[Pomp-commits] r545 - in pkg: . R inst src tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Aug 24 20:26:40 CEST 2011
Author: kingaa
Date: 2011-08-24 20:26:40 +0200 (Wed, 24 Aug 2011)
New Revision: 545
Modified:
pkg/DESCRIPTION
pkg/NAMESPACE
pkg/R/plot-pomp.R
pkg/R/pomp-methods.R
pkg/inst/NEWS
pkg/src/initstate.c
pkg/src/lookup_table.c
pkg/src/pomp_internal.h
pkg/tests/gillespie.Rout.save
pkg/tests/sir.Rout.save
Log:
- improve 'lookup_in_table', which can now handle multiple index values
- as(po,'data.frame'), 'po' a 'pomp' object, now has columns for (interpolated) covariates
- plot(po) behaves as before if 'po' is a 'pomp' object
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2011-08-23 12:05:33 UTC (rev 544)
+++ pkg/DESCRIPTION 2011-08-24 18:26:40 UTC (rev 545)
@@ -2,7 +2,7 @@
Type: Package
Title: Statistical inference for partially observed Markov processes
Version: 0.39-2
-Date: 2011-08-23
+Date: 2011-08-24
Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman
Maintainer: Aaron A. King <kingaa at umich.edu>
URL: http://pomp.r-forge.r-project.org
Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE 2011-08-23 12:05:33 UTC (rev 544)
+++ pkg/NAMESPACE 2011-08-24 18:26:40 UTC (rev 545)
@@ -7,6 +7,7 @@
systematic_resampling,
euler_model_simulator,
euler_model_density,
+ lookup_in_table,
SSA_simulator,
R_Euler_Multinom,D_Euler_Multinom,
pfilter_computations,
Modified: pkg/R/plot-pomp.R
===================================================================
--- pkg/R/plot-pomp.R 2011-08-23 12:05:33 UTC (rev 544)
+++ pkg/R/plot-pomp.R 2011-08-24 18:26:40 UTC (rev 545)
@@ -14,11 +14,18 @@
vars <- names(X)
tpos <- match("time",vars)
if (is.na(tpos))
- stop(sQuote("pomp")," plot error: no data variable labeled ",sQuote("time"),call.=FALSE)
- if (missing(variables))
+ stop(
+ sQuote("pomp"),
+ " plot error: no data variable labeled ",
+ sQuote("time"),
+ call.=FALSE
+ )
+ if (missing(variables)) {
vars <- vars[-tpos]
- else
+ vars <- setdiff(vars,colnames(x at covar))
+ } else {
vars <- variables
+ }
plotpomp <- function (x, time,
xy.labels, xy.lines, panel = lines, nc, xlabel,
type = "l", xlim = NULL, ylim = NULL, xlab = "time",
Modified: pkg/R/pomp-methods.R
===================================================================
--- pkg/R/pomp-methods.R 2011-08-23 12:05:33 UTC (rev 544)
+++ pkg/R/pomp-methods.R 2011-08-24 18:26:40 UTC (rev 545)
@@ -27,6 +27,12 @@
x <- cbind(x,t(from at states))
names(x) <- c(nm,rownames(from at states))
}
+ if (length(from at covar)>0) {
+ nm <- names(x)
+ y <- .Call(lookup_in_table,from at tcovar,from at covar,from at times)
+ x <- cbind(x,t(y))
+ names(x) <- c(nm,rownames(y))
+ }
x
}
)
Modified: pkg/inst/NEWS
===================================================================
--- pkg/inst/NEWS 2011-08-23 12:05:33 UTC (rev 544)
+++ pkg/inst/NEWS 2011-08-24 18:26:40 UTC (rev 545)
@@ -1,4 +1,8 @@
NEWS
+0.39-2
+ o When 'po' is a 'pomp'-class object with covariates, 'as.data.frame(po)' and 'as(po,"data.frame")' now contain columns for the covariates.
+ The latter are interpolated, if necessary, at the observation times.
+
0.39-1
o New facilities for parameter transformation are provided.
New optional arguments 'parameter.transform' and 'parameter.inv.transform' to 'pomp' allow the user to specify transformations between natural and internal parameter scalings.
