[Depmix-commits] r651 - in pkg/depmix: . R src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Feb 12 08:50:29 CET 2016
Author: ingmarvisser
Date: 2016-02-12 08:50:29 +0100 (Fri, 12 Feb 2016)
New Revision: 651
Modified:
pkg/depmix/DESCRIPTION
pkg/depmix/NAMESPACE
pkg/depmix/R/depmix.R
pkg/depmix/src/derdist.h
pkg/depmix/src/hessdist.h
pkg/depmix/src/logl.h
pkg/depmix/src/matrix.h
pkg/depmix/src/mdmm.h
pkg/depmix/src/mgdmm.h
pkg/depmix/src/mmts.h
pkg/depmix/src/mts.h
pkg/depmix/src/npsolfit.h
Log:
=test stuff from development version
Modified: pkg/depmix/DESCRIPTION
===================================================================
--- pkg/depmix/DESCRIPTION 2016-02-12 07:50:14 UTC (rev 650)
+++ pkg/depmix/DESCRIPTION 2016-02-12 07:50:29 UTC (rev 651)
@@ -1,11 +1,11 @@
Package: depmix
-Version: 0.9.13
-Date: 2014-12-21
+Version: 0.9.14
+Date: 2016-02-11
Title: Dependent Mixture Models
Author: Ingmar Visser <i.visser at uva.nl>
Maintainer: Ingmar Visser <i.visser at uva.nl>
Depends: R (>= 3.1.2), MASS
Suggests: Rdonlp2
Additional_repositories: http://R-Forge.R-project.org
-Description: Fit (multigroup) mixtures of latent Markov models on mixed categorical and continuous (timeseries) data. The Rdonlp2 package can optionally be used for optimization of the log-likelihood and is available from R-forge: https://r-forge.r-project.org/R/?group_id=156
+Description: Fits (multigroup) mixtures of latent or hidden Markov models on mixed categorical and continuous (timeseries) data. The Rdonlp2 package can optionally be used for optimization of the log-likelihood and is available from R-forge.
License: GPL-3
\ No newline at end of file
Modified: pkg/depmix/NAMESPACE
===================================================================
--- pkg/depmix/NAMESPACE 2016-02-12 07:50:14 UTC (rev 650)
+++ pkg/depmix/NAMESPACE 2016-02-12 07:50:29 UTC (rev 651)
@@ -2,6 +2,10 @@
import(MASS)
+importFrom("graphics", "layout.show")
+importFrom("stats", "kmeans", "na.omit", "nlm", "optim", "plot.ts",
+ "rmultinom", "rnorm", "runif", "sd", "ts")
+
export(dmm,mgdmm,fitdmm,mixdmm,loglike,oneliner,bootstrap,posterior,
generate,lca,ntimes,itemtypes,dname,replicates,ncov,inames,
nitems,ind,markovdata)
Modified: pkg/depmix/R/depmix.R
===================================================================
--- pkg/depmix/R/depmix.R 2016-02-12 07:50:14 UTC (rev 650)
+++ pkg/depmix/R/depmix.R 2016-02-12 07:50:29 UTC (rev 651)
@@ -14,7 +14,7 @@
# #
###################################
-if(getRversion() >= "2.15.1") utils::globalVariables(c("donlp2", "donlp2Control"))
+# if(getRversion() >= "2.15.1") utils::globalVariables(c("donlp2", "donlp2Control"))
fitdmm <- function(dat,dmm,printlevel=1,poster=TRUE,tdcov=0,ses=TRUE,method="optim",vfactor=15,der=1,iterlim=100,kmst=!dmm$st,kmrep=5,postst=FALSE) {
mod=dmm #keep copy of the original model
@@ -259,7 +259,7 @@
## call npmain to optimize the model (non-linear constraints not implemented yet)
if(method=="donlp") {
- require("Rdonlp2")
+ requireNamespace("Rdonlp2")
bu=bu[which(fixed==1)]
bl=bl[which(fixed==1)]
@@ -293,14 +293,14 @@
}
timeUsed <- system.time(
- res <- donlp2(optpars, logl,
+ res <- Rdonlp2::donlp2(optpars, logl,
par.upper=bu,
par.lower=bl,
A = A,
lin.upper=bulin,
lin.lower=bllin,
nlin = list(),
- control=donlp2Control(),
+ control=Rdonlp2::donlp2Control(),
env=.GlobalEnv, name="Rdonlp2")
)
Modified: pkg/depmix/src/derdist.h
===================================================================
--- pkg/depmix/src/derdist.h 2016-02-12 07:50:14 UTC (rev 650)
+++ pkg/depmix/src/derdist.h 2016-02-12 07:50:29 UTC (rev 651)
@@ -9,7 +9,6 @@
* *
***********************************/
-
#ifndef DERDIST
#define DERDIST 1
@@ -27,6 +26,8 @@
* will be returned
*/
+/* extern "C" { */
+
double dernorm(double x, double mu, double sig, int ms, int logsc);
/*
@@ -40,5 +41,15 @@
* and others .....
