[Pomp-commits] r1159 - pkg/pomp pkg/pomp/R pkg/pomp/inst pkg/pomp/inst/examples pkg/pomp/man pkg/pomp/src pkg/pomp/tests www/content www/vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu May 28 16:55:45 CEST 2015
Author: kingaa
Date: 2015-05-28 16:55:44 +0200 (Thu, 28 May 2015)
New Revision: 1159
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/R/builder.R
pkg/pomp/R/pomp-class.R
pkg/pomp/R/pomp-methods.R
pkg/pomp/R/pomp.R
pkg/pomp/inst/NEWS
pkg/pomp/inst/NEWS.Rd
pkg/pomp/inst/examples/bbs.R
pkg/pomp/inst/examples/blowflies.R
pkg/pomp/inst/examples/dacca.R
pkg/pomp/inst/examples/euler.sir.R
pkg/pomp/inst/examples/gillespie.sir.R
pkg/pomp/inst/examples/gompertz.R
pkg/pomp/inst/examples/ricker.R
pkg/pomp/man/builder.Rd
pkg/pomp/man/pomp-methods.Rd
pkg/pomp/man/pomp.Rd
pkg/pomp/src/partrans.c
pkg/pomp/tests/getting_started.R
pkg/pomp/tests/getting_started.Rout.save
pkg/pomp/tests/partrans.R
pkg/pomp/tests/partrans.Rout.save
pkg/pomp/tests/rw2.Rout.save
pkg/pomp/tests/sir.Rout.save
www/content/NEWS.html
www/vignettes/getting_started.R
www/vignettes/getting_started.Rmd
www/vignettes/pomp.pdf
www/vignettes/pompjss.R
www/vignettes/pompjss.Rnw
www/vignettes/pompjss.pdf
Log:
- the unfortunately named 'pomp' arguments 'parameter.inv.transform' and 'parameter.transform' have been deprecated in favor of the more mnemonic 'toEstimationScale' and 'fromEstimationScale'
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/DESCRIPTION 2015-05-28 14:55:44 UTC (rev 1159)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.64-1
-Date: 2015-05-22
+Version: 0.65-1
+Date: 2015-05-28
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 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/R/builder.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -1,7 +1,7 @@
pompCBuilder <- function (name = NULL, dir = NULL,
statenames, paramnames, covarnames, obsnames,
rmeasure, dmeasure, step.fn, skeleton,
- parameter.transform, parameter.inv.transform,
+ fromEstimationScale, toEstimationScale,
rprior, dprior, globals,
verbose = getOption("verbose",FALSE))
{
@@ -65,19 +65,19 @@
registry <- c("load_stack_incr","load_stack_decr")
## parameter transformation function
- if (!missing(parameter.transform)) {
+ if (!missing(fromEstimationScale)) {
registry <- c(registry,"par_trans")
- cat(file=out,render(header$parameter.transform,name=name))
- cat(file=out,callable.decl(parameter.transform))
- cat(file=out,parameter.transform,footer$parameter.transform)
+ cat(file=out,render(header$fromEstimationScale,name=name))
+ cat(file=out,callable.decl(fromEstimationScale))
+ cat(file=out,fromEstimationScale,footer$fromEstimationScale)
}
## inverse parameter transformation function
- if (!missing(parameter.inv.transform)) {
+ if (!missing(toEstimationScale)) {
registry <- c(registry,"par_untrans")
- cat(file=out,render(header$parameter.inv.transform,name=name))
- cat(file=out,callable.decl(parameter.inv.transform))
- cat(file=out,parameter.inv.transform,footer$parameter.inv.transform)
+ cat(file=out,render(header$toEstimationScale,name=name))
+ cat(file=out,callable.decl(toEstimationScale))
+ cat(file=out,toEstimationScale,footer$toEstimationScale)
}
## rmeasure function
@@ -224,7 +224,7 @@
rmeasure, dmeasure, step.fn, step.fn.delta.t,
skeleton, skeleton.type = c("map","vectorfield"),
skelmap.delta.t = 1,