Modified: pkg/src/initstate.c
===================================================================
--- pkg/src/initstate.c 2011-08-23 12:05:33 UTC (rev 544)
+++ pkg/src/initstate.c 2011-08-24 18:26:40 UTC (rev 545)
@@ -15,7 +15,7 @@
SEXP covar, tcovar, covars;
SEXP paramnames, statenames, mindex;
int *dim, *midx;
- int npar, nrep, nvar, index = 0;
+ int npar, nrep, nvar;
int xdim[2], j, k;
double *p, *pp, *xp, *xpp;
@@ -45,7 +45,7 @@
PROTECT(tcovar = GET_SLOT(object,install("tcovar"))); nprotect++;
if (LENGTH(tcovar) > 0) { // do table lookkup
PROTECT(covar = GET_SLOT(object,install("covar"))); nprotect++;
- PROTECT(covars = lookup_in_table(tcovar,covar,t0,&index)); nprotect++;
+ PROTECT(covars = lookup_in_table(tcovar,covar,t0)); nprotect++;
PROTECT(fcall = LCONS(covars,fcall)); nprotect++;
SET_TAG(fcall,install("covars"));
}
Modified: pkg/src/lookup_table.c
===================================================================
--- pkg/src/lookup_table.c 2011-08-23 12:05:33 UTC (rev 544)
+++ pkg/src/lookup_table.c 2011-08-24 18:26:40 UTC (rev 545)
@@ -4,11 +4,16 @@
#include "pomp_internal.h"
-SEXP lookup_in_table (SEXP ttable, SEXP xtable, SEXP t, int *index) {
+SEXP lookup_in_table (SEXP ttable, SEXP xtable, SEXP t) {
int nprotect = 0;
- int *dim, length, width;
+ int *dim, xdim[2], length, width;
+ int j, nt;
+ double *tp, *xp;
SEXP X;
+ PROTECT(t = AS_NUMERIC(t)); nprotect++;
+ nt = LENGTH(t);
+
dim = INTEGER(GET_DIM(xtable));
length = dim[0]; width = dim[1];
if (length != LENGTH(ttable)) {
@@ -16,12 +21,19 @@
error("incommensurate dimensions in 'lookup_in_table'");
}
- PROTECT(X = NEW_NUMERIC(width)); nprotect++;
- SET_NAMES(X,GET_COLNAMES(GET_DIMNAMES(xtable)));
+ if (nt > 1) {
+ xdim[0] = width; xdim[1] = nt;
+ PROTECT(X = makearray(2,xdim)); nprotect++;
+ setrownames(X,GET_COLNAMES(GET_DIMNAMES(xtable)),2);
+ } else {
+ PROTECT(X = NEW_NUMERIC(width)); nprotect++;
+ SET_NAMES(X,GET_COLNAMES(GET_DIMNAMES(xtable)));
+ }
struct lookup_table tab = {length,width,0,REAL(ttable),REAL(xtable)};
- table_lookup(&tab,*(REAL(t)),REAL(X),0);
-
+ for (j = 0, tp = REAL(t), xp = REAL(X); j < nt; j++, tp++, xp += width)
+ table_lookup(&tab,*tp,xp,0);
+
UNPROTECT(nprotect);
return X;
}
Modified: pkg/src/pomp_internal.h
===================================================================
--- pkg/src/pomp_internal.h 2011-08-23 12:05:33 UTC (rev 544)
+++ pkg/src/pomp_internal.h 2011-08-24 18:26:40 UTC (rev 545)
@@ -38,7 +38,7 @@
SEXP get_pomp_fun (SEXP pfun);
// lookup_table.c
-SEXP lookup_in_table (SEXP ttable, SEXP xtable, SEXP t, int *index);
+SEXP lookup_in_table (SEXP ttable, SEXP xtable, SEXP t);
// resample.c
SEXP systematic_resampling(SEXP weights);
Modified: pkg/tests/gillespie.Rout.save
===================================================================
--- pkg/tests/gillespie.Rout.save 2011-08-23 12:05:33 UTC (rev 544)
+++ pkg/tests/gillespie.Rout.save 2011-08-24 18:26:40 UTC (rev 545)
@@ -103,13 +103,20 @@
>
>
> tail(as(gsir,"data.frame"))
- time reports S I R N cases
-100 1.903846 41 65075 1271 933488 999834 555
-101 1.923077 68 64761 1210 933849 999820 639
-102 1.942308 62 64434 1225 934136 999795 570
