diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index 2c662d9..0ee4bc6 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ -Version: 1.3.0 -Date: 2024-04-11 17:53:24 UTC -SHA: e0de3245e3f28c28c53d86beb987e03ca1a19f4a +Version: 1.3.1 +Date: 2024-09-19 16:57:12 UTC +SHA: e1ec880c397dcaaffc861be9dfe2996f1e3741c9 diff --git a/README.Rmd b/README.Rmd index b22e7d9..3bfb6d4 100644 --- a/README.Rmd +++ b/README.Rmd @@ -57,12 +57,23 @@ model simulators by utilizing its extendable (inheritable) base classes. ## Installation -You can install poems from [GitHub](https://github.com/) using: +You can install poems from the CRAN repository: + +``` r +install.packages("poems") +``` + +Or you can install the development version of poems from [GitHub](https://github.com/) using: ``` r # install.packages("devtools") remotes::install_github("GlobalEcologyLab/poems") ``` + +## The poemsverse + +`poems` can do spatial population models on its own, but it also provides the engine behind two extension packages: [paleopop](https://github.com/GlobalEcologyLab/paleopop) and [epizootic](https://github.com/viralemergence/epizootic). `paleopop` is an extension for simulating populations over very long timescales, and `epizootic` is an extension for simulating disease dynamics in wild populations. + ## Example The following simple example demonstrates how to run a single spatially explicit diff --git a/README.md b/README.md index 1d75b90..f564fc2 100644 --- a/README.md +++ b/README.md @@ -56,13 +56,30 @@ base classes. ## Installation -You can install poems from [GitHub](https://github.com/) using: +You can install poems from the CRAN repository: + +``` r +install.packages("poems") +``` + +Or you can install the development version of poems from +[GitHub](https://github.com/) using: ``` r # install.packages("devtools") remotes::install_github("GlobalEcologyLab/poems") ``` +## The poemsverse + +`poems` can do spatial population models on its own, but it also +provides the engine behind two extension packages: +[paleopop](https://github.com/GlobalEcologyLab/paleopop) and +[epizootic](https://github.com/viralemergence/epizootic). `paleopop` is +an extension for simulating populations over very long timescales, and +`epizootic` is an extension for simulating disease dynamics in wild +populations. + ## Example The following simple example demonstrates how to run a single spatially @@ -111,47 +128,47 @@ results <- population_simulator(pop_model) results # examine #> $all #> $all$abundance -#> [1] 977 1090 1238 1256 1341 +#> [1] 1010 1077 1229 1288 1405 #> #> $all$abundance_stages #> $all$abundance_stages[[1]] -#> [1] 574 643 755 731 847 +#> [1] 604 615 761 744 841 #> #> $all$abundance_stages[[2]] -#> [1] 403 447 483 525 494 +#> [1] 406 462 468 544 564 #> #> #> #> $abundance #> [,1] [,2] [,3] [,4] [,5] -#> [1,] 59 134 157 147 173 -#> [2,] 90 102 157 169 197 -#> [3,] 133 156 192 202 191 -#> [4,] 168 149 154 180 168 -#> [5,] 163 180 178 193 192 -#> [6,] 171 181 192 189 219 -#> [7,] 193 188 208 176 201 +#> [1,] 50 91 143 174 204 +#> [2,] 91 139 167 190 204 +#> [3,] 126 136 162 201 196 +#> [4,] 161 159 175 195 193 +#> [5,] 185 181 182 170 202 +#> [6,] 195 189 195 174 198 +#> [7,] 202 182 205 184 208 #> #> $abundance_stages #> $abundance_stages[[1]] #> [,1] [,2] [,3] [,4] [,5] -#> [1,] 28 76 100 83 108 -#> [2,] 55 56 103 94 133 -#> [3,] 83 91 108 121 115 -#> [4,] 101 96 82 129 86 -#> [5,] 95 109 113 102 141 -#> [6,] 103 105 115 93 132 -#> [7,] 109 110 134 109 132 +#> [1,] 33 54 90 107 134 +#> [2,] 56 83 100 113 126 +#> [3,] 64 79 98 111 103 +#> [4,] 102 82 110 115 114 +#> [5,] 100 113 109 103 118 +#> [6,] 125 107 118 88 126 +#> [7,] 124 97 136 107 120 #> #> $abundance_stages[[2]] #> [,1] [,2] [,3] [,4] [,5] -#> [1,] 31 58 57 64 65 -#> [2,] 35 46 54 75 64 -#> [3,] 50 65 84 81 76 -#> [4,] 67 53 72 51 82 -#> [5,] 68 71 65 91 51 -#> [6,] 68 76 77 96 87 -#> [7,] 84 78 74 67 69 +#> [1,] 17 37 53 67 70 +#> [2,] 35 56 67 77 78 +#> [3,] 62 57 64 90 93 +#> [4,] 59 77 65 80 79 +#> [5,] 85 68 73 67 84 +#> [6,] 70 82 77 86 72 +#> [7,] 78 85 69 77 88 raster::plot(region$raster_from_values(results$abundance[, 5]), main = "Final abundance", xlab = "Longitude (degrees)", ylab = "Latitude (degrees)", zlim = c(0, 300), colNA = "blue" diff --git a/man/figures/README-example-2.png b/man/figures/README-example-2.png index 274f76c..e33636c 100644 Binary files a/man/figures/README-example-2.png and b/man/figures/README-example-2.png differ