- parameter.transform, parameter.inv.transform,
+ fromEstimationScale, toEstimationScale,
rprior, dprior,
globals, ..., save = FALSE) {
@@ -245,8 +245,8 @@
if (missing(statenames)) stop(sQuote("statenames")," must be supplied");
if (missing(paramnames)) stop(sQuote("paramnames")," must be supplied");
- mpt <- missing(parameter.transform)
- mpit <- missing(parameter.inv.transform)
+ mpt <- missing(fromEstimationScale)
+ mpit <- missing(toEstimationScale)
if (xor(mpt,mpit))
stop("if you supply one transformation function, you must supply its inverse")
@@ -260,8 +260,8 @@
dmeasure=dmeasure,
step.fn=step.fn,
skeleton=skeleton,
- parameter.transform=parameter.transform,
- parameter.inv.transform=parameter.inv.transform,
+ fromEstimationScale=fromEstimationScale,
+ toEstimationScale=toEstimationScale,
rprior=rprior,
dprior=dprior,
globals=globals,
@@ -284,8 +284,8 @@
skeleton=render(fnames$skeleton,name=name),
skeleton.type=skeleton.type,
skelmap.delta.t=skelmap.delta.t,
- parameter.transform=render(fnames$parameter.transform,name=name),
- parameter.inv.transform=render(fnames$parameter.inv.transform,name=name),
+ fromEstimationScale=render(fnames$fromEstimationScale,name=name),
+ toEstimationScale=render(fnames$toEstimationScale,name=name),
rprior=render(fnames$rprior,name=name),
dprior=render(fnames$dprior,name=name),
PACKAGE=name,
@@ -316,8 +316,8 @@
dmeasure= "\nvoid __pomp_dmeasure (double *__lik, const double *__y, const double *__x, const double *__p, int give_log, const int *__obsindex, const int *__stateindex, const int *__parindex, const int *__covindex, int __ncovars, const double *__covars, double t)\n{\n",
step.fn="\nvoid __pomp_stepfn (double *__x, const double *__p, const int *__stateindex, const int *__parindex, const int *__covindex, int __covdim, const double *__covars, double t, double dt)\n{\n",
skeleton="\nvoid __pomp_skelfn (double *__f, const double *__x, const double *__p, const int *__stateindex, const int *__parindex, const int *__covindex, int __ncovars, const double *__covars, double t)\n{\n",
- parameter.transform="\nvoid __pomp_par_trans (double *__pt, const double *__p, const int *__parindex)\n{\n",
- parameter.inv.transform="\nvoid __pomp_par_untrans (double *__pt, const double *__p, const int *__parindex)\n{\n",
+ fromEstimationScale="\nvoid __pomp_par_trans (double *__pt, const double *__p, const int *__parindex)\n{\n",
+ toEstimationScale="\nvoid __pomp_par_untrans (double *__pt, const double *__p, const int *__parindex)\n{\n",
rprior="\nvoid __pomp_rprior (double *__p, const int *__parindex)\n{\n",
dprior="\nvoid __pomp_dprior (double *__lik, const double *__p, int give_log, const int *__parindex)\n{\n"
)
@@ -327,8 +327,8 @@
dmeasure= "__pomp_dmeasure",
step.fn="__pomp_stepfn",
skeleton="__pomp_skelfn",
- parameter.transform="__pomp_par_trans",
- parameter.inv.transform="__pomp_par_untrans",
+ fromEstimationScale="__pomp_par_trans",
+ toEstimationScale="__pomp_par_untrans",
rprior="__pomp_rprior",
dprior="__pomp_dprior"
)
@@ -347,8 +347,8 @@
dmeasure="\n}\n\n",
step.fn="\n}\n\n",
skeleton="\n}\n\n",
- parameter.transform="\n}\n\n",
- parameter.inv.transform="\n}\n\n",
+ fromEstimationScale="\n}\n\n",
+ toEstimationScale="\n}\n\n",
rprior="\n}\n\n",
dprior="\n}\n\n",
globals="\n",
Modified: pkg/pomp/R/pomp-class.R