-103 1.961538 49 64055 1258 934441 999754 575
-104 1.980769 53 63765 1225 934740 999730 588
-105 2.000000 60 63451 1290 935012 999753 531
+ time reports S I R N cases seas.1 seas.2
+100 1.903846 41 65075 1271 933488 999834 555 0.5954581 0.06404093
+101 1.923077 68 64761 1210 933849 999820 639 0.6195570 0.07790927
+102 1.942308 62 64434 1225 934136 999795 570 0.6393034 0.09510602
+103 1.961538 49 64055 1258 934441 999754 575 0.6541212 0.11563116
+104 1.980769 53 63765 1225 934740 999730 588 0.6634343 0.13948471
+105 2.000000 60 63451 1290 935012 999753 531 0.6666667 0.16666667
+ seas.3
+100 0.3405010
+101 0.3025338
+102 0.2655906
+103 0.2302477
+104 0.1970810
+105 0.1666667
>
> data(gillespie.sir)
>
Modified: pkg/tests/sir.Rout.save
===================================================================
--- pkg/tests/sir.Rout.save 2011-08-23 12:05:33 UTC (rev 544)
+++ pkg/tests/sir.Rout.save 2011-08-24 18:26:40 UTC (rev 545)
@@ -172,215 +172,215 @@
>
> show(po)
data and states:
- time reports
-1 0.01923077 0
-2 0.03846154 0
-3 0.05769231 0
-4 0.07692308 0
-5 0.09615385 0
-6 0.11538462 0
-7 0.13461538 0
-8 0.15384615 0
-9 0.17307692 0
-10 0.19230769 0
-11 0.21153846 0
-12 0.23076923 0
-13 0.25000000 0
-14 0.26923077 0
-15 0.28846154 0
-16 0.30769231 0
-17 0.32692308 0
-18 0.34615385 0
-19 0.36538462 0
-20 0.38461538 0
-21 0.40384615 0
-22 0.42307692 0
-23 0.44230769 0
-24 0.46153846 0
-25 0.48076923 0
-26 0.50000000 0
-27 0.51923077 0
-28 0.53846154 0
-29 0.55769231 0
-30 0.57692308 0
-31 0.59615385 0
-32 0.61538462 0
-33 0.63461538 0
-34 0.65384615 0
-35 0.67307692 0
-36 0.69230769 0
-37 0.71153846 0
-38 0.73076923 0
-39 0.75000000 0
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-42 0.80769231 0
-43 0.82692308 0
-44 0.84615385 0
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-47 0.90384615 0
-48 0.92307692 0
-49 0.94230769 0
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-51 0.98076923 0
-52 1.00000000 0
-53 1.01923077 0
-54 1.03846154 0
-55 1.05769231 0
-56 1.07692308 0
-57 1.09615385 0
-58 1.11538462 0
-59 1.13461538 0
-60 1.15384615 0
-61 1.17307692 0
-62 1.19230769 0
-63 1.21153846 0
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-65 1.25000000 0
-66 1.26923077 0
-67 1.28846154 0
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-77 1.48076923 0
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-91 1.75000000 0
-92 1.76923077 0
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-116 2.23076923 0
-117 2.25000000 0
-118 2.26923077 0
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-125 2.40384615 0
-126 2.42307692 0
-127 2.44230769 0
-128 2.46153846 0
-129 2.48076923 0
-130 2.50000000 0
-131 2.51923077 0
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-133 2.55769231 0
-134 2.57692308 0
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-138 2.65384615 0
-139 2.67307692 0
-140 2.69230769 0
-141 2.71153846 0
-142 2.73076923 0
-143 2.75000000 0
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-163 3.13461538 0
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-166 3.19230769 0
-167 3.21153846 0
-168 3.23076923 0
-169 3.25000000 0
-170 3.26923077 0
