diff --git a/..Rcheck/00check.log b/..Rcheck/00check.log deleted file mode 100644 index 1dfc05e..0000000 --- a/..Rcheck/00check.log +++ /dev/null @@ -1,14 +0,0 @@ -* using log directory ‘/pkg/Documents/epizootic/..Rcheck’ -* using R version 4.4.1 (2024-06-14) -* using platform: x86_64-pc-linux-gnu -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.5 LTS -* using session charset: UTF-8 -* using option ‘--as-cran’ -* checking for file ‘./DESCRIPTION’ ... ERROR -Required fields missing or empty: - ‘Author’ ‘Maintainer’ -* DONE -Status: 1 ERROR diff --git a/..Rcheck/R_check_bin/R b/..Rcheck/R_check_bin/R deleted file mode 100755 index 3e289bc..0000000 --- a/..Rcheck/R_check_bin/R +++ /dev/null @@ -1,2 +0,0 @@ -echo "'R' should not be used without a path -- see par. 1.6 of the manual" -exit 1 diff --git a/..Rcheck/R_check_bin/Rscript b/..Rcheck/R_check_bin/Rscript deleted file mode 100755 index 6fead74..0000000 --- a/..Rcheck/R_check_bin/Rscript +++ /dev/null @@ -1,2 +0,0 @@ -echo "'Rscript' should not be used without a path -- see par. 1.6 of the manual" -exit 1 diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION new file mode 100644 index 0000000..33daa93 --- /dev/null +++ b/CRAN-SUBMISSION @@ -0,0 +1,3 @@ +Version: 1.0.0 +Date: 2024-09-27 18:22:56 UTC +SHA: a98f40c26e8a84234ef72202f2416410563a8869 diff --git a/DESCRIPTION b/DESCRIPTION index 35c4227..8261e91 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,12 +2,18 @@ Package: epizootic Title: Spatially Explicit Population Models of Disease Transmission in Wildlife Version: 1.0.0 Authors@R: c( - person("July", "Pilowsky", email = "pilowskyj@caryinstitute.org", role = c("aut", "cre"), + person("July", "Pilowsky", email = "pilowskyj@caryinstitute.org", + role = c("aut", "cre"), comment = c(ORCID = "https://orcid.org/0000-0002-6376-2585")), - person("National Science Foundation Biology Integration Institute 2213854", role = "fnd") + person("National Science Foundation Biology Integration Institute 2213854", + role = "fnd") ) -Description: This extension of the pattern-oriented modeling framework of the poems package - provides a collection of modules and functions customized for modeling disease transmission on a population scale in a spatiotemporally explicit manner. This includes seasonal time steps, dispersal functions that track disease state of dispersers, results objects that store disease states, and a population simulator that includes disease dynamics. +Description: This extension of the pattern-oriented modeling framework of the + 'poems' package provides a collection of modules and functions customized + for modeling disease transmission on a population scale in a spatiotemporally + explicit manner. This includes seasonal time steps, dispersal functions that + track disease state of dispersers, results objects that store disease states, + and a population simulator that includes disease dynamics. License: GPL (>= 3) Encoding: UTF-8 Roxygen: list(markdown = TRUE) diff --git a/README.Rmd b/README.Rmd index 654d7f5..a503872 100644 --- a/README.Rmd +++ b/README.Rmd @@ -17,15 +17,21 @@ knitr::opts_chunk$set( [![R-CMD-check](https://github.com/viralemergence/epizootic/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/viralemergence/epizootic/actions/workflows/R-CMD-check.yaml) -[![CRAN status](https://www.r-pkg.org/badges/version/paleopop)](https://CRAN.R-project.org/package=paleopop) -[![Download_count](https://cranlogs.r-pkg.org/badges/grand-total/paleopop)](https://CRAN.R-project.org/package=paleopop) -[![Last commit](https://img.shields.io/github/last-commit/GlobalEcologyLab/paleopop.svg)](https://github.com/GlobalEcologyLab/paleopop/commits/master) +[![CRAN status](https://www.r-pkg.org/badges/version/epizootic)](https://CRAN.R-project.org/package=epizootic) +[![Download_count](https://cranlogs.r-pkg.org/badges/grand-total/epizootic)](https://CRAN.R-project.org/package=epizootic) +[![Last