===================================================================
--- pkg/pomp/R/pomp-class.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/R/pomp-class.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -32,8 +32,8 @@
tcovar = 'numeric',
zeronames = 'character',
has.trans = 'logical',
- par.trans = 'pomp.fun',
- par.untrans = 'pomp.fun',
+ from.trans = 'pomp.fun',
+ to.trans = 'pomp.fun',
solibfile = 'list',
userdata = 'list'
),
@@ -57,8 +57,8 @@
tcovar=numeric(0),
zeronames=character(0),
has.trans=FALSE,
- par.trans=pomp.fun(),
- par.untrans=pomp.fun(),
+ from.trans=pomp.fun(),
+ to.trans=pomp.fun(),
solibfile=list(),
userdata=list()
),
Modified: pkg/pomp/R/pomp-methods.R
===================================================================
--- pkg/pomp/R/pomp-methods.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/R/pomp-methods.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -25,18 +25,20 @@
as.data.frame.pomp <- function (x, row.names, optional, ...) as(x,"data.frame")
## parameter transformations
-partrans.internal <- function (object, params, dir = c("forward","inverse"),
+partrans.internal <- function (object, params,
+ dir = c("fromEstimationScale","toEstimationScale",
+ "forward","inverse"),
.getnativesymbolinfo = TRUE, ...) {
if (!object at has.trans) return(params)
pompLoad(object)
- dir <- switch(match.arg(dir),forward=1L,inverse=-1L)
+ dir <- switch(match.arg(dir),fromEstimationScale=1L,toEstimationScale=-1L,forward=1L,inverse=-1L)
rv <- .Call(do_partrans,object,params,dir,.getnativesymbolinfo)
pompUnload(object)
rv
}
setMethod("partrans","pomp",
- function (object, params, dir = c("forward","inverse"), ...)
+ function (object, params, dir = c("fromEstimationScale","toEstimationScale", "forward","inverse"),...)
partrans.internal(object=object,params=params,dir=dir,...)
)
@@ -168,7 +170,7 @@
function (object, pars, transform = FALSE, ...) {
if (length(object at params)>0) {
if (transform)
- params <- partrans(object,params=object at params,dir="inverse")
+ params <- partrans(object,params=object at params,dir="toEstimationScale")
else
params <- object at params
if (missing(pars))
@@ -198,7 +200,7 @@
if (missing(pars)) { ## replace the whole params slot with 'value'
if (length(value)>0) {
if (transform)
- value <- partrans(object,params=value,dir="forward")
+ value <- partrans(object,params=value,dir="fromEstimationScale")
pars <- names(value)
if (is.null(pars)) {
if (transform)
@@ -220,7 +222,7 @@
names(val) <- pars
val[] <- value
if (transform)
- value <- partrans(object,params=val,dir="forward")
+ value <- partrans(object,params=val,dir="fromEstimationScale")
object at params <- value
} else { ## pre-existing params slot
params <- coef(object,transform=transform)
@@ -240,7 +242,7 @@
}
params[pars] <- val
if (transform)
- params <- partrans(object,params=params,dir="forward")
+ params <- partrans(object,params=params,dir="fromEstimationScale")
object at params <- params
}
}
@@ -296,10 +298,10 @@
}
cat("initializer = \n")
show(object at initializer)
- cat("parameter transform function = \n")
- show(object at par.trans)
- cat("parameter inverse transform function = \n")
- show(object at par.untrans)
+ cat("parameter transformation (to estimation scale) = \n")
+ show(object at to.trans)
+ cat("parameter transformation (from estimation scale) = \n")
