From noreply at r-forge.r-project.org  Thu Jan  1 22:20:25 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  1 Jan 2015 22:20:25 +0100 (CET)
Subject: [Pomp-commits] r1038 - in pkg/pompExamples: . inst/examples src
	tests
Message-ID: <20150101212025.7870F186952@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-01 22:20:25 +0100 (Thu, 01 Jan 2015)
New Revision: 1038

Added:
   pkg/pompExamples/inst/examples/ebola.R
   pkg/pompExamples/src/cholmodel.c
   pkg/pompExamples/src/ebola.c
Modified:
   pkg/pompExamples/DESCRIPTION
   pkg/pompExamples/tests/examples.R
   pkg/pompExamples/tests/pertussis.R
   pkg/pompExamples/tests/pertussis.Rout.save
Log:
- Ebola example
- put Matteo Fasiolo's variant cholera model source code into the package

Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2014-12-31 12:36:42 UTC (rev 1037)
+++ pkg/pompExamples/DESCRIPTION	2015-01-01 21:20:25 UTC (rev 1038)
@@ -1,8 +1,8 @@
 Package: pompExamples
 Type: Package
 Title: Additional pomp examples
-Version: 0.24-1
-Date: 2014-12-31
+Version: 0.25-1
+Date: 2015-01-01
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),
 	   email="kingaa at umich.edu"),

Added: pkg/pompExamples/inst/examples/ebola.R
===================================================================
--- pkg/pompExamples/inst/examples/ebola.R	                        (rev 0)
+++ pkg/pompExamples/inst/examples/ebola.R	2015-01-01 21:20:25 UTC (rev 1038)
@@ -0,0 +1,122 @@
+require(pomp)
+require(plyr)
+require(reshape2)
+
+WHO.situation.report.Oct.1 <- '
+Week,Guinea,Liberia,SierraLeone
+1,2.244,,
+2,2.244,,
+3,0.073,,
+4,5.717,,
+5,3.954,,
+6,5.444,,
+7,3.274,,
+8,5.762,,
+9,7.615,,
+10,7.615,,
+11,27.392,,
+12,17.387,,
+13,27.115,,
+14,29.29,,
+15,27.84,,
+16,16.345,,
+17,10.917,,
+18,11.959,,
+19,11.959,,
+20,8.657,,
+21,26.537,,
+22,47.764,3.517,
+23,26.582,1.043,5.494
+24,32.967,18,57.048
+25,18.707,16.34,76.022
+26,24.322,13.742,36.768
+27,4.719,10.155,81.929
+28,7.081,24.856,102.632
+29,8.527,53.294,69.823
+30,92.227,70.146,81.783
+31,26.423,139.269,99.775
+32,16.549,65.66,88.17
+33,36.819,240.645,90.489
+34,92.08,274.826,161.54
+35,101.03,215.56,168.966
+36,102.113,388.553,186.144
+37,83.016,410.299,220.442
+38,106.674,300.989,258.693
+39,55.522,240.237,299.546
+'
+
+## Population sizes in Guinea, Liberia, and Sierra Leone (census 2014)
+populations <- c(Guinea=10628972,Liberia=4092310,SierraLeone=6190280)
+populations["WestAfrica"] <- sum(populations)
+
+dat <- read.csv(text=WHO.situation.report.Oct.1,stringsAsFactors=FALSE)
+rename(dat,c(Week="week")) -> dat
+dat <- melt(dat,id="week",variable.name="country",value.name="cases")
+mutate(dat,deaths=NA) -> dat
+
+ebolaModel <- function (country=c("Guinea", "SierraLeone", "Liberia", "WestAfrica"),
+                        timestep = 0.01, nstageE = 3L,
+                        type = c("raw","cum"), na.rm = FALSE, least.sq = FALSE) {
+
+  type <- match.arg(type)
+  ctry <- match.arg(country)
+  pop <- unname(populations[ctry])
+
+  ## Incubation period is supposed to be Gamma distributed with shape parameter 3 and mean 11.4 days
+  ## The discrete-time formula is used to calculate the corresponding alpha (cf He et al., Interface 2010)
+  ## Case-fatality ratio is fixed at 0.7 (cf WHO Ebola response team, NEJM 2014)
+  incubation_period <- 11.4/7
+  infectious_period <- 7/7
+  index_case <- 10/pop
+  dt <- timestep
+
+  theta <- c(N=pop,R0=1.4,
+             alpha=-1/(nstageE*dt)*log(1-nstageE*dt/incubation_period),
+             gamma=-log(1-dt/infectious_period)/dt,
+             rho=0.2,cfr=0.7,
+             k=0,
+             S_0=1-index_case,E_0=index_case/2-5e-9,
+             I_0=index_case/2-5e-9,R_0=1e-8)
+
+  dat <- subset(dat,country==ctry,select=-country)
+  if (na.rm) {
+    dat <- mutate(subset(dat,!is.na(cases)),week=week-min(week)+1)
+  }
+  if (type=="cum") {
+    dat <- mutate(dat,cases=cumsum(cases),deaths=cumsum(deaths))
+  }
+
+  print(dat)
+
+  ## Create the pomp object
+  pomp(
+       data=dat,
+       times="week",
+       t0=0,
+       params=theta,
+       obsnames=c("cases","deaths"),
+       statenames=c("S","E1","I","R","N_EI","N_IR"),
+       zeronames=if (type=="raw") c("N_EI","N_IR") else character(0),
+       paramnames=c("N","R0","alpha","gamma","rho","k","cfr",
+         "S_0","E_0","I_0","R_0"),
+       nstageE=nstageE,
+       PACKAGE="pompExamples",
+       dmeasure=if (least.sq) "_ebola_dObsLS" else "_ebola_dObs",
+       rmeasure=if (least.sq) "_ebola_rObsLS" else "_ebola_rObs",
+       rprocess=discrete.time.sim(step.fun="_ebola_rSim",delta.t=timestep),
+       skeleton="_ebola_skel",
+       skeleton.type="vectorfield",
+       parameter.transform="_ebola_par_trans",
+       parameter.inv.transform="_ebola_par_untrans",
+       initializer=function (params, t0, nstageE, ...) {
+         all.state.names <- c("S",paste0("E",1:nstageE),"I","R","N_EI","N_IR")
+         comp.names <- c("S",paste0("E",1:nstageE),"I","R")
+         x0 <- setNames(numeric(length(all.state.names)),all.state.names)
+         frac <- c(params["S_0"],rep(params["E_0"]/nstageE,nstageE),params["I_0"],params["R_0"])
+         x0[comp.names] <- round(params["N"]*frac/sum(frac))
+         x0
+       }
+       ) -> po
+}
+
+c("ebolaModel")

Added: pkg/pompExamples/src/cholmodel.c
===================================================================
--- pkg/pompExamples/src/cholmodel.c	                        (rev 0)
+++ pkg/pompExamples/src/cholmodel.c	2015-01-01 21:20:25 UTC (rev 1038)
@@ -0,0 +1,238 @@
+// -*- C++ -*-
+
+#include <R.h>
+#include <Rmath.h>
+#include "pomp.h"
+
+#define TAU        (p[parindex[0]])
+#define GAMMA      (p[parindex[1]])
+#define EPS        (p[parindex[2]])
+#define DELTA      (p[parindex[3]])
+#define DELTA_I    (p[parindex[4]])
+#define LOGOMEGA   (p[parindex[5]])
+#define SD_BETA    (p[parindex[6]])
+#define BETATREND  (p[parindex[7]])
+#define LOGBETA    (p[parindex[8]])
+#define ALPHA      (p[parindex[9]])
+#define RHO        (p[parindex[10]])
+#define CLIN       (p[parindex[11]])
+#define NBASIS     (p[parindex[12]])
+#define NRSTAGE    (p[parindex[13]])
+#define S0         (p[parindex[14]])
+#define I0         (p[parindex[15]])
+#define RS0        (p[parindex[16]])
+#define RL0        (p[parindex[17]])
+
+#define SUSCEP     (x[stateindex[0]])
+#define INFECT     (x[stateindex[1]])
+#define RSHORT     (x[stateindex[2]])
+#define RLONG      (x[stateindex[3]])
+#define DEATHS     (x[stateindex[4]])
+#define NOISE      (x[stateindex[5]])
+#define COUNT      (x[stateindex[6]])
+
+#define POP        (covar[covindex[0]])
+#define DPOPDT     (covar[covindex[1]])
+#define SEASBASIS  (covar[covindex[2]])
+#define TREND      (covar[covindex[3]])
+
+#define DATADEATHS   (y[obsindex[0]])
+
+void _cholmodel_untrans (double *pt, double *p, int *parindex) 
+{
+  int k, nrstage = (int) NRSTAGE;
+  pt[parindex[0]] = log(TAU);
+  pt[parindex[1]] = log(GAMMA);
+  pt[parindex[2]] = log(EPS);
+  pt[parindex[3]] = log(DELTA);
+  pt[parindex[4]] = log(DELTA_I);
+  pt[parindex[6]] = log(SD_BETA);
+  pt[parindex[9]] = log(ALPHA);
+  pt[parindex[10]] = log(RHO);
+  pt[parindex[11]] = logit(CLIN);
+
+  to_log_barycentric(&pt[parindex[14]],&S0,3+nrstage);
+}
+ 
+void _cholmodel_trans (double *pt, double *p, int *parindex) 
+{
+  int k, nrstage = (int) NRSTAGE;
+  pt[parindex[0]] = exp(TAU);
+  pt[parindex[1]] = exp(GAMMA);
+  pt[parindex[2]] = exp(EPS);
+  pt[parindex[3]] = exp(DELTA);
+  pt[parindex[4]] = exp(DELTA_I);
+  pt[parindex[6]] = exp(SD_BETA);
+  pt[parindex[9]] = exp(ALPHA);
+  pt[parindex[10]] = exp(RHO);
+  pt[parindex[11]] = expit(CLIN);
+
+  from_log_barycentric(&pt[parindex[14]],&S0,3+nrstage);
+}
+
+void _cholmodel_norm_rmeasure (double *y, double *x, double *p, 
+			       int *obsindex, int *stateindex, 
+			       int *parindex, int *covindex,
+			       int ncovars, double *covars, double t)
+{
+  double tol = 1.0e-18;
+  if ((COUNT > 0) || (!(R_FINITE(DEATHS)))) {
+    DATADEATHS = R_NaReal;
+  } else { 
+    DATADEATHS = rnbinom_mu(1 / (TAU*TAU), DEATHS + tol);
+  }
+}
+
+void _cholmodel_norm_dmeasure (double *lik, double *y, double *x, 
+			       double *p, int give_log,
+			       int *obsindex, int *stateindex, 
+			       int *parindex, int *covindex,
+			       int ncovars, double *covars, double t)
+{
+  double tol = 1.0e-18;
+  if ((COUNT>0.0) || (!(R_FINITE(DEATHS)))) {
+    *lik = tol;
+  } else {
+    *lik = dnbinom_mu(DATADEATHS+tol, 1 / (TAU*TAU), DEATHS + tol, 0) + tol;
+  }
+  if (give_log) *lik = log(*lik);
+}
+
+#undef DATADEATHS
+
+
+inline double out_flow(double init, double rate_by_dt)
+{
+
+  return init * (1.0 - exp( - rate_by_dt ));
+
+}
+
+// two-path SIRS cholera model using SDEs
+// exponent (alpha) on I/n
+// only "severe" infections are infectious
+// truncation is not used
+// instead, particles with negative states are killed
+void _cholmodel_two (double *x, const double *p, 
+		     const int *stateindex, const int *parindex, 
+		     const int *covindex,
+		     int covdim, const double *covar, 
+		     double t, double dt)
+{			   // implementation of the SIRS cholera model
+  int nrstage = (int) NRSTAGE;
+  int nbasis  = (int) NBASIS;
+
+  double *pt_r, *pt_w;
+  int j;
+
+  double k_eps = NRSTAGE * EPS;
+ 
+  double gamma_delta_deltaI = GAMMA + DELTA + DELTA_I;
+
+  double keps_div_keps_delta = k_eps / (k_eps + DELTA);
+
+  /* 
+   * Preliminaries
+   */
+
+  double beta = exp(dot_product(nbasis,&SEASBASIS,&LOGBETA)+BETATREND*TREND);
+
+  double omega = exp(dot_product(nbasis,&SEASBASIS,&LOGOMEGA));
+
+  double dw = rgammawn(SD_BETA, dt);  // gamma noise, mean=dt, variance=(beta_sd^2 dt)
+
+  double lambda = omega + (beta * dw/dt) * INFECT/POP;  // Time-dependent force of infection
+
+  /* 
+   * Out-flows from compartments using aboundances at previous time step
+   */
+
+  double S_o = out_flow(SUSCEP, (lambda + DELTA) * dt);
+  double I_o = out_flow(INFECT, gamma_delta_deltaI * dt);
+  double RSH_o = out_flow(RSHORT, (RHO + DELTA) * dt);
+
+  double R_o[nrstage];
+  for (pt_r = &RLONG, pt_w = R_o, j = 0; 
+       j < nrstage; 
+       j++, pt_r++, pt_w++) {
+
+    *pt_w = out_flow(*pt_r, (k_eps + DELTA) * dt); 
+
+  }
+
+  double new_infect = S_o * (lambda / (lambda + DELTA));
+
+  /*
+   * Cholera deaths = (I_o * DELTA_I) / gamma_delta_deltaI are not reborn in SUSCEPT.
+   * To offset this downward bias on total population, we add the average number of (observed) deaths:
+   *
+   * average_chol_death = tot_cholc_deaths / (n_months * n_step)  <----->  29.522 = 354275.0 / (600 * 200) 
+   */
+  double chol_deaths_dt = 29.523;
+  double births = DPOPDT * dt + chol_deaths_dt + S_o * (DELTA / (lambda + DELTA)) + I_o * DELTA / gamma_delta_deltaI + RSH_o * (DELTA / (DELTA + RHO));
+  for (pt_r = R_o, j = 0; 
+       j < nrstage; 
+       j++, pt_r++) {
+
+    births += *pt_r * (DELTA / (k_eps + DELTA)); 
+
+  } 
+
+  /* 
+   * Updating all compartments
+   */
+
+  SUSCEP += - S_o + births + R_o[nrstage-1] * keps_div_keps_delta + RSH_o * (RHO / (RHO + DELTA));
+
+  INFECT += - I_o + CLIN * new_infect;
+
+  RSHORT += - RSH_o + (1 - CLIN) * new_infect;
+
+  for (pt_w = &RLONG, pt_r = R_o, j = 0; 
+       j < nrstage; 
+       j++, pt_r++, pt_w++) {
+
+    if(j == 0)
+      {
+
+	*pt_w += - *pt_r + I_o * (GAMMA / gamma_delta_deltaI); 
+
+      } else {
+
+      *pt_w += - *pt_r + *(pt_r-1) * keps_div_keps_delta;
+
+    } 
+
+  }
+
+  DEATHS += I_o * (DELTA_I / gamma_delta_deltaI);	// cumulative deaths due to disease
+
+  NOISE += (dw-dt) / SD_BETA;
+
+}
+
+#undef GAMMA    
+#undef EPS      
+#undef DELTA    
+#undef DELTA_I  
+#undef LOGOMEGA    
+#undef SD_BETA  
+#undef BETATREND
+#undef LOGBETA  
+#undef ALPHA    
+#undef RHO      
+#undef CLIN     
+#undef NBASIS   
+#undef NRSTAGE  
+
+#undef SUSCEP   
+#undef INFECT   
+#undef RSHORT   
+#undef RLONG    
+#undef DEATHS   
+#undef NOISE    
+#undef COUNT    
+
+#undef POP      
+#undef DPOPDT   
+#undef SEASBASIS

Added: pkg/pompExamples/src/ebola.c
===================================================================
--- pkg/pompExamples/src/ebola.c	                        (rev 0)
+++ pkg/pompExamples/src/ebola.c	2015-01-01 21:20:25 UTC (rev 1038)
@@ -0,0 +1,187 @@
+// SEIR Ebola model
+
+#include <R.h>
+#include <Rmath.h>
+#include <R_ext/Rdynload.h>
+#include <pomp.h>
+
+// State variables
+#define S (x[stateindex[0]]) // Susceptible
+#define E(J) (x[stateindex[1] + (J)]) // Exposed
+#define I (x[stateindex[2]]) // Infected
+#define R (x[stateindex[3]]) // Removed
+#define N_EI (x[stateindex[4]]) // Number of transitions from E to I
+#define N_IR (x[stateindex[5]]) // Number of transitions from I to R
+
+// Variations
+#define DS (f[stateindex[0]]) // Susceptible
+#define DE(J) (f[stateindex[1] + (J)]) // Exposed
+#define DI (f[stateindex[2]]) // Infected
+#define DR (f[stateindex[3]]) // Removed
+#define DN_EI (f[stateindex[4]]) // Number of transitions from E to I
+#define DN_IR (f[stateindex[5]]) // Number of transitions from I to R
+
+// Parameters on the natural scale (all rates are per day)
+#define N (p[parindex[0]]) // Population size
+#define R0 (p[parindex[1]]) // Basic reproduction number
+#define alpha (p[parindex[2]]) // Inverse of latency period
+#define gamma (p[parindex[3]]) // Inverse of duration of infection
+#define rho (p[parindex[4]]) // Reporting probability
+#define k (p[parindex[5]]) // Reporting overdispersion
+#define cfr (p[parindex[6]]) // Case-fatality ratio
+#define IC(J) (p[parindex[7] + (J)]) // Initial conditions
+
+// Parameters on the transformed scale (all rates are per day)
+#define TN (pt[parindex[0]]) // Population size
+#define TR0 (pt[parindex[1]]) // Basic reproduction number
+#define Talpha (pt[parindex[2]]) // Inverse of latency period
+#define Tgamma (pt[parindex[3]]) // Inverse of duration of infection
+#define Trho (pt[parindex[4]]) // Reporting probability
+#define Tk (pt[parindex[5]]) // Reporting overdispersion
+#define Tcfr (pt[parindex[6]]) // Case-fatality ratio
+#define TIC(J) (pt[parindex[7] + (J)]) // Initial conditions
+
+// Observations
+#define cases (y[obsindex[0]]) // Number of reported cases
+#define deaths (y[obsindex[1]]) // Number of reported deaths
+
+// Transforms the parameters to the transformed scale
+void _ebola_par_untrans (double *pt, double *p, int *parindex){
+  TN = log(N);
+  TR0 = log(R0);
+  Talpha = log(alpha);
+  Tgamma = log(gamma);
+  Trho = logit(rho);
+  Tk = log(k);
+  Tcfr = logit(cfr);
+  to_log_barycentric(&(TIC(0)),&(IC(0)),4);
+}
+
+// Transforms the parameters to the natural scale
+void _ebola_par_trans (double *pt, double *p, int *parindex){
+  TN = exp(N);
+  TR0 = exp(R0);
+  Talpha = exp(alpha);
+  Tgamma = exp(gamma);
+  Trho = expit(rho);
+  Tk = exp(k);
+  Tcfr = expit(cfr);
+  from_log_barycentric(&(TIC(0)),&(IC(0)),4);
+}
+
+//  Observation model: hierarchical model for cases and deaths
+// p(R_t, D_t| C_t) = p(R_t | C_t) * p(D_t | C_t, R_t)
+// p(R_t | C_t): Negative binomial with mean rho * C_t and dispersion parameter 1 / k
+// p(D_t | C_t, R_t): Binomial B(R_t, cfr)
+void _ebola_dObs (double *lik, double *y, double *x, double *p, int give_log,
+		  int *obsindex, int *stateindex, int *parindex, int *covindex,
+		  int ncovars, double *covars, double t) {
+  double f;
+  if (k > 0.0)
+    f = dnbinom_mu(nearbyint(cases),1.0/k,rho*N_EI,1);
+  // f += dnbinom_mu(nearbyint(deaths), 1.0 / k, rho * cfr * N_IR, 1);
+  else
+    f = dpois(nearbyint(cases),rho*N_EI,1);
+  *lik = (give_log) ? f : exp(f);
+}
+
+// For least-squares trajectory-matching:
+void _ebola_dObsLS (double *lik, double *y, double *x, double *p, int give_log,
+		    int *obsindex, int *stateindex, int *parindex, int *covindex,
+		    int ncovars, double *covars, double t) {
+  double f;
+  f = dnorm(cases,rho*N_EI,k,1);
+  *lik = (give_log) ? f : exp(f);
+}
+
+void _ebola_rObs (double *y, double *x, double *p,
+		  int *obsindex, int *stateindex, int *parindex, int *covindex,
+		  int ncovars, double *covars, double t)
+{
+  if (k > 0) {
+    cases = rnbinom_mu(1.0/k,rho*N_EI);
+    deaths = rnbinom_mu(1.0/k,rho*cfr*N_IR);
+  } else {
+    cases = rpois(rho*N_EI);
+    deaths = rpois(rho*cfr*N_IR);
+  }
+}
+
+// For least-squares trajectory-matching:
+void _ebola_rObsLS (double *y, double *x, double *p,
+		    int *obsindex, int *stateindex, int *parindex, int *covindex,
+		    int ncovars, double *covars, double t)
+{
+  cases = rnorm(rho*N_EI,k);
+  deaths = NA_REAL;
+}
+
+
+// Process model
+void _ebola_rSim (double *x, const double *p,
+		  const int *stateindex, const int *parindex, const int *covindex,
+		  int covdim, const double *covars,
+		  double t, double dt) {
+
+  // Retrieve user data in the pomp object
+  int *(*get_pomp_userdata_int)(const char *);
+  get_pomp_userdata_int = (int *(*)(const char *)) R_GetCCallable("pomp","get_pomp_userdata_int");
+  int nstageE = *(get_pomp_userdata_int("nstageE")); // Number of stages in the E class
+
+  // Other parameters
+  double lambda, beta;
+  beta = R0 * gamma; // Transmission rate
+  lambda = beta * I / N; // Force of infection
+  int i;
+
+  // Transitions
+
+  // From class S
+  double transS = rbinom(S, 1.0 - exp(- lambda * dt)); // No of infections
+
+  // From class E
+  double transE[nstageE]; // No of transitions between classes E
+  for(i = 0; i < nstageE; i++){
+    transE[i] = rbinom(E(i), 1.0 - exp(- nstageE * alpha * dt));
+  }
+
+  // From class I
+  double transI = rbinom(I, 1.0 - exp(- gamma * dt)); // No of transitions I->R
+
+  // Balance the equations
+  S -= transS;
+  E(0) += transS - transE[0];
+  for(i=1; i < nstageE; i++) {
+    E(i) += transE[i-1] - transE[i];
+  }
+  I += transE[nstageE - 1] - transI;
+  R += transI;
+  N_EI += transE[nstageE - 1]; // No of transitions from E to I
+  N_IR += transI; // No of transitions from I to R
+}
+
+// Continuous-time deterministic skeleton
+void _ebola_skel (double *f, double *x, double *p,
+		  int *stateindex, int *parindex, int *covindex,
+		  int ncovars, double *covars, double t) {
+
+  // Retrieve user data in the pomp object
+  int *(*get_pomp_userdata_int)(const char *);
+  get_pomp_userdata_int = (int *(*)(const char *)) R_GetCCallable("pomp","get_pomp_userdata_int");
+  int nstageE = *(get_pomp_userdata_int("nstageE")); // Number of stages in the E class
+
+  // Other parameters
+  double lambda, beta;
+  beta = R0 * gamma; // Transmission rate
+  lambda = beta * I / N; // Force of infection
+  int i;
+
+  // Balance the equations
+  DS = - lambda * S;
+  DE(0) = lambda * S - nstageE * alpha * E(0);
+  for(i=1; i < nstageE; i++) DE(i) = nstageE * alpha * (E(i - 1) -  E(i));
+  DI = nstageE * alpha * E(nstageE - 1) - gamma * I;
+  DR = gamma * I;
+  DN_EI = nstageE * alpha * E(nstageE - 1);
+  DN_IR = gamma * I;
+}

Modified: pkg/pompExamples/tests/examples.R
===================================================================
--- pkg/pompExamples/tests/examples.R	2014-12-31 12:36:42 UTC (rev 1037)
+++ pkg/pompExamples/tests/examples.R	2015-01-01 21:20:25 UTC (rev 1038)
@@ -22,3 +22,12 @@
 pompExample(bbp)
 pf <- pfilter(simulate(bbp),Np=100,max.fail=Inf)
 tj <- trajectory(bbp)
+
+pompExample(ebola)
+ebolaModel(country="Guinea") -> po
+pf <- pfilter(simulate(po),Np=100)
+tj <- trajectory(po)
+
+ebolaModel(country="SierraLeone",na.rm=TRUE,type='cum') -> po
+pf <- pfilter(simulate(po),Np=100)
+tj <- trajectory(po)

Modified: pkg/pompExamples/tests/pertussis.R
===================================================================
--- pkg/pompExamples/tests/pertussis.R	2014-12-31 12:36:42 UTC (rev 1037)
+++ pkg/pompExamples/tests/pertussis.R	2015-01-01 21:20:25 UTC (rev 1038)
@@ -15,7 +15,7 @@
 y <- trajectory(pertussis.sim(SEIRS.small),as.data.frame=TRUE)
 tail(y)
 
-system.time(pf <- pfilter(pertussis.sim(full.small),seed=3445886L,Np=1000))
+pf <- pfilter(pertussis.sim(full.small),seed=3445886L,Np=1000)
 logLik(pf)
 
 pttest <- function (po, digits = 15) {

Modified: pkg/pompExamples/tests/pertussis.Rout.save
===================================================================
--- pkg/pompExamples/tests/pertussis.Rout.save	2014-12-31 12:36:42 UTC (rev 1037)
+++ pkg/pompExamples/tests/pertussis.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
@@ -1,5 +1,5 @@
 
-R Under development (unstable) (2014-12-14 r67168) -- "Unsuffered Consequences"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -144,9 +144,7 @@
 1040 19.98077    1
 1041 20.00000    1
 > 
-> system.time(pf <- pfilter(pertussis.sim(full.small),seed=3445886L,Np=1000))
-   user  system elapsed 
- 17.801   0.004  17.861 
+> pf <- pfilter(pertussis.sim(full.small),seed=3445886L,Np=1000)
 > logLik(pf)
 [1] -3829.33
 > 
@@ -170,4 +168,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 18.657   0.060  18.801 
+ 23.494   0.034  23.544 


From noreply at r-forge.r-project.org  Thu Jan  1 22:20:29 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  1 Jan 2015 22:20:29 +0100 (CET)
Subject: [Pomp-commits] r1039 - in pkg/pomp: . R tests
Message-ID: <20150101212029.79F01186952@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-01 22:20:29 +0100 (Thu, 01 Jan 2015)
New Revision: 1039

