diff --git a/.gitignore b/.gitignore index 20a167d..65d3394 100644 --- a/.gitignore +++ b/.gitignore @@ -28,3 +28,5 @@ wc10 ## the buffers from article vignettes/articles/buffer_res Meta +/doc/ +/Meta/ diff --git a/docs/articles/buffer_and_randomPoints_files/figure-html/bufferdistance-1.png b/docs/articles/buffer_and_randomPoints_files/figure-html/bufferdistance-1.png index 44eae2b..d3b23d5 100644 Binary files a/docs/articles/buffer_and_randomPoints_files/figure-html/bufferdistance-1.png and b/docs/articles/buffer_and_randomPoints_files/figure-html/bufferdistance-1.png differ diff --git a/docs/articles/buffer_and_randomPoints_files/figure-html/buffermax-1.png b/docs/articles/buffer_and_randomPoints_files/figure-html/buffermax-1.png index 657c382..b580932 100644 Binary files a/docs/articles/buffer_and_randomPoints_files/figure-html/buffermax-1.png and b/docs/articles/buffer_and_randomPoints_files/figure-html/buffermax-1.png differ diff --git a/docs/articles/buffer_and_randomPoints_files/figure-html/buffermean-1.png b/docs/articles/buffer_and_randomPoints_files/figure-html/buffermean-1.png index 4eaca46..b6d686c 100644 Binary files a/docs/articles/buffer_and_randomPoints_files/figure-html/buffermean-1.png and b/docs/articles/buffer_and_randomPoints_files/figure-html/buffermean-1.png differ diff --git a/docs/articles/buffer_and_randomPoints_files/figure-html/buffermedian-1.png b/docs/articles/buffer_and_randomPoints_files/figure-html/buffermedian-1.png index 252764e..db14579 100644 Binary files a/docs/articles/buffer_and_randomPoints_files/figure-html/buffermedian-1.png and b/docs/articles/buffer_and_randomPoints_files/figure-html/buffermedian-1.png differ diff --git a/docs/articles/buffer_and_randomPoints_files/figure-html/centroid-1.png b/docs/articles/buffer_and_randomPoints_files/figure-html/centroid-1.png index 0f54671..1a44e22 100644 Binary files a/docs/articles/buffer_and_randomPoints_files/figure-html/centroid-1.png and b/docs/articles/buffer_and_randomPoints_files/figure-html/centroid-1.png differ diff --git a/docs/articles/buffer_and_randomPoints_files/figure-html/geog-1.png b/docs/articles/buffer_and_randomPoints_files/figure-html/geog-1.png index 1856b23..c3faa23 100644 Binary files a/docs/articles/buffer_and_randomPoints_files/figure-html/geog-1.png and b/docs/articles/buffer_and_randomPoints_files/figure-html/geog-1.png differ diff --git a/docs/articles/buffer_and_randomPoints_files/figure-html/max_env-1.png b/docs/articles/buffer_and_randomPoints_files/figure-html/max_env-1.png index ba026d9..4eadc6b 100644 Binary files a/docs/articles/buffer_and_randomPoints_files/figure-html/max_env-1.png and b/docs/articles/buffer_and_randomPoints_files/figure-html/max_env-1.png differ diff --git a/docs/articles/buffer_and_randomPoints_files/figure-html/plotdataset-1.png b/docs/articles/buffer_and_randomPoints_files/figure-html/plotdataset-1.png index f8a8f2b..f5fa423 100644 Binary files a/docs/articles/buffer_and_randomPoints_files/figure-html/plotdataset-1.png and b/docs/articles/buffer_and_randomPoints_files/figure-html/plotdataset-1.png differ diff --git a/docs/articles/buffer_and_randomPoints_files/figure-html/usr-1.png b/docs/articles/buffer_and_randomPoints_files/figure-html/usr-1.png index 27602e8..16183ff 100644 Binary files a/docs/articles/buffer_and_randomPoints_files/figure-html/usr-1.png and b/docs/articles/buffer_and_randomPoints_files/figure-html/usr-1.png differ diff --git a/docs/articles/buffer_res/envdist_usrshp/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png b/docs/articles/buffer_res/envdist_usrshp/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png index d5b6697..04b20ae 100644 Binary files a/docs/articles/buffer_res/envdist_usrshp/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png and b/docs/articles/buffer_res/envdist_usrshp/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png differ diff --git a/docs/articles/buffer_res/mindist_distance/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png b/docs/articles/buffer_res/mindist_distance/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png index 51617a4..53cd919 100644 Binary files a/docs/articles/buffer_res/mindist_distance/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png and b/docs/articles/buffer_res/mindist_distance/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png differ diff --git a/docs/articles/buffer_res/mindist_maxdist/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png b/docs/articles/buffer_res/mindist_maxdist/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png index e7981b5..c8e4f1a 100644 Binary files a/docs/articles/buffer_res/mindist_maxdist/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png and b/docs/articles/buffer_res/mindist_maxdist/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png differ diff --git a/docs/articles/buffer_res/mindist_meandist/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png b/docs/articles/buffer_res/mindist_meandist/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png index ac4db48..46ce667 100644 Binary files a/docs/articles/buffer_res/mindist_meandist/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png and b/docs/articles/buffer_res/mindist_meandist/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png differ diff --git a/docs/articles/buffer_res/mindist_mediandist/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png b/docs/articles/buffer_res/mindist_mediandist/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png index 9c54770..ad435b4 100644 Binary files a/docs/articles/buffer_res/mindist_mediandist/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png and b/docs/articles/buffer_res/mindist_mediandist/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png differ diff --git a/docs/articles/buffer_res/mindist_usrshp/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png b/docs/articles/buffer_res/mindist_usrshp/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png index be1d13d..929a4ec 100644 Binary files a/docs/articles/buffer_res/mindist_usrshp/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png and b/docs/articles/buffer_res/mindist_usrshp/Abarema_langsdorffii/present/data_setup/sdmdata_Abarema_langsdorffii.png differ diff --git a/docs/articles/modleR.html b/docs/articles/modleR.html index d242164..678179d 100644 --- a/docs/articles/modleR.html +++ b/docs/articles/modleR.html @@ -155,13 +155,6 @@