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-176 3.38461538 0
-177 3.40384615 0
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-179 3.44230769 0
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-181 3.48076923 0
-182 3.50000000 0
-183 3.51923077 0
-184 3.53846154 0
-185 3.55769231 0
-186 3.57692308 0
-187 3.59615385 0
-188 3.61538462 0
-189 3.63461538 0
-190 3.65384615 0
-191 3.67307692 0
-192 3.69230769 0
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-194 3.73076923 0
-195 3.75000000 0
-196 3.76923077 0
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-203 3.90384615 0
-204 3.92307692 0
-205 3.94230769 0
-206 3.96153846 0
-207 3.98076923 0
-208 4.00000000 0
+ time reports seas1 seas2 seas3
+1 0.01923077 0 0.66343428 0.19708101 0.13948471
+2 0.03846154 0 0.65412115 0.23024769 0.11563116
+3 0.05769231 0 0.63930336 0.26559063 0.09510602
+4 0.07692308 0 0.61955697 0.30253376 0.07790927
+5 0.09615385 0 0.59545806 0.34050101 0.06404093
+6 0.11538462 0 0.56758269 0.37891633 0.05350099
+7 0.13461538 0 0.53650693 0.41720362 0.04628945
+8 0.15384615 0 0.50280686 0.45478683 0.04240631
+9 0.17307692 0 0.46705854 0.49108989 0.04185158
+10 0.19230769 0 0.42983804 0.52553672 0.04462525
+11 0.21153846 0 0.39172143 0.55755125 0.05072732
+12 0.23076923 0 0.35328478 0.58655743 0.06015779
+13 0.25000000 0 0.31510417 0.61197917 0.07291667
+14 0.26923077 0 0.27775565 0.63324040 0.08900394
+15 0.28846154 0 0.24181531 0.64976507 0.10841963
+16 0.30769231 0 0.20785920 0.66097709 0.13116371
+17 0.32692308 0 0.17646341 0.66630040 0.15723619
+18 0.34615385 0 0.14817554 0.66521582 0.18660863
+19 0.36538462 0 0.12321252 0.65786560 0.21892187
+20 0.38461538 0 0.10157791 0.64481869 0.25360340
+21 0.40384615 0 0.08327170 0.62665116 0.29007714
+22 0.42307692 0 0.06829389 0.60393908 0.32776703
+23 0.44230769 0 0.05664448 0.57725852 0.36609700
+24 0.46153846 0 0.04832347 0.54718556 0.40449097
+25 0.48076923 0 0.04333087 0.51429625 0.44237289
+26 0.50000000 0 0.04166667 0.47916667 0.47916667
+27 0.51923077 0 0.04333087 0.44237289 0.51429625
+28 0.53846154 0 0.04832347 0.40449097 0.54718556
+29 0.55769231 0 0.05664448 0.36609700 0.57725852
+30 0.57692308 0 0.06829389 0.32776703 0.60393908
+31 0.59615385 0 0.08327170 0.29007714 0.62665116
+32 0.61538462 0 0.10157791 0.25360340 0.64481869
+33 0.63461538 0 0.12321252 0.21892187 0.65786560
+34 0.65384615 0 0.14817554 0.18660863 0.66521582
+35 0.67307692 0 0.17646341 0.15723619 0.66630040
+36 0.69230769 0 0.20785920 0.13116371 0.66097709
+37 0.71153846 0 0.24181531 0.10841963 0.64976507
+38 0.73076923 0 0.27775565 0.08900394 0.63324040
+39 0.75000000 0 0.31510417 0.07291667 0.61197917
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+51 0.98076923 0 0.66343428 0.13948471 0.19708101
+52 1.00000000 0 0.66666667 0.16666667 0.16666667
+53 1.01923077 0 0.66343428 0.19708101 0.13948471
+54 1.03846154 0 0.65412115 0.23024769 0.11563116
+55 1.05769231 0 0.63930336 0.26559063 0.09510602
+56 1.07692308 0 0.61955697 0.30253376 0.07790927
+57 1.09615385 0 0.59545806 0.34050101 0.06404093
+58 1.11538462 0 0.56758269 0.37891633 0.05350099