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/example.R
   pkg/pomp/tests/bbs-trajmatch.Rout.save
   pkg/pomp/tests/bbs.Rout.save
   pkg/pomp/tests/blowflies.Rout.save
   pkg/pomp/tests/dacca.Rout.save
   pkg/pomp/tests/dimchecks.Rout.save
   pkg/pomp/tests/fhn.Rout.save
   pkg/pomp/tests/filtfail.Rout.save
   pkg/pomp/tests/gillespie.Rout.save
   pkg/pomp/tests/gompertz.Rout.save
   pkg/pomp/tests/logistic.Rout.save
   pkg/pomp/tests/ou2-abc.Rout.save
   pkg/pomp/tests/ou2-bsmc.Rout.save
   pkg/pomp/tests/ou2-bsmc2.Rout.save
   pkg/pomp/tests/ou2-forecast.Rout.save
   pkg/pomp/tests/ou2-kalman.Rout.save
   pkg/pomp/tests/ou2-mif-fp.Rout.save
   pkg/pomp/tests/ou2-mif.Rout.save
   pkg/pomp/tests/ou2-mif2.Rout.save
   pkg/pomp/tests/ou2-nlf.Rout.save
   pkg/pomp/tests/ou2-pmcmc.Rout.save
   pkg/pomp/tests/ou2-probe.Rout.save
   pkg/pomp/tests/ou2-procmeas.Rout.save
   pkg/pomp/tests/ou2-simulate.Rout.save
   pkg/pomp/tests/ou2-trajmatch.Rout.save
   pkg/pomp/tests/partrans.Rout.save
   pkg/pomp/tests/pfilter.Rout.save
   pkg/pomp/tests/pomppomp.Rout.save
   pkg/pomp/tests/prior.Rout.save
   pkg/pomp/tests/ricker-bsmc.Rout.save
   pkg/pomp/tests/ricker-probe.Rout.save
   pkg/pomp/tests/ricker-spect.Rout.save
   pkg/pomp/tests/ricker.Rout.save
   pkg/pomp/tests/rw2.Rout.save
   pkg/pomp/tests/sir.Rout.save
   pkg/pomp/tests/skeleton.Rout.save
   pkg/pomp/tests/steps.Rout.save
   pkg/pomp/tests/synlik.Rout.save
   pkg/pomp/tests/verhulst.Rout.save
Log:
- minor cosmetic tweak
- update all .Rout.save files

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/DESCRIPTION	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.56-1
-Date: 2014-12-16
+Version: 0.56-2
+Date: 2015-01-01
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),

Modified: pkg/pomp/R/example.R
===================================================================
--- pkg/pomp/R/example.R	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/R/example.R	2015-01-01 21:20:29 UTC (rev 1039)
@@ -28,7 +28,7 @@
                get(objs$value[i],envir=evalEnv),
                envir=envir)
       }
-      cat("newly created pomp object(s):\n",objs$value,"\n")
+      cat("newly created object(s):\n",objs$value,"\n")
       obj <- NULL
     } else {
       stop(sQuote("envir")," must be an environment or NULL")

Modified: pkg/pomp/tests/bbs-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/bbs-trajmatch.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,15 +16,11 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > pompExample(bbs)
-newly created pomp object(s):
+newly created object(s):
  bbs 
 > 
 > guess <- c(
@@ -72,8 +68,8 @@
 > options(warn=2)
 > ofun <- traj.match.objfun(window(bbs,end=3),est=c("beta","gamma"),transform=TRUE,maxsteps=10,rtol=1e-6)
 > try(optim(fn=ofun,par=c(0,-1),method="Nelder-Mead",control=list(reltol=1e-10)))
-DLSODA-  At current T (=R1), MXSTEP (=I1) steps
-      taken on this call before reaching TOUT
+DLSODA-  At current T (=R1), MXSTEP (=I1) steps   
+      taken on this call before reaching TOUT     
 In above message, I1 = 10
  
 In above message, R1 = 0.609738
@@ -84,4 +80,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.795   0.053   2.839 
+  2.725   0.017   2.733 

Modified: pkg/pomp/tests/bbs.Rout.save
===================================================================
--- pkg/pomp/tests/bbs.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/bbs.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -20,7 +20,7 @@
 Loading required package: nloptr
 > 
 > pompExample(bbs)
-newly created pomp object(s):
+newly created object(s):
  bbs 
 > 
 > set.seed(48857734L)
@@ -69,4 +69,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  6.716   0.076   6.831 
+  7.769   0.051   7.832 

Modified: pkg/pomp/tests/blowflies.Rout.save
===================================================================
--- pkg/pomp/tests/blowflies.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/blowflies.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,15 +16,11 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > pompExample(blowflies)
-newly created pomp object(s):
+newly created object(s):
  blowflies1 blowflies2 
 > 
 > init.state(blowflies1)
@@ -74,4 +70,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.430   0.051   1.473 
+  1.493   0.039   1.519 

Modified: pkg/pomp/tests/dacca.Rout.save
===================================================================
--- pkg/pomp/tests/dacca.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/dacca.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,17 +16,13 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > set.seed(1420306530L)
 > 
 > pompExample(dacca)
-newly created pomp object(s):
+newly created object(s):
  dacca 
 > 
 > x <- as.data.frame(dacca)
@@ -111,4 +107,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 13.216   0.040  13.260 
+ 14.817   0.035  14.853 

Modified: pkg/pomp/tests/dimchecks.Rout.save
===================================================================
--- pkg/pomp/tests/dimchecks.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/dimchecks.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,17 +16,13 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > set.seed(1420306530L)
 > 
 > pompExample(ricker)
-newly created pomp object(s):
+newly created object(s):
  ricker 
 > po <- ricker
 > 
@@ -156,7 +152,7 @@
 > stopifnot(identical(g1,g3[,4:6,]))
 > 
 > pompExample(gompertz)
-newly created pomp object(s):
+newly created object(s):
  gompertz 
 > p <- parmat(coef(gompertz),5)
 > f1 <- partrans(gompertz,p,"inv")
@@ -166,4 +162,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.532   0.037   0.555 
+  0.489   0.041   0.517 

Modified: pkg/pomp/tests/fhn.Rout.save
===================================================================
--- pkg/pomp/tests/fhn.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/fhn.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,12 +16,8 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > pdf.options(useDingbats=FALSE)
 > pdf(file="fhn.pdf")
@@ -95,4 +91,4 @@
 > 
 > proc.time()
    user  system elapsed 
-   0.99    0.04    1.02 
+  0.927   0.060   0.950 

Modified: pkg/pomp/tests/filtfail.Rout.save
===================================================================
--- pkg/pomp/tests/filtfail.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/filtfail.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,12 +16,8 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > set.seed(834454394L)
 > 
@@ -120,4 +116,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.572   0.031   0.581 
+  0.489   0.053   0.529 

Modified: pkg/pomp/tests/gillespie.Rout.save
===================================================================
--- pkg/pomp/tests/gillespie.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/gillespie.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,12 +16,8 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > params <- c(
 +             nu=1/70,
@@ -121,7 +117,7 @@
 105 0.1666667
 > 
 > pompExample(gillespie.sir)
-newly created pomp object(s):
+newly created object(s):
  gillespie.sir 
 > 
 > tail(as.data.frame(simulate(gillespie.sir,times=time(gsir),t0=timezero(gsir),seed=1165270654L)))
@@ -135,4 +131,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.637   0.064   2.693 
+  2.565   0.041   2.592 

Modified: pkg/pomp/tests/gompertz.Rout.save
===================================================================
--- pkg/pomp/tests/gompertz.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/gompertz.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,16 +16,12 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > options(digits=4)
 > 
 > pompExample(gompertz)
-newly created pomp object(s):
+newly created object(s):
  gompertz 
 > 
 > po <- gompertz
@@ -137,4 +133,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.762   0.063   1.806 
+  1.797   0.038   1.822 

Modified: pkg/pomp/tests/logistic.Rout.save
===================================================================
--- pkg/pomp/tests/logistic.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/logistic.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,12 +16,8 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > po <- pomp(
 +            data=rbind(obs=rep(0,1000)),
@@ -126,4 +122,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.911   0.033   0.933 
+  0.874   0.030   0.887 

Modified: pkg/pomp/tests/ou2-abc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-abc.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-abc.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -18,14 +18,10 @@
 > ### OU2 test of abc for pomp
 > 
 > library(pomp) 
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > 
 > pdf(file='ou2-abc.pdf')
@@ -135,4 +131,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 11.588   0.056  11.647 
+ 11.085   0.055  11.138 

Modified: pkg/pomp/tests/ou2-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-bsmc.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,16 +16,12 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > set.seed(398585L)
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > 
 > time(ou2) <- 1:10
@@ -63,7 +59,7 @@
 > post <- smc$post
 > 
 > print(etime <- toc-tic)
-Time difference of 3.021244 secs
+Time difference of 3.430529 secs
 > 
 > print(
 +       cbind(
@@ -105,4 +101,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  4.967   0.053   5.012 
+  5.498   0.064   5.527 

Modified: pkg/pomp/tests/ou2-bsmc2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc2.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-bsmc2.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -21,7 +21,7 @@
 > 
 > set.seed(398585L)
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > 
 > time(ou2) <- 1:10
@@ -56,7 +56,7 @@
 > post <- smc$post
 > 
 > print(etime <- toc-tic)
-Time difference of 2.042303 secs
+Time difference of 2.234756 secs
 > 
 > print(
 +       cbind(
@@ -98,4 +98,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  3.576   0.104   3.707 
+  3.846   0.045   3.881 

Modified: pkg/pomp/tests/ou2-forecast.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-forecast.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-forecast.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,17 +16,13 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > set.seed(921625222L)
 > 
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > tm <- time(ou2)
 > y <- obs(ou2)
@@ -65,4 +61,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.456   0.016   1.463 
+  1.376   0.042   1.402 

Modified: pkg/pomp/tests/ou2-kalman.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-kalman.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-kalman.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,12 +16,8 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > set.seed(577639485L)
 > 
@@ -72,7 +68,7 @@
 + }
 > 
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > 
 > # true coefficients
@@ -168,7 +164,7 @@
     117 function evaluations used
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 3.49406 secs
+Time difference of 3.235065 secs
 > tic <- Sys.time()
 > print(loglik.mle <- -kalm.fit1$value,digits=4)
 [1] -477.2
@@ -192,4 +188,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  4.096   0.029   4.104 
+  3.769   0.026   3.787 

Modified: pkg/pomp/tests/ou2-mif-fp.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif-fp.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-mif-fp.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,15 +16,11 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > 
 > set.seed(64857673L)
@@ -74,4 +70,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 23.726   0.048  23.790 
+ 24.537   0.066  24.614 

Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-mif.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,15 +16,11 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > 
 > set.seed(64857673L)
@@ -285,4 +281,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 14.330   0.061  14.397 
+ 13.791   0.053  13.848 

Modified: pkg/pomp/tests/ou2-mif2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif2.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-mif2.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,15 +16,11 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > 
 > pdf(file="ou2-mif2.pdf")
@@ -139,4 +135,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 63.315   0.042  63.432 
+ 62.157   0.075  62.274 

Modified: pkg/pomp/tests/ou2-nlf.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-nlf.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-nlf.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,17 +16,13 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > set.seed(583615606L)
 > 
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > estnames=c("alpha.2","alpha.3","tau")
 > theta.truth <- coef(ou2)
@@ -89,4 +85,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  5.413   0.023   5.433 
+  5.003   0.037   5.037 

Modified: pkg/pomp/tests/ou2-pmcmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-pmcmc.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-pmcmc.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,15 +16,11 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > 
 > dprior.ou2 <- function (params, log, ...) {
@@ -118,4 +114,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 27.262   0.036  27.325 
+ 26.822   0.042  26.880 

Modified: pkg/pomp/tests/ou2-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-probe.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-probe.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,18 +16,14 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > set.seed(1066L)
 > 
 > pdf(file="ou2-probe.pdf")
 > 
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > 
 > pm.ou2 <- probe(
@@ -297,7 +293,7 @@
 sim.5 0.5542739 0.6216561 -0.4089672 -0.7236761  0.06850115
 > 
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > 
 > good <- probe(
@@ -344,4 +340,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  8.873   0.076   8.949 
+  8.501   0.048   8.545 

Modified: pkg/pomp/tests/ou2-procmeas.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-procmeas.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-procmeas.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,15 +16,11 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > 
 > po <- window(ou2,end=10)
@@ -58,4 +54,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.526   0.044   0.560 
+  0.493   0.037   0.495 

Modified: pkg/pomp/tests/ou2-simulate.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-simulate.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-simulate.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,15 +16,11 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > 
 > ## fix some parameters
@@ -39,7 +35,7 @@
 > ou2.sim <- simulate(ou2,params=p,nsim=100,seed=32043858)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 0.006201267 secs
+Time difference of 0.007747889 secs
 > 
 > coef(ou2,c('x1.0','x2.0')) <- c(-50,50)
 > 
@@ -50,4 +46,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.523   0.016   0.530 
+  0.501   0.022   0.507 

Modified: pkg/pomp/tests/ou2-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-trajmatch.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-trajmatch.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,17 +16,13 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > set.seed(93885485L)
 > 
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > true.p <- coef(ou2)
 > simdata <- simulate(ou2,nsim=5,params=true.p,seed=394885)
@@ -159,7 +155,7 @@
 > stopifnot(fit$convergence==0)
 > 
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > p <- coef(ou2)
 > ou2 at params <- numeric(0)
@@ -179,4 +175,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.771   0.065   1.824 
+  1.740   0.048   1.765 

Modified: pkg/pomp/tests/partrans.Rout.save
===================================================================
--- pkg/pomp/tests/partrans.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/partrans.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,15 +16,11 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > pompExample(gompertz)
-newly created pomp object(s):
+newly created object(s):
  gompertz 
 > 
 > pars <- coef(gompertz)
@@ -56,4 +52,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.500   0.053   0.522 
+  0.492   0.020   0.494 

Modified: pkg/pomp/tests/pfilter.Rout.save
===================================================================
--- pkg/pomp/tests/pfilter.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/pfilter.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,15 +16,11 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > 
 > set.seed(9994847L)
@@ -49,7 +45,7 @@
   -479.61      0.46 
 > 
 > pompExample(euler.sir)
-newly created pomp object(s):
+newly created object(s):
  euler.sir 
 > pf <- pfilter(euler.sir,Np=100,seed=394343L)
 > print(coef(pf))
@@ -81,4 +77,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 10.454   0.035  10.489 
+  9.887   0.037   9.924 

Modified: pkg/pomp/tests/pomppomp.Rout.save
===================================================================
--- pkg/pomp/tests/pomppomp.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/pomppomp.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,15 +16,11 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > pompExample(ricker)
-newly created pomp object(s):
+newly created object(s):
  ricker 
 > y1 <- obs(simulate(ricker,seed=1066L))
 > r2 <- pomp(ricker,measurement.model=y~pois(lambda=N*phi))
@@ -59,4 +55,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.562   0.032   0.582 
+  0.489   0.030   0.504 

Modified: pkg/pomp/tests/prior.Rout.save
===================================================================
--- pkg/pomp/tests/prior.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/prior.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,15 +16,11 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
  ou2 
 > coef(ou2,"alpha.sd") <- 5
 Warning message:
@@ -76,4 +72,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.697   0.016   0.703 
+  0.683   0.025   0.694 

Modified: pkg/pomp/tests/ricker-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-bsmc.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ricker-bsmc.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,15 +16,11 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > pompExample(ricker)
-newly created pomp object(s):
+newly created object(s):
  ricker 
 > 
 > pdf(file="ricker-bsmc.pdf")
@@ -58,4 +54,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  3.035   0.057   3.068 
+  2.571   0.057   2.614 

Modified: pkg/pomp/tests/ricker-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-probe.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ricker-probe.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,15 +16,11 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > pompExample(ricker)
-newly created pomp object(s):
+newly created object(s):
  ricker 
 > 
 > pdf(file="ricker-probe.pdf")
@@ -301,4 +297,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 14.323   0.079  14.418 
+ 13.643   0.070  13.713 

Modified: pkg/pomp/tests/ricker-spect.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-spect.Rout.save	2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ricker-spect.Rout.save	2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
 
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -16,17 +16,13 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: mvtnorm
 Loading required package: subplex
 Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
 > 
 > pdf(file="ricker-spect.pdf")
 > 
 > pompExample(ricker)
-newly created pomp object(s):
+newly created object(s):
  ricker 
 > 
 > set.seed(6457673L)
@@ -74,4 +70,4 @@
 > 
 > proc.time()
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 1039

From noreply at r-forge.r-project.org  Fri Jan  2 00:13:41 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri,  2 Jan 2015 00:13:41 +0100 (CET)
Subject: [Pomp-commits] r1040 - pkg/pompExamples
Message-ID: <20150101231341.A9EA2185E0A@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-02 00:13:41 +0100 (Fri, 02 Jan 2015)
New Revision: 1040

Modified:
   pkg/pompExamples/DESCRIPTION
Log:
- add plyr and reshape2 to Suggests field

Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2015-01-01 21:20:29 UTC (rev 1039)
+++ pkg/pompExamples/DESCRIPTION	2015-01-01 23:13:41 UTC (rev 1040)
@@ -17,6 +17,7 @@
 URL: http://pomp.r-forge.r-project.org
 Description: More 'pomp' examples.
 Depends: R(>= 3.0.0), stats, graphics, pomp(>= 0.56-1)
+Suggests: plyr, reshape2
 License: GPL (>= 2)
 LazyData: false
 BuildVignettes: true


From noreply at r-forge.r-project.org  Fri Jan  2 03:39:52 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri,  2 Jan 2015 03:39:52 +0100 (CET)
Subject: [Pomp-commits] r1041 - in pkg/pompExamples: . inst/examples
Message-ID: <20150102023952.69117185183@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-02 03:39:51 +0100 (Fri, 02 Jan 2015)
New Revision: 1041

Modified:
   pkg/pompExamples/DESCRIPTION
   pkg/pompExamples/inst/examples/ebola.R
Log:
- fix bug

Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2015-01-01 23:13:41 UTC (rev 1040)
+++ pkg/pompExamples/DESCRIPTION	2015-01-02 02:39:51 UTC (rev 1041)
@@ -1,7 +1,7 @@
 Package: pompExamples
 Type: Package
 Title: Additional pomp examples
-Version: 0.25-1
+Version: 0.25-2
 Date: 2015-01-01
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),

Modified: pkg/pompExamples/inst/examples/ebola.R
===================================================================
--- pkg/pompExamples/inst/examples/ebola.R	2015-01-01 23:13:41 UTC (rev 1040)
+++ pkg/pompExamples/inst/examples/ebola.R	2015-01-02 02:39:51 UTC (rev 1041)
@@ -3,7 +3,7 @@
 require(reshape2)
 
 WHO.situation.report.Oct.1 <- '
-Week,Guinea,Liberia,SierraLeone
+week,Guinea,Liberia,SierraLeone
 1,2.244,,
 2,2.244,,
 3,0.073,,
@@ -50,7 +50,6 @@
 populations["WestAfrica"] <- sum(populations)
 
 dat <- read.csv(text=WHO.situation.report.Oct.1,stringsAsFactors=FALSE)
-rename(dat,c(Week="week")) -> dat
 dat <- melt(dat,id="week",variable.name="country",value.name="cases")
 mutate(dat,deaths=NA) -> dat
 
@@ -78,7 +77,14 @@
              S_0=1-index_case,E_0=index_case/2-5e-9,
              I_0=index_case/2-5e-9,R_0=1e-8)
 
-  dat <- subset(dat,country==ctry,select=-country)
+  if (ctry=="WestAfrica") {
+    dat <- ddply(dat,~week,summarize,
+                 cases=sum(cases,na.rm=TRUE),
+                 deaths=sum(deaths,na.rm=TRUE))
+  } else {
+    dat <- subset(dat,country==ctry,select=-country)
+  }
+
   if (na.rm) {
     dat <- mutate(subset(dat,!is.na(cases)),week=week-min(week)+1)
   }
@@ -86,8 +92,6 @@
     dat <- mutate(dat,cases=cumsum(cases),deaths=cumsum(deaths))
   }
 
-  print(dat)
-
   ## Create the pomp object
   pomp(
        data=dat,
@@ -99,7 +103,7 @@
        zeronames=if (type=="raw") c("N_EI","N_IR") else character(0),
        paramnames=c("N","R0","alpha","gamma","rho","k","cfr",
          "S_0","E_0","I_0","R_0"),
-       nstageE=nstageE,
+       nstageE=as.integer(nstageE),
        PACKAGE="pompExamples",
        dmeasure=if (least.sq) "_ebola_dObsLS" else "_ebola_dObs",
        rmeasure=if (least.sq) "_ebola_rObsLS" else "_ebola_rObs",


From noreply at r-forge.r-project.org  Fri Jan  2 15:04:39 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri,  2 Jan 2015 15:04:39 +0100 (CET)
Subject: [Pomp-commits] r1042 - in pkg/pompExamples: . inst/examples tests
Message-ID: <20150102140439.2A0A018795C@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-02 15:04:38 +0100 (Fri, 02 Jan 2015)
New Revision: 1042

Added:
   pkg/pompExamples/tests/bbp.R
   pkg/pompExamples/tests/bbp.Rout.save
   pkg/pompExamples/tests/ebola.R
   pkg/pompExamples/tests/ebola.Rout.save
   pkg/pompExamples/tests/parus.R
   pkg/pompExamples/tests/parus.Rout.save
Removed:
   pkg/pompExamples/tests/examples.R
Modified:
   pkg/pompExamples/DESCRIPTION
   pkg/pompExamples/inst/examples/ebola.R
   pkg/pompExamples/tests/budmoth.Rout.save
   pkg/pompExamples/tests/pertussis.Rout.save
Log:
- fix ebola example
- rearrange tests directory

Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2015-01-02 02:39:51 UTC (rev 1041)
+++ pkg/pompExamples/DESCRIPTION	2015-01-02 14:04:38 UTC (rev 1042)
@@ -1,8 +1,8 @@
 Package: pompExamples
 Type: Package
 Title: Additional pomp examples
-Version: 0.25-2
-Date: 2015-01-01
+Version: 0.25-3
+Date: 2015-01-02
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),
 	   email="kingaa at umich.edu"),

Modified: pkg/pompExamples/inst/examples/ebola.R
===================================================================
--- pkg/pompExamples/inst/examples/ebola.R	2015-01-02 02:39:51 UTC (rev 1041)
+++ pkg/pompExamples/inst/examples/ebola.R	2015-01-02 14:04:38 UTC (rev 1042)
@@ -54,6 +54,7 @@
 mutate(dat,deaths=NA) -> dat
 
 ebolaModel <- function (country=c("Guinea", "SierraLeone", "Liberia", "WestAfrica"),
+                        data = NULL,
                         timestep = 0.01, nstageE = 3L,
                         type = c("raw","cum"), na.rm = FALSE, least.sq = FALSE) {
 
@@ -77,14 +78,18 @@
              S_0=1-index_case,E_0=index_case/2-5e-9,
              I_0=index_case/2-5e-9,R_0=1e-8)
 
-  if (ctry=="WestAfrica") {
-    dat <- ddply(dat,~week,summarize,
-                 cases=sum(cases,na.rm=TRUE),
-                 deaths=sum(deaths,na.rm=TRUE))
+  if (is.null(data)) {
+    if (ctry=="WestAfrica") {
+      dat <- ddply(dat,~week,summarize,
+                   cases=sum(cases,na.rm=TRUE),
+                   deaths=sum(deaths,na.rm=TRUE))
+    } else {
+      dat <- subset(dat,country==ctry,select=-country)
+    }
   } else {
-    dat <- subset(dat,country==ctry,select=-country)
+    dat <- data
   }
-
+    
   if (na.rm) {
     dat <- mutate(subset(dat,!is.na(cases)),week=week-min(week)+1)
   }

Added: pkg/pompExamples/tests/bbp.R
===================================================================
--- pkg/pompExamples/tests/bbp.R	                        (rev 0)
+++ pkg/pompExamples/tests/bbp.R	2015-01-02 14:04:38 UTC (rev 1042)
@@ -0,0 +1,7 @@
+library(pompExamples)
+
+set.seed(47575684L)
+
+pompExample(bbp)
+pf <- pfilter(simulate(bbp),Np=100,max.fail=Inf)
+tj <- trajectory(bbp)

Added: pkg/pompExamples/tests/bbp.Rout.save
===================================================================
--- pkg/pompExamples/tests/bbp.Rout.save	                        (rev 0)
+++ pkg/pompExamples/tests/bbp.Rout.save	2015-01-02 14:04:38 UTC (rev 1042)
@@ -0,0 +1,33 @@
+
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(pompExamples)
+Loading required package: pomp
+Loading required package: subplex
+Loading required package: nloptr
+> 
+> set.seed(47575684L)
+> 
+> pompExample(bbp)
+newly created pomp object(s):
+ bbp 
+> pf <- pfilter(simulate(bbp),Np=100,max.fail=Inf)
+> tj <- trajectory(bbp)
+> 
+> proc.time()
+   user  system elapsed 
+  0.573   0.038   0.597 

Modified: pkg/pompExamples/tests/budmoth.Rout.save
===================================================================
--- pkg/pompExamples/tests/budmoth.Rout.save	2015-01-02 02:39:51 UTC (rev 1041)
+++ pkg/pompExamples/tests/budmoth.Rout.save	2015-01-02 14:04:38 UTC (rev 1042)
@@ -127,4 +127,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.649   0.033   0.670 
+  0.614   0.056   0.652 

Added: pkg/pompExamples/tests/ebola.R
===================================================================
--- pkg/pompExamples/tests/ebola.R	                        (rev 0)
+++ pkg/pompExamples/tests/ebola.R	2015-01-02 14:04:38 UTC (rev 1042)
@@ -0,0 +1,15 @@
+library(pompExamples)
+
+set.seed(47575684L)
+
+pompExample(ebola)
+ebolaModel(country="Guinea") -> po
+pf <- pfilter(simulate(po),Np=100)
+tj <- trajectory(po)
+
+ebolaModel(country="SierraLeone",na.rm=TRUE,type='cum') -> po
+pf <- pfilter(simulate(po),Np=100)
+tj <- trajectory(po)
+dd <- simulate(po,as.data.frame=TRUE,obs=TRUE)
+dd$week <- dd$time
+po <- ebolaModel(data=subset(dd,select=c(week,cases,deaths)))

Added: pkg/pompExamples/tests/ebola.Rout.save
===================================================================
--- pkg/pompExamples/tests/ebola.Rout.save	                        (rev 0)
+++ pkg/pompExamples/tests/ebola.Rout.save	2015-01-02 14:04:38 UTC (rev 1042)
@@ -0,0 +1,43 @@
+
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(pompExamples)
+Loading required package: pomp
+Loading required package: subplex
+Loading required package: nloptr
+> 
+> set.seed(47575684L)
+> 
+> pompExample(ebola)
+Loading required package: plyr
+Loading required package: reshape2
+newly created pomp object(s):
+ ebolaModel 
+> ebolaModel(country="Guinea") -> po
+> pf <- pfilter(simulate(po),Np=100)
+> tj <- trajectory(po)
+> 
+> ebolaModel(country="SierraLeone",na.rm=TRUE,type='cum') -> po
+> pf <- pfilter(simulate(po),Np=100)
+> tj <- trajectory(po)
+> dd <- simulate(po,as.data.frame=TRUE,obs=TRUE)
+> dd$week <- dd$time
+> po <- ebolaModel(data=subset(dd,select=c(week,cases,deaths)))
+> 
+> proc.time()
+   user  system elapsed 
+  1.100   0.034   1.119 

Deleted: pkg/pompExamples/tests/examples.R
===================================================================
--- pkg/pompExamples/tests/examples.R	2015-01-02 02:39:51 UTC (rev 1041)
+++ pkg/pompExamples/tests/examples.R	2015-01-02 14:04:38 UTC (rev 1042)
@@ -1,33 +0,0 @@
-library(pompExamples)
-
-set.seed(47575684L)
-
-po <- pompExample(parus,proc="Ricker",meas="lognormal",envir=NULL)
-pf <- pfilter(simulate(po$parus),Np=100,max.fail=Inf)
-tj <- trajectory(po$parus)
-
-po <- pompExample(parus,proc="Ricker",meas="negbin",envir=NULL)
-pf <- pfilter(simulate(po$parus),Np=100,max.fail=Inf)
-
-po <- pompExample(parus,proc="Ricker",meas="Poisson",envir=NULL)
-pf <- pfilter(simulate(po$parus),Np=100,max.fail=Inf)
-
-po <- pompExample(parus,proc="Gompertz",meas="Poisson",envir=NULL)
-pf <- pfilter(simulate(po[[1]]),Np=100,max.fail=Inf)
-tj <- trajectory(po[[1]])
-
-po <- pompExample(parus,proc="Gompertz",meas="lognormal",envir=NULL)
-pf <- pfilter(simulate(po$parus),Np=100,max.fail=Inf)
-
-pompExample(bbp)
-pf <- pfilter(simulate(bbp),Np=100,max.fail=Inf)
-tj <- trajectory(bbp)
-
-pompExample(ebola)
-ebolaModel(country="Guinea") -> po
-pf <- pfilter(simulate(po),Np=100)
-tj <- trajectory(po)
-
-ebolaModel(country="SierraLeone",na.rm=TRUE,type='cum') -> po
-pf <- pfilter(simulate(po),Np=100)
-tj <- trajectory(po)

