sdmverse 0.1.0.9020: app fix following review

NEWS.md

@@ -1,3 +1,7 @@
+sdmverse 0.1.0.9020
+
+-   app fix following review
+
 sdmverse 0.1.0.9019
 
 -   #38 cleaning

R/plot_table.R

@@ -83,8 +83,10 @@ plot_table <- function(
     theme_bw() +
     scale_x_discrete(position = "top") +
     theme(
-      axis.text.x.top =  element_text(color = pkg_cols, angle = 90, size = 14,
-                                      hjust = 0, vjust = 0.5, face = "bold"),
+      axis.text.x.top = element_text(
+        color = pkg_cols, angle = 90, size = 14,
+        hjust = 0, vjust = 0.5, face = "bold"
+      ),
       axis.text.y = element_text(size = 14),
       axis.title = element_blank(),
       legend.position = "none"

inst/app/server.R

@@ -4,7 +4,10 @@ library(dplyr)
 
 shinyServer(function(input, output) {
   # packages
-  packages <- sdmverse::prep_table(where = "online")
+  packages <- sdmverse::list_packages(where = "online") %>%
+    select(
+      -author, -cran, -description, -manuscript_citation
+    )
 
   # to further play with the table
   tab <- reactive({

inst/extdata/packages/bamm.yaml

@@ -1,29 +1,12 @@
 name : bamm
 title: "Species Distribution Models as a Function of Biotic, Abiotic and
        Movement Factors (BAM)"
-version: 0.4.3
-author: "Luis Osorio-Olvera, Jorge Soberón"
+version: 0.5.0
+author: "Luis Osorio-Olvera, Jorge Soberón, Rusby G. Contreras-Díaz"
 maintainer: "Luis Osorio-Olvera <[email protected]>"
 cran: yes
 repository: "https://github.com/luismurao/bamm"
-description: "Species Distribution Modeling (SDM) is a practical methodology
- that aims to estimate the area of distribution of a species. However,
- most of the work has focused on estimating static expressions of the
- correlation between environmental variables. The outputs of
- correlative species distribution models can be interpreted
- as maps of the suitable environment for a species but not generally as maps
- of its actual distribution.
- Soberón and Peterson (2005) <doi:10.17161/bi.v2i0.4> presented
- the BAM scheme, a heuristic framework that states that the occupied area of
- a species occurs on sites that have been accessible through dispersal (M) and
- have both favorable biotic (B) and abiotic conditions (A).
- The 'bamm' package implements classes and functions to operate on each element
- of the BAM and by using a cellular automata model where the occupied area
- of a species at time t is estimated by the multiplication of three
- binary matrices: one matrix represents movements (M), another
- abiotic -niche- tolerances (A), and a third, biotic interactions (B).
- The theoretical background of the package can be found in
- Soberón and Osorio-Olvera (2022) <arXiv:2212.06308>."
+description: "Species Distribution Modeling (SDM) is a practical methodology that aims to estimate the area of distribution of a species. However, most of the work has focused on estimating static expressions of the correlation between environmental variables. The outputs of correlative species distribution models can be interpreted as maps of the suitable environment for a species but not generally as maps of its actual distribution. Soberón and Peterson (2005) <doi:10.17161/bi.v2i0.4> presented the BAM scheme, a heuristic framework that states that the occupied area of a species occurs on sites that have been accessible through dispersal (M) and have both favorable biotic (B) and abiotic conditions (A). The 'bamm' package implements classes and functions to operate on each element of the BAM and by using a cellular automata model where the occupied area of a species at time t is estimated by the multiplication of three binary matrices: one matrix represents movements (M), another abiotic -niche- tolerances (A), and a third, biotic interactions (B). The theoretical background of the package can be found in Soberón and Osorio-Olvera (2023) <doi:10.1111/jbi.14587>."
 occ_acquisition: no
 occ_cleaning: no
 data_integration: no

inst/extdata/packages/biomod2.yaml

@@ -1,6 +1,6 @@
 name: biomod2
 title: Ensemble Platform for Species Distribution Modeling
-version: 4.2-5
+version: 4.2-5-2
 author: "Wilfried Thuiller, Damien Georges, Maya Gueguen, Robin Engler, Frank Breiner, Bruno Lafourcade, Remi Patin, Helene Blancheteau"
 maintainer: Maya Gueguen <[email protected]>
 cran: yes

inst/extdata/packages/ecospat.yaml

@@ -1,6 +1,6 @@
 name: ecospat
 title: "Spatial Ecology Miscellaneous Methods"
-version: 4.1.0
+version: 4.1.1
 author: "Olivier Broennimann, Valeria Di Cola, Blaise Petitpierre, Frank Breiner, Daniel Scherrer, Manuela D`Amen, Christophe Randin, Robin Engler, Wim Hordijk, Heidi Mod, Julien Pottier, Mirko Di Febbraro, Loic Pellissier, Dorothea Pio, Ruben Garcia Mateo, Anne Dubuis, Luigi Maiorano, Achilleas Psomas, Charlotte Ndiribe, Nicolas Salamin, Niklaus Zimmermann, Flavien Collart, Valentin Verdon, Tyler Smith, Antoine Guisan"
 maintainer: "Olivier Broennimann <[email protected]>"
 cran: yes

