documentation improvement

Author: kingaa

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 5.11.0.0
-Date: 2024-09-11
+Version: 5.11.0.1
+Date: 2024-10-04
 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/accumulators.R

@@ -6,13 +6,13 @@
 ##' @rdname accumvars
 ##' @family implementation information
 ##' @seealso \code{\link{sir}}
-##'
 ##' @details
 ##' In formulating models, one sometimes wishes to define a state variable that will accumulate some quantity over the interval between successive observations.
 ##' \pkg{pomp} provides a facility to make such features more convenient.
-##' Specifically, variables named in the \code{pomp}'s \code{accumvars} argument will be set to zero immediately following each observation.
-##' See \code{\link{sir}} and the tutorials on the \href{https://kingaa.github.io/pomp/}{package website} for examples.
-##'
+##' Specifically, if \eqn{a} is a state-variable named in the \code{pomp}'s \code{accumvars} argument, then for each interval \eqn{(t_k,t_{k+1})}{(t[k],t[k+1])}, \eqn{k=0,1,2,\dots}, \eqn{a} will be set to zero at prior to any \code{\link{rprocess}} computation over that interval.
+##' Deterministic trajectory computation is handled slightly differently:
+##' see \code{\link{flow}}.
+##' For examples, see \code{\link{sir}} and the tutorials on the \href{https://kingaa.github.io/pomp/}{package website}.
 ##' @example examples/accumulators.R
 ##'
 NULL

R/flow.R

@@ -29,7 +29,11 @@
 ##' @return
 ##' \code{flow} returns an array of dimensions \code{nvar} x \code{nrep} x \code{ntimes}.
 ##' If \code{x} is the returned matrix, \code{x[i,j,k]} is the i-th component of the state vector at time \code{times[k]} given parameters \code{params[,j]}.
-##'
+##' @section Accumulator variables:
+##' When there are accumulator variables (as determined by the \code{\link{accumvars}} argument), their handling in the continuous-time (vectorfield) case differs from that in the discrete-time (map) case.
+##' In the latter, accumulator variables are set to zero at the beginning of each interval \eqn{(t_k,t_{k+1})}{(t[k],t[k+1])}, \eqn{k=0,1,2,\dots} over which flow computation is required.
+##' In the former, the flow computation proceeds over the entire set of intervals required, and accumulator variables are then differenced.
+##' That is, the value \eqn{a_k}{a[k]} of accumulator variable \eqn{a} at times \eqn{t_k}{t[k]}, \eqn{k=1,2,\dots} will be \eqn{A_k-A_{k-1}}{A[k]-A[k-1]}, where \eqn{A_k}{A[k]} is the solution of the corresponding differential equation at \eqn{t_k}{t[k]}.
 NULL
 
 setGeneric(

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 _5._1_1._1:
+
+        • The help-page discussion of accumulator variables has been
+          expanded and clarified.
+
 _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _5._1_0._1:
 
         • An improper typecast in the C snippet system, which was

inst/NEWS.Rd

@@ -1,5 +1,10 @@
 \name{NEWS}
 \title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 5.11.1}{
+  \itemize{
+    \item The help-page discussion of accumulator variables has been expanded and clarified.
+  }
+}
 \section{Changes in \pkg{pomp} version 5.10.1}{
   \itemize{
     \item An improper typecast in the C snippet system, which was resolvable by many compilers but threw an error under recent versions of \pkg{clang} on MacOS, has been repaired.