Copied: pkg/pompExamples/tests/parus.R (from rev 1041, pkg/pompExamples/tests/examples.R)
===================================================================
--- pkg/pompExamples/tests/parus.R	                        (rev 0)
+++ pkg/pompExamples/tests/parus.R	2015-01-02 14:04:38 UTC (rev 1042)
@@ -0,0 +1,20 @@
+library(pompExamples)
+
+set.seed(47575684L)
+
+po <- pompExample(parus,proc="Ricker",meas="lognormal",envir=NULL)
+pf <- pfilter(simulate(po$parus),Np=100,max.fail=Inf)
+tj <- trajectory(po$parus)
+
+po <- pompExample(parus,proc="Ricker",meas="negbin",envir=NULL)
+pf <- pfilter(simulate(po$parus),Np=100,max.fail=Inf)
+
+po <- pompExample(parus,proc="Ricker",meas="Poisson",envir=NULL)
+pf <- pfilter(simulate(po$parus),Np=100,max.fail=Inf)
+
+po <- pompExample(parus,proc="Gompertz",meas="Poisson",envir=NULL)
+pf <- pfilter(simulate(po[[1]]),Np=100,max.fail=Inf)
+tj <- trajectory(po[[1]])
+
+po <- pompExample(parus,proc="Gompertz",meas="lognormal",envir=NULL)
+pf <- pfilter(simulate(po$parus),Np=100,max.fail=Inf)

Added: pkg/pompExamples/tests/parus.Rout.save
===================================================================
--- pkg/pompExamples/tests/parus.Rout.save	                        (rev 0)
+++ pkg/pompExamples/tests/parus.Rout.save	2015-01-02 14:04:38 UTC (rev 1042)
@@ -0,0 +1,44 @@
+
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(pompExamples)
+Loading required package: pomp
+Loading required package: subplex
+Loading required package: nloptr
+> 
+> set.seed(47575684L)
+> 
+> po <- pompExample(parus,proc="Ricker",meas="lognormal",envir=NULL)
+> pf <- pfilter(simulate(po$parus),Np=100,max.fail=Inf)
+> tj <- trajectory(po$parus)
+> 
+> po <- pompExample(parus,proc="Ricker",meas="negbin",envir=NULL)
+> pf <- pfilter(simulate(po$parus),Np=100,max.fail=Inf)
+> 
+> po <- pompExample(parus,proc="Ricker",meas="Poisson",envir=NULL)
+> pf <- pfilter(simulate(po$parus),Np=100,max.fail=Inf)
+> 
+> po <- pompExample(parus,proc="Gompertz",meas="Poisson",envir=NULL)
+> pf <- pfilter(simulate(po[[1]]),Np=100,max.fail=Inf)
+> tj <- trajectory(po[[1]])
+> 
+> po <- pompExample(parus,proc="Gompertz",meas="lognormal",envir=NULL)
+> pf <- pfilter(simulate(po$parus),Np=100,max.fail=Inf)
+> 
+> proc.time()
+   user  system elapsed 
+  0.572   0.037   0.596 

Modified: pkg/pompExamples/tests/pertussis.Rout.save
===================================================================
--- pkg/pompExamples/tests/pertussis.Rout.save	2015-01-02 02:39:51 UTC (rev 1041)
+++ pkg/pompExamples/tests/pertussis.Rout.save	2015-01-02 14:04:38 UTC (rev 1042)
@@ -168,4 +168,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 23.494   0.034  23.544 
+ 23.697   0.033  23.738 


From noreply at r-forge.r-project.org  Fri Jan  2 15:04:49 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri,  2 Jan 2015 15:04:49 +0100 (CET)
Subject: [Pomp-commits] r1043 - in pkg/pomp: . R inst man
Message-ID: <20150102140449.712F918795C@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-02 15:04:49 +0100 (Fri, 02 Jan 2015)
New Revision: 1043

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/simulate-pomp.R
   pkg/pomp/inst/NEWS
   pkg/pomp/inst/NEWS.Rd
   pkg/pomp/man/simulate-pomp.Rd
Log:
- new 'include.data' argument to 'simulate'

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-01-02 14:04:38 UTC (rev 1042)
+++ pkg/pomp/DESCRIPTION	2015-01-02 14:04:49 UTC (rev 1043)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.56-2
-Date: 2015-01-01
+Version: 0.57-1
+Date: 2015-01-02
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),

Modified: pkg/pomp/R/simulate-pomp.R
===================================================================
--- pkg/pomp/R/simulate-pomp.R	2015-01-02 14:04:38 UTC (rev 1042)
+++ pkg/pomp/R/simulate-pomp.R	2015-01-02 14:04:49 UTC (rev 1043)
@@ -3,6 +3,7 @@
 simulate.internal <- function (object, nsim = 1, seed = NULL, params,
                                states = FALSE, obs = FALSE,
                                times, t0, as.data.frame = FALSE,
+                               include.data = FALSE,
                                .getnativesymbolinfo = TRUE, ...) {
 
   if (missing(times))
@@ -18,6 +19,7 @@
   obs <- as.logical(obs)
   states <- as.logical(states)
   as.data.frame <- as.logical(as.data.frame)
+  include.data <- as.logical(include.data)
 
   if (missing(params))
     params <- coef(object)
@@ -109,6 +111,11 @@
         retval$sim <- factor(1)
       }
     }
+
+    if (include.data) {
+      od <- as.data.frame(object)
+      retval <- merge(od,retval,sort=FALSE)
+    }
     
   }
 
@@ -119,8 +126,9 @@
           "simulate",
           signature=signature(object="pomp"),
           definition=function (object, nsim = 1, seed = NULL, params,
-                               states = FALSE, obs = FALSE,
-                               times, t0, as.data.frame = FALSE, ...)
+            states = FALSE, obs = FALSE,
+            times, t0, as.data.frame = FALSE, include.data = FALSE,
+            ...)
           simulate.internal(
                             object=object,
                             nsim=nsim,
@@ -131,6 +139,7 @@
                             times=times,
                             t0=t0,
                             as.data.frame=as.data.frame,
+                            include.data=include.data,
                             ...
                             )
           )

Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS	2015-01-02 14:04:38 UTC (rev 1042)
+++ pkg/pomp/inst/NEWS	2015-01-02 14:04:49 UTC (rev 1043)
@@ -1,5 +1,12 @@
 _N_e_w_s _f_o_r _p_a_c_k_a_g_e '_p_o_m_p'
 
+_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._5_7-_1:
+
+        ? ?simulate? has a new argument, ?include.data?, that when used
+          in conjuncion with ?as.data.frame=TRUE? will include the
+          actual data in the resulting data frame along with the
+          simulations.
+
 _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._5_6-_1:
 
         ? Revamped the ?pompExample? function.  A search path for

Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd	2015-01-02 14:04:38 UTC (rev 1042)
+++ pkg/pomp/inst/NEWS.Rd	2015-01-02 14:04:49 UTC (rev 1043)
@@ -1,5 +1,10 @@
 \name{NEWS}
 \title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 0.57-1}{
+  \itemize{
+    \item \code{simulate} has a new argument, \code{include.data}, that when used in conjuncion with \code{as.data.frame=TRUE} will include the actual data in the resulting data frame along with the simulations.
+  }
+}
 \section{Changes in \pkg{pomp} version 0.56-1}{
   \itemize{
     \item Revamped the \code{pompExample} function.

Modified: pkg/pomp/man/simulate-pomp.Rd
===================================================================
--- pkg/pomp/man/simulate-pomp.Rd	2015-01-02 14:04:38 UTC (rev 1042)
+++ pkg/pomp/man/simulate-pomp.Rd	2015-01-02 14:04:49 UTC (rev 1043)
@@ -9,7 +9,7 @@
 \usage{
 \S4method{simulate}{pomp}(object, nsim = 1, seed = NULL, params,
          states = FALSE, obs = FALSE, times, t0,
-         as.data.frame = FALSE, \dots)
+         as.data.frame = FALSE, include.data = FALSE, \dots)
 }
 \arguments{
   \item{object}{An object of class \code{pomp}.}
@@ -34,8 +34,11 @@
     \code{t0} specifies the start time (the time at which the initial conditions hold).
     The default for \code{times} is is \code{times=time(object,t0=FALSE)} and \code{t0=timezero(object)}, respectively.
   }
-  \item{as.data.frame}{
-    logical; if \code{TRUE}, return the result as a data-frame.
+  \item{as.data.frame, include.data}{
+    logical; if \code{as.data.frame=TRUE}, the results are returned as a data-frame.
+    A factor variable, \sQuote{sim}, distinguishes one simulation from another.
+    If, in addition, \code{include.data=TRUE}, the original data are included as an additional \sQuote{simulation}.
+    If \code{as.data.frame=FALSE}, \code{include.data} is ignored.
   }
   \item{\dots}{further arguments that are currently ignored.}
 }
@@ -64,6 +67,8 @@
 pompExample(ou2)
 x <- simulate(ou2,seed=3495485,nsim=10)
 x <- simulate(ou2,seed=3495485,nsim=10,states=TRUE,obs=TRUE)
+x <- simulate(ou2,seed=3495485,nsim=10,obs=TRUE,
+              as.data.frame=TRUE,include.data=TRUE)
 }
 \author{Aaron A. King \email{kingaa at umich dot edu}}
 \seealso{\link{pomp}}


From noreply at r-forge.r-project.org  Wed Jan  7 00:07:54 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  7 Jan 2015 00:07:54 +0100 (CET)
Subject: [Pomp-commits] r1044 - in pkg/pompExamples: . inst/examples src
	tests
Message-ID: <20150106230754.53D4C18431B@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-07 00:07:54 +0100 (Wed, 07 Jan 2015)
New Revision: 1044

Removed:
   pkg/pompExamples/src/ebola.c
Modified:
   pkg/pompExamples/DESCRIPTION
   pkg/pompExamples/inst/examples/ebola.R
   pkg/pompExamples/tests/bbp.Rout.save
   pkg/pompExamples/tests/budmoth.Rout.save
   pkg/pompExamples/tests/ebola.Rout.save
   pkg/pompExamples/tests/parus.Rout.save
   pkg/pompExamples/tests/pertussis.Rout.save
Log:
- pull Ebola example back to using on-the-fly compiled codes

Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2015-01-02 14:04:49 UTC (rev 1043)
+++ pkg/pompExamples/DESCRIPTION	2015-01-06 23:07:54 UTC (rev 1044)
@@ -1,8 +1,8 @@
 Package: pompExamples
 Type: Package
 Title: Additional pomp examples
-Version: 0.25-3
-Date: 2015-01-02
+Version: 0.25-4
+Date: 2015-01-05
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),
 	   email="kingaa at umich.edu"),

Modified: pkg/pompExamples/inst/examples/ebola.R
===================================================================
--- pkg/pompExamples/inst/examples/ebola.R	2015-01-02 14:04:49 UTC (rev 1043)
+++ pkg/pompExamples/inst/examples/ebola.R	2015-01-06 23:07:54 UTC (rev 1044)
@@ -53,6 +53,117 @@
 dat <- melt(dat,id="week",variable.name="country",value.name="cases")
 mutate(dat,deaths=NA) -> dat
 
+
+paruntrans <- Csnippet('
+  double *IC = &S_0;
+  double *TIC = &TS_0;
+  TN = log(N);
+  TR0 = log(R0);
+  Talpha = log(alpha);
+  Tgamma = log(gamma);
+  Trho = logit(rho);
+  Tk = log(k);
+  Tcfr = logit(cfr);
+  to_log_barycentric(TIC,IC,4);
+')
+
+partrans <- Csnippet('
+  double *IC = &S_0;
+  double *TIC = &TS_0;
+  TN = exp(N);
+  TR0 = exp(R0);
+  Talpha = exp(alpha);
+  Tgamma = exp(gamma);
+  Trho = expit(rho);
+  Tk = exp(k);
+  Tcfr = expit(cfr);
+  from_log_barycentric(TIC,IC,4);
+')
+
+##  Observation model: hierarchical model for cases and deaths
+## p(R_t, D_t| C_t) = p(R_t | C_t) * p(D_t | C_t, R_t)
+## p(R_t | C_t): Negative binomial with mean rho * C_t and dispersion parameter 1 / k
+## p(D_t | C_t, R_t): Binomial B(R_t, cfr)
+
+dObs <- Csnippet('
+  double f;
+  if (k > 0.0)
+    f = dnbinom_mu(nearbyint(cases),1.0/k,rho*N_EI,1);
+  else
+    f = dpois(nearbyint(cases),rho*N_EI,1);
+  lik = (give_log) ? f : exp(f);
+')
+
+dObsLS <- Csnippet('
+  double f;
+  f = dnorm(cases,rho*N_EI,k,1);
+  lik = (give_log) ? f : exp(f);
+')
+
+rObs <- Csnippet('
+  if (k > 0) {
+    cases = rnbinom_mu(1.0/k,rho*N_EI);
+    deaths = rnbinom_mu(1.0/k,rho*cfr*N_IR);
+  } else {
+    cases = rpois(rho*N_EI);
+    deaths = rpois(rho*cfr*N_IR);
+  }')
+
+rObsLS <- Csnippet('
+  cases = rnorm(rho*N_EI,k);
+  deaths = NA_REAL;
+')
+
+rSim <- Csnippet('
+  double lambda, beta;
+  double *E = &E1;
+  beta = R0 * gamma; // Transmission rate
+  lambda = beta * I / N; // Force of infection
+  int i;
+
+  // Transitions
+  // From class S
+  double transS = rbinom(S, 1.0 - exp(- lambda * dt)); // No of infections
+  // From class E
+  double transE[nstageE]; // No of transitions between classes E
+  for(i = 0; i < nstageE; i++){
+    transE[i] = rbinom(E[i], 1.0 - exp(- nstageE * alpha * dt));
+  }
+  // From class I
+  double transI = rbinom(I, 1.0 - exp(- gamma * dt)); // No of transitions I->R
+
+  // Balance the equations
+  S -= transS;
+  E[0] += transS - transE[0];
+  for(i=1; i < nstageE; i++) {
+    E[i] += transE[i-1] - transE[i];
+  }
+  I += transE[nstageE - 1] - transI;
+  R += transI;
+  N_EI += transE[nstageE - 1]; // No of transitions from E to I
+  N_IR += transI; // No of transitions from I to R
+')
+
+skel <- Csnippet('
+  double lambda, beta;
+  double *E = &E1;
+  double *DE = &DE1;
+  beta = R0 * gamma; // Transmission rate
+  lambda = beta * I / N; // Force of infection
+  int i;
+
+  // Balance the equations
+  DS = - lambda * S;
+  DE[0] = lambda * S - nstageE * alpha * E[0];
+  for (i=1; i < nstageE; i++)
+    DE[i] = nstageE * alpha * (E[i-1]-E[i]);
+  DI = nstageE * alpha * E[nstageE-1] - gamma * I;
+  DR = gamma * I;
+  DN_EI = nstageE * alpha * E[nstageE-1];
+  DN_IR = gamma * I;
+')
+
+
 ebolaModel <- function (country=c("Guinea", "SierraLeone", "Liberia", "WestAfrica"),
                         data = NULL,
                         timestep = 0.01, nstageE = 3L,
@@ -69,7 +180,10 @@
   infectious_period <- 7/7
   index_case <- 10/pop
   dt <- timestep
+  nstageE <- as.integer(nstageE)
 
+  globs <- paste0("static int nstageE = ",nstageE,";");
+
   theta <- c(N=pop,R0=1.4,
              alpha=-1/(nstageE*dt)*log(1-nstageE*dt/incubation_period),
              gamma=-log(1-dt/infectious_period)/dt,
@@ -89,7 +203,7 @@
   } else {
     dat <- data
   }
-    
+
   if (na.rm) {
     dat <- mutate(subset(dat,!is.na(cases)),week=week-min(week)+1)
   }
@@ -103,20 +217,20 @@
        times="week",
        t0=0,
        params=theta,
+       globals=globs,
        obsnames=c("cases","deaths"),
        statenames=c("S","E1","I","R","N_EI","N_IR"),
        zeronames=if (type=="raw") c("N_EI","N_IR") else character(0),
        paramnames=c("N","R0","alpha","gamma","rho","k","cfr",
          "S_0","E_0","I_0","R_0"),
-       nstageE=as.integer(nstageE),
-       PACKAGE="pompExamples",
-       dmeasure=if (least.sq) "_ebola_dObsLS" else "_ebola_dObs",
-       rmeasure=if (least.sq) "_ebola_rObsLS" else "_ebola_rObs",
-       rprocess=discrete.time.sim(step.fun="_ebola_rSim",delta.t=timestep),
-       skeleton="_ebola_skel",
+       nstageE=nstageE,
+       dmeasure=if (least.sq) dObsLS else dObs,
+       rmeasure=if (least.sq) rObsLS else rObs,
+       rprocess=discrete.time.sim(step.fun=rSim,delta.t=timestep),
+       skeleton=skel,
        skeleton.type="vectorfield",
-       parameter.transform="_ebola_par_trans",
-       parameter.inv.transform="_ebola_par_untrans",
+       parameter.transform=partrans,
+       parameter.inv.transform=paruntrans,
        initializer=function (params, t0, nstageE, ...) {
          all.state.names <- c("S",paste0("E",1:nstageE),"I","R","N_EI","N_IR")
          comp.names <- c("S",paste0("E",1:nstageE),"I","R")

Deleted: pkg/pompExamples/src/ebola.c
===================================================================
--- pkg/pompExamples/src/ebola.c	2015-01-02 14:04:49 UTC (rev 1043)
+++ pkg/pompExamples/src/ebola.c	2015-01-06 23:07:54 UTC (rev 1044)
@@ -1,187 +0,0 @@
-// SEIR Ebola model
-
-#include <R.h>
-#include <Rmath.h>
-#include <R_ext/Rdynload.h>
-#include <pomp.h>
-
-// State variables
-#define S (x[stateindex[0]]) // Susceptible
-#define E(J) (x[stateindex[1] + (J)]) // Exposed
-#define I (x[stateindex[2]]) // Infected
-#define R (x[stateindex[3]]) // Removed
-#define N_EI (x[stateindex[4]]) // Number of transitions from E to I
-#define N_IR (x[stateindex[5]]) // Number of transitions from I to R
-
-// Variations
-#define DS (f[stateindex[0]]) // Susceptible
-#define DE(J) (f[stateindex[1] + (J)]) // Exposed
-#define DI (f[stateindex[2]]) // Infected
-#define DR (f[stateindex[3]]) // Removed
-#define DN_EI (f[stateindex[4]]) // Number of transitions from E to I
-#define DN_IR (f[stateindex[5]]) // Number of transitions from I to R
-
-// Parameters on the natural scale (all rates are per day)
-#define N (p[parindex[0]]) // Population size
-#define R0 (p[parindex[1]]) // Basic reproduction number
-#define alpha (p[parindex[2]]) // Inverse of latency period
-#define gamma (p[parindex[3]]) // Inverse of duration of infection
-#define rho (p[parindex[4]]) // Reporting probability
-#define k (p[parindex[5]]) // Reporting overdispersion
-#define cfr (p[parindex[6]]) // Case-fatality ratio
-#define IC(J) (p[parindex[7] + (J)]) // Initial conditions
-
-// Parameters on the transformed scale (all rates are per day)
-#define TN (pt[parindex[0]]) // Population size
-#define TR0 (pt[parindex[1]]) // Basic reproduction number
-#define Talpha (pt[parindex[2]]) // Inverse of latency period
-#define Tgamma (pt[parindex[3]]) // Inverse of duration of infection
-#define Trho (pt[parindex[4]]) // Reporting probability
-#define Tk (pt[parindex[5]]) // Reporting overdispersion
-#define Tcfr (pt[parindex[6]]) // Case-fatality ratio
-#define TIC(J) (pt[parindex[7] + (J)]) // Initial conditions
-
-// Observations
-#define cases (y[obsindex[0]]) // Number of reported cases
-#define deaths (y[obsindex[1]]) // Number of reported deaths
-
-// Transforms the parameters to the transformed scale
-void _ebola_par_untrans (double *pt, double *p, int *parindex){
-  TN = log(N);
-  TR0 = log(R0);
-  Talpha = log(alpha);
-  Tgamma = log(gamma);
-  Trho = logit(rho);
-  Tk = log(k);
-  Tcfr = logit(cfr);
-  to_log_barycentric(&(TIC(0)),&(IC(0)),4);
-}
-
-// Transforms the parameters to the natural scale
-void _ebola_par_trans (double *pt, double *p, int *parindex){
-  TN = exp(N);
-  TR0 = exp(R0);
-  Talpha = exp(alpha);
-  Tgamma = exp(gamma);
-  Trho = expit(rho);
-  Tk = exp(k);
-  Tcfr = expit(cfr);
-  from_log_barycentric(&(TIC(0)),&(IC(0)),4);
-}
-
-//  Observation model: hierarchical model for cases and deaths
-// p(R_t, D_t| C_t) = p(R_t | C_t) * p(D_t | C_t, R_t)
-// p(R_t | C_t): Negative binomial with mean rho * C_t and dispersion parameter 1 / k
-// p(D_t | C_t, R_t): Binomial B(R_t, cfr)
-void _ebola_dObs (double *lik, double *y, double *x, double *p, int give_log,
-		  int *obsindex, int *stateindex, int *parindex, int *covindex,
-		  int ncovars, double *covars, double t) {
-  double f;
-  if (k > 0.0)
-    f = dnbinom_mu(nearbyint(cases),1.0/k,rho*N_EI,1);
-  // f += dnbinom_mu(nearbyint(deaths), 1.0 / k, rho * cfr * N_IR, 1);
-  else
-    f = dpois(nearbyint(cases),rho*N_EI,1);
-  *lik = (give_log) ? f : exp(f);
-}
-
-// For least-squares trajectory-matching:
-void _ebola_dObsLS (double *lik, double *y, double *x, double *p, int give_log,
-		    int *obsindex, int *stateindex, int *parindex, int *covindex,
-		    int ncovars, double *covars, double t) {
-  double f;
-  f = dnorm(cases,rho*N_EI,k,1);
-  *lik = (give_log) ? f : exp(f);
-}
-
-void _ebola_rObs (double *y, double *x, double *p,
-		  int *obsindex, int *stateindex, int *parindex, int *covindex,
-		  int ncovars, double *covars, double t)
-{
-  if (k > 0) {
-    cases = rnbinom_mu(1.0/k,rho*N_EI);
-    deaths = rnbinom_mu(1.0/k,rho*cfr*N_IR);
-  } else {
-    cases = rpois(rho*N_EI);
-    deaths = rpois(rho*cfr*N_IR);
-  }
-}
-
-// For least-squares trajectory-matching:
-void _ebola_rObsLS (double *y, double *x, double *p,
-		    int *obsindex, int *stateindex, int *parindex, int *covindex,
-		    int ncovars, double *covars, double t)
-{
-  cases = rnorm(rho*N_EI,k);
-  deaths = NA_REAL;
-}
-
-
-// Process model
-void _ebola_rSim (double *x, const double *p,
-		  const int *stateindex, const int *parindex, const int *covindex,
-		  int covdim, const double *covars,
-		  double t, double dt) {
-
-  // Retrieve user data in the pomp object
-  int *(*get_pomp_userdata_int)(const char *);
-  get_pomp_userdata_int = (int *(*)(const char *)) R_GetCCallable("pomp","get_pomp_userdata_int");
-  int nstageE = *(get_pomp_userdata_int("nstageE")); // Number of stages in the E class
-
-  // Other parameters
-  double lambda, beta;
-  beta = R0 * gamma; // Transmission rate
-  lambda = beta * I / N; // Force of infection
-  int i;
-
-  // Transitions
-
-  // From class S
-  double transS = rbinom(S, 1.0 - exp(- lambda * dt)); // No of infections
-
-  // From class E
-  double transE[nstageE]; // No of transitions between classes E
-  for(i = 0; i < nstageE; i++){
-    transE[i] = rbinom(E(i), 1.0 - exp(- nstageE * alpha * dt));
-  }
-
-  // From class I
-  double transI = rbinom(I, 1.0 - exp(- gamma * dt)); // No of transitions I->R
-
-  // Balance the equations
-  S -= transS;
-  E(0) += transS - transE[0];
-  for(i=1; i < nstageE; i++) {
-    E(i) += transE[i-1] - transE[i];
-  }
-  I += transE[nstageE - 1] - transI;
-  R += transI;
-  N_EI += transE[nstageE - 1]; // No of transitions from E to I
-  N_IR += transI; // No of transitions from I to R
-}
-
-// Continuous-time deterministic skeleton
-void _ebola_skel (double *f, double *x, double *p,
-		  int *stateindex, int *parindex, int *covindex,
-		  int ncovars, double *covars, double t) {
-
-  // Retrieve user data in the pomp object
-  int *(*get_pomp_userdata_int)(const char *);
-  get_pomp_userdata_int = (int *(*)(const char *)) R_GetCCallable("pomp","get_pomp_userdata_int");
-  int nstageE = *(get_pomp_userdata_int("nstageE")); // Number of stages in the E class
-
-  // Other parameters
-  double lambda, beta;
-  beta = R0 * gamma; // Transmission rate
-  lambda = beta * I / N; // Force of infection
-  int i;
-
-  // Balance the equations
-  DS = - lambda * S;
-  DE(0) = lambda * S - nstageE * alpha * E(0);
-  for(i=1; i < nstageE; i++) DE(i) = nstageE * alpha * (E(i - 1) -  E(i));
-  DI = nstageE * alpha * E(nstageE - 1) - gamma * I;
-  DR = gamma * I;
-  DN_EI = nstageE * alpha * E(nstageE - 1);
-  DN_IR = gamma * I;
-}

Modified: pkg/pompExamples/tests/bbp.Rout.save
===================================================================
--- pkg/pompExamples/tests/bbp.Rout.save	2015-01-02 14:04:49 UTC (rev 1043)
+++ pkg/pompExamples/tests/bbp.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
@@ -23,11 +23,11 @@
 > set.seed(47575684L)
 > 
 > pompExample(bbp)
-newly created pomp object(s):
+newly created object(s):
  bbp 
 > pf <- pfilter(simulate(bbp),Np=100,max.fail=Inf)
 > tj <- trajectory(bbp)
 > 
 > proc.time()
    user  system elapsed 
-  0.573   0.038   0.597 
+  0.728   0.028   0.786 

Modified: pkg/pompExamples/tests/budmoth.Rout.save
===================================================================
--- pkg/pompExamples/tests/budmoth.Rout.save	2015-01-02 14:04:49 UTC (rev 1043)
+++ pkg/pompExamples/tests/budmoth.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
@@ -127,4 +127,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.614   0.056   0.652 
+  0.732   0.060   0.818 

