Minor modifications to get into CRAN

panelPomp-org · Sep 12, 2024 · cdf4c47 · cdf4c47
2 parents 66dd6c7 + a1c09ee
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -39,3 +39,7 @@ check
 ^(.+?)\.tar\.gz
 ^(.+?)\.tgz
 ^(.+?)\.zip
+^revdep$
+^cran-comments\.md$
+^CRAN-SUBMISSION$
+^\.github$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,6 @@ Package: panelPomp
 Type: Package
 Title: Inference for Panel Partially Observed Markov Processes
 Version: 1.4.0.0
-Date: 2023-09-04
 Authors@R: c(person(given="Carles",family="Breto",role="aut",email="[email protected]",comment=c(ORCID="0000-0003-4695-4902")),
 	person(given=c("Edward","L."),family="Ionides",role="aut",comment=c(ORCID="0000-0002-4190-0174")),
 	person(given=c("Aaron","A."),family="King",role="aut",comment=c(ORCID="0000-0001-6159-3207")),

diff --git a/README.md b/README.md
@@ -4,14 +4,11 @@
 
 ### an *R* package for inference on panel partially observed Markov processes
 
-[![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)
-[![CRAN Status](https://www.r-pkg.org/badges/version/panelPomp)](https://cran.r-project.org/package=panelPomp)
-[![Last CRAN release date](https://www.r-pkg.org/badges/last-release/panelPomp)](https://cran.r-project.org/package=panelPomp)
-[![R-CMD-check](https://github.com/cbreto/panelPomp/actions/workflows/r-cmd-check.yml/badge.svg)](https://github.com/cbreto/panelPomp/actions/workflows/r-cmd-check.yml) [![binary-build](https://github.com/cbreto/panelPomp/actions/workflows/binary-build.yml/badge.svg)](https://github.com/cbreto/panelPomp/actions/workflows/binary-build.yml) [![test-coverage](https://github.com/cbreto/panelPomp/actions/workflows/test-coverage.yml/badge.svg)](https://github.com/cbreto/panelPomp/actions/workflows/test-coverage.yml) [![codecov](https://codecov.io/gh/cbreto/panelPomp/branch/master/graph/badge.svg?token=1vT9TJfHGP)](https://app.codecov.io/gh/cbreto/panelPomp)
+[![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) [![CRAN Status](https://www.r-pkg.org/badges/version/panelPomp)](https://cran.r-project.org/package=panelPomp) [![Last CRAN release date](https://www.r-pkg.org/badges/last-release/panelPomp)](https://cran.r-project.org/package=panelPomp) [![R-CMD-check](https://github.com/panelPomp-org/panelPomp/actions/workflows/r-cmd-check.yml/badge.svg)](https://github.com/panelPomp-org/panelPomp/actions/workflows/r-cmd-check.yml) [![binary-build](https://github.com/panelPomp-org/panelPomp/actions/workflows/binary-build.yml/badge.svg)](https://github.com/panelPomp-org/panelPomp/actions/workflows/binary-build.yml) [![test-coverage](https://github.com/panelPomp-org/panelPomp/actions/workflows/test-coverage.yml/badge.svg)](https://github.com/panelPomp-org/panelPomp/actions/workflows/test-coverage.yml)
 
 This package allows performing data analysis based on panel partially-observed Markov process (PanelPOMP) models. To implement such models, simulate them and fit them to panel data, 'panelPomp' extends some of the facilities provided for time series data by the 'pomp' package. Implemented methods include filtering (panel particle filtering) and maximum likelihood estimation (Panel Iterated Filtering) as proposed in Bretó, Ionides and King (2020) "Panel Data Analysis via Mechanistic Models" [\<doi:10.1080/01621459.2019.1604367\>](https://doi.org/10.1080/01621459.2019.1604367).
 