*/
+/* double squared(double x); */
+
+// the second and third to last integer arguments determine for which
+// combination of parameters the hessian is returned, ie 1 for mu and
+//2 for sigma, if logsc=1 the log will be returned (not functional)
+
+double hessnorm(double x, double mu, double sig, int ms1, int ms2, int logsc);
+
+/* } // end extern "C" */
+
#endif
Modified: pkg/depmix/src/hessdist.h
===================================================================
--- pkg/depmix/src/hessdist.h 2016-02-12 07:50:14 UTC (rev 650)
+++ pkg/depmix/src/hessdist.h 2016-02-12 07:50:29 UTC (rev 651)
@@ -12,13 +12,15 @@
#ifndef HESSDIST
#define HESSDIST 1
-
+
#include <stdio.h>
#include <stdlib.h>
#include <R.h>
#include <Rmath.h>
+/* extern "C" { */
+
//constant M_PI=3.141592653589793238462643383280 from Rmath.h
double squared(double x);
@@ -30,7 +32,7 @@
double hessnorm(double x, double mu, double sig, int ms1, int ms2, int logsc);
//this puts the return value in x (for use directly from R)
-void Rhessnorm(double *x, double *mu, double *sig, int *ms1, int *ms2, int *logsc, double *value);
+/* void Rhessnorm(double *x, double *mu, double *sig, int *ms1, int *ms2, int *logsc, double *value); */
// to be implemented:
@@ -39,4 +41,7 @@
// double hessweibull(double x, double sh, double sc, int shsc1, int shsc2, int logsc);
// double hessgamma(double x, double sh, double sc, int shsc1, int shsc2, int logsc);
+/* } */
+
+
#endif
\ No newline at end of file
Modified: pkg/depmix/src/logl.h
===================================================================
--- pkg/depmix/src/logl.h 2016-02-12 07:50:14 UTC (rev 650)
+++ pkg/depmix/src/logl.h 2016-02-12 07:50:29 UTC (rev 651)
@@ -13,11 +13,11 @@
#include "matrix.h"
-extern "C" {
-
#include <R.h>
#include <Rmath.h>
+extern "C" {
+
//these routines set up the model and set up the data in formats that are readable by loglikelihood
void mixModelSetUp(int *ngroups, int *nrcomp, int *nstates, int *nitems, int *itemtypes, double *pars, int *xm, int *print);
void covSetUp(int *ngroups, int *nrcomp, int *nstates, int *nitems, int *itemtypes, double *pars, int *xm, int *print);
Modified: pkg/depmix/src/matrix.h
===================================================================
--- pkg/depmix/src/matrix.h 2016-02-12 07:50:14 UTC (rev 650)
+++ pkg/depmix/src/matrix.h 2016-02-12 07:50:29 UTC (rev 651)
@@ -5,10 +5,10 @@
#include <stdio.h>
#include <stdlib.h>
-extern "C" {
- #include <R.h>
+/* extern "C" { */
+#include <R.h>
/* static int matrixConst; */
-}
+/* } */
#define MATRIXBOUNDS 1
Modified: pkg/depmix/src/mdmm.h
===================================================================
--- pkg/depmix/src/mdmm.h 2016-02-12 07:50:14 UTC (rev 650)
+++ pkg/depmix/src/mdmm.h 2016-02-12 07:50:29 UTC (rev 651)
@@ -19,15 +19,15 @@
#include <stdio.h>
#include <stdlib.h>
-extern "C" {
- #include <R.h>
- #include <Rmath.h>
- #include "derdist.h"
- #include "hessdist.h"
-}
+#include <R.h>
+#include <Rmath.h>
#include "matrix.h"
+extern "C" {
+#include "derdist.h"
+}
+
#define MDMMBOUNDS 1
class mdmm {
Modified: pkg/depmix/src/mgdmm.h
===================================================================
--- pkg/depmix/src/mgdmm.h 2016-02-12 07:50:14 UTC (rev 650)
+++ pkg/depmix/src/mgdmm.h 2016-02-12 07:50:29 UTC (rev 651)
@@ -18,10 +18,10 @@
#include <stdio.h>
#include <stdlib.h>
-extern "C" {
- #include <R.h>
- #include <Rmath.h>
-}
+/* extern "C" { */
+#include <R.h>
+#include <Rmath.h>
+/* } */
#include "matrix.h"
#include "mdmm.h"
Modified: pkg/depmix/src/mmts.h
===================================================================
--- pkg/depmix/src/mmts.h 2016-02-12 07:50:14 UTC (rev 650)
+++ pkg/depmix/src/mmts.h 2016-02-12 07:50:29 UTC (rev 651)
@@ -20,9 +20,9 @@
#include <stdio.h>
#include <stdlib.h>
-extern "C" {
- #include <R.h>
-}
+/* extern "C" { */
+#include <R.h>
+/* } */
#include "matrix.h"
#include "mts.h"
Modified: pkg/depmix/src/mts.h
===================================================================
--- pkg/depmix/src/mts.h 2016-02-12 07:50:14 UTC (rev 650)
+++ pkg/depmix/src/mts.h 2016-02-12 07:50:29 UTC (rev 651)
@@ -24,9 +24,9 @@
#include <stdio.h>
#include <stdlib.h>
-extern "C" {
- #include <R.h>
-}
+/* extern "C" { */
+#include <R.h>
+/* } */
#include "matrix.h"
Modified: pkg/depmix/src/npsolfit.h
===================================================================
--- pkg/depmix/src/npsolfit.h 2016-02-12 07:50:14 UTC (rev 650)
+++ pkg/depmix/src/npsolfit.h 2016-02-12 07:50:29 UTC (rev 651)
@@ -6,6 +6,9 @@
#include <stdlib.h>
/* #include <fstream.h> */
+#include <R.h>
+#include <Rmath.h>
+
extern "C" {
//globals needed in npsolc and funobj
@@ -15,8 +18,6 @@
double *fixedvalues;
int npars;
-#include <R.h>
-#include <Rmath.h>
/************************************************************/
/* */
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