Modified: pkg/pompExamples/tests/ebola.Rout.save
===================================================================
--- pkg/pompExamples/tests/ebola.Rout.save	2015-01-02 14:04:49 UTC (rev 1043)
+++ pkg/pompExamples/tests/ebola.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
@@ -25,19 +25,43 @@
 > pompExample(ebola)
 Loading required package: plyr
 Loading required package: reshape2
-newly created pomp object(s):
+newly created object(s):
  ebolaModel 
 > ebolaModel(country="Guinea") -> po
+make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
+gcc -std=gnu99 -I/usr/local/apps/R/R-3.1.2/lib64/R/include -DNDEBUG  -I/usr/local/include    -I/usr/local/apps/R/R-3.1.2/lib64/R/library/pomp/include -fpic  -g -O2  -c /tmp/RtmpU0NeMt/pomp2583FF7C2A2A.c -o /tmp/RtmpU0NeMt/pomp2583FF7C2A2A.o
+gcc -std=gnu99 -shared -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -L/usr/local/lib64 -o /tmp/RtmpU0NeMt/pomp2583FF7C2A2A.so /tmp/RtmpU0NeMt/pomp2583FF7C2A2A.o -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -lR
+make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
+make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
+make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
+model codes written to '/tmp/RtmpU0NeMt/pomp2583FF7C2A2A.c' 
+link to shared-object library '/tmp/RtmpU0NeMt/pomp2583FF7C2A2A.so' 
 > pf <- pfilter(simulate(po),Np=100)
 > tj <- trajectory(po)
 > 
 > ebolaModel(country="SierraLeone",na.rm=TRUE,type='cum') -> po
+make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
+gcc -std=gnu99 -I/usr/local/apps/R/R-3.1.2/lib64/R/include -DNDEBUG  -I/usr/local/include    -I/usr/local/apps/R/R-3.1.2/lib64/R/library/pomp/include -fpic  -g -O2  -c /tmp/RtmpU0NeMt/pompDA1B7D4C88B1.c -o /tmp/RtmpU0NeMt/pompDA1B7D4C88B1.o
+gcc -std=gnu99 -shared -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -L/usr/local/lib64 -o /tmp/RtmpU0NeMt/pompDA1B7D4C88B1.so /tmp/RtmpU0NeMt/pompDA1B7D4C88B1.o -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -lR
+make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
+make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
+make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
+model codes written to '/tmp/RtmpU0NeMt/pompDA1B7D4C88B1.c' 
+link to shared-object library '/tmp/RtmpU0NeMt/pompDA1B7D4C88B1.so' 
 > pf <- pfilter(simulate(po),Np=100)
 > tj <- trajectory(po)
 > dd <- simulate(po,as.data.frame=TRUE,obs=TRUE)
 > dd$week <- dd$time
 > po <- ebolaModel(data=subset(dd,select=c(week,cases,deaths)))
+make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
+gcc -std=gnu99 -I/usr/local/apps/R/R-3.1.2/lib64/R/include -DNDEBUG  -I/usr/local/include    -I/usr/local/apps/R/R-3.1.2/lib64/R/library/pomp/include -fpic  -g -O2  -c /tmp/RtmpU0NeMt/pompBF9800D29D72.c -o /tmp/RtmpU0NeMt/pompBF9800D29D72.o
+gcc -std=gnu99 -shared -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -L/usr/local/lib64 -o /tmp/RtmpU0NeMt/pompBF9800D29D72.so /tmp/RtmpU0NeMt/pompBF9800D29D72.o -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -lR
+make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
+make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
+make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
+model codes written to '/tmp/RtmpU0NeMt/pompBF9800D29D72.c' 
+link to shared-object library '/tmp/RtmpU0NeMt/pompBF9800D29D72.so' 
 > 
 > proc.time()
    user  system elapsed 
-  1.100   0.034   1.119 
+  2.032   0.228   3.798 

Modified: pkg/pompExamples/tests/parus.Rout.save
===================================================================
--- pkg/pompExamples/tests/parus.Rout.save	2015-01-02 14:04:49 UTC (rev 1043)
+++ pkg/pompExamples/tests/parus.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
@@ -41,4 +41,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.572   0.037   0.596 
+  0.716   0.060   0.806 

Modified: pkg/pompExamples/tests/pertussis.Rout.save
===================================================================
--- pkg/pompExamples/tests/pertussis.Rout.save	2015-01-02 14:04:49 UTC (rev 1043)
+++ pkg/pompExamples/tests/pertussis.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
@@ -168,4 +168,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 23.697   0.033  23.738 
+ 18.417   0.068  18.567 


From noreply at r-forge.r-project.org  Wed Jan  7 00:08:16 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  7 Jan 2015 00:08:16 +0100 (CET)
Subject: [Pomp-commits] r1045 - in pkg/pomp: . R src tests
Message-ID: <20150106230816.1AC1D18431B@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-07 00:08:15 +0100 (Wed, 07 Jan 2015)
New Revision: 1045

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/trajectory-pomp.R
   pkg/pomp/src/dmeasure.c
   pkg/pomp/src/dprocess.c
   pkg/pomp/src/initstate.c
   pkg/pomp/src/pomp_internal.h
   pkg/pomp/src/rmeasure.c
   pkg/pomp/src/rprior.c
   pkg/pomp/src/rprocess.c
   pkg/pomp/src/skeleton.c
   pkg/pomp/tests/bbs-trajmatch.Rout.save
   pkg/pomp/tests/bbs.Rout.save
   pkg/pomp/tests/blowflies.Rout.save
   pkg/pomp/tests/dacca.Rout.save
   pkg/pomp/tests/dimchecks.Rout.save
   pkg/pomp/tests/fhn.Rout.save
   pkg/pomp/tests/filtfail.Rout.save
   pkg/pomp/tests/gillespie.Rout.save
   pkg/pomp/tests/gompertz.Rout.save
   pkg/pomp/tests/logistic.Rout.save
   pkg/pomp/tests/ou2-abc.Rout.save
   pkg/pomp/tests/ou2-bsmc.Rout.save
   pkg/pomp/tests/ou2-bsmc2.Rout.save
   pkg/pomp/tests/ou2-forecast.Rout.save
   pkg/pomp/tests/ou2-kalman.Rout.save
   pkg/pomp/tests/ou2-mif-fp.Rout.save
   pkg/pomp/tests/ou2-mif.Rout.save
   pkg/pomp/tests/ou2-mif2.Rout.save
   pkg/pomp/tests/ou2-nlf.Rout.save
   pkg/pomp/tests/ou2-pmcmc.Rout.save
   pkg/pomp/tests/ou2-probe.Rout.save
   pkg/pomp/tests/ou2-procmeas.R
   pkg/pomp/tests/ou2-procmeas.Rout.save
   pkg/pomp/tests/ou2-simulate.Rout.save
   pkg/pomp/tests/ou2-trajmatch.Rout.save
   pkg/pomp/tests/partrans.Rout.save
   pkg/pomp/tests/pfilter.Rout.save
   pkg/pomp/tests/pomppomp.Rout.save
   pkg/pomp/tests/prior.Rout.save
   pkg/pomp/tests/ricker-bsmc.Rout.save
   pkg/pomp/tests/ricker-probe.Rout.save
   pkg/pomp/tests/ricker-spect.Rout.save
   pkg/pomp/tests/ricker.Rout.save
   pkg/pomp/tests/rw2.Rout.save
   pkg/pomp/tests/sir.Rout.save
   pkg/pomp/tests/skeleton.Rout.save
   pkg/pomp/tests/steps.Rout.save
   pkg/pomp/tests/synlik.Rout.save
   pkg/pomp/tests/verhulst.Rout.save
Log:
- use names on dimnames of arrays returned by basic pomp methods

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/DESCRIPTION	2015-01-06 23:08:15 UTC (rev 1045)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.57-1
-Date: 2015-01-02
+Version: 0.57-2
+Date: 2015-01-06
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),

Modified: pkg/pomp/R/trajectory-pomp.R
===================================================================
--- pkg/pomp/R/trajectory-pomp.R	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/R/trajectory-pomp.R	2015-01-06 23:08:15 UTC (rev 1045)
@@ -91,6 +91,8 @@
 
   }
 
+  dimnames(x) <- setNames(dimnames(x),c("variable","rep","time"))
+
   if (as.data.frame) {
     x <- lapply(
                 seq_len(ncol(x)),

Modified: pkg/pomp/src/dmeasure.c
===================================================================
--- pkg/pomp/src/dmeasure.c	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/src/dmeasure.c	2015-01-06 23:08:15 UTC (rev 1045)
@@ -129,7 +129,9 @@
   // create array to store results
   {
     int dim[2] = {nreps, ntimes};
+    const char *dimnm[2] = {"rep","time"};
     PROTECT(F = makearray(2,dim)); nprotect++; 
+    fixdimnames(F,dimnm,2);
   }
 
   // now do computations

Modified: pkg/pomp/src/dprocess.c
===================================================================
--- pkg/pomp/src/dprocess.c	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/src/dprocess.c	2015-01-06 23:08:15 UTC (rev 1045)
@@ -109,7 +109,10 @@
     UNPROTECT(nprotect);
     error("dprocess error: user 'dprocess' must return a %d x %d array",nreps,ntimes-1);
   }
-
+  {
+    const char *dimnms[2] = {"rep","time"};
+    fixdimnames(X,dimnms,2);
+  }
   UNPROTECT(nprotect);
   return X;
 }

Modified: pkg/pomp/src/initstate.c
===================================================================
--- pkg/pomp/src/initstate.c	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/src/initstate.c	2015-01-06 23:08:15 UTC (rev 1045)
@@ -18,6 +18,7 @@
   int npar, nrep, nvar;
   int xdim[2], j, k;
   double *p, *pp, *xp, *xpp;
+  const char *dimnms[2] = {"variable","rep"};
 
   PROTECT(params = as_matrix(params)); nprotect++;
   dim = INTEGER(GET_DIM(params));
@@ -76,6 +77,7 @@
   xdim[0] = nvar; xdim[1] = nrep;
   PROTECT(x = makearray(2,xdim)); nprotect++;
   setrownames(x,statenames,2);
+  fixdimnames(x,dimnms,2);
   xpp = REAL(x);
 
   for (k = 0; k < nvar; k++) xpp[k] = xp[k];

Modified: pkg/pomp/src/pomp_internal.h
===================================================================
--- pkg/pomp/src/pomp_internal.h	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/src/pomp_internal.h	2015-01-06 23:08:15 UTC (rev 1045)
@@ -13,7 +13,6 @@
 # define MATCHNAMES(X,N,W) (matchnames(GET_NAMES(X),(N),(W)))
 # define MATCHROWNAMES(X,N,W) (matchnames(GET_ROWNAMES(GET_DIMNAMES(X)),(N),(W)))
 # define MATCHCOLNAMES(X,N,W) (matchnames(GET_COLNAMES(GET_DIMNAMES(X)),(N),(W)))
-# define MATCH_CHAR_TO_ROWNAMES(X,N,A) (match_char_to_names(GET_ROWNAMES(GET_DIMNAMES(X)),(N),(A)))
 
 // lookup-table structure, as used internally
 typedef struct lookup_table {
@@ -77,27 +76,25 @@
 void unset_pomp_userdata (void);
 
 static R_INLINE SEXP makearray (int rank, int *dim) {
-  int nprotect = 0;
   int *dimp, k;
   double *xp;
   SEXP dimx, x;
-  PROTECT(dimx = NEW_INTEGER(rank)); nprotect++;
+  PROTECT(dimx = NEW_INTEGER(rank));
   dimp = INTEGER(dimx); 
   for (k = 0; k < rank; k++) dimp[k] = dim[k];
-  PROTECT(x = allocArray(REALSXP,dimx)); nprotect++;
+  PROTECT(x = allocArray(REALSXP,dimx));
   xp = REAL(x);
   for (k = 0; k < length(x); k++) xp[k] = NA_REAL;
-  UNPROTECT(nprotect);
+  UNPROTECT(2);
   return x;
 }
 
 static R_INLINE SEXP matchnames (SEXP x, SEXP names, const char *where) {
-  int nprotect = 0;
   int n = length(names);
   int *idx, k;
   SEXP index, nm;
-  PROTECT(nm = AS_CHARACTER(names)); nprotect++;
-  PROTECT(index = match(x,names,0)); nprotect++;
+  PROTECT(nm = AS_CHARACTER(names));
+  PROTECT(index = match(x,names,0));
   idx = INTEGER(index);
   for (k = 0; k < n; k++) {
     if (idx[k]==0) 
@@ -106,31 +103,10 @@
 	    where);
     idx[k] -= 1;
   }
-  UNPROTECT(nprotect);
+  UNPROTECT(2);
   return index;
 }
 
-static R_INLINE SEXP match_char_to_names (SEXP x, int n, char **names) {
-  int nprotect = 0;
-  int *idx, k;
-  SEXP index, nm;
-  PROTECT(nm = NEW_CHARACTER(n)); nprotect++;
-  for (k = 0; k < n; k++) {
-    SET_STRING_ELT(nm,k,mkChar(names[k]));
-  }
-  PROTECT(index = match(x,nm,0)); nprotect++;
-  idx = INTEGER(index);
-  for (k = 0; k < n; k++) {
-    if (idx[k]==0) {
-      UNPROTECT(nprotect);
-      error("variable %s not specified",names[k]);
-    }
-    idx[k] -= 1;
-  }
-  UNPROTECT(nprotect);
-  return index;
-}
-
 static R_INLINE SEXP name_index (SEXP names, SEXP object, const char *slot) {
   SEXP slotnames, index;
   PROTECT(slotnames = GET_SLOT(object,install(slot)));
@@ -144,12 +120,27 @@
 }
 
 static R_INLINE void setrownames (SEXP x, SEXP names, int n) {
-  int nprotect = 0;
   SEXP dimnms, nm;
-  PROTECT(nm = AS_CHARACTER(names)); nprotect++;
-  PROTECT(dimnms = allocVector(VECSXP,n)); nprotect++;
+  PROTECT(nm = AS_CHARACTER(names));
+  PROTECT(dimnms = allocVector(VECSXP,n));
   SET_ELEMENT(dimnms,0,nm);	// set row names
   SET_DIMNAMES(x,dimnms);
+  UNPROTECT(2);
+}
+
+static R_INLINE void fixdimnames (SEXP x, const char **names, int n) {
+  int nprotect = 0;
+  int i;
+  SEXP dimnames, nm;
+  PROTECT(dimnames = GET_DIMNAMES(x)); nprotect++;
+  if (isNull(dimnames)) {
+    PROTECT(dimnames = allocVector(VECSXP,n)); nprotect++;
+  }
+  PROTECT(nm = allocVector(VECSXP,n)); nprotect++;
+  for (i = 0; i < n; i++)
+    SET_ELEMENT(nm,i,mkChar(names[i]));
+  SET_NAMES(dimnames,nm);
+  SET_DIMNAMES(x,dimnames);
   UNPROTECT(nprotect);
 }
 

Modified: pkg/pomp/src/rmeasure.c
===================================================================
--- pkg/pomp/src/rmeasure.c	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/src/rmeasure.c	2015-01-06 23:08:15 UTC (rev 1045)
@@ -61,8 +61,10 @@
 
   {
     int dim[3] = {nobs, nreps, ntimes};
+    const char *dimnm[3] = {"variable","rep","time"};
     PROTECT(Y = makearray(3,dim)); nprotect++; 
     setrownames(Y,Onames,3);
+    fixdimnames(Y,dimnm,3);
   }
 
   // extract the user-defined function

Modified: pkg/pomp/src/rprior.c
===================================================================
--- pkg/pomp/src/rprior.c	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/src/rprior.c	2015-01-06 23:08:15 UTC (rev 1045)
@@ -20,6 +20,7 @@
   SEXP Pnames, P, fn, fcall;
   SEXP pompfun;
   int *dim;
+  const char *dimnms[2] = {"variable","rep"};
 
   PROTECT(params = as_matrix(params)); nprotect++;
   dim = INTEGER(GET_DIM(params));
@@ -144,5 +145,6 @@
   }
 
   UNPROTECT(nprotect);
+  fixdimnames(P,dimnms,2);
   return P;
 }

Modified: pkg/pomp/src/rprocess.c
===================================================================
--- pkg/pomp/src/rprocess.c	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/src/rprocess.c	2015-01-06 23:08:15 UTC (rev 1045)
@@ -14,6 +14,7 @@
   int *xdim, nvars, npars, nreps, nrepsx, ntimes, off;
   SEXP X, Xoff, copy, fn, fcall, rho;
   SEXP dimXstart, dimP, dimX;
+  const char *dimnm[3] = {"variable","rep","time"};
 
   PROTECT(gnsi = duplicate(gnsi)); nprotect++;
 
@@ -113,10 +114,12 @@
     xdim[2] -= off;
     PROTECT(Xoff = makearray(3,xdim)); nprotect++;
     setrownames(Xoff,GET_ROWNAMES(GET_DIMNAMES(X)),3);
+    fixdimnames(Xoff,dimnm,3);
     memcpy(REAL(Xoff),REAL(X)+off*nvars*nreps,(ntimes-off)*nvars*nreps*sizeof(double));
     UNPROTECT(nprotect);
     return Xoff;
   } else {
+    fixdimnames(X,dimnm,3);
     UNPROTECT(nprotect);
     return X;
   }

Modified: pkg/pomp/src/skeleton.c
===================================================================
--- pkg/pomp/src/skeleton.c	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/src/skeleton.c	2015-01-06 23:08:15 UTC (rev 1045)
@@ -131,8 +131,10 @@
   // set up the array to hold results
   {
     int dim[3] = {nvars, nreps, ntimes};
+    const char *dimnms[3] = {"variable","rep","time"};
     PROTECT(F = makearray(3,dim)); nprotect++; 
     setrownames(F,Snames,3);
+    fixdimnames(F,dimnms,3);
   }
 
   // first do setup

Modified: pkg/pomp/tests/bbs-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/bbs-trajmatch.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -80,4 +80,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.725   0.017   2.733 
+  2.480   0.052   2.555 

Modified: pkg/pomp/tests/bbs.Rout.save
===================================================================
--- pkg/pomp/tests/bbs.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/bbs.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -69,4 +69,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  7.769   0.051   7.832 
+  7.008   0.076   7.124 

Modified: pkg/pomp/tests/blowflies.Rout.save
===================================================================
--- pkg/pomp/tests/blowflies.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/blowflies.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -24,45 +24,47 @@
  blowflies1 blowflies2 
 > 
 > init.state(blowflies1)
-     [,1]
-N1  397.0
-N2  450.5
-N3  504.0
-N4  590.0
-N5  676.0
-N6  738.5
-N7  801.0
-N8  829.5
-N9  858.0
-N10 884.5
-N11 911.0
-N12 926.5
-N13 942.0
-N14 945.0
-N15 948.0
-R     0.0
-S     0.0
-e     0.0
-eps   0.0
+        rep
+variable  [,1]
+     N1  397.0
+     N2  450.5
+     N3  504.0
+     N4  590.0
+     N5  676.0
+     N6  738.5
+     N7  801.0
+     N8  829.5
+     N9  858.0
+     N10 884.5
+     N11 911.0
+     N12 926.5
+     N13 942.0
+     N14 945.0
+     N15 948.0
+     R     0.0
+     S     0.0
+     e     0.0
+     eps   0.0
 > x1 <- simulate(blowflies1)
 > f1 <- pfilter(blowflies1,Np=1000,seed=599688L)
 > logLik(f1)
 [1] -1466.694
 > 
 > init.state(blowflies2)
-    [,1]
-N1   397
-N2   504
-N3   676
-N4   801
-N5   858
-N6   911
-N7   942
-N8   948
-R      0
-S      0
-e      0
-eps    0
+        rep
+variable [,1]
+     N1   397
+     N2   504
+     N3   676
+     N4   801
+     N5   858
+     N6   911
+     N7   942
+     N8   948
+     R      0
+     S      0
+     e      0
+     eps    0
 > x2 <- simulate(blowflies2)
 > f2 <- pfilter(blowflies2,Np=1000,seed=599688L)
 > logLik(f2)
@@ -70,4 +72,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.493   0.039   1.519 
+  1.304   0.044   1.380 

Modified: pkg/pomp/tests/dacca.Rout.save
===================================================================
--- pkg/pomp/tests/dacca.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/dacca.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -107,4 +107,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 14.817   0.035  14.853 
+ 10.852   0.064  10.968 

Modified: pkg/pomp/tests/dimchecks.Rout.save
===================================================================
--- pkg/pomp/tests/dimchecks.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/dimchecks.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -29,19 +29,22 @@
 > pars <- coef(po)
 > xstart <- init.state(po,params=pars)
 > rprocess(po,xstart,times=0:5,params=pars)[,1,]
-  [,1]      [,2]        [,3]        [,4]      [,5]       [,6]
-N    7 0.4578051 11.78599703 0.004766933 0.2732487 14.6301023
-e    0 0.4727782 -0.09397106 0.173032749 0.2534460  0.4537029
+        time
+variable [,1]      [,2]        [,3]        [,4]      [,5]       [,6]
+       N    7 0.4578051 11.78599703 0.004766933 0.2732487 14.6301023
+       e    0 0.4727782 -0.09397106 0.173032749 0.2534460  0.4537029
 > 
 > rprocess(po,xstart=parmat(xstart,5),times=0:5,params=pars)[,3,]
-  [,1]       [,2]      [,3]       [,4]       [,5]      [,6]
-N    7  0.1788532 8.0265735 0.11906954  4.1101032 4.7809853
-e    0 -0.4671001 0.1828009 0.01576817 -0.1394347 0.4613017
+        time
+variable [,1]       [,2]      [,3]       [,4]       [,5]      [,6]
+       N    7  0.1788532 8.0265735 0.11906954  4.1101032 4.7809853
+       e    0 -0.4671001 0.1828009 0.01576817 -0.1394347 0.4613017
 > 
 > rprocess(po,xstart=xstart,times=0:5,params=parmat(pars,3))[,3,]
-  [,1]      [,2]       [,3]       [,4]      [,5]      [,6]
-N    7 0.3200483  7.9793435  0.1061246 6.3880659 0.5943893
-e    0 0.1148066 -0.2638123 -0.1406537 0.4036972 0.2134135
+        time
+variable [,1]      [,2]       [,3]       [,4]      [,5]      [,6]
+       N    7 0.3200483  7.9793435  0.1061246 6.3880659 0.5943893
+       e    0 0.1148066 -0.2638123 -0.1406537 0.4036972 0.2134135
 > 
 > try(
 +     rprocess(po,xstart=parmat(xstart,2),times=0:5,params=parmat(pars,3))[,,3]
@@ -50,9 +53,10 @@
   rprocess error: larger number of replicates is not a multiple of smaller
 > 
 > rprocess(po,xstart=parmat(xstart,2),times=0:5,params=parmat(pars,6))[,,3]
-        [,1]       [,2]       [,3]       [,4]      [,5]        [,6]
-N 11.4232929 11.3881039  4.8636396  7.1427117 9.4874566  9.65359657
-e  0.1987878  0.2241485 -0.5425199 -0.1655866 0.2008968 -0.09235699
+        rep
+variable       [,1]       [,2]       [,3]       [,4]      [,5]        [,6]
+       N 11.4232929 11.3881039  4.8636396  7.1427117 9.4874566  9.65359657
+       e  0.1987878  0.2241485 -0.5425199 -0.1655866 0.2008968 -0.09235699
 > 
 > x <- rprocess(po,xstart=parmat(xstart,2),times=0:5,params=parmat(pars,8))
 > 
@@ -68,72 +72,85 @@
 > rmeasure(po,x=x,params=parmat(pars,4),times=0:5)
 , , 1
 
-  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
-y   95   77   70   84   75   65   55   73
+        rep
+variable [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
+       y   95   77   70   84   75   65   55   73
 
 , , 2
 
-  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
-y    6    2    4    9    3    1    2    1
+        rep
+variable [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
+       y    6    2    4    9    3    1    2    1
 
 , , 3
 
-  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
-y  107   67   95   99   74   54   36   74
+        rep
+variable [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
+       y  107   67   95   99   74   54   36   74
 
 , , 4
 
-  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
-y    0    7    0    0    1    4   10    5
+        rep
+variable [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
+       y    0    7    0    0    1    4   10    5
 
 , , 5
 
-  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
-y    7  178   14    1   82  190  200   88
+        rep
+variable [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
+       y    7  178   14    1   82  190  200   88
 
 , , 6
 
-  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
-y  216    0  190  106    1    0    0    0
+        rep
+variable [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
+       y  216    0  190  106    1    0    0    0
 
 > 
 > x <- rprocess(po,xstart=xstart,times=0:5,params=pars)
 > rmeasure(po,x=x,params=parmat(pars,2),times=0:5)
 , , 1
 
-  [,1] [,2]
-y   79   73
+        rep
+variable [,1] [,2]
+       y   79   73
 
 , , 2
 
-  [,1] [,2]
-y    1    1
+        rep
+variable [,1] [,2]
+       y    1    1
 
 , , 3
 
-  [,1] [,2]
-y   73   51
+        rep
+variable [,1] [,2]
+       y   73   51
 
 , , 4
 
-  [,1] [,2]
-y   10   12
+        rep
+variable [,1] [,2]
+       y   10   12
 
 , , 5
 
-  [,1] [,2]
-y  193  186
+        rep
+variable [,1] [,2]
+       y  193  186
 
 , , 6
 
-  [,1] [,2]
-y    0    0
+        rep
+variable [,1] [,2]
+       y    0    0
 
 > 
 > y <- rmeasure(po,x=x,params=parmat(pars,4),times=0:5)
 > dmeasure(po,x=x,y=y[,2,,drop=F],params=pars,times=0:5)
-            [,1]     [,2]       [,3]      [,4]       [,5]      [,6]
-[1,] 0.002350788 0.268881 0.04825714 0.1309304 0.02090266 0.9998435
+      time
+rep           [,1]     [,2]       [,3]      [,4]       [,5]      [,6]
+  [1,] 0.002350788 0.268881 0.04825714 0.1309304 0.02090266 0.9998435
 > 
 > x <- rprocess(po,xstart=parmat(xstart,3),times=0:5,params=pars)
 > y <- rmeasure(po,x=x,params=pars,times=0:5)
@@ -162,4 +179,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.489   0.041   0.517 
+  0.560   0.092   0.677 

Modified: pkg/pomp/tests/fhn.Rout.save
===================================================================
--- pkg/pomp/tests/fhn.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/fhn.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -44,15 +44,17 @@
 > skeleton(fhn,x,t=c(0,3),params=params)
 , , 1
 
-   [,1]      [,2]
-V -0.40 -6.666667
-R -0.05  0.100000
+        rep
+variable  [,1]      [,2]
+       V -0.40 -6.666667
+       R -0.05  0.100000
 
 , , 2
 
-       [,1] [,2]
-V 0.9333333  5.0
-R 0.4500000  0.2
+        rep
+variable      [,1] [,2]
+       V 0.9333333  5.0
+       R 0.4500000  0.2
 
 > y <- trajectory(fhn,params=params,hmax=0.1)
 > invisible(y[,,599:601])
@@ -91,4 +93,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.927   0.060   0.950 
+  1.084   0.064   1.285 

Modified: pkg/pomp/tests/filtfail.Rout.save
===================================================================
--- pkg/pomp/tests/filtfail.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/filtfail.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -116,4 +116,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.489   0.053   0.529 
+  0.576   0.068   0.660 

Modified: pkg/pomp/tests/gillespie.Rout.save
===================================================================
--- pkg/pomp/tests/gillespie.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/gillespie.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -131,4 +131,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.565   0.041   2.592 
+  2.564   0.048   2.635 

Modified: pkg/pomp/tests/gompertz.Rout.save
===================================================================
--- pkg/pomp/tests/gompertz.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/gompertz.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -133,4 +133,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.797   0.038   1.822 
+  1.576   0.052   1.652 

