From 941f160263428d7afefa44e9f63f455014cc55c2 Mon Sep 17 00:00:00 2001 From: "Aaron A. King" Date: Tue, 23 Jan 2024 09:36:16 -0500 Subject: [PATCH] update --- DESCRIPTION | 4 +- R/transformations.R | 7 +- README.md | 13 +- inst/doc/index.html | 412 ++++++++++++++++++++++++++++++++++++++++- inst/doc/index.md | 8 +- man/transformations.Rd | 7 +- 6 files changed, 428 insertions(+), 23 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index c98fb6cab..696d91188 100644 --- a/DESCRIPTION +++ b/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="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/transformations.R b/R/transformations.R index c51be1a1d..15373d044 100644 --- a/R/transformations.R +++ b/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{ diff --git a/README.md b/README.md index 3b1b0181b..cd743c9a6 100644 --- a/README.md +++ b/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/). diff --git a/inst/doc/index.html b/inst/doc/index.html index 6b856ee70..b488733e8 100644 --- a/inst/doc/index.html +++ b/inst/doc/index.html @@ -1,3 +1,365 @@ + + + + + + + + + + + + + +pomp + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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