commit](https://img.shields.io/github/last-commit/GlobalEcologyLab/epizootic.svg)](https://github.com/viralemergence/epizootic/commits/master) `epizootic` is an extension to `poems`, a spatially-explicit, process-explicit, pattern-oriented framework for modeling population dynamics. This extension adds functionality for modeling disease dynamics in wildlife. It also adds capability for seasonality and for unique dispersal dynamics for each life cycle stage. ## Installation +You can install the latest release on CRAN with: + +``` r +install.packages("epizootic") +``` + You can install the latest version of epizootic from [GitHub](https://github.com/) with: ``` r diff --git a/README.md b/README.md index ddc3265..819bf87 100644 --- a/README.md +++ b/README.md @@ -7,10 +7,10 @@ [![R-CMD-check](https://github.com/viralemergence/epizootic/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/viralemergence/epizootic/actions/workflows/R-CMD-check.yaml) [![CRAN -status](https://www.r-pkg.org/badges/version/paleopop)](https://CRAN.R-project.org/package=paleopop) -[![Download_count](https://cranlogs.r-pkg.org/badges/grand-total/paleopop)](https://CRAN.R-project.org/package=paleopop) +status](https://www.r-pkg.org/badges/version/epizootic)](https://CRAN.R-project.org/package=epizootic) +[![Download_count](https://cranlogs.r-pkg.org/badges/grand-total/epizootic)](https://CRAN.R-project.org/package=epizootic) [![Last -commit](https://img.shields.io/github/last-commit/GlobalEcologyLab/paleopop.svg)](https://github.com/GlobalEcologyLab/paleopop/commits/master) +commit](https://img.shields.io/github/last-commit/GlobalEcologyLab/epizootic.svg)](https://github.com/viralemergence/epizootic/commits/master) `epizootic` is an extension to `poems`, a spatially-explicit, @@ -21,6 +21,12 @@ unique dispersal dynamics for each life cycle stage. ## Installation +You can install the latest release on CRAN with: + +``` r +install.packages("epizootic") +``` + You can install the latest version of epizootic from [GitHub](https://github.com/) with: diff --git a/man/epizootic-package.Rd b/man/epizootic-package.Rd index 2904abe..9dcfdd1 100644 --- a/man/epizootic-package.Rd +++ b/man/epizootic-package.Rd @@ -6,7 +6,7 @@ \alias{epizootic-package} \title{epizootic: Spatially Explicit Population Models of Disease Transmission in Wildlife} \description{ -This extension of the pattern-oriented modeling framework of the poems package provides a collection of modules and functions customized for modeling disease transmission on a population scale in a spatiotemporally explicit manner. This includes seasonal time steps, dispersal functions that track disease state of dispersers, results objects that store disease states, and a population simulator that includes disease dynamics. +This extension of the pattern-oriented modeling framework of the 'poems' package provides a collection of modules and functions customized for modeling disease transmission on a population scale in a spatiotemporally explicit manner. This includes seasonal time steps, dispersal functions that track disease state of dispersers, results objects that store disease states, and a population simulator that includes disease dynamics. } \seealso{ Useful links: diff --git a/man/figures/README-disease_simulator-1.png b/man/figures/README-disease_simulator-1.png index ec28fea..2b40e42 100644 Binary files a/man/figures/README-disease_simulator-1.png and b/man/figures/README-disease_simulator-1.png differ diff --git a/man/figures/README-disease_simulator-2.png b/man/figures/README-disease_simulator-2.png index ba32beb..c42f28e 100644 Binary files a/man/figures/README-disease_simulator-2.png and b/man/figures/README-disease_simulator-2.png differ