Modified: pkg/pomp/tests/logistic.Rout.save
===================================================================
--- pkg/pomp/tests/logistic.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/logistic.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -76,8 +76,9 @@
 +                ),
 +       digits=4
 +       )
-         [,1]      [,2]      [,3]      [,4]      [,5]
-[1,] 0.001204 0.0005132 0.0005411 0.0007547 0.0005974
+      time
+rep        [,1]      [,2]      [,3]      [,4]      [,5]
+  [1,] 0.001204 0.0005132 0.0005411 0.0007547 0.0005974
 > 
 > print(
 +       dmeasure(
@@ -90,8 +91,9 @@
 +                ),
 +       digits=4
 +       )
-       [,1]   [,2]   [,3]   [,4]   [,5]   [,6]
-[1,] -7.915 -8.896 -7.992 -8.196 -11.12 -7.946
+      time
+rep      [,1]   [,2]   [,3]   [,4]   [,5]   [,6]
+  [1,] -7.915 -8.896 -7.992 -8.196 -11.12 -7.946
 > 
 > print(
 +       drop(
@@ -122,4 +124,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.874   0.030   0.887 
+  0.976   0.052   1.175 

Modified: pkg/pomp/tests/ou2-abc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-abc.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-abc.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -131,4 +131,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 11.085   0.055  11.138 
+  9.612   0.100   9.906 

Modified: pkg/pomp/tests/ou2-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-bsmc.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -59,7 +59,7 @@
 > post <- smc$post
 > 
 > print(etime <- toc-tic)
-Time difference of 3.430529 secs
+Time difference of 2.789886 secs
 > 
 > print(
 +       cbind(
@@ -101,4 +101,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  5.498   0.064   5.527 
+  4.688   0.064   4.785 

Modified: pkg/pomp/tests/ou2-bsmc2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc2.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-bsmc2.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -56,7 +56,7 @@
 > post <- smc$post
 > 
 > print(etime <- toc-tic)
-Time difference of 2.234756 secs
+Time difference of 2.022153 secs
 > 
 > print(
 +       cbind(
@@ -98,4 +98,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  3.846   0.045   3.881 
+  3.588   0.084   3.697 

Modified: pkg/pomp/tests/ou2-forecast.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-forecast.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-forecast.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -61,4 +61,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.376   0.042   1.402 
+  1.420   0.036   1.559 

Modified: pkg/pomp/tests/ou2-kalman.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-kalman.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-kalman.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -164,7 +164,7 @@
     117 function evaluations used
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 3.235065 secs
+Time difference of 3.309699 secs
 > tic <- Sys.time()
 > print(loglik.mle <- -kalm.fit1$value,digits=4)
 [1] -477.2
@@ -188,4 +188,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  3.769   0.026   3.787 
+  3.960   0.044   4.036 

Modified: pkg/pomp/tests/ou2-mif-fp.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif-fp.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-mif-fp.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -70,4 +70,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 24.537   0.066  24.614 
+ 19.413   0.056  19.690 

Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-mif.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -281,4 +281,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 13.791   0.053  13.848 
+ 11.452   0.064  11.704 

Modified: pkg/pomp/tests/ou2-mif2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif2.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-mif2.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -135,4 +135,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 62.157   0.075  62.274 
+ 49.355   0.040  49.763 

Modified: pkg/pomp/tests/ou2-nlf.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-nlf.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-nlf.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -85,4 +85,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  5.003   0.037   5.037 
+  4.380   0.092   6.425 

Modified: pkg/pomp/tests/ou2-pmcmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-pmcmc.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-pmcmc.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -114,4 +114,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 26.822   0.042  26.880 
+ 24.125   0.068  24.493 

Modified: pkg/pomp/tests/ou2-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-probe.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-probe.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -340,4 +340,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  8.501   0.048   8.545 
+  7.892   0.092   8.187 

Modified: pkg/pomp/tests/ou2-procmeas.R
===================================================================
--- pkg/pomp/tests/ou2-procmeas.R	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-procmeas.R	2015-01-06 23:08:15 UTC (rev 1045)
@@ -23,8 +23,8 @@
 x <- simulate(po,states=T,params=coef(po))
 dp2 <- dprocess(po,x=x,times=time(po),params=coef(po),log=T)
 dp3 <- dprocess(po,x=x,times=time(po),params=pmat,log=T)
-stopifnot(identical(rbind(dp2,dp2,dp2),dp3))
+stopifnot(identical(rbind(dp2,dp2,dp2),unname(dp3)))
 
 dm2 <- dmeasure(po,x=x,y=obs(po),times=time(po),params=coef(po),log=T)
 dm3 <- dmeasure(po,x=x,y=obs(po),times=time(po),params=pmat,log=T)
-stopifnot(identical(rbind(dm2,dm2,dm2),dm3))
+stopifnot(identical(rbind(dm2,dm2,dm2),unname(dm3)))

Modified: pkg/pomp/tests/ou2-procmeas.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-procmeas.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-procmeas.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -46,12 +46,12 @@
 > x <- simulate(po,states=T,params=coef(po))
 > dp2 <- dprocess(po,x=x,times=time(po),params=coef(po),log=T)
 > dp3 <- dprocess(po,x=x,times=time(po),params=pmat,log=T)
-> stopifnot(identical(rbind(dp2,dp2,dp2),dp3))
+> stopifnot(identical(rbind(dp2,dp2,dp2),unname(dp3)))
 > 
 > dm2 <- dmeasure(po,x=x,y=obs(po),times=time(po),params=coef(po),log=T)
 > dm3 <- dmeasure(po,x=x,y=obs(po),times=time(po),params=pmat,log=T)
-> stopifnot(identical(rbind(dm2,dm2,dm2),dm3))
+> stopifnot(identical(rbind(dm2,dm2,dm2),unname(dm3)))
 > 
 > proc.time()
    user  system elapsed 
-  0.493   0.037   0.495 
+  0.408   0.048   0.479 

Modified: pkg/pomp/tests/ou2-simulate.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-simulate.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-simulate.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -35,7 +35,7 @@
 > ou2.sim <- simulate(ou2,params=p,nsim=100,seed=32043858)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 0.007747889 secs
+Time difference of 0.006910086 secs
 > 
 > coef(ou2,c('x1.0','x2.0')) <- c(-50,50)
 > 
@@ -46,4 +46,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.501   0.022   0.507 
+  0.508   0.040   0.572 

Modified: pkg/pomp/tests/ou2-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-trajmatch.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-trajmatch.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -175,4 +175,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.740   0.048   1.765 
+  1.712   0.060   1.801 

Modified: pkg/pomp/tests/partrans.Rout.save
===================================================================
--- pkg/pomp/tests/partrans.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/partrans.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -52,4 +52,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.492   0.020   0.494 
+  0.600   0.060   0.678 

Modified: pkg/pomp/tests/pfilter.Rout.save
===================================================================
--- pkg/pomp/tests/pfilter.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/pfilter.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -77,4 +77,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  9.887   0.037   9.924 
+  8.448   0.080   8.699 

Modified: pkg/pomp/tests/pomppomp.Rout.save
===================================================================
--- pkg/pomp/tests/pomppomp.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/pomppomp.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -55,4 +55,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.489   0.030   0.504 
+  0.580   0.064   0.663 

Modified: pkg/pomp/tests/prior.Rout.save
===================================================================
--- pkg/pomp/tests/prior.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/prior.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -53,18 +53,19 @@
 > 
 > stopifnot(all.equal(mean(dprior(po,params=parmat(coef(po),3))),dnorm(x=0,mean=0,sd=5)^4))
 > rprior(po,params=coef(po))
-               [,1]
-alpha.1  -2.2417803
-alpha.2   0.7708391
-alpha.3  -3.2398829
-alpha.4   9.9993334
-sigma.1   3.0000000
-sigma.2  -0.5000000
-sigma.3   2.0000000
-tau       1.0000000
-x1.0     -3.0000000
-x2.0      4.0000000
-alpha.sd  5.0000000
+          rep
+variable         [,1]
+  alpha.1  -2.2417803
+  alpha.2   0.7708391
+  alpha.3  -3.2398829
+  alpha.4   9.9993334
+  sigma.1   3.0000000
+  sigma.2  -0.5000000
+  sigma.3   2.0000000
+  tau       1.0000000
+  x1.0     -3.0000000
+  x2.0      4.0000000
+  alpha.sd  5.0000000
 > 
 > coef(po,"alpha.sd") <- 1
 > mean(dprior(po,params=rprior(po,params=parmat(coef(po),10000)),log=TRUE))+0.5*(1+log(2*pi))*4
@@ -72,4 +73,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.683   0.025   0.694 
+  0.736   0.056   0.809 

Modified: pkg/pomp/tests/ricker-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-bsmc.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ricker-bsmc.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -54,4 +54,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.571   0.057   2.614 
+  2.604   0.072   2.860 

Modified: pkg/pomp/tests/ricker-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-probe.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ricker-probe.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -297,4 +297,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 13.643   0.070  13.713 
+ 11.976   0.072  12.278 

Modified: pkg/pomp/tests/ricker-spect.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-spect.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ricker-spect.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -70,4 +70,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.504   0.018   2.511 
+  2.284   0.084   3.241 

Modified: pkg/pomp/tests/ricker.Rout.save
===================================================================
--- pkg/pomp/tests/ricker.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ricker.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -83,4 +83,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.554   0.038   0.579 
+  0.704   0.048   0.884 

Modified: pkg/pomp/tests/rw2.Rout.save
===================================================================
--- pkg/pomp/tests/rw2.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/rw2.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -164,7 +164,7 @@
     }
     y
 }
-<environment: 0x1c9a9f8>
+<environment: 0x24441b8>
 measurement model density, dmeasure = 
 function (y, x, t, params, log, covars, ...) 
 {
@@ -177,7 +177,7 @@
         f
     else exp(f)
 }
-<environment: 0x1c9a9f8>
+<environment: 0x24441b8>
 prior simulator, rprior = 
 function not specified
 prior density, dprior = 
@@ -342,4 +342,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.879   0.041   0.908 
+  0.992   0.040   1.052 

Modified: pkg/pomp/tests/sir.Rout.save
===================================================================
--- pkg/pomp/tests/sir.Rout.save	2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/sir.Rout.save	2015-01-06 23:08:15 UTC (rev 1045)
@@ -192,7 +192,7 @@
         method = 0L, zeronames = zeronames, tcovar = tcovar, 
         covar = covar, args = pairlist(...), gnsi = .getnativesymbolinfo)
 }
-<environment: 0x151f968>
+<environment: 0x24f3bf8>
 process model density, dprocess = 
 function (x, times, params, ..., tcovar, covar, log = FALSE, 
     .getnativesymbolinfo = TRUE) 
@@ -201,7 +201,7 @@
         params = params, tcovar = tcovar, covar = covar, log = log, 
         args = pairlist(...), gnsi = .getnativesymbolinfo)
 }
-<environment: 0x1272bc8>
+<environment: 0x228d048>
 measurement model simulator, rmeasure = 
 function (x, t, params, covars, ...) 
 {
@@ -274,7 +274,7 @@
 > x <- simulate(po,nsim=3)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 0.9468338 secs
+Time difference of 0.8555272 secs
 > 
 > pdf(file='sir.pdf')
 > 
@@ -291,7 +291,7 @@
 > X3 <- trajectory(po,times=t3,hmax=1/52)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 0.560688 secs
+Time difference of 0.5343869 secs
 > plot(t3,X3['I',1,],type='l')
 > 
 > f1 <- dprocess(
@@ -322,14 +322,16 @@
 +                params=params
 +                )
 > print(h1[c("S","I","R"),,],digits=4)
-      [,1]     [,2]      [,3]      [,4]     [,5]   [,6]     [,7]   [,8]
-S  32161.6  31582.4  32142.21  31758.36  31639.0  32006  31953.5  31666
-I   -318.4   -218.9    -88.93     21.52    128.7    218    309.2    403
-R -31855.2 -31375.0 -32064.98 -31792.40 -31780.0 -32236 -32276.8 -32083
-      [,9]    [,10]    [,11]    [,12]    [,13]  [,14]  [,15]  [,16]
-S  31017.5  29782.5  29443.9  28916.7  27997.1  27494  26434  25448
-I    518.5    675.3    768.6    868.8    996.8   1074   1187   1278
-R -31549.7 -30472.3 -30226.0 -29798.8 -29007.2 -28580 -27634 -26740
+        time
+variable     [,1]     [,2]      [,3]      [,4]     [,5]   [,6]     [,7]   [,8]
+       S  32161.6  31582.4  32142.21  31758.36  31639.0  32006  31953.5  31666
+       I   -318.4   -218.9    -88.93     21.52    128.7    218    309.2    403
+       R -31855.2 -31375.0 -32064.98 -31792.40 -31780.0 -32236 -32276.8 -32083
+        time
+variable     [,9]    [,10]    [,11]    [,12]    [,13]  [,14]  [,15]  [,16]
+       S  31017.5  29782.5  29443.9  28916.7  27997.1  27494  26434  25448
+       I    518.5    675.3    768.6    868.8    996.8   1074   1187   1278
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 1045

From noreply at r-forge.r-project.org  Wed Jan  7 04:26:44 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  7 Jan 2015 04:26:44 +0100 (CET)
Subject: [Pomp-commits] r1046 - in pkg/pomp: . R inst man
Message-ID: <20150107032644.8F026187270@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-07 04:26:44 +0100 (Wed, 07 Jan 2015)
New Revision: 1046

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/NAMESPACE
   pkg/pomp/R/builder.R
   pkg/pomp/R/generics.R
   pkg/pomp/R/pomp-class.R
   pkg/pomp/R/pomp.R
   pkg/pomp/inst/NEWS
   pkg/pomp/inst/NEWS.Rd
   pkg/pomp/man/pomp.Rd
Log:
- new 'pompLoad' and 'pompUnload' convenience functions for working with shared-object files associated with pomps

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-01-06 23:08:15 UTC (rev 1045)
+++ pkg/pomp/DESCRIPTION	2015-01-07 03:26:44 UTC (rev 1046)
@@ -1,7 +1,7 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.57-2
+Version: 0.58-1
 Date: 2015-01-06
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),

Modified: pkg/pomp/NAMESPACE
===================================================================
--- pkg/pomp/NAMESPACE	2015-01-06 23:08:15 UTC (rev 1045)
+++ pkg/pomp/NAMESPACE	2015-01-07 03:26:44 UTC (rev 1046)
@@ -56,6 +56,7 @@
 exportMethods(
               pomp,
               plot,show,print,coerce,summary,logLik,window,"$",
+              pompLoad,pompUnload,
               dprocess,rprocess,rmeasure,dmeasure,init.state,skeleton,
               dprior,rprior,
               data.array,obs,partrans,coef,"coef<-",

Modified: pkg/pomp/R/builder.R
===================================================================
--- pkg/pomp/R/builder.R	2015-01-06 23:08:15 UTC (rev 1045)
+++ pkg/pomp/R/builder.R	2015-01-07 03:26:44 UTC (rev 1046)
@@ -46,8 +46,11 @@
                globals=globals,
                link=link,
                save=save
-               ) -> name
+               ) -> bret
 
+  name <- bret[1]
+  solib <- bret[2]
+
   pomp(
        data=data,
        times=times,
@@ -71,19 +74,26 @@
        paramnames=paramnames,
        tcovar=tcovar,
        covar=covar,
-       ...
+       ...,
+       .solibfile=solib
        )
 }
 
-pompLink <- function (name) {
-  solib <- paste0(name,.Platform$dynlib.ext)
-  dyn.load(solib)
-}
+setMethod("pompLoad",
+          signature=signature(object='pomp'),
+          definition = function (object) {
+            for (lib in object at solibfile)
+              dyn.load(lib)
+            invisible(NULL)
+          })
 
-pompUnlink <- function (name) {
-  solib <- paste0(name,.Platform$dynlib.ext)
-  dyn.unload(solib)
-}
+setMethod("pompUnload",
+          signature=signature(object='pomp'),
+          definition = function (object) {
+            for (lib in object at solibfile)
+              dyn.unload(lib)
+            invisible(NULL)
+          })
 
 define <- list(
                var="#define {%variable%}\t({%ptr%}[{%ilist%}[{%index%}]])\n",
@@ -295,15 +305,9 @@
     cat("model codes written to",sQuote(modelfile),
         "\nlink to shared-object library",sQuote(solib),"\n")
 
-  if (link) {
-    if (save) {
-      pompLink(name)
-    } else {
-      pompLink(file.path(tempdir(),name))
-    }
-  }
+  if (link) dyn.load(solib)
 
-  invisible(name)
+  invisible(c(name,solib))
 }
 
 cleanForC <- function (text) {
@@ -333,3 +337,4 @@
   }
   do.call(paste0,retval)
 }
+

Modified: pkg/pomp/R/generics.R
===================================================================
--- pkg/pomp/R/generics.R	2015-01-06 23:08:15 UTC (rev 1045)
+++ pkg/pomp/R/generics.R	2015-01-07 03:26:44 UTC (rev 1046)
@@ -88,3 +88,7 @@
 
 ## continue an iteration
 setGeneric("continue",function(object,...)standardGeneric("continue"))
+
+## dynamic loading and unloading
+setGeneric("pompLoad",function(object,...)standardGeneric("pompLoad"))
+setGeneric("pompUnload",function(object,...)standardGeneric("pompUnload"))

Modified: pkg/pomp/R/pomp-class.R
===================================================================
--- pkg/pomp/R/pomp-class.R	2015-01-06 23:08:15 UTC (rev 1045)
+++ pkg/pomp/R/pomp-class.R	2015-01-07 03:26:44 UTC (rev 1046)
@@ -34,6 +34,7 @@
            has.trans = 'logical',
            par.trans = 'pomp.fun',
            par.untrans = 'pomp.fun',
+           solibfile = 'character',
            userdata = 'list'
            ),
          prototype=prototype(
@@ -58,6 +59,7 @@
            has.trans=FALSE,
            par.trans=pomp.fun(),
            par.untrans=pomp.fun(),
+           solibfile=character(0),
            userdata=list()
            ),
          validity=function (object) {

Modified: pkg/pomp/R/pomp.R
===================================================================
--- pkg/pomp/R/pomp.R	2015-01-06 23:08:15 UTC (rev 1045)
+++ pkg/pomp/R/pomp.R	2015-01-07 03:26:44 UTC (rev 1046)
@@ -9,14 +9,18 @@
                               obsnames, statenames, paramnames, covarnames,
                               zeronames, PACKAGE,
                               parameter.transform, parameter.inv.transform,
-                              globals,
-                              userdata) {
+                              globals, userdata, ..., .solibfile) {
 
   ## preliminary error checking
   if (missing(data)) stop(sQuote("data")," is a required argument")
   if (missing(times)) stop(sQuote("times")," is a required argument")
   if (missing(t0)) stop(sQuote("t0")," is a required argument")
   if (missing(params)) params <- numeric(0)
+  if (missing(.solibfile)) .solibfile <- character(0)
+  
+  if (missing(userdata)) userdata <- list()
+  added.userdata <- list(...)
+  userdata[names(added.userdata)] <- added.userdata
 
   ## name of shared object library
   if (missing(PACKAGE)) PACKAGE <- NULL
@@ -147,10 +151,14 @@
                            ),
                    silent=FALSE
                    )
-    if (inherits(PACKAGE,"try-error"))
+    if (inherits(PACKAGE,"try-error")) {
       stop("error in building shared-object library from Csnippets")
+    } else {
+      .solibfile <- c(.solibfile,libname[2L])
+      libname <- libname[1L]
+    }
   } else {
-    libname <- ""
+    libname <- ''
   }
   
   ## handle rprocess
@@ -363,6 +371,7 @@
       has.trans = has.trans,
       par.trans = par.trans,
       par.untrans = par.untrans,
+      solibfile = .solibfile,
       userdata = userdata
       )
 }
@@ -483,8 +492,8 @@
                              rmeasure=rmeasure,
                              dmeasure=dmeasure,
                              measurement.model=measurement.model,
-                             dprior = dprior,
-                             rprior = rprior,
+                             dprior=dprior,
+                             rprior=rprior,
                              skeleton=skeleton,
                              skeleton.type=skeleton.type,
                              skelmap.delta.t=skelmap.delta.t,
@@ -501,7 +510,7 @@
                              parameter.transform=parameter.transform,
                              parameter.inv.transform=parameter.inv.transform,
                              globals=globals,
-                             userdata=list(...)
+                             ...
                              )
           }
           )
@@ -527,8 +536,8 @@
                              rmeasure=rmeasure,
                              dmeasure=dmeasure,
                              measurement.model=measurement.model,
-                             dprior = dprior,
-                             rprior = rprior,
+                             dprior=dprior,
+                             rprior=rprior,
                              skeleton=skeleton,
                              skeleton.type=skeleton.type,
                              skelmap.delta.t=skelmap.delta.t,
@@ -545,7 +554,7 @@
                              parameter.transform=parameter.transform,
                              parameter.inv.transform=parameter.inv.transform,
                              globals=globals,
-                             userdata=list(...)
+                             ...
                              )
           }
           )
@@ -572,8 +581,8 @@
                              rmeasure=rmeasure,
                              dmeasure=dmeasure,
                              measurement.model=measurement.model,
-                             dprior = dprior,
-                             rprior = rprior,
+                             dprior=dprior,
+                             rprior=rprior,
                              skeleton=skeleton,
                              skeleton.type=skeleton.type,
                              skelmap.delta.t=skelmap.delta.t,
@@ -590,7 +599,7 @@
                              parameter.transform=parameter.transform,
                              parameter.inv.transform=parameter.inv.transform,
                              globals=globals,
-                             userdata=list(...)
+                             ...
                              )
           }
           )
@@ -659,10 +668,6 @@
               }
             }
 
-            userdata <- data at userdata
-            added.userdata <- list(...)
-            userdata[names(added.userdata)] <- added.userdata
-
             if (missing(obsnames)) obsnames <- character(0)
             if (missing(statenames)) statenames <- character(0)
             if (missing(paramnames)) paramnames <- character(0)
@@ -677,8 +682,8 @@
                              dprocess=dprocess,
                              rmeasure=rmeasure,
                              dmeasure=dmeasure,
-                             dprior = dprior,
-                             rprior = rprior,
+                             dprior=dprior,
+                             rprior=rprior,
                              skeleton=skeleton,
                              skeleton.type=skeleton.type,
                              skelmap.delta.t=skelmap.delta.t,
@@ -695,7 +700,8 @@
                              parameter.inv.transform=par.untrans,
                              params=params,
                              globals=globals,
-                             userdata=userdata
+                             userdata=data at userdata,
+                             ...
                              )
           }
           )

Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS	2015-01-06 23:08:15 UTC (rev 1045)
+++ pkg/pomp/inst/NEWS	2015-01-07 03:26:44 UTC (rev 1046)
@@ -1,5 +1,12 @@
 _N_e_w_s _f_o_r _p_a_c_k_a_g_e '_p_o_m_p'
 
+_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._5_8-_1:
+
+        ? A ?pomp? object created with ?Csnippet?s or ?pompBuilder?
+          will now remember its associated shared-object file, which
+          can be unloaded and reloaded using the new ?pompUnload? and
+          ?pompLoad? methods.
+
 _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._5_7-_1:
 
         ? ?simulate? has a new argument, ?include.data?, that when used

Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd	2015-01-06 23:08:15 UTC (rev 1045)
+++ pkg/pomp/inst/NEWS.Rd	2015-01-07 03:26:44 UTC (rev 1046)
@@ -1,5 +1,10 @@
 \name{NEWS}
 \title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 0.58-1}{
+  \itemize{
+    \item A \code{pomp} object created with \code{Csnippet}s or \code{pompBuilder} will now remember its associated shared-object file, which can be unloaded and reloaded using the new \code{pompUnload} and \code{pompLoad} methods.
+  }
+}
 \section{Changes in \pkg{pomp} version 0.57-1}{
   \itemize{
     \item \code{simulate} has a new argument, \code{include.data}, that when used in conjuncion with \code{as.data.frame=TRUE} will include the actual data in the resulting data frame along with the simulations.

Modified: pkg/pomp/man/pomp.Rd
===================================================================
--- pkg/pomp/man/pomp.Rd	2015-01-06 23:08:15 UTC (rev 1045)
+++ pkg/pomp/man/pomp.Rd	2015-01-07 03:26:44 UTC (rev 1046)
@@ -9,6 +9,12 @@
 \alias{pomp,pomp-method}
 \alias{pomp-pomp}
 \alias{pomp-class}
+\alias{pompLoad}
+\alias{pompLoad-pomp}
+\alias{pompLoad,pomp-method}
+\alias{pompUnload}
+\alias{pompUnload-pomp}
+\alias{pompUnload,pomp-method}
 \title{Partially-observed Markov process object.}
 \description{
   This function creates a \code{pomp} object,
@@ -38,6 +44,8 @@
        initializer, rprior, dprior, params, covar, tcovar,
        obsnames, statenames, paramnames, covarnames, zeronames,
        PACKAGE, parameter.transform, parameter.inv.transform, globals)
+\S4method{pompLoad}{pomp}(object)
+\S4method{pompUnload}{pomp}(object)
 }
 \arguments{
   \item{data, times}{
@@ -185,8 +193,11 @@
   \item{globals}{
     optional character;
     C code that will be included in the source for (and therefore hard-coded into) the shared-object library created when the call to \code{pomp} uses \code{Csnippets}.
-    If no \code{Csnippets} are used, \code{globals} has no effect.
+    If no \code{Csnippet}s are used, \code{globals} has no effect.
   }
+  \item{object}{
+    a \code{pomp} object.
+  }
   \item{\dots}{
     Any additional arguments given to \code{pomp} will be stored in the \code{\link[=pomp-class]{pomp}} object and passed as arguments to each of the basic functions whenever they are evaluated.
   }
@@ -313,6 +324,13 @@
          )
 }
 }
+\section{Dynamically linked codes}{
+  \code{pompLoad} and \code{pompUnload} cause any compiled codes associated with \code{object} to be dynamically linked or unlinked, respectively.
+  When 
+  \code{Csnippet}s are used in the construction of a \code{pomp} object, the resulting shared-object library is dynamically loaded (linked) at the time of its construction.
+  A subsequent call to \code{pompUnload} will unload the shared object library;
+  it can afterward be reloaded via a call to \code{pompLoad}.
+}
 \section{Warning}{
   Some error checking is done by \code{pomp}, but complete error checking is impossible.  
   If the user-specified functions do not conform to the above specifications (see Details), then the results may be invalid.