inst/extdata/packages/enmSdmX.yaml

@@ -1,6 +1,6 @@
 name: "enmSdmX"
 title: "Species Distribution Modeling and Ecological Niche Modeling"
-version: 1.1.5
+version: 1.1.6
 author: "Adam B. Smith"
 maintainer: "Adam B. Smith <[email protected]>"
 cran: yes

inst/extdata/packages/kissmig.yaml

@@ -1,11 +1,11 @@
 name: kissmig
 title: "a Keep It Simple Species Migration Model"
-version: 1.0-4
+version: 1.0-5
 author: "Michael P. Nobis, Signe Normand"
 maintainer: "Michael P. Nobis <[email protected]>"
 cran: yes
 repository: ""
-description: "Simulating species migration and range dynamics under stable or changing environmental conditions based on a simple, raster-based, stochastic migration model. Providing accessibility from an origin or previous distribution for niche-based species distribution models. Nobis & Normand (2014) <doi:10.1111/ecog.00930>."
+description: "Simulating species migration and range dynamics under stable or changing environmental conditions based on a simple, raster-based, deterministic or stochastic migration model. Kissmig runs on binary or quantitative suitability maps, which are pre-calculated with niche-based habitat suitability models (also called ecological niche models (ENMs) or species distribution models (SDMs)). Nobis & Normand (2014), <doi:10.1111/ecog.00930>."
 occ_acquisition: no
 occ_cleaning: no
 data_integration: no

inst/extdata/packages/occCite.yml

@@ -1,6 +1,6 @@
 name : occCite
 title: "Querying and Managing Large Biodiversity Occurrence Datasets"
-version: 0.5.6
+version: 0.5.7
 author: "Hannah L. Owens, Cory Merow, Brian Maitner, Jamie M. Kass, Vijay Barve, Robert P. Guralnick, Damiano Oldoni for rOpenSci, see)"
 maintainer: "Hannah L. Owens <[email protected]>"
 cran: yes

inst/extdata/packages/sdm.yaml

@@ -1,6 +1,6 @@
 name : "sdm"
 title: "Species Distribution Modelling"
-version: 1.2-40
+version: 1.2-46
 author: "Babak Naimi, Miguel B. Araujo"
 maintainer: "Babak Naimi <[email protected]>"
 cran: yes

inst/extdata/packages/wallace.yaml

@@ -1,10 +1,7 @@
 name : wallace
 title: "A Modular Platform for Reproducible Modeling of Species Niches and Distributions"
-version: 2.1.2
-author: "Jamie M. Kass, Gonzalo E. Pinilla-Buitrago, Andrea Paz, Bethany A. Johnson,
-Valentina Grisales-Betancur, Dean Attali, Matthew E. Aiello-Lammens, Cory Merow,
-Mary E. Blair, Robert P. Anderson, Sarah I. Meenan, Olivier Broennimann, Peter J. Galante,
-Brian S. Maitner, Hannah L. Owens, Sara Varela, Bruno Vilela, Robert Muscarella"
+version: 2.1.3
+author: "Bethany A. Johnson, Jamie M. Kass, Gonzalo E. Pinilla-Buitrago, Andrea Paz, Valentina Grisales-Betancur, Dean Attali, Matthew E. Aiello-Lammens, Cory Merow, Mary E. Blair, Robert P. Anderson, Sarah I. Meenan, Olivier Broennimann, Peter J. Galante, Brian S. Maitner, Hannah L. Owens, Sara Varela, Bruno Vilela, Robert Muscarella"
 maintainer: "Mary E. Blair <[email protected]>"
 cran: yes
 repository: "https://github.com/wallaceEcoMod/wallace"

inst/scripts/ms_figs.R

@@ -2,22 +2,30 @@ library(dplyr)
 
 d <- prep_table(where = "online")
 
-d <- filter(d, name != "rgbif",
-            name != "ibis.iSDM",
-            name != "dismo") |>
-  select(-mod_mechanistic,
-         -mod_multispecies)
+d <- filter(
+  d, name != "rgbif",
+  name != "ibis.iSDM",
+  name != "dismo"
+) |>
+  select(
+    -mod_mechanistic,
+    -mod_multispecies
+  )
 
 pal <- RColorBrewer::brewer.pal(n = 5, name = "Dark2")
 
 pdf("fig3.pdf", height = 5, width = 9.7)
-plot_dendrogram(d, k = 5, cex = 0.7, diff_method = "binary",
-                k_colors = pal, horiz = TRUE, main = "")
+plot_dendrogram(d,
+  k = 5, cex = 0.7, diff_method = "binary",
+  k_colors = pal, horiz = TRUE, main = ""
+)
 dev.off()
 
-clust <- plot_dendrogram(d, k = 5, cex = 1, diff_method = "binary",
-                         k_colors = pal, horiz = TRUE, main = "",
-                         return_clust = TRUE)
+clust <- plot_dendrogram(d,
+  k = 5, cex = 1, diff_method = "binary",
+  k_colors = pal, horiz = TRUE, main = "",
+  return_clust = TRUE
+)
 pkg_order <- rev(clust$labels[clust$order])
 
 pkg_cols <- pkg_order
@@ -31,7 +39,8 @@ pkg_cols[32:33] <- pal[1]
 
 pdf("fig2.pdf", height = 7, width = 16)
 plot_table(d,
-           pkg_order = pkg_order,
-           pkg_cols = pkg_cols,
-           remove_empty_cats = TRUE)
+  pkg_order = pkg_order,
+  pkg_cols = pkg_cols,
+  remove_empty_cats = TRUE
+)
 dev.off()