+59 1.13461538 0 0.53650693 0.41720362 0.04628945
+60 1.15384615 0 0.50280686 0.45478683 0.04240631
+61 1.17307692 0 0.46705854 0.49108989 0.04185158
+62 1.19230769 0 0.42983804 0.52553672 0.04462525
+63 1.21153846 0 0.39172143 0.55755125 0.05072732
+64 1.23076923 0 0.35328478 0.58655743 0.06015779
+65 1.25000000 0 0.31510417 0.61197917 0.07291667
+66 1.26923077 0 0.27775565 0.63324040 0.08900394
+67 1.28846154 0 0.24181531 0.64976507 0.10841963
+68 1.30769231 0 0.20785920 0.66097709 0.13116371
+69 1.32692308 0 0.17646341 0.66630040 0.15723619
+70 1.34615385 0 0.14817554 0.66521582 0.18660863
+71 1.36538462 0 0.12321252 0.65786560 0.21892187
+72 1.38461538 0 0.10157791 0.64481869 0.25360340
+73 1.40384615 0 0.08327170 0.62665116 0.29007714
+74 1.42307692 0 0.06829389 0.60393908 0.32776703
+75 1.44230769 0 0.05664448 0.57725852 0.36609700
+76 1.46153846 0 0.04832347 0.54718556 0.40449097
+77 1.48076923 0 0.04333087 0.51429625 0.44237289
+78 1.50000000 0 0.04166667 0.47916667 0.47916667
+79 1.51923077 0 0.04333087 0.44237289 0.51429625
+80 1.53846154 0 0.04832347 0.40449097 0.54718556
+81 1.55769231 0 0.05664448 0.36609700 0.57725852
+82 1.57692308 0 0.06829389 0.32776703 0.60393908
+83 1.59615385 0 0.08327170 0.29007714 0.62665116
+84 1.61538462 0 0.10157791 0.25360340 0.64481869
+85 1.63461538 0 0.12321252 0.21892187 0.65786560
+86 1.65384615 0 0.14817554 0.18660863 0.66521582
+87 1.67307692 0 0.17646341 0.15723619 0.66630040
+88 1.69230769 0 0.20785920 0.13116371 0.66097709
+89 1.71153846 0 0.24181531 0.10841963 0.64976507
+90 1.73076923 0 0.27775565 0.08900394 0.63324040
+91 1.75000000 0 0.31510417 0.07291667 0.61197917
+92 1.76923077 0 0.35328478 0.06015779 0.58655743
+93 1.78846154 0 0.39172143 0.05072732 0.55755125
+94 1.80769231 0 0.42983804 0.04462525 0.52553672
+95 1.82692308 0 0.46705854 0.04185158 0.49108989
+96 1.84615385 0 0.50280686 0.04240631 0.45478683
+97 1.86538462 0 0.53650693 0.04628945 0.41720362
+98 1.88461538 0 0.56758269 0.05350099 0.37891633
+99 1.90384615 0 0.59545806 0.06404093 0.34050101
+100 1.92307692 0 0.61955697 0.07790927 0.30253376
+101 1.94230769 0 0.63930336 0.09510602 0.26559063
+102 1.96153846 0 0.65412115 0.11563116 0.23024769
+103 1.98076923 0 0.66343428 0.13948471 0.19708101
+104 2.00000000 0 0.66666667 0.16666667 0.16666667
+105 2.01923077 0 0.66343428 0.19708101 0.13948471
+106 2.03846154 0 0.65412115 0.23024769 0.11563116
+107 2.05769231 0 0.63930336 0.26559063 0.09510602
+108 2.07692308 0 0.61955697 0.30253376 0.07790927
+109 2.09615385 0 0.59545806 0.34050101 0.06404093
+110 2.11538462 0 0.56758269 0.37891633 0.05350099
+111 2.13461538 0 0.53650693 0.41720362 0.04628945
+112 2.15384615 0 0.50280686 0.45478683 0.04240631
+113 2.17307692 0 0.46705854 0.49108989 0.04185158
+114 2.19230769 0 0.42983804 0.52553672 0.04462525
+115 2.21153846 0 0.39172143 0.55755125 0.05072732
+116 2.23076923 0 0.35328478 0.58655743 0.06015779
+117 2.25000000 0 0.31510417 0.61197917 0.07291667
+118 2.26923077 0 0.27775565 0.63324040 0.08900394
+119 2.28846154 0 0.24181531 0.64976507 0.10841963
+120 2.30769231 0 0.20785920 0.66097709 0.13116371
+121 2.32692308 0 0.17646341 0.66630040 0.15723619