From noreply at r-forge.r-project.org  Wed Jan  7 11:54:30 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  7 Jan 2015 11:54:30 +0100 (CET)
Subject: [Pomp-commits] r1047 - in pkg/pomp: . R inst man
Message-ID: <20150107105430.12A54184950@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-07 11:54:29 +0100 (Wed, 07 Jan 2015)
New Revision: 1047

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/builder.R
   pkg/pomp/R/pomp.R
   pkg/pomp/inst/NEWS
   pkg/pomp/inst/NEWS.Rd
   pkg/pomp/man/pomp.Rd
Log:
- compiler messages are now suppressed by default
- pomp, pompCBuilder, pompLoad, and pompUnload all have new 'verbose' option

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-01-07 03:26:44 UTC (rev 1046)
+++ pkg/pomp/DESCRIPTION	2015-01-07 10:54:29 UTC (rev 1047)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.58-1
-Date: 2015-01-06
+Version: 0.58-2
+Date: 2015-01-07
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),

Modified: pkg/pomp/R/builder.R
===================================================================
--- pkg/pomp/R/builder.R	2015-01-07 03:26:44 UTC (rev 1046)
+++ pkg/pomp/R/builder.R	2015-01-07 10:54:29 UTC (rev 1047)
@@ -79,20 +79,34 @@
        )
 }
 
+pompLoad.internal <- function (object, ...,
+                               verbose = getOption("verbose",FALSE)) {
+  for (lib in object at solibfile) {
+    if (verbose) cat("loading",sQuote(lib),"\n")
+    dyn.load(lib)
+  }
+  invisible(NULL)
+}
+
+pompUnload.internal <- function (object, ...,
+                                 verbose = getOption("verbose",FALSE)) {
+  for (lib in object at solibfile) {
+    if (verbose) cat("unloading",sQuote(lib),"\n")
+    dyn.unload(lib)
+  }
+  invisible(NULL)
+}
+
 setMethod("pompLoad",
           signature=signature(object='pomp'),
-          definition = function (object) {
-            for (lib in object at solibfile)
-              dyn.load(lib)
-            invisible(NULL)
+          definition = function (object, ...) {
+            pompLoad.internal(object,...)
           })
 
 setMethod("pompUnload",
           signature=signature(object='pomp'),
-          definition = function (object) {
-            for (lib in object at solibfile)
-              dyn.unload(lib)
-            invisible(NULL)
+          definition = function (object, ...) {
+            pompUnload.internal(object,...)
           })
 
 define <- list(
@@ -161,7 +175,8 @@
 pompCBuilder <- function (name, statenames, paramnames, covarnames, obsnames,
                           rmeasure, dmeasure, step.fn, skeleton,
                           parameter.transform, parameter.inv.transform,
-                          rprior, dprior, globals, save = FALSE, link = TRUE)
+                          rprior, dprior, globals, save = FALSE, link = TRUE,
+                          verbose = getOption("verbose",FALSE))
 {
 
   if (missing(name))
@@ -297,11 +312,12 @@
   rv <- system2(
                 command=R.home("bin/R"),
                 args=c("CMD","SHLIB","-o",solib,modelfile),
-                env=cflags
+                env=cflags,
+                stdout=if (verbose) "" else NULL
                 )
   if (rv!=0)
     stop("cannot compile shared-object library ",sQuote(solib))
-  else
+  else if (verbose)
     cat("model codes written to",sQuote(modelfile),
         "\nlink to shared-object library",sQuote(solib),"\n")
 

Modified: pkg/pomp/R/pomp.R
===================================================================
--- pkg/pomp/R/pomp.R	2015-01-07 03:26:44 UTC (rev 1046)
+++ pkg/pomp/R/pomp.R	2015-01-07 10:54:29 UTC (rev 1047)
@@ -9,7 +9,8 @@
                               obsnames, statenames, paramnames, covarnames,
                               zeronames, PACKAGE,
                               parameter.transform, parameter.inv.transform,
-                              globals, userdata, ..., .solibfile) {
+                              globals, userdata, ..., .solibfile,
+                              verbose = getOption("verbose",FALSE)) {
 
   ## preliminary error checking
   if (missing(data)) stop(sQuote("data")," is a required argument")
@@ -144,7 +145,8 @@
                                   covarnames=covarnames,
                                   globals=globals,
                                   link=TRUE,
-                                  save=FALSE
+                                  save=FALSE,
+                                  verbose=verbose
                                   ),
                              snips
                              )

Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS	2015-01-07 03:26:44 UTC (rev 1046)
+++ pkg/pomp/inst/NEWS	2015-01-07 10:54:29 UTC (rev 1047)
@@ -2,6 +2,12 @@
 
 _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._5_8-_1:
 
+        ? Compiler messages are now suppressed by default when
+          ?Csnippet?s are used in construction of a ?pomp? object.
+          These can be enabled by setting ?options(verbose=TRUE)?.
+
+_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._5_8-_1:
+
         ? A ?pomp? object created with ?Csnippet?s or ?pompBuilder?
           will now remember its associated shared-object file, which
           can be unloaded and reloaded using the new ?pompUnload? and

Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd	2015-01-07 03:26:44 UTC (rev 1046)
+++ pkg/pomp/inst/NEWS.Rd	2015-01-07 10:54:29 UTC (rev 1047)
@@ -2,6 +2,12 @@
 \title{News for package `pomp'}
 \section{Changes in \pkg{pomp} version 0.58-1}{
   \itemize{
+    \item Compiler messages are now suppressed by default when \code{Csnippet}s are used in construction of a \code{pomp} object.
+    These can be enabled by setting \code{options(verbose=TRUE)}.
+  }
+}
+\section{Changes in \pkg{pomp} version 0.58-1}{
+  \itemize{
     \item A \code{pomp} object created with \code{Csnippet}s or \code{pompBuilder} will now remember its associated shared-object file, which can be unloaded and reloaded using the new \code{pompUnload} and \code{pompLoad} methods.
   }
 }

Modified: pkg/pomp/man/pomp.Rd
===================================================================
--- pkg/pomp/man/pomp.Rd	2015-01-07 03:26:44 UTC (rev 1046)
+++ pkg/pomp/man/pomp.Rd	2015-01-07 10:54:29 UTC (rev 1047)
@@ -44,8 +44,8 @@
        initializer, rprior, dprior, params, covar, tcovar,
        obsnames, statenames, paramnames, covarnames, zeronames,
        PACKAGE, parameter.transform, parameter.inv.transform, globals)
-\S4method{pompLoad}{pomp}(object)
-\S4method{pompUnload}{pomp}(object)
+\S4method{pompLoad}{pomp}(object, \dots)
+\S4method{pompUnload}{pomp}(object, \dots)
 }
 \arguments{
   \item{data, times}{


From noreply at r-forge.r-project.org  Fri Jan  9 14:03:04 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri,  9 Jan 2015 14:03:04 +0100 (CET)
Subject: [Pomp-commits] r1048 - in pkg/pomp: . R
Message-ID: <20150109130304.1D671187819@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-09 14:03:03 +0100 (Fri, 09 Jan 2015)
New Revision: 1048

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/simulate-pomp.R
Log:
- fix bug with 'simulate' when 'include.data=TRUE'

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-01-07 10:54:29 UTC (rev 1047)
+++ pkg/pomp/DESCRIPTION	2015-01-09 13:03:03 UTC (rev 1048)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.58-2
-Date: 2015-01-07
+Version: 0.58-3
+Date: 2015-01-09
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),

Modified: pkg/pomp/R/simulate-pomp.R
===================================================================
--- pkg/pomp/R/simulate-pomp.R	2015-01-07 10:54:29 UTC (rev 1047)
+++ pkg/pomp/R/simulate-pomp.R	2015-01-09 13:03:03 UTC (rev 1048)
@@ -79,7 +79,7 @@
                       as.data.frame(t(retval$obs)),
                       as.data.frame(t(retval$states))
                       )
-      retval$sim <- factor(seq_len(nsim))
+      retval$sim <- as.character(seq_len(nsim))
       retval$time <- rep(times,each=nsim)
       retval <- retval[order(retval$sim,retval$time),]
     } else if (obs || states) {
@@ -90,7 +90,7 @@
       dim(retval) <- c(dm[1L],prod(dm[-1L]))
       rownames(retval) <- nm
       retval <- as.data.frame(t(retval))
-      retval$sim <- factor(seq_len(nsim))
+      retval$sim <- as.character(seq_len(nsim))
       retval$time <- rep(times,each=nsim)
       retval <- retval[order(retval$sim,retval$time),]
     } else {
@@ -105,18 +105,22 @@
                          }
                          )
         retval <- do.call(rbind,retval)
-        retval$sim <- factor(retval$sim)
+        retval$sim <- as.character(retval$sim)
       } else {
         retval <- as.data.frame(retval)
-        retval$sim <- factor(1)
+        retval$sim <- "1"
       }
     }
 
     if (include.data) {
       od <- as.data.frame(object)
-      retval <- merge(od,retval,sort=FALSE)
+      od$sim <- "data"
+      od <- od[names(retval)]
+      retval <- rbind(od,retval)
     }
-    
+
+    retval$sim <- factor(retval$sim)
+
   }
 
   retval


From noreply at r-forge.r-project.org  Sat Jan 10 13:36:12 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat, 10 Jan 2015 13:36:12 +0100 (CET)
Subject: [Pomp-commits] r1049 - in pkg/pomp: . R src
Message-ID: <20150110123612.759C2187896@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-10 13:36:12 +0100 (Sat, 10 Jan 2015)
New Revision: 1049

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/pfilter.R
   pkg/pomp/src/pfilter.c
Log:
- attach names to dimnames of states and parameter arrays in pfilter computations

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-01-09 13:03:03 UTC (rev 1048)
+++ pkg/pomp/DESCRIPTION	2015-01-10 12:36:12 UTC (rev 1049)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.58-3
-Date: 2015-01-09
+Version: 0.58-4
+Date: 2015-01-10
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),

Modified: pkg/pomp/R/pfilter.R
===================================================================
--- pkg/pomp/R/pfilter.R	2015-01-09 13:03:03 UTC (rev 1048)
+++ pkg/pomp/R/pfilter.R	2015-01-10 12:36:12 UTC (rev 1049)
@@ -301,10 +301,12 @@
     
     if (save.states) {
       xparticles[[nt]] <- x
+      dimnames(xparticles[[nt]]) <- setNames(dimnames(xparticles[[nt]]),c("variable","rep"))
     }
     
     if (save.params) {
       pparticles[[nt]] <- params
+      dimnames(pparticles[[nt]]) <- setNames(dimnames(pparticles[[nt]]),c("variable","rep"))
     }
     
     if (verbose && (nt%%5==0))

Modified: pkg/pomp/src/pfilter.c
===================================================================
--- pkg/pomp/src/pfilter.c	2015-01-09 13:03:03 UTC (rev 1048)
+++ pkg/pomp/src/pfilter.c	2015-01-10 12:36:12 UTC (rev 1049)
@@ -59,6 +59,7 @@
   SEXP rw_names, ess, fail, loglik;
   SEXP newstates = R_NilValue, newparams = R_NilValue;
   SEXP retval, retvalnames;
+  const char *dimnm[2] = {"variable","rep"};
   double *xpm = 0, *xpv = 0, *xfm = 0, *xw = 0, *xx = 0, *xp = 0;
   SEXP dimX, dimP, newdim, Xnames, Pnames, pindex;
   int *dim, *pidx, lv, np;
@@ -225,6 +226,7 @@
     xdim[0] = nvars; xdim[1] = np;
     PROTECT(newstates = makearray(2,xdim)); nprotect++;
     setrownames(newstates,Xnames,2);
+    fixdimnames(newstates,dimnm,2);
     ss = REAL(x);
     st = REAL(newstates);
 
@@ -233,6 +235,7 @@
       xdim[0] = npars; xdim[1] = np;
       PROTECT(newparams = makearray(2,xdim)); nprotect++;
       setrownames(newparams,Pnames,2);
+      fixdimnames(newparams,dimnm,2);
       ps = REAL(params);
       pt = REAL(newparams);
     }
@@ -255,6 +258,7 @@
     dim[0] = nvars; dim[1] = nreps;
     SET_DIM(x,newdim);
     setrownames(x,Xnames,2);
+    fixdimnames(x,dimnm,2);
 
   }
 


From noreply at r-forge.r-project.org  Thu Jan 22 17:10:29 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 22 Jan 2015 17:10:29 +0100 (CET)
Subject: [Pomp-commits] r1050 - in pkg/pomp: . R tests
Message-ID: <20150122161029.988C218596C@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-22 17:10:29 +0100 (Thu, 22 Jan 2015)
New Revision: 1050

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/simulate-pomp.R
   pkg/pomp/tests/bbs.R
   pkg/pomp/tests/bbs.Rout.save
Log:
- fix bug in 'simulate' that shows up when 'include.dir=TRUE'

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-01-10 12:36:12 UTC (rev 1049)
+++ pkg/pomp/DESCRIPTION	2015-01-22 16:10:29 UTC (rev 1050)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.58-4
-Date: 2015-01-10
+Version: 0.58-5
+Date: 2015-01-15
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),

Modified: pkg/pomp/R/simulate-pomp.R
===================================================================
--- pkg/pomp/R/simulate-pomp.R	2015-01-10 12:36:12 UTC (rev 1049)
+++ pkg/pomp/R/simulate-pomp.R	2015-01-22 16:10:29 UTC (rev 1050)
@@ -115,8 +115,7 @@
     if (include.data) {
       od <- as.data.frame(object)
       od$sim <- "data"
-      od <- od[names(retval)]
-      retval <- rbind(od,retval)
+      retval <- merge(od,retval,all=TRUE)
     }
 
     retval$sim <- factor(retval$sim)

Modified: pkg/pomp/tests/bbs.R
===================================================================
--- pkg/pomp/tests/bbs.R	2015-01-10 12:36:12 UTC (rev 1049)
+++ pkg/pomp/tests/bbs.R	2015-01-22 16:10:29 UTC (rev 1050)
@@ -25,3 +25,7 @@
 
 fit3 <- traj.match(bbs,est=c("beta","sigma"),transform=TRUE)
 signif(coef(fit3),3)
+
+sim1 <- simulate(bbs,nsim=20,as.data.frame=TRUE,include.data=TRUE)
+sim2 <- simulate(bbs,nsim=20,as.data.frame=TRUE,obs=TRUE,include.data=TRUE)
+sim3 <- simulate(bbs,nsim=20,as.data.frame=TRUE,states=TRUE,include.data=TRUE)

Modified: pkg/pomp/tests/bbs.Rout.save
===================================================================
--- pkg/pomp/tests/bbs.Rout.save	2015-01-10 12:36:12 UTC (rev 1049)
+++ pkg/pomp/tests/bbs.Rout.save	2015-01-22 16:10:29 UTC (rev 1050)
@@ -67,6 +67,10 @@
      S.0      I.0      R.0 
    0.999    0.001    0.000 
 > 
+> sim1 <- simulate(bbs,nsim=20,as.data.frame=TRUE,include.data=TRUE)
+> sim2 <- simulate(bbs,nsim=20,as.data.frame=TRUE,obs=TRUE,include.data=TRUE)
+> sim3 <- simulate(bbs,nsim=20,as.data.frame=TRUE,states=TRUE,include.data=TRUE)
+> 
 > proc.time()
    user  system elapsed 
-  7.008   0.076   7.124 
+  7.153   0.049   7.193 


From noreply at r-forge.r-project.org  Thu Jan 22 17:10:34 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 22 Jan 2015 17:10:34 +0100 (CET)
Subject: [Pomp-commits] r1051 - pkg/pomp
Message-ID: <20150122161034.8876618596C@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-22 17:10:34 +0100 (Thu, 22 Jan 2015)
New Revision: 1051

Modified:
   pkg/pomp/DESCRIPTION
Log:
- the recent changes to pompExample are not compatible with R <=3.1.1

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-01-22 16:10:29 UTC (rev 1050)
+++ pkg/pomp/DESCRIPTION	2015-01-22 16:10:34 UTC (rev 1051)
@@ -2,7 +2,7 @@
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
 Version: 0.58-5
-Date: 2015-01-15
+Date: 2015-01-16
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),
@@ -18,7 +18,7 @@
 	  )
 URL: http://pomp.r-forge.r-project.org
 Description: Inference methods for partially observed Markov processes (AKA stochastic dynamical systems, state-space models)
-Depends: R(>= 3.0.0), methods, subplex, nloptr
+Depends: R(>= 3.1.2), methods, subplex, nloptr
 Imports: stats, graphics, mvtnorm, deSolve, coda
 License: GPL(>= 2)
 LazyData: true


From noreply at r-forge.r-project.org  Thu Jan 22 17:10:39 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 22 Jan 2015 17:10:39 +0100 (CET)
Subject: [Pomp-commits] r1052 - in pkg/pomp: . R
Message-ID: <20150122161039.2D9EC18596C@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-22 17:10:38 +0100 (Thu, 22 Jan 2015)
New Revision: 1052

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/example.R
Log:
- restore compatibility with R>=3.0.0

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-01-22 16:10:34 UTC (rev 1051)
+++ pkg/pomp/DESCRIPTION	2015-01-22 16:10:38 UTC (rev 1052)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.58-5
-Date: 2015-01-16
+Version: 0.58-6
+Date: 2015-01-22
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),
@@ -18,7 +18,7 @@
 	  )
 URL: http://pomp.r-forge.r-project.org
 Description: Inference methods for partially observed Markov processes (AKA stochastic dynamical systems, state-space models)
-Depends: R(>= 3.1.2), methods, subplex, nloptr
+Depends: R(>= 3.0.0), methods, subplex, nloptr
 Imports: stats, graphics, mvtnorm, deSolve, coda
 License: GPL(>= 2)
 LazyData: true

Modified: pkg/pomp/R/example.R
===================================================================
--- pkg/pomp/R/example.R	2015-01-22 16:10:34 UTC (rev 1051)
+++ pkg/pomp/R/example.R	2015-01-22 16:10:38 UTC (rev 1052)
@@ -11,7 +11,11 @@
       print(avlbl[[dir]])
     }
   } else {
-    evalEnv <- list2env(list(...))
+## the following needed from R/3.0.0 to R/3.1.1:
+    dots <- list(...)
+    evalEnv <- if (length(dots)>0) list2env(list(...)) else new.env()
+## the following will work from R/3.1.2
+##  evalEnv <- list2env(list(...))
     file <- c(lapply(exampleDirs,list.files,
                      pattern=paste0(example,".R"),
                      full.names=TRUE),


From noreply at r-forge.r-project.org  Fri Jan 23 15:50:30 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 23 Jan 2015 15:50:30 +0100 (CET)
Subject: [Pomp-commits] r1053 - in pkg: . pompExamples
	pompExamples/inst/examples pompExamples/vignettes
Message-ID: <20150123145030.3A82F187946@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-23 15:50:29 +0100 (Fri, 23 Jan 2015)
New Revision: 1053

Added:
   pkg/pompExamples/inst/examples/bsflu.R
   pkg/pompExamples/inst/examples/bsflu3.R
   pkg/pompExamples/vignettes/Makefile
   pkg/pompExamples/vignettes/bsflu-mf1.rds
   pkg/pompExamples/vignettes/bsflu-mf3.rds
   pkg/pompExamples/vignettes/bsflu-tm1.rds
   pkg/pompExamples/vignettes/bsflu-tm3.rds
   pkg/pompExamples/vignettes/bsflu.Rmd
   pkg/pompExamples/vignettes/bsflu.html
Modified:
   pkg/Makefile
   pkg/pompExamples/DESCRIPTION
Log:
- add boarding-school flu vignette to the pompExamples package

Modified: pkg/Makefile
===================================================================
--- pkg/Makefile	2015-01-22 16:10:38 UTC (rev 1052)
+++ pkg/Makefile	2015-01-23 14:50:29 UTC (rev 1053)
@@ -45,6 +45,9 @@
 	cp pomp.pdf ../www/vignettes
 	$(RCMD) Rdconv -t html pomp/inst/NEWS.Rd -o ../www/content/NEWS.html
 
+pompExamples.vignettes: pompExamples.install
+	(cd pompExamples/vignettes; make)
+
 %.data: %.install
 	cd $*/inst/data-R; make
 

Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2015-01-22 16:10:38 UTC (rev 1052)
+++ pkg/pompExamples/DESCRIPTION	2015-01-23 14:50:29 UTC (rev 1053)
@@ -1,8 +1,8 @@
 Package: pompExamples
 Type: Package
 Title: Additional pomp examples
-Version: 0.25-4
-Date: 2015-01-05
+Version: 0.26-1
+Date: 2015-01-23
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),
 	   email="kingaa at umich.edu"),
@@ -16,9 +16,10 @@
 	  person(given=c("Helen"),family="Wearing",role=c("ctb")))
 URL: http://pomp.r-forge.r-project.org
 Description: More 'pomp' examples.
-Depends: R(>= 3.0.0), stats, graphics, pomp(>= 0.56-1)
-Suggests: plyr, reshape2
+Depends: R(>= 3.0.0), stats, graphics, pomp(>= 0.58-6)
+Suggests: plyr, reshape2, knitr, ggplot2
 License: GPL (>= 2)
 LazyData: false
 BuildVignettes: true
+VignetteBuilder: knitr
 Collate: aaa.R pertussis.R

Added: pkg/pompExamples/inst/examples/bsflu.R
===================================================================
--- pkg/pompExamples/inst/examples/bsflu.R	                        (rev 0)
+++ pkg/pompExamples/inst/examples/bsflu.R	2015-01-23 14:50:29 UTC (rev 1053)
@@ -0,0 +1,109 @@
+## data read from graph in Anonymous (1978) 'Influenza in a boarding school' Brit. Med. J. 1:578.
+## cases are recorded with error of +/- 1 case
+## 763 boys were at risk, 512 boys spent time away from class
+flu <- read.csv(text="
+date,confined,convalescent
+1978-01-22,1,0
+1978-01-23,6,0
+1978-01-24,26,0
+1978-01-25,73,1
+1978-01-26,222,8
+1978-01-27,293,16
+1978-01-28,258,99
+1978-01-29,236,160
+1978-01-30,191,173
+1978-01-31,124,162
+1978-02-01,69,150
+1978-02-02,26,89
+1978-02-03,11,44
+1978-02-04,4,22
+",colClasses=c(date='Date'))
+flu$day <- flu$date-min(flu$date)+1
+units(flu$day) <- "days"
+flu$day <- as.numeric(flu$day)
+
+partrans <- "
+ TBeta = exp(Beta);
+ Tinf_pd = exp(inf_pd);
+ Trho = expit(rho);
+ Tsfrac = expit(sfrac);
+"
+
+paruntrans <- "
+ TBeta = log(Beta);
+ Tinf_pd = log(inf_pd);
+ Trho = logit(rho);
+ Tsfrac = logit(sfrac);
+"
+
+dmeas <- "
+  lik = dpois(confined,rho*R+1e-6,give_log);
+"
+
+rmeas <- "
+  confined = rpois(rho*R+1e-6);
+  convalescent = rpois(rho*C);
+"
+
+stochsim <- "
+  double t1 = rbinom(S,1-exp(-Beta*I*dt));
+  double t2 = rbinom(I,1-exp(-dt/inf_pd));
+  double t3 = rbinom(R,1-exp(-dt/conf_pd));
+  double t4 = rbinom(C,1-exp(-dt/conv_pd));
+  S -= t1;
+  I += t1 - t2;
+  R += t2 - t3;
+  C += t3 - t4;
+"
+
+skel <- "
+  double dt = 1.0/24.0;
+  double t1 = S*(1-exp(-Beta*I*dt));
+  double t2 = I*(1-exp(-dt/inf_pd));
+  double t3 = R*(1-exp(-dt/conf_pd));
+  double t4 = C*(1-exp(-dt/conv_pd));
+  DS = S - t1;
+  DI = I + t1 - t2;
+  DR = R + t2 - t3;
+  DC = C + t3 - t4;
+"
+
+pomp(
+     data=flu[c("day","confined","convalescent")],
+     times="day",
+     t0=0,
+     params=c(
+       Beta=0.004,
+       inf.pd=0.7,
+       conf.pd=sum(flu$confined)/512,
+       conv.pd=sum(flu$convalescent)/512,
+       rho=0.9,
+       sfrac=762/763
+       ),
+     rprocess=euler.sim(
+       step.fun=Csnippet(stochsim),
+       delta.t=1/24
+       ),
+     skeleton=Csnippet(skel),
+     skelmap.delta.t=1/24,
+     skeleton.type="map",
+     rmeasure=Csnippet(rmeas),
+     dmeasure=Csnippet(dmeas),
+     parameter.transform=Csnippet(partrans),
+     parameter.inv.transform=Csnippet(paruntrans),
+     obsnames = c("confined","convalescent"),
+     statenames=c("S","I","R","C"),
+     paramnames=c(
+       "Beta",
+       "inf.pd","conf.pd","conv.pd",
+       "rho","sfrac"
+       ),
+     initializer=function(params, t0, ...) {
+       x0 <- setNames(numeric(4),c("S","I","R","C"))
+       S.0 <- round(763*params["sfrac"])
+       x0[c("S","I")] <- c(S.0,763-S.0)
+       x0
+     }
+     ) -> bsflu
+
+c("bsflu")

Added: pkg/pompExamples/inst/examples/bsflu3.R
===================================================================
--- pkg/pompExamples/inst/examples/bsflu3.R	                        (rev 0)
+++ pkg/pompExamples/inst/examples/bsflu3.R	2015-01-23 14:50:29 UTC (rev 1053)
@@ -0,0 +1,117 @@
+## data read from graph in Anonymous (1978) 'Influenza in a boarding school' Brit. Med. J. 1:578.
+## cases are recorded with error of +/- 1 case
+## 763 boys were at risk, 512 boys spent time away from class
+flu <- read.csv(text="
+date,confined,convalescent
+1978-01-22,1,0
+1978-01-23,6,0
+1978-01-24,26,0
+1978-01-25,73,1
+1978-01-26,222,8
+1978-01-27,293,16
+1978-01-28,258,99
+1978-01-29,236,160
+1978-01-30,191,173
+1978-01-31,124,162
+1978-02-01,69,150
+1978-02-02,26,89
+1978-02-03,11,44
+1978-02-04,4,22
+",colClasses=c(date='Date'))
+flu$day <- flu$date-min(flu$date)+1
+units(flu$day) <- "days"
+flu$day <- as.numeric(flu$day)
+
+partrans <- "
+ TBeta = exp(Beta);
+ Tinf_pd = exp(inf_pd);
+ Trho = expit(rho);
+ Tsfrac = expit(sfrac);
+"
+
+paruntrans <- "
+ TBeta = log(Beta);
+ Tinf_pd = log(inf_pd);
+ Trho = logit(rho);
+ Tsfrac = logit(sfrac);
+"
+
+dmeas <- "
+  lik = dpois(confined,rho*(R1+R2+R3)+1e-6,give_log);
+"
+
+rmeas <- "
+  confined = rpois(rho*(R1+R2+R3)+1e-6);
+  convalescent = rpois(rho*C);
+"
+
+stochsim <- "
+  double t1 = rbinom(S,1-exp(-Beta*I*dt));
+  double t2 = rbinom(I,1-exp(-dt/inf_pd));
+  double t3a = rbinom(R1,1-exp(-3*dt/conf_pd));
+  double t3b = rbinom(R2,1-exp(-3*dt/conf_pd));
+  double t3c = rbinom(R3,1-exp(-3*dt/conf_pd));
+  double t4 = rbinom(C,1-exp(-dt/conv_pd));
+  S -= t1;
+  I += t1 - t2;
+  R1 += t2 - t3a;
+  R2 += t3a - t3b;
+  R3 += t3b - t3c;
+  C += t3c - t4;
+"
+
+skel <- "
+  double dt = 1.0/24.0;
+  double t1 = S*(1-exp(-Beta*I*dt));
+  double t2 = I*(1-exp(-dt/inf_pd));
+  double t3a = R1*(1-exp(-3*dt/conf_pd));
+  double t3b = R2*(1-exp(-3*dt/conf_pd));
+  double t3c = R3*(1-exp(-3*dt/conf_pd));
+  double t4 = C*(1-exp(-dt/conv_pd));
+  DS = S - t1;
+  DI = I + t1 - t2;
+  DR1 = R1 + t2 - t3a;
+  DR2 = R2 + t3a - t3b;
+  DR3 = R3 + t3b - t3c;
+  DC = C + t3c - t4;
+"
+
+pomp(
+     data=flu[c("day","confined","convalescent")],
+     times="day",
+     t0=0,
+     params=c(
+       Beta=0.004,
+       inf.pd=0.7,
+       conf.pd=sum(flu$confined)/512,
+       conv.pd=sum(flu$convalescent)/512,
+       rho=0.9,
+       sfrac=762/763
+       ),
+     rprocess=euler.sim(
+       step.fun=Csnippet(stochsim),
+       delta.t=1/24
+       ),
+     skeleton=Csnippet(skel),
+     skelmap.delta.t=1/24,
+     skeleton.type="map",
+     rmeasure=Csnippet(rmeas),
+     dmeasure=Csnippet(dmeas),
+     parameter.transform=Csnippet(partrans),
+     parameter.inv.transform=Csnippet(paruntrans),
+     obsnames = c("confined","convalescent"),
+     statenames=c("S","I","R1","R2","R3","C"),
+     paramnames=c(
+       "Beta",
+       "inf.pd","conf.pd","conv.pd",
+       "rho","sfrac"
+       ),
+     initializer=function(params, t0, ...) {
+       x0 <- setNames(numeric(6),c("S","I","R1","R2","R3","C"))
+       S.0 <- round(763*params["sfrac"])
+       x0[c("S","I")] <- c(S.0,763-S.0)
+       x0
+     }
+     ) -> bsflu3
+
+c("bsflu3")

Added: pkg/pompExamples/vignettes/Makefile
===================================================================
--- pkg/pompExamples/vignettes/Makefile	                        (rev 0)
+++ pkg/pompExamples/vignettes/Makefile	2015-01-23 14:50:29 UTC (rev 1053)
@@ -0,0 +1,10 @@
+RSCRIPT = Rscript --vanilla
+RM = rm -f
+
+vignettes: bsflu.html
+	$(RM) -r figure
+
+%.html: %.Rmd
+	$(RSCRIPT) -e 'knitr::knit("$*.Rmd")'
+	$(RSCRIPT) -e 'markdown::markdownToHTML("$*.md","$*.html")'
+	$(RM) $*.md

Added: pkg/pompExamples/vignettes/bsflu-mf1.rds
===================================================================
--- pkg/pompExamples/vignettes/bsflu-mf1.rds	                        (rev 0)
+++ pkg/pompExamples/vignettes/bsflu-mf1.rds	2015-01-23 14:50:29 UTC (rev 1053)
@@ -0,0 +1 @@
+???b```b`fdb`b2????
1???m[Y{`|?o?n??M????nJ??????5?w?`???????!???Fy????:??e``a?X8?4k^bnj1?!vD?-'?='3??????S?,N?%?0??yiz)P{r>:??e.???Y[?V???????r=?{xA??$?
???s?a??	r?$?$?
??M??
???&~

\ No newline at end of file

Added: pkg/pompExamples/vignettes/bsflu-mf3.rds
===================================================================
--- pkg/pompExamples/vignettes/bsflu-mf3.rds	                        (rev 0)
+++ pkg/pompExamples/vignettes/bsflu-mf3.rds	2015-01-23 14:50:29 UTC (rev 1053)
@@ -0,0 +1,4 @@
+???b```b`fdb`b2????
1?
??|??c?`|?]_??V??????|>?????1???>??C?