-The latest version of the package can be installed from this GitHub source using `devtools::install_github('cbreto/panelPomp')`
+The latest version of the package can be installed from this GitHub source using `devtools::install_github('panelPomp-org/panelPomp')`
 
 Installing the current CRAN version is also possible using `install.packages("panelPomp")`
 

diff --git a/inst/NEWS b/inst/NEWS
@@ -1,4 +1,4 @@
-_N_e_w_s _f_o_r _p_a_c_k_a_g_e '_p_a_n_e_l_P_o_m_p'
+_N_e_w_s _f_o_r _t_h_e '_p_a_n_e_l_P_o_m_p' _p_a_c_k_a_g_e
 
 _C_h_a_n_g_e_s _i_n '_p_a_n_e_l_P_o_m_p' _v_e_r_s_i_o_n _1._4._0._0:
 

diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
@@ -1,5 +1,5 @@
 \name{NEWS}
-\title{News for package `panelPomp'}
+\title{News for the \pkg{panelPomp} package}
 \section{Changes in \pkg{panelPomp} version 1.4.0.0}{
   \itemize{
     \item Changed package maintainers

diff --git a/revdep/.gitignore b/revdep/.gitignore
@@ -2,3 +2,5 @@
 *.Rcheck
 Library/
 PACKAGES*
+library.noindex/
+checks.noindex/
diff --git a/revdep/README.md b/revdep/README.md
@@ -0,0 +1,27 @@
+# Platform
+
+|field    |value                                    |
+|:--------|:----------------------------------------|
+|version  |R version 4.4.1 (2024-06-14)             |
+|os       |macOS Sonoma 14.6.1                      |
+|system   |x86_64, darwin20                         |
+|ui       |RStudio                                  |
+|language |(EN)                                     |
+|collate  |en_US.UTF-8                              |
+|ctype    |en_US.UTF-8                              |
+|tz       |America/Detroit                          |
+|date     |2024-09-06                               |
+|rstudio  |2024.04.2+764 Chocolate Cosmos (desktop) |
+|pandoc   |3.1.5 @ /usr/local/bin/pandoc            |
+
+# Dependencies
+
+|package    | old|new     |Δ  |
+|:----------|---:|:-------|:--|
+|panelPomp  | 1.1|1.4.0.0 |*  |
+|data.table |  NA|1.16.0  |*  |
+|digest     |  NA|0.6.37  |*  |
+|mvtnorm    |  NA|1.3-1   |*  |
+
+# Revdeps
+
diff --git a/revdep/cran.md b/revdep/cran.md
@@ -0,0 +1,7 @@
+## revdepcheck results
+
+We checked 0 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 0 new problems
+ * We failed to check 0 packages
+
diff --git a/revdep/failures.md b/revdep/failures.md
@@ -0,0 +1 @@
+*Wow, no problems at all. :)*
diff --git a/revdep/problems.md b/revdep/problems.md
@@ -0,0 +1 @@
+*Wow, no problems at all. :)*
diff --git a/vignettes/getting-started.Rmd b/vignettes/getting-started.Rmd
@@ -36,7 +36,7 @@ Panel data arise when time series are measured on a collection of units.
 When the time series for each unit is modeled as a partially observed Markov process (POMP) the collection of these models is a PanelPOMP.
 The `panelPomp` package provides facilities for inference on panel data using PanelPOMP models. 
 Monte Carlo methods used for POMP models require adaptation for PanelPOMP models due to the higher dimensionality of panel data.
-This package builds on the functionality and tools of the popular [`pomp` R package](kingaa.github.io/pomp), providing a computationally efficient framework that can be used to simulate from, fit, and diagnose PanelPOMP models. 
+This package builds on the functionality and tools of the popular [`pomp` R package](https://kingaa.github.io/pomp/), providing a computationally efficient framework that can be used to simulate from, fit, and diagnose PanelPOMP models. 
 As such, a basic working knowledge of the `pomp` package is recommended. 
 Here we cover some of the necessary basics. 
 See [Getting Started With `pomp`](https://kingaa.github.io/pomp/vignettes/getting_started.html) for an introductory Vignette to the `pomp` package.