Installingremotes::install_github("mrmaxent/maxnet")
-

Shiny app -

-

A shiny application currently available at: https://github.com/Model-R/modleR_shiny_app uses a -previous version of this workflow and is currently being updated to this -newest version.

-
-

The workflow

The workflow consists of mainly four functions that should be used @@ -680,9 +673,9 @@

Algorithmic consensus with which_final = "raw_mean", models_dir = test_folder, overwrite = TRUE) #argument from writeRaster -#> [1] "Thu Aug 3 11:15:36 2023" +#> [1] "Thu Aug 3 12:31:43 2023" #> [1] "DONE!" -#> [1] "Thu Aug 3 11:15:54 2023"

+#> [1] "Thu Aug 3 12:31:57 2023"
 plot(ens)

diff --git a/docs/articles/projection.html b/docs/articles/projection.html index be0e369..f941bdc 100644 --- a/docs/articles/projection.html +++ b/docs/articles/projection.html @@ -306,7 +306,7 @@

Final model projection models_dir = "./projections/", proj_dir = "present", overwrite = TRUE) -
## [1] "Thu Aug  3 11:12:33 2023"
+
## [1] "Thu Aug  3 12:28:46 2023"
## [1] "DONE svme !"

For the projected models, each proj_dir has to have the name of the projection

@@ -318,7 +318,7 @@

Proj1 models_dir = "./projections/", proj_dir = "proj1", overwrite = TRUE) -
## [1] "Thu Aug  3 11:12:37 2023"
+
## [1] "Thu Aug  3 12:28:50 2023"
## [1] "DONE svme !"
 knitr::include_graphics("./projections/Abarema_langsdorffii/proj1/final_models/Abarema_langsdorffii_svme_raw_mean.png")
@@ -332,7 +332,7 @@

Proj2 models_dir = "./projections/", proj_dir = "proj2", overwrite = TRUE) -
## [1] "Thu Aug  3 11:12:38 2023"
+
## [1] "Thu Aug  3 12:28:52 2023"
## [1] "DONE svme !"
 knitr::include_graphics("./projections/Abarema_langsdorffii/proj2/final_models/Abarema_langsdorffii_svme_raw_mean.png")
@@ -346,7 +346,7 @@

Proj3 models_dir = "./projections/", proj_dir = "proj3", overwrite = TRUE) -
## [1] "Thu Aug  3 11:12:43 2023"
+
## [1] "Thu Aug  3 12:28:56 2023"
## [1] "DONE svme !"
 knitr::include_graphics("./projections/Abarema_langsdorffii/proj3/final_models/Abarema_langsdorffii_svme_raw_mean.png")
@@ -360,7 +360,7 @@