+ ????O????P???? ?(?????	?Y?sS??
?? ?l9??9??P'??W?
+`qJ-I?)??K?+H???????e.sQF>??????d4?p??????
+? ?????Xs4L?+%?$Qhln*??????~

\ No newline at end of file

Added: pkg/pompExamples/vignettes/bsflu-tm1.rds
===================================================================
--- pkg/pompExamples/vignettes/bsflu-tm1.rds	                        (rev 0)
+++ pkg/pompExamples/vignettes/bsflu-tm1.rds	2015-01-23 14:50:29 UTC (rev 1053)
@@ -0,0 +1 @@
+???b```b`fdb`b2????
1????U?F?7`|???ds?'Mu????K?`mm??8P??y??]?,???M8??W?????,L`?X8?4k^bnj1?!vD?-'?='3??????S?,N?%?0??yiz)P{r>:??e.???Y[?V???????r=?{xA??$?
???s?a??	r?$?$?
??M??
????~

\ No newline at end of file

Added: pkg/pompExamples/vignettes/bsflu-tm3.rds
===================================================================
--- pkg/pompExamples/vignettes/bsflu-tm3.rds	                        (rev 0)
+++ pkg/pompExamples/vignettes/bsflu-tm3.rds	2015-01-23 14:50:29 UTC (rev 1053)
@@ -0,0 +1,4 @@
+???b```b`fdb`b2????
1?
???*S,Ua|????+?v7???_??x?T????!????T?K?F??2p??????CX????0pi?????b C?8? [N~zNf6??	???BX?RKaJ3???
+R?<??|tn??\????8?(1?-?E??z0????
H?tG'?$?
+?JI,I???
+??Q&~

\ No newline at end of file

Added: pkg/pompExamples/vignettes/bsflu.Rmd
===================================================================
--- pkg/pompExamples/vignettes/bsflu.Rmd	                        (rev 0)
+++ pkg/pompExamples/vignettes/bsflu.Rmd	2015-01-23 14:50:29 UTC (rev 1053)
@@ -0,0 +1,183 @@
+%\VignetteIndexEntry{Boarding-school influenza example}
+%\VignetteEngine{knitr::knitr}
+
+# Boarding-School Flu Outbreak Analysis  
+***Aaron A. King***
+
+```{r setup,include=FALSE}
+require(pomp)
+require(plyr)
+require(reshape2)
+options(stringsAsFactors=FALSE,keep.source=TRUE,encoding="UTF-8")
+
+require(ggplot2)
+theme_set(theme_bw())
+
+require(knitr)
+opts_knit$set(out.format="html")
+opts_chunk$set(
+  progress=TRUE,
+  prompt=FALSE,tidy=FALSE,highlight=TRUE,
+  strip.white=TRUE,
+  warning=FALSE,message=FALSE,error=FALSE,
+  echo=TRUE,cache=FALSE,
+  results='markup',
+  fig.show='asis',
+  fig.height=5,fig.width=10,
+  dpi=100
+  )
+
+require(pompExamples)
+set.seed(862663052L)
+```
+
+First, a little function to cache the results of expensive computations.
+
+```{r juliaChild}
+juliaChild <- function (file, expr) {
+  if (file.exists(file)) {
+    readRDS(file)
+    } else {
+      val <- eval(expr)
+      saveRDS(val,file=file)
+      val
+      }
+  }
+```
+
+## Flu model with exponentially-distributed waiting times
+
+```{r bsflu1,cache=FALSE}
+pompExample(bsflu)
+coef(bsflu)
+```
+```{r plot1}
+simdat <- simulate(bsflu,nsim=10,obs=TRUE,as.data.frame=TRUE,include.data=TRUE)
+ggplot(data=melt(simdat,id=c("sim","time")),
+       mapping=aes(x=time,y=value,group=interaction(variable,sim),
+                   color=variable,size=sim=="data",alpha=sim=="data"))+
+  geom_line()+
+  scale_alpha_manual(values=c(`TRUE`=1,`FALSE`=0.5))+
+  scale_size_manual(values=c(`TRUE`=2,`FALSE`=1))
+```
+
+### Trajectory matching
+
+```{r tm1}
+juliaChild("bsflu-tm1.rds",{
+  traj.match(bsflu,est=c("Beta","inf.pd","rho"),transform=TRUE) -> tm
+  traj.match(tm,method='subplex') -> tm
+  data.frame(loglik=logLik(tm),loglik.se=0,as.list(coef(tm)))
+}) -> tm1
+```
+```{r tm1-simplot}
+simdat <- simulate(bsflu,params=unlist(tm1),nsim=10,
+                   obs=TRUE,as.data.frame=TRUE,include.data=TRUE)
+ggplot(data=melt(simdat,id=c("sim","time")),
+       mapping=aes(x=time,y=value,group=interaction(variable,sim),
+                   color=variable,size=sim=="data",alpha=sim=="data"))+
+  geom_line()+
+  scale_alpha_manual(values=c(`TRUE`=1,`FALSE`=0.5))+
+  scale_size_manual(values=c(`TRUE`=2,`FALSE`=1))
+```
+
+### Iterated filtering
+
+```{r mf1}
+juliaChild("bsflu-mf1.rds",{
+  mif(bsflu,rw.sd=c(Beta=0.05,inf.pd=0.05,rho=0.05),
+      cooling.fraction=0.9,var.factor=2,
+      Nmif=50,Np=1000,method='mif2',transform=TRUE) -> mf
+  mif(mf,Nmif=50,cooling.fraction=0.5) -> mf
+  mif(mf,Nmif=50,cooling.fraction=0.1) -> mf
+  ll <- unname(logmeanexp(raply(5,logLik(pfilter(mf))),se=TRUE))
+  data.frame(loglik=ll[1],loglik.se=ll[2],as.list(coef(mf)))
+}) -> mf1
+```
+```{r mf1-simplot}
+simdat <- simulate(bsflu,params=unlist(mf1),nsim=10,
+                   obs=TRUE,as.data.frame=TRUE,include.data=TRUE)
+ggplot(data=melt(simdat,id=c("sim","time")),
+       mapping=aes(x=time,y=value,group=interaction(variable,sim),
+                   color=variable,size=sim=="data",alpha=sim=="data"))+
+  geom_line()+
+  scale_alpha_manual(values=c(`TRUE`=1,`FALSE`=0.5))+
+  scale_size_manual(values=c(`TRUE`=2,`FALSE`=1))
+```
+
+## Model with Erlang(3) confinement period
+
+```{r bsflu3,cache=FALSE}
+pompExample(bsflu3)
+coef(bsflu3)
+```
+```{r plot3}
+simdat <- simulate(bsflu3,nsim=10,obs=TRUE,as.data.frame=TRUE,include.data=TRUE)
+ggplot(data=melt(simdat,id=c("sim","time")),
+       mapping=aes(x=time,y=value,group=interaction(variable,sim),
+                   color=variable,size=sim=="data",alpha=sim=="data"))+
+  geom_line()+
+  scale_alpha_manual(values=c(`TRUE`=1,`FALSE`=0.5))+
+  scale_size_manual(values=c(`TRUE`=2,`FALSE`=1))
+```
+
+### Trajectory matching
+
+```{r tm3}
+juliaChild("bsflu-tm3.rds",{
+  traj.match(bsflu3,est=c("Beta","inf.pd","rho"),transform=TRUE) -> tm
+  traj.match(tm,method='subplex') -> tm
+  data.frame(loglik=logLik(tm),loglik.se=0,as.list(coef(tm)))
+}) -> tm3
+```
+```{r tm3-simplot}
+simdat <- simulate(bsflu3,params=unlist(tm3),nsim=10,
+                   obs=TRUE,as.data.frame=TRUE,include.data=TRUE)
+ggplot(data=melt(simdat,id=c("sim","time")),
+       mapping=aes(x=time,y=value,group=interaction(variable,sim),
+                   color=variable,size=sim=="data",alpha=sim=="data"))+
+  geom_line()+
+  scale_alpha_manual(values=c(`TRUE`=1,`FALSE`=0.5))+
+  scale_size_manual(values=c(`TRUE`=2,`FALSE`=1))
+```
+
+### Iterated filtering
+
+```{r mf3}
+juliaChild("bsflu-mf3.rds",{
+  mif(bsflu3,rw.sd=c(Beta=0.05,inf.pd=0.05,rho=0.05),
+      cooling.fraction=0.9,var.factor=2,
+      Nmif=50,Np=1000,method='mif2',transform=TRUE) -> mf
+  mif(mf,Nmif=50,cooling.fraction=0.5) -> mf
+  mif(mf,Nmif=50,cooling.fraction=0.1) -> mf
+  ll <- unname(logmeanexp(raply(5,logLik(pfilter(mf))),se=TRUE))
+  data.frame(loglik=ll[1],loglik.se=ll[2],as.list(coef(mf)))
+}) -> mf3
+```
+```{r mf3-simplot}
+simdat <- simulate(bsflu3,params=unlist(mf3),nsim=10,
+                   obs=TRUE,as.data.frame=TRUE,include.data=TRUE)
+ggplot(data=melt(simdat,id=c("sim","time")),
+       mapping=aes(x=time,y=value,group=interaction(variable,sim),
+                   color=variable,size=sim=="data",alpha=sim=="data"))+
+  geom_line()+
+  scale_alpha_manual(values=c(`TRUE`=1,`FALSE`=0.5))+
+  scale_size_manual(values=c(`TRUE`=2,`FALSE`=1))
+```
+
+## Model comparison
+
+```{r comp}
+tb <- ldply(list(det1=tm1,stoch1=mf1,det3=tm3,stoch3=mf3),.id="model")
+kable(tb)
+```
+
+```{r probes,fig.height=6,fig.width=6}
+plist <- list(probe.acf("confined",lags=c(2),type="cov",transform=sqrt),
+              probe.ccf(c("confined","convalescent"),lags=c(0,3),transform=sqrt),
+              tot=function (x) apply(x,1,sum))
+plot(probe(bsflu,params=unlist(tm1),nsim=500,probes=plist))
+plot(probe(bsflu,params=unlist(mf1),nsim=500,probes=plist))
+plot(probe(bsflu3,params=unlist(tm3),nsim=500,probes=plist))
+plot(probe(bsflu3,params=unlist(mf3),nsim=500,probes=plist))
+```

Added: pkg/pompExamples/vignettes/bsflu.html
===================================================================
--- pkg/pompExamples/vignettes/bsflu.html	                        (rev 0)
+++ pkg/pompExamples/vignettes/bsflu.html	2015-01-23 14:50:29 UTC (rev 1053)
@@ -0,0 +1,460 @@
+<!DOCTYPE html>
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
+
+<title>Boarding-School Flu Outbreak Analysis</title>
+
+<script type="text/javascript">
+window.onload = function() {
+  var imgs = document.getElementsByTagName('img'), i, img;
+  for (i = 0; i < imgs.length; i++) {
+    img = imgs[i];
+    // center an image if it is the only element of its parent
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+      img.parentElement.style.textAlign = 'center';
+  }
+};
+</script>
+
+<!-- Styles for R syntax highlighter -->
+<style type="text/css">
+   pre .operator,
+   pre .paren {
+     color: rgb(104, 118, 135)
+   }
+
+   pre .literal {
+     color: #990073
+   }
+
+   pre .number {
+     color: #099;
+   }
+
+   pre .comment {
+     color: #998;
+     font-style: italic
+   }
+
+   pre .keyword {
+     color: #900;
+     font-weight: bold
+   }
+
+   pre .identifier {
+     color: rgb(0, 0, 0);
+   }
+
+   pre .string {
+     color: #d14;
+   }
+</style>
+
+<!-- R syntax highlighter -->
+<script type="text/javascript">
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+}
+
+ at media print {
+   * {
+      background: transparent !important;
+      color: black !important;
+      filter:none !important;
+      -ms-filter: none !important;
+   }
+
+   body {
+      font-size:12pt;
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+   }
+
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+      padding-right: 1em;
+      page-break-inside: avoid;
+   }
+
+   tr, img {
+      page-break-inside: avoid;
+   }
+
+   img {
+      max-width: 100% !important;
+   }
+
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+      margin: 15mm 20mm 15mm 10mm;
+   }
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+      margin: 15mm 10mm 15mm 20mm;
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+}
+</style>
+
+
+
+</head>
+
+<body>
+<h1>Boarding-School Flu Outbreak Analysis</h1>
+
+<p><strong><em>Aaron A. King</em></strong></p>
+
+<p>First, a little function to cache the results of expensive computations.</p>
+
+<pre><code class="r">juliaChild &lt;- function (file, expr) {
+  if (file.exists(file)) {
+    readRDS(file)
+    } else {
+      val &lt;- eval(expr)
+      saveRDS(val,file=file)
+      val
+      }
+  }
+</code></pre>
+
+<h2>Flu model with exponentially-distributed waiting times</h2>
+
+<pre><code class="r">pompExample(bsflu)
+</code></pre>
+
+<pre><code>## newly created object(s):
+##  bsflu
+</code></pre>
+
+<pre><code class="r">coef(bsflu)
+</code></pre>
+
+<pre><code>##      Beta    inf.pd   conf.pd   conv.pd       rho     sfrac 
+## 0.0040000 0.7000000 3.0078125 1.8046875 0.9000000 0.9986894
+</code></pre>
+
+<pre><code class="r">simdat &lt;- simulate(bsflu,nsim=10,obs=TRUE,as.data.frame=TRUE,include.data=TRUE)
+ggplot(data=melt(simdat,id=c(&quot;sim&quot;,&quot;time&quot;)),
+       mapping=aes(x=time,y=value,group=interaction(variable,sim),
+                   color=variable,size=sim==&quot;data&quot;,alpha=sim==&quot;data&quot;))+
+  geom_line()+
+  scale_alpha_manual(values=c(`TRUE`=1,`FALSE`=0.5))+
+  scale_size_manual(values=c(`TRUE`=2,`FALSE`=1))
+</code></pre>
+
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 1053

From noreply at r-forge.r-project.org  Fri Jan 23 15:50:34 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 23 Jan 2015 15:50:34 +0100 (CET)
Subject: [Pomp-commits] r1054 - pkg/pompExamples
Message-ID: <20150123145034.3F02B187946@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-23 15:50:34 +0100 (Fri, 23 Jan 2015)
New Revision: 1054

Modified:
   pkg/pompExamples/DESCRIPTION
Log:
- add markdown to Suggests

Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2015-01-23 14:50:29 UTC (rev 1053)
+++ pkg/pompExamples/DESCRIPTION	2015-01-23 14:50:34 UTC (rev 1054)
@@ -17,7 +17,7 @@
 URL: http://pomp.r-forge.r-project.org
 Description: More 'pomp' examples.
 Depends: R(>= 3.0.0), stats, graphics, pomp(>= 0.58-6)
-Suggests: plyr, reshape2, knitr, ggplot2
+Suggests: plyr, reshape2, ggplot2, knitr, markdown
 License: GPL (>= 2)
 LazyData: false
 BuildVignettes: true


From noreply at r-forge.r-project.org  Sat Jan 24 16:19:48 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat, 24 Jan 2015 16:19:48 +0100 (CET)
Subject: [Pomp-commits] r1055 - pkg/pompExamples/vignettes
Message-ID: <20150124151948.99447187924@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-24 16:19:48 +0100 (Sat, 24 Jan 2015)
New Revision: 1055

Added:
   pkg/pompExamples/vignettes/parus-mf.rds
   pkg/pompExamples/vignettes/parus-tm1.rds
   pkg/pompExamples/vignettes/parus.Rmd
   pkg/pompExamples/vignettes/parus.html
Log:
- vignette on Parus major example

Added: pkg/pompExamples/vignettes/parus-mf.rds
===================================================================
--- pkg/pompExamples/vignettes/parus-mf.rds	                        (rev 0)
+++ pkg/pompExamples/vignettes/parus-mf.rds	2015-01-24 15:19:48 UTC (rev 1055)
@@ -0,0 +1,3 @@
+???b```b`fdb`b2???;?
1????_???Q????%)???
+?wH_????\m8?[p???s????{??3_????2~\}R?0??,?@?5/17??;"???????
+?qBxz??P
Fo?fJqfzn"?S??Z?0???Y?Y?_???& ??t?%?$???JI,I?K+???
HP??U

\ No newline at end of file

Added: pkg/pompExamples/vignettes/parus-tm1.rds
===================================================================
--- pkg/pompExamples/vignettes/parus-tm1.rds	                        (rev 0)
+++ pkg/pompExamples/vignettes/parus-tm1.rds	2015-01-24 15:19:48 UTC (rev 1055)
@@ -0,0 +1 @@
+???b```b`fdb`b2???;?
1???;???}???w?????)8???G????a|?e+??gY????????/??O???X????0pi?????b C?? [N~zNf6??	???B?a?"?)?????0NIFj	????g?f%gQ~??Z^P?4	???????XsL?+%?$Q/????T??U

\ No newline at end of file

Added: pkg/pompExamples/vignettes/parus.Rmd
===================================================================
--- pkg/pompExamples/vignettes/parus.Rmd	                        (rev 0)
+++ pkg/pompExamples/vignettes/parus.Rmd	2015-01-24 15:19:48 UTC (rev 1055)
@@ -0,0 +1,107 @@
+%\VignetteIndexEntry{Parus major example}
+%\VignetteEngine{knitr::knitr}
+
+# Analysis of Parus Major data from Wytham Wood  
+***Aaron A. King***
+
+```{r setup,include=FALSE}
+require(pomp)
+require(plyr)
+require(reshape2)
+options(stringsAsFactors=FALSE,keep.source=TRUE,encoding="UTF-8")
+
+require(ggplot2)
+theme_set(theme_bw())
+
+require(knitr)
+opts_knit$set(out.format="html")
+opts_chunk$set(
+  progress=TRUE,
+  prompt=FALSE,tidy=FALSE,highlight=TRUE,
+  strip.white=TRUE,
+  warning=FALSE,message=FALSE,error=FALSE,
+  echo=TRUE,cache=FALSE,
+  results='markup',
+  fig.show='asis',
+  fig.height=5,fig.width=10,
+  dpi=100
+  )
+
+require(pompExamples)
+set.seed(862663052L)
+```
+
+First, a little function to cache the results of expensive computations.
+
+```{r juliaChild}
+juliaChild <- function (file, expr) {
+  if (file.exists(file)) {
+    readRDS(file)
+    } else {
+      val <- eval(expr)
+      saveRDS(val,file=file)
+      val
+      }
+  }
+```
+
+### Load and plot the data
+
+```{r}
+pompExample(parus,proc='Gompertz',meas='Poisson')
+plot(parus)
+coef(parus)
+logLik(traj.match(parus))
+```
+
+## Trajectory matching
+
+```{r}
+juliaChild("parus-tm1.rds",{
+  tm <- parus
+  coef(tm,"theta") <- NA
+  traj.match(tm,est=c("K","r","sigma"),transform=T) -> tm
+  traj.match(tm,method='subplex') -> tm
+  data.frame(loglik=logLik(tm),loglik.se=0,as.list(coef(tm)))
+  }) -> tm
+```
+```{r}
+ggplot(data=simulate(parus,params=unlist(tm),nsim=10,obs=TRUE,
+                     as.data.frame=TRUE,include.data=TRUE),
+       mapping=aes(x=time,y=pop,group=sim,alpha=sim=="data"))+
+  geom_line()
+```
+
+## Iterated filtering
+
+```{r}
+juliaChild("parus-mf.rds",{
+  mf <- parus
+  coef(mf,"theta") <- NA
+  mif(mf,rw.sd=c(K=0.02,r=0.02,sigma=0.02),
+      cooling.fraction=0.8,var.factor=2,
+      Nmif=50,Np=2000,method='mif2',
+      cooling.type='hyperbolic') -> mf
+  continue(mf,Nmif=250) -> mf
+  mif(mf) -> mf
+  mif(mf,Np=5000) -> mf
+  mif(mf,Np=5000) -> mf
+  mif(mf,Np=5000) -> mf
+  continue(mf,Nmif=50) -> mf
+  plot(mf)
+  ll <- unname(logmeanexp(raply(5,logLik(pfilter(mf))),se=TRUE))
+  data.frame(loglik=ll[1],loglik.se=ll[2],as.list(coef(mf)))
+}) -> mf
+```
+```{r}
+ggplot(data=simulate(parus,params=unlist(mf),nsim=10,obs=TRUE,
+                     as.data.frame=TRUE,include.data=TRUE),
+       mapping=aes(x=time,y=pop,group=sim,alpha=sim=="data"))+
+  geom_line()
+```
+
+## Comparison
+
+```{r}
+kable(ldply(list(det=tm,stoch=mf),.id='model'))
+```

Added: pkg/pompExamples/vignettes/parus.html
===================================================================
--- pkg/pompExamples/vignettes/parus.html	                        (rev 0)
+++ pkg/pompExamples/vignettes/parus.html	2015-01-24 15:19:48 UTC (rev 1055)
@@ -0,0 +1,196 @@
+<!DOCTYPE html>
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+
+<head>
+
+<meta charset="utf-8">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="pandoc" />
+
+<meta name="author" content />
+
+
+<title></title>
+
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 1055

From noreply at r-forge.r-project.org  Sat Jan 24 16:19:52 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat, 24 Jan 2015 16:19:52 +0100 (CET)
Subject: [Pomp-commits] r1056 - pkg/pompExamples
Message-ID: <20150124151952.30FDE187924@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-24 16:19:51 +0100 (Sat, 24 Jan 2015)
New Revision: 1056

Modified:
   pkg/pompExamples/DESCRIPTION
Log:
- vignette for Parus major example

Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2015-01-24 15:19:48 UTC (rev 1055)
+++ pkg/pompExamples/DESCRIPTION	2015-01-24 15:19:51 UTC (rev 1056)
@@ -1,8 +1,8 @@
 Package: pompExamples
 Type: Package
 Title: Additional pomp examples
-Version: 0.26-1
-Date: 2015-01-23
+Version: 0.26-2
+Date: 2015-01-24
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),
 	   email="kingaa at umich.edu"),


From noreply at r-forge.r-project.org  Mon Jan 26 02:27:50 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 26 Jan 2015 02:27:50 +0100 (CET)
Subject: [Pomp-commits] r1057 - in pkg/pompExamples: . vignettes
Message-ID: <20150126012750.D10DB185FC1@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-26 02:27:50 +0100 (Mon, 26 Jan 2015)
New Revision: 1057

Modified:
   pkg/pompExamples/DESCRIPTION
   pkg/pompExamples/vignettes/parus-tm1.rds
   pkg/pompExamples/vignettes/parus.Rmd
   pkg/pompExamples/vignettes/parus.html
Log:
- update

Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2015-01-24 15:19:51 UTC (rev 1056)
+++ pkg/pompExamples/DESCRIPTION	2015-01-26 01:27:50 UTC (rev 1057)
@@ -1,7 +1,7 @@
 Package: pompExamples
 Type: Package
 Title: Additional pomp examples
-Version: 0.26-2
+Version: 0.26-3
 Date: 2015-01-24
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),

Modified: pkg/pompExamples/vignettes/parus-tm1.rds
===================================================================
--- pkg/pompExamples/vignettes/parus-tm1.rds	2015-01-24 15:19:51 UTC (rev 1056)
+++ pkg/pompExamples/vignettes/parus-tm1.rds	2015-01-26 01:27:50 UTC (rev 1057)
@@ -1 +1,2 @@
-???b```b`fdb`b2???;?
1???;???}???w?????)8???G????a|?e+??gY????????/??O???X????0pi?????b C?? [N~zNf6??	???B?a?"?)?????0NIFj	????g?f%gQ~??Z^P?4	???????XsL?+%?$Q/????T??U

\ No newline at end of file
+???b```b`fdb`b2???;?
1???;???}???w?8???eB<?t8Z]@???? &?"?????@?????	????H??%??`?@?r??s2??<NO?8*??
+c?L)?L?M?qJ2RK`f?=4+9????`?????
H???????b??`?\)?%?ziE@?@?? ?h?U