+ show(object at from.trans)
if (length(coef(object))>0) {
cat("parameter(s):\n")
print(coef(object))
Modified: pkg/pomp/R/pomp.R
===================================================================
--- pkg/pomp/R/pomp.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/R/pomp.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -8,7 +8,8 @@
params, covar, tcovar,
obsnames, statenames, paramnames, covarnames,
zeronames, PACKAGE,
- parameter.transform, parameter.inv.transform,
+ fromEstimationScale, toEstimationScale,
+ parameter.transform = NULL, parameter.inv.transform = NULL,
globals, userdata, ...,
.solibfile, .filename, .filedir,
verbose = getOption("verbose",FALSE)) {
@@ -39,9 +40,39 @@
if (missing(dmeasure)) dmeasure <- NULL
if (missing(rprior)) rprior <- NULL
if (missing(dprior)) dprior <- NULL
- if (missing(parameter.transform)) parameter.transform <- NULL
- if (missing(parameter.inv.transform)) parameter.inv.transform <- NULL
+ if (missing(fromEstimationScale)) fromEstimationScale <- NULL
+ if (missing(toEstimationScale)) toEstimationScale <- NULL
+ ## deal with deprecated arguments
+ if (!is.null(parameter.transform)) {
+ warning("the ",sQuote("parameter.transform")," argument of ",
+ sQuote("pomp")," is deprecated, ",
+ "and will be removed in a future release.\n",
+ "Use ",sQuote("fromEstimationScale")," instead.",call.=FALSE)
+ if (!is.null(fromEstimationScale) && !is(fromEstimationScale,"pomp.fun")) {
+ warning("both ",sQuote("fromEstimationScale")," and ",
+ sQuote("parameter.transform")," have been specified in a call to ",
+ sQuote("pomp"),".\n",
+ "The latter will be ignored.",call.=FALSE)
+ } else {
+ fromEstimationScale <- parameter.transform
+ }
+ }
+ if (!is.null(parameter.inv.transform)) {
+ warning("the ",sQuote("parameter.inv.transform")," argument of ",
+ sQuote("pomp")," is deprecated, ",
+ "and will be removed in a future release.\n",
+ "Use ",sQuote("toEstimationScale")," instead.",call.=FALSE)
+ if (!is.null(toEstimationScale) && !is(toEstimationScale,"pomp.fun")) {
+ warning("both ",sQuote("toEstimationScale")," and ",
+ sQuote("parameter.inv.transform")," have been specified in a call to ",
+ sQuote("pomp"),".\n",
+ "The latter will be ignored.",call.=FALSE)
+ } else {
+ toEstimationScale <- parameter.inv.transform
+ }
+ }
+
## defaults for names of states, parameters, and accumulator variables
if (missing(statenames)) statenames <- character(0)
if (missing(paramnames)) paramnames <- character(0)
@@ -60,7 +91,7 @@
storage.mode(data) <- 'double'
if (missing(obsnames) || length(obsnames)==0) obsnames <- rownames(data)
obsnames <- as.character(obsnames)
-
+
## check times
if (!is.numeric(times) || !all(diff(times)>0))
stop("pomp error: ",sQuote("times")," must be an increasing numeric vector")
@@ -132,10 +163,10 @@
snips <- c(snips,rprior=rprior at text)
if (is(dprior,"Csnippet"))
snips <- c(snips,dprior=dprior at text)
- if (is(parameter.transform,"Csnippet"))
- snips <- c(snips,parameter.transform=parameter.transform at text)
- if (is(parameter.inv.transform,"Csnippet"))
- snips <- c(snips,parameter.inv.transform=parameter.inv.transform at text)
+ if (is(fromEstimationScale,"Csnippet"))
+ snips <- c(snips,fromEstimationScale=fromEstimationScale at text)
+ if (is(toEstimationScale,"Csnippet"))
