diff --git a/.Rbuildignore b/.Rbuildignore index 9d504068..5f9a099f 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -12,6 +12,7 @@ ^www ^yaml ^Makefile +^TAGS ^rules.mk ^tests/Makefile ^tests/(.+?)\.png$ diff --git a/.gitignore b/.gitignore index 3cacef97..d43e420e 100644 --- a/.gitignore +++ b/.gitignore @@ -20,6 +20,7 @@ rchk\.out *.gcno *.pdf *.sif +/TAGS /scripts check lib diff --git a/DESCRIPTION b/DESCRIPTION index 5a08626a..babcddf7 100644 --- a/DESCRIPTION +++ b/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="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")), diff --git a/R/kalman.R b/R/kalman.R index 5cd4866b..42269264 100644 --- a/R/kalman.R +++ b/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) diff --git a/R/probe_match.R b/R/probe_match.R index 1e10248a..9e4cb6a6 100644 --- a/R/probe_match.R +++ b/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. @@ -26,10 +31,8 @@ ##' 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. @@ -37,11 +40,9 @@ ##' 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"),...) } ) - diff --git a/man/macros/citations.Rd b/man/macros/citations.Rd index d436e3f7..bbd4ddb8 100644 --- a/man/macros/citations.Rd +++ b/man/macros/citations.Rd @@ -2,82 +2,82 @@ \newcommand{\Akinshin2023}{A. Akinshin. Weighted quantile estimators. arXiv:2304.07265, 2023. \doi{10.48550/arxiv.2304.07265}.} -\newcommand{\Anderson2001}{J.L. Anderson. An ensemble adjustment Kalman filter for data assimilation. \emph{Monthly Weather Review} \bold{129}, 2884--2903, 2001.} +\newcommand{\Anderson2001}{J.L. Anderson. An ensemble adjustment Kalman filter for data assimilation. \emph{Monthly Weather Review} \bold{129}, 2884--2903, 2001. \doi{10.1175/1520-0493(2001)129<2884:AEAKFF>2.0.CO;2}.} -\newcommand{\Andrieu2009}{C. Andrieu and G.O. Roberts. 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