\ No newline at end of file

Modified: pkg/pompExamples/vignettes/parus.Rmd
===================================================================
--- pkg/pompExamples/vignettes/parus.Rmd	2015-01-24 15:19:51 UTC (rev 1056)
+++ pkg/pompExamples/vignettes/parus.Rmd	2015-01-26 01:27:50 UTC (rev 1057)
@@ -50,17 +50,46 @@
 ```{r}
 pompExample(parus,proc='Gompertz',meas='Poisson')
 plot(parus)
+```
+
+## Model description
+
+### Process model
+
+If `proc="Gompertz"`, then the population size, $N_t$ follows the stochastic Gompertz model
+$$N_{t} = K^{1-S}\,N_{t-1}^S\,\epsilon_t,$$
+where $S=e^r$ and $\epsilon_t\stackrel{i.i.d.}{\sim}\mathrm{Lognormal}(0,\sigma)$.
+
+If `proc="Ricker"`, the state process is the stochastic Ricker model
+$$N_{t} = N_{t-1}\,\exp\left(r\,\left(1-\frac{N_{t-1}}{K}\right)\right)\,\epsilon_t,$$
+where, again, $\epsilon_t\stackrel{i.i.d.}{\sim}\mathrm{Lognormal}(0,\sigma)$.
+
+### Measurement model
+
+There are three alternative measurement models.
+
+If `meas="Poisson"`, the measurement process is
+$$\mathrm{pop}_{t} \sim \mathrm{Poisson}(N_t).$$
+
+If `meas="negbin"`, the measurement process is
+$$\mathrm{pop}_{t} \sim \mathrm{Negbin}(N_t,\theta),$$
+i.e., $\mathrm{pop}_t$ has mean $N_t$ and variance $N_t+\frac{N_t^2}{\theta}$.
+
+If `meas="lognormal"`, the measurement process is
+$$\mathrm{pop}_{t} \sim \mathrm{Lognormal}(\log(N_t),\theta).$$
+
+```{r}
 coef(parus)
-logLik(traj.match(parus))
 ```
 
 ## Trajectory matching
 
 ```{r}
+logLik(traj.match(parus))
 juliaChild("parus-tm1.rds",{
   tm <- parus
-  coef(tm,"theta") <- NA
-  traj.match(tm,est=c("K","r","sigma"),transform=T) -> tm
+  coef(tm,c("sigma","theta")) <- c(0,NA)
+  traj.match(tm,est=c("K","r"),transform=T) -> tm
   traj.match(tm,method='subplex') -> tm
   data.frame(loglik=logLik(tm),loglik.se=0,as.list(coef(tm)))
   }) -> tm
@@ -69,7 +98,9 @@
 ggplot(data=simulate(parus,params=unlist(tm),nsim=10,obs=TRUE,
                      as.data.frame=TRUE,include.data=TRUE),
        mapping=aes(x=time,y=pop,group=sim,alpha=sim=="data"))+
-  geom_line()
+  geom_line()+
+  scale_alpha_manual(name="",labels=c(`TRUE`='data',`FALSE`='simulation'),
+                     values=c(`TRUE`=1,`FALSE`=0.2))
 ```
 
 ## Iterated filtering
@@ -91,17 +122,19 @@
   plot(mf)
   ll <- unname(logmeanexp(raply(5,logLik(pfilter(mf))),se=TRUE))
   data.frame(loglik=ll[1],loglik.se=ll[2],as.list(coef(mf)))
-}) -> mf
+  }) -> mf
 ```
 ```{r}
 ggplot(data=simulate(parus,params=unlist(mf),nsim=10,obs=TRUE,
                      as.data.frame=TRUE,include.data=TRUE),
        mapping=aes(x=time,y=pop,group=sim,alpha=sim=="data"))+
-  geom_line()
+  geom_line()+
+  scale_alpha_manual(name="",labels=c(`TRUE`='data',`FALSE`='simulation'),
+                     values=c(`TRUE`=1,`FALSE`=0.2))
 ```
 
 ## Comparison
 
 ```{r}
-kable(ldply(list(det=tm,stoch=mf),.id='model'))
+kable(ldply(list(det.gomp.poisson=tm,stoch.gomp.poisson=mf),.id='model'))
 ```

Modified: pkg/pompExamples/vignettes/parus.html
===================================================================
--- pkg/pompExamples/vignettes/parus.html	2015-01-24 15:19:51 UTC (rev 1056)
+++ pkg/pompExamples/vignettes/parus.html	2015-01-26 01:27:50 UTC (rev 1057)
@@ -82,26 +82,43 @@
 ##  parus</code></pre>
 <pre class="r"><code>plot(parus)</code></pre>
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 1057

From noreply at r-forge.r-project.org  Mon Jan 26 02:35:51 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 26 Jan 2015 02:35:51 +0100 (CET)
Subject: [Pomp-commits] r1058 - in pkg/pomp: . R tests
Message-ID: <20150126013551.92F54185FC1@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-26 02:35:51 +0100 (Mon, 26 Jan 2015)
New Revision: 1058

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/pomp-methods.R
   pkg/pomp/tests/ou2-mif.Rout.save
Log:
- dimnames of arrays returned by 'states' and 'obs' will have names

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-01-26 01:27:50 UTC (rev 1057)
+++ pkg/pomp/DESCRIPTION	2015-01-26 01:35:51 UTC (rev 1058)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.58-6
-Date: 2015-01-22
+Version: 0.58-7
+Date: 2015-01-25
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),

Modified: pkg/pomp/R/pomp-methods.R
===================================================================
--- pkg/pomp/R/pomp-methods.R	2015-01-26 01:27:50 UTC (rev 1057)
+++ pkg/pomp/R/pomp-methods.R	2015-01-26 01:35:51 UTC (rev 1058)
@@ -44,7 +44,9 @@
     vars <- varnames
   else if (!all(vars%in%varnames))
     stop("some elements of ",sQuote("vars")," correspond to no observed variable")
-  object at data[vars,,drop=FALSE]
+  y <- object at data[vars,,drop=FALSE]
+  dimnames(y) <- list(variable=rownames(y),time=time(object))
+  y
 }
 
 ## a simple method to extract the data array
@@ -52,20 +54,20 @@
 setMethod("data.array","pomp",obs.internal)
 
 ## a simple method to extract the array of states
-setMethod(
-          "states",
-          "pomp",
-          function (object, vars, ...) {
-            if (length(object at states)==0) {
-              NULL
-            } else {
-              if (missing(vars))
-                vars <- seq(length=nrow(object at states))
-              object at states[vars,,drop=FALSE]
-            }
-          }
-          )
+states.internal <- function (object, vars, ...) {
+  if (length(object at states)==0) {
+    NULL
+  } else {
+    if (missing(vars))
+      vars <- seq(length=nrow(object at states))
+    x <- object at states[vars,,drop=FALSE]
+    dimnames(x) <- list(variable=rownames(x),time=time(object))
+    x
+  }
+}
 
+setMethod("states","pomp",states.internal)
+
 ## a simple method to extract the vector of times
 setMethod(
           "time",

Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save	2015-01-26 01:27:50 UTC (rev 1057)
+++ pkg/pomp/tests/ou2-mif.Rout.save	2015-01-26 01:35:51 UTC (rev 1058)
@@ -26,12 +26,14 @@
 > set.seed(64857673L)
 > 
 > obs(window(ou2,end=20,start=15))
-        [,1]       [,2]       [,3]      [,4]      [,5]      [,6]
-y1  8.598190   2.199643  -1.134924 -2.564136 -4.915368 -4.338996
-y2 -4.903347 -10.251144 -10.362431 -8.168859 -7.220312 -2.310222
+        time
+variable        15         16         17        18        19        20
+      y1  8.598190   2.199643  -1.134924 -2.564136 -4.915368 -4.338996
+      y2 -4.903347 -10.251144 -10.362431 -8.168859 -7.220312 -2.310222
 > obs(window(ou2,end=5),"y1")
-        [,1]      [,2]     [,3]     [,4]     [,5]
-y1 -1.700816 0.2421701 3.767589 5.685888 3.774526
+        time
+variable         1         2        3        4        5
+      y1 -1.700816 0.2421701 3.767589 5.685888 3.774526
 > 
 > fit1.pfilter <- pfilter(ou2,Np=1000)
 > cat("coefficients at `truth'\n")
@@ -281,4 +283,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 11.452   0.064  11.704 
+ 14.827   0.050  14.879 


From noreply at r-forge.r-project.org  Wed Jan 28 13:34:07 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 28 Jan 2015 13:34:07 +0100 (CET)
Subject: [Pomp-commits] r1059 - pkg/pompExamples
Message-ID: <20150128123407.F0AA11876DD@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-28 13:34:07 +0100 (Wed, 28 Jan 2015)
New Revision: 1059

Modified:
   pkg/pompExamples/DESCRIPTION
Log:
bump

Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2015-01-26 01:35:51 UTC (rev 1058)
+++ pkg/pompExamples/DESCRIPTION	2015-01-28 12:34:07 UTC (rev 1059)
@@ -1,8 +1,8 @@
 Package: pompExamples
 Type: Package
 Title: Additional pomp examples
-Version: 0.26-3
-Date: 2015-01-24
+Version: 0.26-4
+Date: 2015-01-28
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),
 	   email="kingaa at umich.edu"),


From noreply at r-forge.r-project.org  Wed Jan 28 14:33:26 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 28 Jan 2015 14:33:26 +0100 (CET)
Subject: [Pomp-commits] r1060 - pkg/pompExamples/vignettes
Message-ID: <20150128133326.8F8D4186041@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-28 14:33:25 +0100 (Wed, 28 Jan 2015)
New Revision: 1060

Modified:
   pkg/pompExamples/vignettes/bsflu.Rmd
   pkg/pompExamples/vignettes/bsflu.html
   pkg/pompExamples/vignettes/parus.Rmd
   pkg/pompExamples/vignettes/parus.html
Log:
- replace 'juliaChild' with 'bake'

Modified: pkg/pompExamples/vignettes/bsflu.Rmd
===================================================================
--- pkg/pompExamples/vignettes/bsflu.Rmd	2015-01-28 12:34:07 UTC (rev 1059)
+++ pkg/pompExamples/vignettes/bsflu.Rmd	2015-01-28 13:33:25 UTC (rev 1060)
@@ -33,8 +33,8 @@
 
 First, a little function to cache the results of expensive computations.
 
-```{r juliaChild}
-juliaChild <- function (file, expr) {
+```{r bake}
+bake <- function (file, expr) {
   if (file.exists(file)) {
     readRDS(file)
     } else {
@@ -64,11 +64,11 @@
 ### Trajectory matching
 
 ```{r tm1}
-juliaChild("bsflu-tm1.rds",{
+bake("bsflu-tm1.rds",{
   traj.match(bsflu,est=c("Beta","inf.pd","rho"),transform=TRUE) -> tm
   traj.match(tm,method='subplex') -> tm
   data.frame(loglik=logLik(tm),loglik.se=0,as.list(coef(tm)))
-}) -> tm1
+  }) -> tm1
 ```
 ```{r tm1-simplot}
 simdat <- simulate(bsflu,params=unlist(tm1),nsim=10,
@@ -84,7 +84,7 @@
 ### Iterated filtering
 
 ```{r mf1}
-juliaChild("bsflu-mf1.rds",{
+bake("bsflu-mf1.rds",{
   mif(bsflu,rw.sd=c(Beta=0.05,inf.pd=0.05,rho=0.05),
       cooling.fraction=0.9,var.factor=2,
       Nmif=50,Np=1000,method='mif2',transform=TRUE) -> mf
@@ -92,7 +92,7 @@
   mif(mf,Nmif=50,cooling.fraction=0.1) -> mf
   ll <- unname(logmeanexp(raply(5,logLik(pfilter(mf))),se=TRUE))
   data.frame(loglik=ll[1],loglik.se=ll[2],as.list(coef(mf)))
-}) -> mf1
+  }) -> mf1
 ```
 ```{r mf1-simplot}
 simdat <- simulate(bsflu,params=unlist(mf1),nsim=10,
@@ -124,11 +124,11 @@
 ### Trajectory matching
 
 ```{r tm3}
-juliaChild("bsflu-tm3.rds",{
+bake("bsflu-tm3.rds",{
   traj.match(bsflu3,est=c("Beta","inf.pd","rho"),transform=TRUE) -> tm
   traj.match(tm,method='subplex') -> tm
   data.frame(loglik=logLik(tm),loglik.se=0,as.list(coef(tm)))
-}) -> tm3
+  }) -> tm3
 ```
 ```{r tm3-simplot}
 simdat <- simulate(bsflu3,params=unlist(tm3),nsim=10,
@@ -144,7 +144,7 @@
 ### Iterated filtering
 
 ```{r mf3}
-juliaChild("bsflu-mf3.rds",{
+bake("bsflu-mf3.rds",{
   mif(bsflu3,rw.sd=c(Beta=0.05,inf.pd=0.05,rho=0.05),
       cooling.fraction=0.9,var.factor=2,
       Nmif=50,Np=1000,method='mif2',transform=TRUE) -> mf
@@ -152,7 +152,7 @@
   mif(mf,Nmif=50,cooling.fraction=0.1) -> mf
   ll <- unname(logmeanexp(raply(5,logLik(pfilter(mf))),se=TRUE))
   data.frame(loglik=ll[1],loglik.se=ll[2],as.list(coef(mf)))
-}) -> mf3
+  }) -> mf3
 ```
 ```{r mf3-simplot}
 simdat <- simulate(bsflu3,params=unlist(mf3),nsim=10,

Modified: pkg/pompExamples/vignettes/bsflu.html
===================================================================
--- pkg/pompExamples/vignettes/bsflu.html	2015-01-28 12:34:07 UTC (rev 1059)
+++ pkg/pompExamples/vignettes/bsflu.html	2015-01-28 13:33:25 UTC (rev 1060)
@@ -1,213 +1,72 @@
 <!DOCTYPE html>
-<html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
 
-<title>Boarding-School Flu Outbreak Analysis</title>
+<html xmlns="http://www.w3.org/1999/xhtml">
 
-<script type="text/javascript">
-window.onload = function() {
-  var imgs = document.getElementsByTagName('img'), i, img;
-  for (i = 0; i < imgs.length; i++) {
-    img = imgs[i];
-    // center an image if it is the only element of its parent
-    if (img.parentElement.childElementCount === 1)
-      img.parentElement.style.textAlign = 'center';
-  }
-};
-</script>
+<head>
 
-<!-- Styles for R syntax highlighter -->
-<style type="text/css">
-   pre .operator,
-   pre .paren {
-     color: rgb(104, 118, 135)
-   }
+<meta charset="utf-8">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="pandoc" />
 
-   pre .literal {
-     color: #990073
-   }
+<meta name="author" content />
 
-   pre .number {
-     color: #099;
-   }
 
-   pre .comment {
-     color: #998;
-     font-style: italic
-   }
+<title></title>
 
-   pre .keyword {
-     color: #900;
-     font-weight: bold
-   }
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 1060

From noreply at r-forge.r-project.org  Wed Jan 28 14:33:32 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 28 Jan 2015 14:33:32 +0100 (CET)
Subject: [Pomp-commits] r1061 - pkg/pompExamples/man
Message-ID: <20150128133332.EF4EC186041@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-28 14:33:32 +0100 (Wed, 28 Jan 2015)
New Revision: 1061

Modified:
   pkg/pompExamples/man/parus.Rd
Log:
- link to vignette

Modified: pkg/pompExamples/man/parus.Rd
===================================================================
--- pkg/pompExamples/man/parus.Rd	2015-01-28 13:33:25 UTC (rev 1060)
+++ pkg/pompExamples/man/parus.Rd	2015-01-28 13:33:32 UTC (rev 1061)
@@ -38,4 +38,5 @@
 pompExample(parus,proc="Gompertz",meas="lognormal")
 plot(simulate(parus))
 }
+\seealso{\code{vignette("parus")}}
 \keyword{models,datasets}


From noreply at r-forge.r-project.org  Wed Jan 28 15:30:54 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 28 Jan 2015 15:30:54 +0100 (CET)
Subject: [Pomp-commits] r1062 - pkg/pomp/src
Message-ID: <20150128143054.692D318681D@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-28 15:30:53 +0100 (Wed, 28 Jan 2015)
New Revision: 1062

Modified:
   pkg/pomp/src/Makevars
Log:
- tiny change

Modified: pkg/pomp/src/Makevars
===================================================================
--- pkg/pomp/src/Makevars	2015-01-28 13:33:32 UTC (rev 1061)
+++ pkg/pomp/src/Makevars	2015-01-28 14:30:53 UTC (rev 1062)
@@ -1 +1 @@
- PKG_LIBS =  $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)


From noreply at r-forge.r-project.org  Wed Jan 28 15:30:56 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 28 Jan 2015 15:30:56 +0100 (CET)
Subject: [Pomp-commits] r1063 - in pkg/pompExamples: . src tests
Message-ID: <20150128143056.D924018681D@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-28 15:30:56 +0100 (Wed, 28 Jan 2015)
New Revision: 1063

Removed:
   pkg/pompExamples/src/Makevars
Modified:
   pkg/pompExamples/DESCRIPTION
   pkg/pompExamples/src/budmoth.c
   pkg/pompExamples/src/cholmodel.c
   pkg/pompExamples/tests/bbp.Rout.save
   pkg/pompExamples/tests/budmoth.Rout.save
   pkg/pompExamples/tests/ebola.Rout.save
   pkg/pompExamples/tests/parus.Rout.save
   pkg/pompExamples/tests/pertussis.Rout.save
Log:
- remove unneeded Makevars (use LinkingTo field instead)

Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/DESCRIPTION	2015-01-28 14:30:56 UTC (rev 1063)
@@ -18,6 +18,7 @@
 Description: More 'pomp' examples.
 Depends: R(>= 3.0.0), stats, graphics, pomp(>= 0.58-6)
 Suggests: plyr, reshape2, ggplot2, knitr, markdown
+LinkingTo: pomp
 License: GPL (>= 2)
 LazyData: false
 BuildVignettes: true

Deleted: pkg/pompExamples/src/Makevars
===================================================================
--- pkg/pompExamples/src/Makevars	2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/src/Makevars	2015-01-28 14:30:56 UTC (rev 1063)
@@ -1,2 +0,0 @@
-POMP_INC = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e 'library(pomp); cat(system.file("include",package="pomp"))')
-PKG_CFLAGS = -I $(POMP_INC)

Modified: pkg/pompExamples/src/budmoth.c
===================================================================
--- pkg/pompExamples/src/budmoth.c	2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/src/budmoth.c	2015-01-28 14:30:56 UTC (rev 1063)
@@ -65,7 +65,6 @@
 		       int *stateindex, int *parindex, int *covindex, 
 		       int ncovars, double *covars, double t) 
 {
-  double Q, N, S;
   double tol = 1e-6;
 
   f[stateindex[0]] = ALPHA;	// ALPHA equation
@@ -142,10 +141,7 @@
 		      const int *stateindex, const int *parindex, const int *covindex,
 		      int covdim, const double *covar)
 {
-  double noise;
   double sig2lambda;
-  double Q, N, S;
-  double tol = 1e-6;
   double f1, f2, f3;
 
   // check the discrete-time assumption

Modified: pkg/pompExamples/src/cholmodel.c
===================================================================
--- pkg/pompExamples/src/cholmodel.c	2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/src/cholmodel.c	2015-01-28 14:30:56 UTC (rev 1063)
@@ -40,7 +40,7 @@
 
 void _cholmodel_untrans (double *pt, double *p, int *parindex) 
 {
-  int k, nrstage = (int) NRSTAGE;
+  int nrstage = (int) NRSTAGE;
   pt[parindex[0]] = log(TAU);
   pt[parindex[1]] = log(GAMMA);
   pt[parindex[2]] = log(EPS);
@@ -56,7 +56,7 @@
  
 void _cholmodel_trans (double *pt, double *p, int *parindex) 
 {
-  int k, nrstage = (int) NRSTAGE;
+  int nrstage = (int) NRSTAGE;
   pt[parindex[0]] = exp(TAU);
   pt[parindex[1]] = exp(GAMMA);
   pt[parindex[2]] = exp(EPS);

Modified: pkg/pompExamples/tests/bbp.Rout.save
===================================================================
--- pkg/pompExamples/tests/bbp.Rout.save	2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/tests/bbp.Rout.save	2015-01-28 14:30:56 UTC (rev 1063)
@@ -30,4 +30,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.728   0.028   0.786 
+  0.575   0.045   0.608 

Modified: pkg/pompExamples/tests/budmoth.Rout.save
===================================================================
--- pkg/pompExamples/tests/budmoth.Rout.save	2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/tests/budmoth.Rout.save	2015-01-28 14:30:56 UTC (rev 1063)
@@ -127,4 +127,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.732   0.060   0.818 
+  0.626   0.053   0.668 

Modified: pkg/pompExamples/tests/ebola.Rout.save
===================================================================
--- pkg/pompExamples/tests/ebola.Rout.save	2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/tests/ebola.Rout.save	2015-01-28 14:30:56 UTC (rev 1063)
@@ -28,40 +28,16 @@
 newly created object(s):
  ebolaModel 
 > ebolaModel(country="Guinea") -> po
-make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-gcc -std=gnu99 -I/usr/local/apps/R/R-3.1.2/lib64/R/include -DNDEBUG  -I/usr/local/include    -I/usr/local/apps/R/R-3.1.2/lib64/R/library/pomp/include -fpic  -g -O2  -c /tmp/RtmpU0NeMt/pomp2583FF7C2A2A.c -o /tmp/RtmpU0NeMt/pomp2583FF7C2A2A.o
-gcc -std=gnu99 -shared -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -L/usr/local/lib64 -o /tmp/RtmpU0NeMt/pomp2583FF7C2A2A.so /tmp/RtmpU0NeMt/pomp2583FF7C2A2A.o -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -lR
-make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-model codes written to '/tmp/RtmpU0NeMt/pomp2583FF7C2A2A.c' 
-link to shared-object library '/tmp/RtmpU0NeMt/pomp2583FF7C2A2A.so' 
 > pf <- pfilter(simulate(po),Np=100)
 > tj <- trajectory(po)
 > 
 > ebolaModel(country="SierraLeone",na.rm=TRUE,type='cum') -> po
-make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-gcc -std=gnu99 -I/usr/local/apps/R/R-3.1.2/lib64/R/include -DNDEBUG  -I/usr/local/include    -I/usr/local/apps/R/R-3.1.2/lib64/R/library/pomp/include -fpic  -g -O2  -c /tmp/RtmpU0NeMt/pompDA1B7D4C88B1.c -o /tmp/RtmpU0NeMt/pompDA1B7D4C88B1.o
-gcc -std=gnu99 -shared -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -L/usr/local/lib64 -o /tmp/RtmpU0NeMt/pompDA1B7D4C88B1.so /tmp/RtmpU0NeMt/pompDA1B7D4C88B1.o -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -lR
-make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-model codes written to '/tmp/RtmpU0NeMt/pompDA1B7D4C88B1.c' 
-link to shared-object library '/tmp/RtmpU0NeMt/pompDA1B7D4C88B1.so' 
 > pf <- pfilter(simulate(po),Np=100)
 > tj <- trajectory(po)
 > dd <- simulate(po,as.data.frame=TRUE,obs=TRUE)
 > dd$week <- dd$time
 > po <- ebolaModel(data=subset(dd,select=c(week,cases,deaths)))
-make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-gcc -std=gnu99 -I/usr/local/apps/R/R-3.1.2/lib64/R/include -DNDEBUG  -I/usr/local/include    -I/usr/local/apps/R/R-3.1.2/lib64/R/library/pomp/include -fpic  -g -O2  -c /tmp/RtmpU0NeMt/pompBF9800D29D72.c -o /tmp/RtmpU0NeMt/pompBF9800D29D72.o
-gcc -std=gnu99 -shared -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -L/usr/local/lib64 -o /tmp/RtmpU0NeMt/pompBF9800D29D72.so /tmp/RtmpU0NeMt/pompBF9800D29D72.o -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -lR
-make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-model codes written to '/tmp/RtmpU0NeMt/pompBF9800D29D72.c' 
-link to shared-object library '/tmp/RtmpU0NeMt/pompBF9800D29D72.so' 
 > 
 > proc.time()
    user  system elapsed 
-  2.032   0.228   3.798 
+  1.837   0.246   2.034 

Modified: pkg/pompExamples/tests/parus.Rout.save
===================================================================
--- pkg/pompExamples/tests/parus.Rout.save	2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/tests/parus.Rout.save	2015-01-28 14:30:56 UTC (rev 1063)
@@ -41,4 +41,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.716   0.060   0.806 
+  0.638   0.025   0.650 

Modified: pkg/pompExamples/tests/pertussis.Rout.save
===================================================================
--- pkg/pompExamples/tests/pertussis.Rout.save	2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/tests/pertussis.Rout.save	2015-01-28 14:30:56 UTC (rev 1063)
@@ -168,4 +168,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 18.417   0.068  18.567 
+ 23.862   0.074  23.943 


From noreply at r-forge.r-project.org  Thu Jan 29 13:08:31 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 29 Jan 2015 13:08:31 +0100 (CET)
Subject: [Pomp-commits] r1064 - pkg/pompExamples
Message-ID: <20150129120831.A0A6818758A@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-29 13:08:31 +0100 (Thu, 29 Jan 2015)
New Revision: 1064

Modified:
   pkg/pompExamples/DESCRIPTION
Log:
bump

Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2015-01-28 14:30:56 UTC (rev 1063)
+++ pkg/pompExamples/DESCRIPTION	2015-01-29 12:08:31 UTC (rev 1064)
@@ -1,8 +1,8 @@
 Package: pompExamples
 Type: Package
 Title: Additional pomp examples
-Version: 0.26-4
-Date: 2015-01-28
+Version: 0.26-5
+Date: 2015-01-29
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),
 	   email="kingaa at umich.edu"),


From noreply at r-forge.r-project.org  Sat Jan 31 16:59:25 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat, 31 Jan 2015 16:59:25 +0100 (CET)
Subject: [Pomp-commits] r1065 - pkg/pomp/R
Message-ID: <20150131155925.EAE14187987@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-31 16:59:25 +0100 (Sat, 31 Jan 2015)
New Revision: 1065

Modified:
   pkg/pomp/R/builder.R
Log:
- small change to the way 'pompCBuilder' picks the name of the file

Modified: pkg/pomp/R/builder.R
===================================================================
--- pkg/pomp/R/builder.R	2015-01-29 12:08:31 UTC (rev 1064)
+++ pkg/pomp/R/builder.R	2015-01-31 15:59:25 UTC (rev 1065)
@@ -172,23 +172,27 @@
   paste0("  error(\"'",name,"' not defined\");")
 }
 
-pompCBuilder <- function (name, statenames, paramnames, covarnames, obsnames,
+randomName <- function (stem = "pomp", size = 2) {
+  paste0(stem,
+         paste(
+               format(
+                      as.hexmode(ceiling(runif(n=size,max=2^24))),
+                      upper.case=TRUE
+                      ),
+               collapse=""
+               )
+         )
+}
+
+pompCBuilder <- function (name = NULL,
+                          statenames, paramnames, covarnames, obsnames,
                           rmeasure, dmeasure, step.fn, skeleton,
                           parameter.transform, parameter.inv.transform,
                           rprior, dprior, globals, save = FALSE, link = TRUE,
                           verbose = getOption("verbose",FALSE))
 {
 
-  if (missing(name))
-    name <- paste0("pomp",
-                   paste(
-                         format(
-                                as.hexmode(ceiling(runif(n=2,max=2^24))),
-                                upper.case=TRUE
-                                ),
-                         collapse=""
-                         )
-                   )
+  if (is.null(name)) name <- randomName()
 
   has.trans <- !(missing(parameter.transform))
 


From noreply at r-forge.r-project.org  Sat Jan 31 16:59:50 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat, 31 Jan 2015 16:59:50 +0100 (CET)
Subject: [Pomp-commits] r1066 - pkg/pomp
Message-ID: <20150131155950.19BD5187987@r-forge.r-project.org>

Author: kingaa
Date: 2015-01-31 16:59:49 +0100 (Sat, 31 Jan 2015)
New Revision: 1066

Modified:
   pkg/pomp/DESCRIPTION
Log:
- update version number

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-01-31 15:59:25 UTC (rev 1065)
+++ pkg/pomp/DESCRIPTION	2015-01-31 15:59:49 UTC (rev 1066)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.58-7
-Date: 2015-01-25
+Version: 0.58-8
+Date: 2015-01-31
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),