include DOI for references

.Rbuildignore

@@ -12,6 +12,7 @@
 ^www
 ^yaml
 ^Makefile
+^TAGS
 ^rules.mk
 ^tests/Makefile
 ^tests/(.+?)\.png$

.gitignore

@@ -20,6 +20,7 @@ rchk\.out
 *.gcno
 *.pdf
 *.sif
+/TAGS
 /scripts
 check
 lib

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 5.10.0.0
-Date: 2024-07-01
+Version: 5.10.0.1
+Date: 2024-07-02
 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/kalman.R

@@ -17,7 +17,6 @@
 ##' @inheritParams pfilter
 ##' @inheritParams pomp
 ##' @param Np integer; the number of particles to use, i.e., the size of the ensemble.
-##' 
 ##' @return
 ##' An object of class \sQuote{kalmand_pomp}.
 ##' @references
@@ -186,7 +185,7 @@ enkf_internal <- function (object, Np, ..., verbose) {
   Np <- as.integer(Np)
   if (length(Np)>1 || !is.finite(Np) || isTRUE(Np<=0))
     pStop_(sQuote("Np")," should be a single positive integer.")
-  
+
   params <- coef(object)
 
   t <- time(object)
@@ -213,7 +212,7 @@ enkf_internal <- function (object, Np, ..., verbose) {
     ## advance ensemble according to state process
     X <- rprocess(object,x0=X,t0=tt[k],times=tt[k+1],params=params,.gnsi=first)
     rn <- rownames(X)
-    
+
     predMeans[,k] <- pm <- rowMeans(X) # prediction mean
     Y <- emeasure(object,x=X,times=tt[k+1],params=params,.gnsi=first)
     ym <- rowMeans(Y)                  # forecast mean
@@ -236,7 +235,7 @@ enkf_internal <- function (object, Np, ..., verbose) {
 
     dn <- dim(R)[c(1L,2L)]
     dim(R) <- dn
-    
+
     sqrtR <- tryCatch(
       t(chol(R)), ## t(sqrtR)%*%sqrtR == R
       error = function (e) {
@@ -380,7 +379,7 @@ eakf_internal <- function (object, Np, ..., verbose) {
   Np <- as.integer(Np)
   if (length(Np)>1 || !is.finite(Np) || isTRUE(Np<=0))
     pStop_(sQuote("Np")," should be a single positive integer.")
-  
+
   params <- coef(object)
 
   t <- time(object)

R/probe_match.R

@@ -16,8 +16,13 @@
 ##' @family summary statistic-based methods
 ##' @family estimation methods
 ##' @family methods based on maximization
-##' @seealso \code{\link[stats]{optim}} \code{\link[subplex]{subplex}} \code{\link[nloptr]{nloptr}}
+##' @references
+##'
+##' \Kendall1999
 ##'
+##' \Wood2010
+##'
+##' @seealso \code{\link[stats]{optim}} \code{\link[subplex]{subplex}} \code{\link[nloptr]{nloptr}}
 ##' @param est character vector; the names of parameters to be estimated.
 ##' @param fail.value optional numeric scalar;
 ##' if non-\code{NA}, this value is substituted for non-finite values of the objective function.
@@ -26,22 +31,18 @@
 ##' When fitting, it is often best to fix the seed of the random-number generator (RNG).
 ##' This is accomplished by setting \code{seed} to an integer.
 ##' By default, \code{seed = NULL}, which does not alter the RNG state.
-##' 
 ##' @inheritParams probe
 ##' @inheritParams pomp
-##'
 ##' @return
 ##' \code{probe_objfun} constructs a stateful objective function for probe matching.
 ##' Specifically, \code{probe_objfun} returns an object of class \sQuote{probe_match_objfun}, which is a function suitable for use in an \code{\link[stats]{optim}}-like optimizer.
 ##' In particular, this function takes a single numeric-vector argument that is assumed to contain the parameters named in \code{est}, in that order.
 ##' When called, it will return the negative synthetic log likelihood for the probes specified.
 ##' It is a stateful function:
 ##' Each time it is called, it will remember the values of the parameters and its estimate of the synthetic likelihood.
-##'
 ##' @inheritSection pomp Note for Windows users
 ##' @inheritSection objfun Important Note
 ##' @inheritSection objfun Warning! Objective functions based on C snippets
-##'
 ##' @example examples/probe_match.R
 ##'
 NULL
@@ -293,4 +294,3 @@ setMethod(
     plot(as(x,"probed_pomp"),...)
   }
 )
-