+ snips <- c(snips,toEstimationScale=toEstimationScale at text)
if (length(snips)>0) {
libname <- try(
do.call(
@@ -288,44 +319,44 @@
}
## handle parameter transformations
- mpt <- is.null(parameter.transform)
- mpit <- is.null(parameter.inv.transform)
+ mpt <- is.null(fromEstimationScale)
+ mpit <- is.null(toEstimationScale)
if (xor(mpt,mpit)) {
- stop("if one of ",sQuote("parameter.transform"),", ",
- sQuote("parameter.inv.transform"),
+ stop("if one of ",sQuote("fromEstimationScale"),", ",
+ sQuote("toEstimationScale"),
" is supplied, then so must the other")
}
has.trans <- !mpt
if (has.trans) {
- par.trans <- pomp.fun(
- f=parameter.transform,
- PACKAGE=PACKAGE,
- proto=quote(par.trans(params,...)),
- slotname="parameter.transform",
- libname=libname,
- statenames=statenames,
- paramnames=paramnames,
- obsnames=obsnames,
- covarnames=covarnames
- )
- par.untrans <- pomp.fun(
- f=parameter.inv.transform,
- PACKAGE=PACKAGE,
- proto=quote(par.untrans(params,...)),
- slotname="parameter.inv.transform",
- libname=libname,
- statenames=statenames,
- paramnames=paramnames,
- obsnames=obsnames,
- covarnames=covarnames
- )
+ from.trans <- pomp.fun(
+ f=fromEstimationScale,
+ PACKAGE=PACKAGE,
+ proto=quote(from.trans(params,...)),
+ slotname="fromEstimationScale",
+ libname=libname,
+ statenames=statenames,
+ paramnames=paramnames,
+ obsnames=obsnames,
+ covarnames=covarnames
+ )
+ to.trans <- pomp.fun(
+ f=toEstimationScale,
+ PACKAGE=PACKAGE,
+ proto=quote(to.trans(params,...)),
+ slotname="toEstimationScale",
+ libname=libname,
+ statenames=statenames,
+ paramnames=paramnames,
+ obsnames=obsnames,
+ covarnames=covarnames
+ )
} else {
- par.trans <- pomp.fun()
- par.untrans <- pomp.fun()
+ from.trans <- pomp.fun()
+ to.trans <- pomp.fun()
}
if (has.trans &&
- par.trans at mode==pompfunmode$undef &&
- par.untrans at mode==pompfunmode$undef
+ from.trans at mode==pompfunmode$undef &&
+ to.trans at mode==pompfunmode$undef
) has.trans <- FALSE
if (nrow(covar)>0) {
@@ -381,8 +412,8 @@
tcovar = tcovar,
zeronames = zeronames,
has.trans = has.trans,
- par.trans = par.trans,
- par.untrans = par.untrans,
+ from.trans = from.trans,
+ to.trans = to.trans,
solibfile = .solibfile,
userdata = userdata
)
@@ -477,7 +508,7 @@
initializer, rprior, dprior,
params, covar, tcovar,
obsnames, statenames, paramnames, covarnames, zeronames,
- PACKAGE, parameter.transform, parameter.inv.transform,
+ PACKAGE, fromEstimationScale, toEstimationScale,
globals) {
data <- t(sapply(data,as.numeric))
@@ -519,8 +550,8 @@
covarnames=covarnames,
zeronames=zeronames,
PACKAGE=PACKAGE,
- parameter.transform=parameter.transform,
- parameter.inv.transform=parameter.inv.transform,
+ fromEstimationScale=fromEstimationScale,
+ toEstimationScale=toEstimationScale,
globals=globals,
...
)
@@ -536,7 +567,7 @@
skelmap.delta.t = 1,
initializer, rprior, dprior, params, covar, tcovar,
obsnames, statenames, paramnames, covarnames, zeronames,
- PACKAGE, parameter.transform, parameter.inv.transform,
+ PACKAGE, fromEstimationScale, toEstimationScale,
globals) {
pomp.constructor(
@@ -563,8 +594,8 @@
covarnames=covarnames,
zeronames=zeronames,
PACKAGE=PACKAGE,
- parameter.transform=parameter.transform,
- parameter.inv.transform=parameter.inv.transform,
+ fromEstimationScale=fromEstimationScale,
+ toEstimationScale=toEstimationScale,
globals=globals,
...
