update

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 5.5.2.1
-Date: 2024-01-22
+Version: 5.5.2.2
+Date: 2024-01-23
 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/transformations.R

@@ -42,8 +42,9 @@ expit <- function (x) {
 ##' @param X numeric; a vector containing the quantities to be transformed according to the log-barycentric transformation.
 ##'
 ##' @details
-##' The log-barycentric transformation takes a vector \eqn{X_i}{Xi}, \eqn{i=1,\dots,n}, to a vector \eqn{Y_i}{Yi}, where \deqn{Y_i = \log\frac{X_i}{\sum_j X_j}.}{Yi = log(Xi/sum(Xj)).}
-##' If \eqn{X} is an \eqn{n}-vector, it takes every simplex defined by \eqn{\sum_i X_i = c}{sum(Xi)=c}, \eqn{c} constant, to n-dimensional Euclidean space \eqn{R^n}{R^n}.
+##' The log-barycentric transformation takes a vector \eqn{X\in{R^{n}_+}}{X in the non-negative cone of R^n}, to a vector \eqn{Y\in{R^n}}{Y in R^n}, where \deqn{Y_i = \log\frac{X_i}{\sum_j X_j}.}{Yi = log(Xi/sum(X)).}
+##' The transformation is not one-to-one.
+##' However, for each \eqn{c>0}, it maps the simplex \eqn{\{X\in{R^n_+}:\sum_i X_i = c\}}{sum(X)=c} bijectively onto \eqn{n}-dimensional Euclidean space \eqn{R^n}.
 ##'
 log_barycentric <- function (X) {
   .Call(P_LogBarycentricTransform,X)
@@ -56,7 +57,7 @@ log_barycentric <- function (X) {
 ##'
 ##' @details
 ##' The inverse of the log-barycentric transformation is implemented as \code{inv_log_barycentric}.
-##' Note that it is not a true inverse, in the sense that it takes \eqn{R^n} to the \emph{unit} simplex, \eqn{\sum_i X_i = 1}{sum(Xi)=1}.
+##' Note that it is not a true inverse, in the sense that it takes \eqn{R^n} to the \emph{unit} simplex, \eqn{\{X\in{R^n_+}:\sum_i X_i = 1\}}{sum(X)=1}.
 ##' Thus, \preformatted{
 ##'     log_barycentric(inv_log_barycentric(Y)) == Y,
 ##' } but \preformatted{

README.md

@@ -4,17 +4,18 @@
 
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![Development Release](https://img.shields.io/github/release/kingaa/pomp.svg)](https://github.com/kingaa/pomp/releases/latest)
-[![CRAN Status](https://www.r-pkg.org/badges/version/pomp)](https://cran.r-project.org/package=pomp)
-[![Last CRAN release date](https://www.r-pkg.org/badges/last-release/pomp)](https://cran.r-project.org/package=pomp)
+[![CRAN Status](https://www.r-pkg.org/badges/version/pomp?color=blue)](https://cran.r-project.org/package=pomp)
+[![Last CRAN release date](https://www.r-pkg.org/badges/last-release/pomp?color=blue)](https://cran.r-project.org/package=pomp)
 [![R-CMD-check](https://github.com/kingaa/pomp/actions/workflows/r-cmd-check.yml/badge.svg)](https://github.com/kingaa/pomp/actions/workflows/r-cmd-check.yml)
 [![binary-build](https://github.com/kingaa/pomp/actions/workflows/binary-build.yml/badge.svg)](https://github.com/kingaa/pomp/actions/workflows/binary-build.yml)
 [![test-coverage](https://github.com/kingaa/pomp/actions/workflows/test-coverage.yml/badge.svg)](https://github.com/kingaa/pomp/actions/workflows/test-coverage.yml)
 [![codecov](https://codecov.io/gh/kingaa/pomp/branch/master/graph/badge.svg)](https://app.codecov.io/gh/kingaa/pomp)
-![CRAN mirror monthly downloads](https://cranlogs.r-pkg.org/badges/last-month/pomp)
-![CRAN mirror total downloads](https://cranlogs.r-pkg.org/badges/grand-total/pomp)
+![CRAN mirror monthly downloads](https://cranlogs.r-pkg.org/badges/last-month/pomp?color=yellow)
+![CRAN mirror total downloads](https://cranlogs.r-pkg.org/badges/grand-total/pomp?color=yellow)
 [![Dependencies](https://tinyverse.netlify.app/badge/pomp)](https://tinyverse.netlify.app/)
-[![manual](https://img.shields.io/badge/manual-HTML-informational)](https://kingaa.github.io/pomp/manual/)
-[![pdf-manual](https://img.shields.io/badge/manual-PDF-informational)](https://kingaa.github.io/pomp/manual/pdf/)
+[![manual](https://img.shields.io/badge/manual-HTML-brown)](https://kingaa.github.io/pomp/manual/)
+[![pdf-manual](https://img.shields.io/badge/manual-PDF-brown)](https://kingaa.github.io/pomp/manual/pdf/)
+[![doxygen](https://img.shields.io/badge/doxygen-HTML-brown)](https://kingaa.github.io/manuals/pomp/source/html/index.html)
 
 For installation instructions and user guides, see [the package website](https://kingaa.github.io/pomp/).
 

inst/doc/index.md

@@ -124,10 +124,6 @@ dt {
 
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