+122 2.34615385 0 0.14817554 0.66521582 0.18660863
+123 2.36538462 0 0.12321252 0.65786560 0.21892187
+124 2.38461538 0 0.10157791 0.64481869 0.25360340
+125 2.40384615 0 0.08327170 0.62665116 0.29007714
+126 2.42307692 0 0.06829389 0.60393908 0.32776703
+127 2.44230769 0 0.05664448 0.57725852 0.36609700
+128 2.46153846 0 0.04832347 0.54718556 0.40449097
+129 2.48076923 0 0.04333087 0.51429625 0.44237289
+130 2.50000000 0 0.04166667 0.47916667 0.47916667
+131 2.51923077 0 0.04333087 0.44237289 0.51429625
+132 2.53846154 0 0.04832347 0.40449097 0.54718556
+133 2.55769231 0 0.05664448 0.36609700 0.57725852
+134 2.57692308 0 0.06829389 0.32776703 0.60393908
+135 2.59615385 0 0.08327170 0.29007714 0.62665116
+136 2.61538462 0 0.10157791 0.25360340 0.64481869
+137 2.63461538 0 0.12321252 0.21892187 0.65786560
+138 2.65384615 0 0.14817554 0.18660863 0.66521582
+139 2.67307692 0 0.17646341 0.15723619 0.66630040
+140 2.69230769 0 0.20785920 0.13116371 0.66097709
+141 2.71153846 0 0.24181531 0.10841963 0.64976507
+142 2.73076923 0 0.27775565 0.08900394 0.63324040
+143 2.75000000 0 0.31510417 0.07291667 0.61197917
+144 2.76923077 0 0.35328478 0.06015779 0.58655743
+145 2.78846154 0 0.39172143 0.05072732 0.55755125
+146 2.80769231 0 0.42983804 0.04462525 0.52553672
+147 2.82692308 0 0.46705854 0.04185158 0.49108989
+148 2.84615385 0 0.50280686 0.04240631 0.45478683
+149 2.86538462 0 0.53650693 0.04628945 0.41720362
+150 2.88461538 0 0.56758269 0.05350099 0.37891633
+151 2.90384615 0 0.59545806 0.06404093 0.34050101
+152 2.92307692 0 0.61955697 0.07790927 0.30253376
+153 2.94230769 0 0.63930336 0.09510602 0.26559063
+154 2.96153846 0 0.65412115 0.11563116 0.23024769
+155 2.98076923 0 0.66343428 0.13948471 0.19708101
+156 3.00000000 0 0.66666667 0.16666667 0.16666667
+157 3.01923077 0 0.66343428 0.19708101 0.13948471
+158 3.03846154 0 0.65412115 0.23024769 0.11563116
+159 3.05769231 0 0.63930336 0.26559063 0.09510602
+160 3.07692308 0 0.61955697 0.30253376 0.07790927
+161 3.09615385 0 0.59545806 0.34050101 0.06404093
+162 3.11538462 0 0.56758269 0.37891633 0.05350099
+163 3.13461538 0 0.53650693 0.41720362 0.04628945
+164 3.15384615 0 0.50280686 0.45478683 0.04240631
+165 3.17307692 0 0.46705854 0.49108989 0.04185158
+166 3.19230769 0 0.42983804 0.52553672 0.04462525
+167 3.21153846 0 0.39172143 0.55755125 0.05072732
+168 3.23076923 0 0.35328478 0.58655743 0.06015779
+169 3.25000000 0 0.31510417 0.61197917 0.07291667
+170 3.26923077 0 0.27775565 0.63324040 0.08900394
+171 3.28846154 0 0.24181531 0.64976507 0.10841963
+172 3.30769231 0 0.20785920 0.66097709 0.13116371
+173 3.32692308 0 0.17646341 0.66630040 0.15723619
+174 3.34615385 0 0.14817554 0.66521582 0.18660863
+175 3.36538462 0 0.12321252 0.65786560 0.21892187
+176 3.38461538 0 0.10157791 0.64481869 0.25360340
+177 3.40384615 0 0.08327170 0.62665116 0.29007714
+178 3.42307692 0 0.06829389 0.60393908 0.32776703
+179 3.44230769 0 0.05664448 0.57725852 0.36609700
+180 3.46153846 0 0.04832347 0.54718556 0.40449097
+181 3.48076923 0 0.04333087 0.51429625 0.44237289
+182 3.50000000 0 0.04166667 0.47916667 0.47916667
+183 3.51923077 0 0.04333087 0.44237289 0.51429625