)
@@ -581,7 +612,7 @@
skelmap.delta.t = 1,
initializer, rprior, dprior, params, covar, tcovar,
obsnames, statenames, paramnames, covarnames, zeronames,
- PACKAGE, parameter.transform, parameter.inv.transform,
+ PACKAGE, fromEstimationScale, toEstimationScale,
globals) {
pomp.constructor(
@@ -608,8 +639,8 @@
covarnames=covarnames,
zeronames=zeronames,
PACKAGE=PACKAGE,
- parameter.transform=parameter.transform,
- parameter.inv.transform=parameter.inv.transform,
+ fromEstimationScale=fromEstimationScale,
+ toEstimationScale=toEstimationScale,
globals=globals,
...
)
@@ -624,7 +655,7 @@
skeleton, skeleton.type, skelmap.delta.t,
initializer, rprior, dprior, params, covar, tcovar,
obsnames, statenames, paramnames, covarnames, zeronames,
- PACKAGE, parameter.transform, parameter.inv.transform,
+ PACKAGE, fromEstimationScale, toEstimationScale,
globals) {
if (missing(times)) times <- data at times
@@ -660,23 +691,23 @@
if (missing(skeleton.type)) skeleton.type <- data at skeleton.type
if (missing(skeleton)) skeleton <- data at skeleton
if (missing(skelmap.delta.t)) skelmap.delta.t <- data at skelmap.delta.t
- if (missing(parameter.transform)) {
- if (missing(parameter.inv.transform)) {
- par.trans <- data at par.trans
- par.untrans <- data at par.untrans
+ if (missing(fromEstimationScale)) {
+ if (missing(toEstimationScale)) {
+ from.trans <- data at from.trans
+ to.trans <- data at to.trans
} else {
- stop("pomp error: if ",sQuote("parameter.inv.transform"),
+ stop("pomp error: if ",sQuote("toEstimationScale"),
" is supplied, then " ,
- sQuote("parameter.transform")," must also be supplied")
+ sQuote("fromEstimationScale")," must also be supplied")
}
} else {
- if (missing(parameter.inv.transform)) {
- stop("pomp error: if ",sQuote("parameter.transform"),
+ if (missing(toEstimationScale)) {
+ stop("pomp error: if ",sQuote("fromEstimationScale"),
" is supplied, then " ,
- sQuote("parameter.inv.transform")," must also be supplied")
+ sQuote("toEstimationScale")," must also be supplied")
} else {
- par.trans <- parameter.transform
- par.untrans <- parameter.inv.transform
+ from.trans <- fromEstimationScale
+ to.trans <- toEstimationScale
}
}
@@ -708,8 +739,8 @@
covarnames=covarnames,
zeronames=zeronames,
PACKAGE=PACKAGE,
- parameter.transform=par.trans,
- parameter.inv.transform=par.untrans,
+ fromEstimationScale=from.trans,
+ toEstimationScale=to.trans,
params=params,
globals=globals,
.solibfile=data at solibfile,
Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/NEWS 2015-05-28 14:55:44 UTC (rev 1159)
@@ -1,5 +1,14 @@
_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._6_5-_1:
+
+ • The unfortunately named ‘pomp’ arguments
+ ‘parameter.transform’ and ‘parameter.inv.transform’ have been
+ deprecated in favor of the more mnemonic ‘toEstimationScale’
+ and ‘fromEstimationScale’. Using the old arguments will
+ result in the same behavior as previously, but a warning will
+ be generated.
+
_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_4-_1:
• The ‘mif’ option ‘cooling.fraction’ has been replaced by the
Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/NEWS.Rd 2015-05-28 14:55:44 UTC (rev 1159)
@@ -1,5 +1,11 @@
\name{NEWS}
\title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 0.65-1}{
+ \itemize{
+ \item The unfortunately named \code{pomp} arguments \code{parameter.transform} and \code{parameter.inv.transform} have been deprecated in favor of the more mnemonic \code{toEstimationScale} and \code{fromEstimationScale}.
