update NEWS; catch a few stragglers

Author: kingaa

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 6.0.2.0
-Date: 2024-12-12
+Version: 6.0.2.2
+Date: 2024-12-15
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa@umich.edu",comment=c(ORCID="0000-0001-6159-3207")),
 	  person(given=c("Edward","L."),family="Ionides",role="aut",comment=c(ORCID="0000-0002-4190-0174"))	,
 	  person(given="Carles",family="Bretó",role="aut",comment=c(ORCID="0000-0003-4695-4902")),

R/objfun.R

@@ -100,7 +100,7 @@ setMethod(
 setMethod(
   "simulate",
   signature=signature(object="objfun"),
-  definition=function (object, seed = NULL, ...) {
+  definition=function (object, seed = NULL,...) {
     simulate(as(object,"pomp"),seed=seed,...)
   }
 )
@@ -110,7 +110,7 @@ setMethod(
 setMethod(
   "probe",
   signature=signature(data="objfun"),
-  definition=function (data, seed = NULL, ...) {
+  definition=function (data, ..., seed = NULL) {
     probe(as(data,"pomp"),seed=seed,...)
   }
 )
@@ -130,7 +130,7 @@ setMethod(
 setMethod(
   "spect",
   signature=signature(data="objfun"),
-  definition=function (data, seed = NULL, ...) {
+  definition=function (data, ..., seed = NULL) {
     spect(as(data,"pomp"),seed=seed,...)
   }
 )
@@ -143,7 +143,8 @@ setMethod(
   definition = function (object, ...) {
     object@env$.gnsi <- TRUE
     pompLoad_internal(object@env$object,...)
-  })
+  }
+)
 
 ##' @rdname load
 ##' @export
@@ -153,4 +154,5 @@ setMethod(
   definition = function (object, ...) {
     object@env$.gnsi <- TRUE
     pompUnload_internal(object@env$object,...)
-  })
+  }
+)

R/pfilter.R

@@ -125,8 +125,8 @@ setMethod(
   signature=signature(data="data.frame"),
   definition=function (
     data,
-    Np,
     ...,
+    Np,
     params, rinit, rprocess, dmeasure,
     pred.mean = FALSE,
     pred.var = FALSE,
@@ -201,8 +201,9 @@ setMethod(
   "pfilter",
   signature=signature(data="pfilterd_pomp"),
   function (
-    data, Np,
+    data,
     ...,
+    Np,
     verbose = getOption("verbose", FALSE)
   ) {
 
@@ -214,8 +215,7 @@ setMethod(
 )
 
 pfilter_internal <- function (
-  object, Np,
-  ...,
+  object, ..., Np,
   pred.mean = FALSE, pred.var = FALSE, filter.mean = FALSE,
   filter.traj = FALSE, cooling, cooling.m,
   save.states = c("no", "filter", "prediction",

R/pmcmc.R

@@ -222,7 +222,11 @@ setMethod(
 setMethod(
   "continue",
   signature=signature(object="pmcmcd_pomp"),
-  function (object, Nmcmc = 1, ...) {
+  function (
+    object,
+    ...,
+    Nmcmc = 1
+  ) {
 
     ndone <- object@Nmcmc
     accepts <- object@accepts

R/wpfilter.R

@@ -83,8 +83,8 @@ setMethod(
   signature=signature(data="data.frame"),
   definition=function (
     data,
-    Np,
     ...,
+    Np,
     params, rinit, rprocess, dmeasure,
     trigger = 1, target = 0.5,
     verbose = getOption("verbose", FALSE)
@@ -116,8 +116,8 @@ setMethod(
   signature=signature(data="pomp"),
   definition=function (
     data,
-    Np,
     ...,
+    Np,
     trigger = 1, target = 0.5,
     verbose = getOption("verbose", FALSE)
   ) {

inst/NEWS

@@ -1,5 +1,10 @@
 _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 _6._0._2:
+
+        • The ‘save.states’ option to ‘pfilter’ has changed.  See
+          ‘?pfilter’ and ‘?saved_states’ for details.
+
 _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _6._0._1:
 
         • In calls to ‘pomp’ elementary and inference algorithms, it is

inst/NEWS.Rd

@@ -1,5 +1,11 @@
 \name{NEWS}
 \title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 6.0.2}{
+  \itemize{
+    \item The \code{save.states} option to \code{pfilter} has changed.
+    See \code{?pfilter} and \code{?saved_states} for details.
+  }
+}
 \section{Changes in \pkg{pomp} version 6.0.1}{
   \itemize{
     \item In calls to \pkg{pomp} elementary and inference algorithms, it is now necessary to pass all arguments by name.