+184 3.53846154 0 0.04832347 0.40449097 0.54718556
+185 3.55769231 0 0.05664448 0.36609700 0.57725852
+186 3.57692308 0 0.06829389 0.32776703 0.60393908
+187 3.59615385 0 0.08327170 0.29007714 0.62665116
+188 3.61538462 0 0.10157791 0.25360340 0.64481869
+189 3.63461538 0 0.12321252 0.21892187 0.65786560
+190 3.65384615 0 0.14817554 0.18660863 0.66521582
+191 3.67307692 0 0.17646341 0.15723619 0.66630040
+192 3.69230769 0 0.20785920 0.13116371 0.66097709
+193 3.71153846 0 0.24181531 0.10841963 0.64976507
+194 3.73076923 0 0.27775565 0.08900394 0.63324040
+195 3.75000000 0 0.31510417 0.07291667 0.61197917
+196 3.76923077 0 0.35328478 0.06015779 0.58655743
+197 3.78846154 0 0.39172143 0.05072732 0.55755125
+198 3.80769231 0 0.42983804 0.04462525 0.52553672
+199 3.82692308 0 0.46705854 0.04185158 0.49108989
+200 3.84615385 0 0.50280686 0.04240631 0.45478683
+201 3.86538462 0 0.53650693 0.04628945 0.41720362
+202 3.88461538 0 0.56758269 0.05350099 0.37891633
+203 3.90384615 0 0.59545806 0.06404093 0.34050101
+204 3.92307692 0 0.61955697 0.07790927 0.30253376
+205 3.94230769 0 0.63930336 0.09510602 0.26559063
+206 3.96153846 0 0.65412115 0.11563116 0.23024769
+207 3.98076923 0 0.66343428 0.13948471 0.19708101
+208 4.00000000 0 0.66666667 0.16666667 0.16666667
zero time, t0 = 0
parameter(s) unspecified
process model simulator, rprocess =
@@ -394,7 +394,7 @@
zeronames = zeronames, tcovar = tcovar, covar = covar,
args = pairlist(...))
}
-<environment: 0x1513c10>
+<environment: 0x14e87b8>
process model density, dprocess =
function (x, times, params, ..., statenames = character(0), paramnames = character(0),
covarnames = character(0), tcovar, covar, log = FALSE)
@@ -404,7 +404,7 @@
covarnames = covarnames, tcovar = tcovar, covar = covar,
log = log, args = pairlist(...))
}
-<environment: 0x1edb848>
+<environment: 0x193a340>
measurement model simulator, rmeasure =
function (x, t, params, covars, ...)
{
@@ -463,11 +463,11 @@
parameter transform function =
function (params, ...)
params
-<environment: 0x1057aa0>
+<environment: 0x15beeb0>
parameter inverse transform function =
function (params, ...)
params
-<environment: 0x1057aa0>
+<environment: 0x15beeb0>
userdata =
$zeronames
[1] "cases"
@@ -479,7 +479,7 @@
> x <- simulate(po,params=log(params),nsim=3)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 2.048561 secs
+Time difference of 2.027774 secs
>
> pdf(file='sir.pdf')
>
@@ -496,7 +496,7 @@
> X3 <- trajectory(po,params=log(params),times=t3,hmax=1/52)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 2.724916 secs
+Time difference of 2.722191 secs
> plot(t3,X3['I',1,],type='l')
>
> f1 <- dprocess(
@@ -556,7 +556,7 @@
> x <- simulate(po,nsim=100)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 2.509698 secs
+Time difference of 2.520875 secs
> plot(x[[1]],variables=c("S","I","R","cases","W"))
>
> t3 <- seq(0,20,by=1/52)
@@ -564,7 +564,7 @@
> X4 <- trajectory(po,times=t3,hmax=1/52)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 0.153466 secs
+Time difference of 0.1533842 secs
> plot(t3,X4['I',1,],type='l')
>
> g2 <- dmeasure(
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