+ Using the old arguments will result in the same behavior as previously, but a warning will be generated.
+ }
+}
\section{Changes in \pkg{pomp} version 0.64-1}{
\itemize{
\item The \code{mif} option \code{cooling.fraction} has been replaced by the more descriptive \code{cooling.fraction.50}.
Modified: pkg/pomp/inst/examples/bbs.R
===================================================================
--- pkg/pomp/inst/examples/bbs.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/examples/bbs.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -57,12 +57,12 @@
"S.0","I.0","R.0"
),
logitvar="rho",
- parameter.inv.transform=function (params, logvar, logitvar, ...) {
+ toEstimationScale=function (params, logvar, logitvar, ...) {
params[logvar] <- log(params[logvar])
params[logitvar] <- qlogis(params[logitvar])
params
},
- parameter.transform=function (params, logvar, logitvar, ...) {
+ fromEstimationScale=function (params, logvar, logitvar, ...) {
params[logvar] <- exp(params[logvar])
params[logitvar] <- plogis(params[logitvar])
params
Modified: pkg/pomp/inst/examples/blowflies.R
===================================================================
--- pkg/pomp/inst/examples/blowflies.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/examples/blowflies.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -892,10 +892,10 @@
approx(x=day,y=y,xout=seq(from=0,to=14,by=1),rule=2)$y
),
# y.init=c(948, 948, 942, 930, 911, 885, 858, 833.7, 801, 748.3, 676, 589.8, 504, 434.9, 397),
- parameter.inv.transform=function(params,...) {
+ toEstimationScale=function(params,...) {
log(params)
},
- parameter.transform=function(params,...) {
+ fromEstimationScale=function(params,...) {
exp(params)
},
initializer=function (params, t0, y.init, ...) {
Modified: pkg/pomp/inst/examples/dacca.R
===================================================================
--- pkg/pomp/inst/examples/dacca.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/examples/dacca.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -128,8 +128,8 @@
all.state.names=c("S","I","Rs",paste("R",1:nrstage,sep=''),"M","W","count"),
comp.names=c("S","I","Rs",paste("R",1:nrstage,sep='')),
comp.ic.names=c("S.0","I.0","Rs.0",paste("R",1:nrstage,".0",sep='')),
- parameter.transform="_cholmodel_trans",
- parameter.inv.transform="_cholmodel_untrans",
+ fromEstimationScale="_cholmodel_trans",
+ toEstimationScale="_cholmodel_untrans",
initializer = function (params, t0, covars, nrstage, comp.ic.names, comp.names, all.state.names, ...) {
states <- numeric(length(all.state.names))
names(states) <- all.state.names
Modified: pkg/pomp/inst/examples/euler.sir.R
===================================================================
--- pkg/pomp/inst/examples/euler.sir.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/examples/euler.sir.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -243,8 +243,8 @@
zeronames=c("cases"),
comp.names=c("S","I","R"),
ic.names=c("S.0","I.0","R.0"),
- parameter.transform="_sir_par_trans",
- parameter.inv.transform="_sir_par_untrans",
+ fromEstimationScale="_sir_par_trans",
+ toEstimationScale="_sir_par_untrans",
nbasis=3L,
degree=3L,
period=1.0,
Modified: pkg/pomp/inst/examples/gillespie.sir.R
===================================================================
--- pkg/pomp/inst/examples/gillespie.sir.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/examples/gillespie.sir.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -570,8 +570,8 @@
zeronames=c("cases"),
comp.names=c("S","I","R"),
ic.names=c("S.0","I.0","R.0"),
- parameter.transform="_sir_par_trans",
- parameter.inv.transform="_sir_par_untrans",
+ fromEstimationScale="_sir_par_trans",
+ toEstimationScale="_sir_par_untrans",
nbasis=3L,
degree=3L,
period=1.0,
