update old documentation

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 6.1.0.0
-Date: 2025-01-08
+Version: 6.1.0.1
+Date: 2025-02-08
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="[email protected]",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/rprocess_spec.R

@@ -102,15 +102,14 @@
 ##'     rprocess = gillespie(rate.fun = f, v, hmax = Inf)
 ##' }
 ##' to \code{pomp}, where \code{f} gives the rates of the elementary events.
-##' Here, \code{f} may be an \R function of the form
-##' \preformatted{
-##'     f(j, x, t, params, ...)
-##' }
+##' Here, \code{f} may be furnished as an \R function or as a C snippet.
+##' If \code{f} is an \R function, its arguments should come from the state variables, parameters, covariates, and time.
+##' It must also have the arguments \sQuote{\code{j}} and \sQuote{\code{...}}.
 ##' When \code{f} is called,
-##' the integer \code{j} will be the number of the elementary event (corresponding to the column the matrix \code{v}, see below),
-##' \code{x} will be a named numeric vector containing the value of the state process at time \code{t} and
-##' \code{params} is a named numeric vector containing parameters.
+##' the integer \code{j} will indicate the elementary event (corresponding to the column the matrix \code{v}, see below).
 ##' \code{f} should return a single numerical value, representing the rate of that elementary event at that point in state space and time.
+##' If \code{f} is supplied as a C snippet, the parameters, latent state variables, covariates, and time will be visible in the context wherein the snippet is executed, as will the integer \sQuote{\code{j}}.
+##' The purpose of the C snippet is to fill the double-precision variable \sQuote{\code{rate}} with the corresponding event rate.
 ##'
 ##' Here, the stoichiometric matrix \code{v} specifies the continuous-time Markov process in terms of its elementary events.
 ##' It should have dimensions \code{nvar} x \code{nevent}, where \code{nvar} is the number of state variables and \code{nevent} is the number of elementary events.
@@ -119,9 +118,6 @@
 ##' The rows of \code{v} should have names corresponding to the state variables.
 ##' If any of the row names of \code{v} cannot be found among the state variables or if any row names of \code{v} are duplicated, an error will occur.
 ##'
-##' It is also possible to provide a C snippet via the \code{rate.fun} argument to \code{gillespie}.
-##' Such a snippet should assign the correct value to a \code{rate} variable depending on the value of \code{j}.
-##' The same variables will be available as for the C code provided to \code{gillespie_hl}.
 ##' This lower-level interface may be preferable if it is easier to write code that calculates the correct rate based on \code{j} rather than to write a snippet for each possible value of \code{j}.
 ##' For example, if the number of possible values of \code{j} is large and the rates vary according to a few simple rules, the lower-level interface may provide the easier way of specifying the model.
 ##'