[Pomp-commits] r1141 - pkg/pomp pkg/pomp/R pkg/pomp/inst/include pkg/pomp/src www/vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Mar 13 19:43:51 CET 2015
Author: kingaa
Date: 2015-03-13 19:43:50 +0100 (Fri, 13 Mar 2015)
New Revision: 1141
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/R/pomp.R
pkg/pomp/inst/include/pomp.h
pkg/pomp/src/pomp.h
www/vignettes/pomp.pdf
www/vignettes/pompjss.pdf
Log:
- improve warnings in 'pomp' when covariate table is supplied but not used
- make 'reulermultinom' and 'deulermultinom' R_INLINE
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2015-03-13 18:42:28 UTC (rev 1140)
+++ pkg/pomp/DESCRIPTION 2015-03-13 18:43:50 UTC (rev 1141)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.62-8
-Date: 2015-03-06
+Version: 0.62-9
+Date: 2015-03-14
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.R
===================================================================
--- pkg/pomp/R/pomp.R 2015-03-13 18:42:28 UTC (rev 1140)
+++ pkg/pomp/R/pomp.R 2015-03-13 18:43:50 UTC (rev 1141)
@@ -335,21 +335,24 @@
)
warning("a covariate table has been given, yet the ",
sQuote("skeleton")," function does not have ",
- sQuote("covars")," as a formal argument",call.=FALSE)
+ sQuote("covars")," as a formal argument: see ",
+ sQuote("?pomp"),call.=FALSE)
if (
(rmeasure at mode==pompfunmode$Rfun)
&&!("covars"%in%names(formals(rmeasure at R.fun)))
)
warning("a covariate table has been given, yet the ",
sQuote("rmeasure")," function does not have ",
- sQuote("covars")," as a formal argument",call.=FALSE)
+ sQuote("covars")," as a formal argument: see ",
+ sQuote("?pomp"),call.=FALSE)
if (
(dmeasure at mode==pompfunmode$Rfun)
&&!("covars"%in%names(formals(dmeasure at R.fun)))
)
warning("a covariate table has been given, yet the ",
sQuote("dmeasure")," function does not have ",
- sQuote("covars")," as a formal argument",call.=FALSE)
+ sQuote("covars")," as a formal argument: see ",
+ sQuote("?pomp"),call.=FALSE)
}
if ((length(tcovar)>0)&&((min(tcovar)>t0)||(max(tcovar)<max(times))))
Modified: pkg/pomp/inst/include/pomp.h
===================================================================
--- pkg/pomp/inst/include/pomp.h 2015-03-13 18:42:28 UTC (rev 1140)
+++ pkg/pomp/inst/include/pomp.h 2015-03-13 18:43:50 UTC (rev 1141)
@@ -65,8 +65,8 @@
// But note that when reulermultinom is called inside a pomp 'rprocess',
// there is no need to call {Get,Put}RNGState() as this is handled by pomp
-static void reulermultinom (int m, double size, double *rate,
- double dt, double *trans) {
+static R_INLINE void reulermultinom (int m, double size, double *rate,
+ double dt, double *trans) {
double p = 0.0;
int j, k;
if ((size < 0.0) || (dt < 0.0) || (floor(size+0.5) != size)) {
@@ -114,8 +114,8 @@
// See '?deulermultinom' and vignettes for more on the Euler-multinomial
// distributions.
-static double deulermultinom (int m, double size, double *rate, double dt,
- double *trans, int give_log) {
+static R_INLINE double deulermultinom (int m, double size, double *rate,
+ double dt, double *trans, int give_log) {
double p = 0.0;
double n = 0.0;
double ff = 0.0;
Modified: pkg/pomp/src/pomp.h
===================================================================
--- pkg/pomp/src/pomp.h 2015-03-13 18:42:28 UTC (rev 1140)
+++ pkg/pomp/src/pomp.h 2015-03-13 18:43:50 UTC (rev 1141)
@@ -65,8 +65,8 @@
// But note that when reulermultinom is called inside a pomp 'rprocess',
// there is no need to call {Get,Put}RNGState() as this is handled by pomp
-static void reulermultinom (int m, double size, double *rate,
- double dt, double *trans) {
+static R_INLINE void reulermultinom (int m, double size, double *rate,
+ double dt, double *trans) {
double p = 0.0;
int j, k;
if ((size < 0.0) || (dt < 0.0) || (floor(size+0.5) != size)) {
@@ -114,8 +114,8 @@
// See '?deulermultinom' and vignettes for more on the Euler-multinomial
// distributions.
-static double deulermultinom (int m, double size, double *rate, double dt,
- double *trans, int give_log) {
+static R_INLINE double deulermultinom (int m, double size, double *rate,
+ double dt, double *trans, int give_log) {
double p = 0.0;
double n = 0.0;
double ff = 0.0;
Modified: www/vignettes/pomp.pdf
===================================================================
--- www/vignettes/pomp.pdf 2015-03-13 18:42:28 UTC (rev 1140)
+++ www/vignettes/pomp.pdf 2015-03-13 18:43:50 UTC (rev 1141)
@@ -1,41 +1,43 @@
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[TRUNCATED]
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