Modified: pkg/pomp/inst/examples/gompertz.R
===================================================================
--- pkg/pomp/inst/examples/gompertz.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/examples/gompertz.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -119,10 +119,10 @@
paramnames=c("r","K","sigma","tau"),
statenames=c("X"),
obsnames=c("Y"),
- parameter.transform=function(params,...){
+ fromEstimationScale=function(params,...){
exp(params)
},
- parameter.inv.transform=function(params,...){
+ toEstimationScale=function(params,...){
log(params)
}
) -> gompertz
Modified: pkg/pomp/inst/examples/ricker.R
===================================================================
--- pkg/pomp/inst/examples/ricker.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/examples/ricker.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -69,11 +69,11 @@
paramnames=c("r","sigma","phi"),
statenames=c("N","e"),
obsnames=c("y"),
- parameter.inv.transform=function(params,...) {
+ toEstimationScale=function(params,...) {
params[c("r","sigma","phi","N.0")] <- log(params[c("r","sigma","phi","N.0")])
params
},
- parameter.transform=function(params,...) {
+ fromEstimationScale=function(params,...) {
params[c("r","sigma","phi","N.0")] <- exp(params[c("r","sigma","phi","N.0")])
params
},
Modified: pkg/pomp/man/builder.Rd
===================================================================
--- pkg/pomp/man/builder.Rd 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/man/builder.Rd 2015-05-28 14:55:44 UTC (rev 1159)
@@ -12,7 +12,7 @@
rmeasure, dmeasure, step.fn, step.fn.delta.t,
skeleton, skeleton.type = c("map","vectorfield"),
skelmap.delta.t = 1,
- parameter.transform, parameter.inv.transform,
+ fromEstimationScale, toEstimationScale,
rprior, dprior, globals, \dots, save = FALSE)
}
\arguments{
@@ -44,10 +44,10 @@
As in \code{\link{pomp}}, \code{skeleton.type} indicates whether the skeleton is a map (discrete-time) or vectorfield (continuous-time).
If the former, \code{skelmap.delta.t} is the time-step of the map.
}
- \item{parameter.transform, parameter.inv.transform}{
+ \item{fromEstimationScale, toEstimationScale}{
optional C codes that implement parameter transformations.
- \code{parameter.transform} maps parameters from the estimation scale to the natural scale;
- \code{parameter.inv.transformation} maps them from the natural scale to the estimation scale.
+ \code{toEstimationScale} maps parameters from the model scale to the estimation scale.
+ \code{fromEstimationScale} maps them from the estimation scale to the model scale;
}
\item{rprior, dprior}{
C codes implementing the prior distribution
Modified: pkg/pomp/man/pomp-methods.Rd
===================================================================
--- pkg/pomp/man/pomp-methods.Rd 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/man/pomp-methods.Rd 2015-05-28 14:55:44 UTC (rev 1159)
@@ -47,7 +47,8 @@
\S4method{coef}{pomp}(object, pars, transform = FALSE, \dots)
\S4method{coef}{pomp}(object, pars, transform = FALSE, \dots) <- value
\S4method{obs}{pomp}(object, vars, \dots)
-\S4method{partrans}{pomp}(object, params, dir = c("forward","inverse"), \dots)
+\S4method{partrans}{pomp}(object, params, dir = c("fromEstimationScale",
+ "toEstimationScale","forward","inverse"), \dots)
\S4method{plot}{pomp}(x, y, variables, panel = lines,
nc = NULL, yax.flip = FALSE,
mar = c(0, 5.1, 0, if (yax.flip) 5.1 else 2.1),
Modified: pkg/pomp/man/pomp.Rd
===================================================================
--- pkg/pomp/man/pomp.Rd 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/man/pomp.Rd 2015-05-28 14:55:44 UTC (rev 1159)
@@ -24,24 +24,24 @@
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 1159
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