Proj4 models_dir = "./projections/", proj_dir = "proj4", overwrite = TRUE) -
## [1] "Thu Aug  3 11:12:47 2023"
+
## [1] "Thu Aug  3 12:29:00 2023"
## [1] "DONE svme !"
 knitr::include_graphics("./projections/Abarema_langsdorffii/proj4/final_models/Abarema_langsdorffii_svme_raw_mean.png")
diff --git a/docs/articles/projection_files/figure-html/enm1-1.png b/docs/articles/projection_files/figure-html/enm1-1.png index 323f41d..7689c93 100644 Binary files a/docs/articles/projection_files/figure-html/enm1-1.png and b/docs/articles/projection_files/figure-html/enm1-1.png differ diff --git a/docs/articles/projections/Abarema_langsdorffii/proj1/final_models/Abarema_langsdorffii_svme_raw_mean.png b/docs/articles/projections/Abarema_langsdorffii/proj1/final_models/Abarema_langsdorffii_svme_raw_mean.png index 506f398..aa7e484 100644 Binary files a/docs/articles/projections/Abarema_langsdorffii/proj1/final_models/Abarema_langsdorffii_svme_raw_mean.png and b/docs/articles/projections/Abarema_langsdorffii/proj1/final_models/Abarema_langsdorffii_svme_raw_mean.png differ diff --git a/docs/articles/projections/Abarema_langsdorffii/proj1/partitions/svme_cont_Abarema_langsdorffii_1_1.png b/docs/articles/projections/Abarema_langsdorffii/proj1/partitions/svme_cont_Abarema_langsdorffii_1_1.png index e3665bc..a2606d8 100644 Binary files a/docs/articles/projections/Abarema_langsdorffii/proj1/partitions/svme_cont_Abarema_langsdorffii_1_1.png and b/docs/articles/projections/Abarema_langsdorffii/proj1/partitions/svme_cont_Abarema_langsdorffii_1_1.png differ diff --git a/docs/articles/projections/Abarema_langsdorffii/proj1/partitions/svme_cont_Abarema_langsdorffii_2_1.png b/docs/articles/projections/Abarema_langsdorffii/proj1/partitions/svme_cont_Abarema_langsdorffii_2_1.png index 0cb3caf..18dd19d 100644 Binary files a/docs/articles/projections/Abarema_langsdorffii/proj1/partitions/svme_cont_Abarema_langsdorffii_2_1.png and b/docs/articles/projections/Abarema_langsdorffii/proj1/partitions/svme_cont_Abarema_langsdorffii_2_1.png differ diff --git a/docs/articles/projections/Abarema_langsdorffii/proj1/partitions/svme_cont_Abarema_langsdorffii_3_1.png b/docs/articles/projections/Abarema_langsdorffii/proj1/partitions/svme_cont_Abarema_langsdorffii_3_1.png index dec0153..8381ca6 100644 Binary files a/docs/articles/projections/Abarema_langsdorffii/proj1/partitions/svme_cont_Abarema_langsdorffii_3_1.png and b/docs/articles/projections/Abarema_langsdorffii/proj1/partitions/svme_cont_Abarema_langsdorffii_3_1.png differ diff --git a/docs/articles/projections/Abarema_langsdorffii/proj2/final_models/Abarema_langsdorffii_svme_raw_mean.png b/docs/articles/projections/Abarema_langsdorffii/proj2/final_models/Abarema_langsdorffii_svme_raw_mean.png index e3426b3..0929874 100644 Binary files a/docs/articles/projections/Abarema_langsdorffii/proj2/final_models/Abarema_langsdorffii_svme_raw_mean.png and b/docs/articles/projections/Abarema_langsdorffii/proj2/final_models/Abarema_langsdorffii_svme_raw_mean.png differ diff --git a/docs/articles/projections/Abarema_langsdorffii/proj3/final_models/Abarema_langsdorffii_svme_raw_mean.png b/docs/articles/projections/Abarema_langsdorffii/proj3/final_models/Abarema_langsdorffii_svme_raw_mean.png index e27b4f4..28972d8 100644 Binary files a/docs/articles/projections/Abarema_langsdorffii/proj3/final_models/Abarema_langsdorffii_svme_raw_mean.png and b/docs/articles/projections/Abarema_langsdorffii/proj3/final_models/Abarema_langsdorffii_svme_raw_mean.png differ diff --git a/docs/articles/projections/Abarema_langsdorffii/proj4/final_models/Abarema_langsdorffii_svme_raw_mean.png b/docs/articles/projections/Abarema_langsdorffii/proj4/final_models/Abarema_langsdorffii_svme_raw_mean.png index a3870cd..c3f4d9f 100644 Binary files a/docs/articles/projections/Abarema_langsdorffii/proj4/final_models/Abarema_langsdorffii_svme_raw_mean.png and b/docs/articles/projections/Abarema_langsdorffii/proj4/final_models/Abarema_langsdorffii_svme_raw_mean.png differ diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 09793cd..b126fd1 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -5,5 +5,5 @@ articles: buffer_and_randomPoints: buffer_and_randomPoints.html projection: projection.html modleR: modleR.html -last_built: 2023-08-03T18:06Z +last_built: 2023-08-03T19:23Z diff --git a/docs/reference/figures/README-plot_final-1.png b/docs/reference/figures/README-plot_final-1.png index 01b8d7b..f245af1 100644 Binary files a/docs/reference/figures/README-plot_final-1.png and b/docs/reference/figures/README-plot_final-1.png differ diff --git a/vignettes/modleR.Rmd b/vignettes/modleR.Rmd index 2e943af..010dcfa 100644 --- a/vignettes/modleR.Rmd +++ b/vignettes/modleR.Rmd @@ -66,10 +66,6 @@ remotes::install_github("marlonecobos/kuenm") remotes::install_github("mrmaxent/maxnet") ``` -# Shiny app - -A shiny application currently available at: https://github.com/Model-R/modleR_shiny_app -uses a previous version of this workflow and is currently being updated to this newest version. # The workflow