sdmverse 0.1.0.9023: inst/scripts/ms_figs.R to examples sections

NEWS.md

@@ -1,3 +1,7 @@
+sdmverse 0.1.0.9023
+
+-   inst/scripts/ms_figs.R to examples sections
+
 sdmverse 0.1.0.9022
 
 -   app update with M. Noblis suggestions

R/plot_dendrogram.R

@@ -25,46 +25,27 @@ NULL
 #'
 #' @examples
 #' \donttest{
-#' # fetch data
-#' table <- prep_table()
-#'
-#' # a rectangular dendrogram
-#' rect <- plot_dendrogram(
-#'   table = table,
-#'   dist_method = "binary",
-#'   k = nrow(table),
-#'   k_colors = "jco",
-#'   rect = TRUE,
-#'   rect_border = "jco",
-#'   rect_fill = TRUE,
-#'   type = "rectangle",
+#' library(dplyr)
+#' d <- prep_table(where = "online") %>%
+#'   filter(
+#'     name != "rgbif",
+#'     name != "ibis.iSDM",
+#'     name != "dismo"
+#'   ) %>%
+#'   select(
+#'     -mod_mechanistic,
+#'     -mod_multispecies
+#'   )
+#' plot_dendrogram(
+#'   d,
+#'   k = 5,
+#'   cex = 0.7,
+#'   diff_method = "binary",
 #'   horiz = TRUE,
-#'   main = "Species distribution modeling software",
-#'   sub = date(),
-#'   cex = 1.4
-#' )
-#'
-#' # a phylogenic plot
-#' phylo <- plot_dendrogram(
-#'   table = table,
-#'   dist_method = "binary",
-#'   k = nrow(table),
-#'   k_colors = "jco",
-#'   rect = TRUE,
-#'   rect_border = "jco",
-#'   type = "phylogenic",
-#'   repel = TRUE,
-#'   main = "Species distribution modeling software",
-#'   sub = date(),
-#'   cex = 1
+#'   main = ""
 #' )
 #' }
 #'
-#' \dontrun{
-#' library(patchwork)
-#' rect + phylo
-#' }
-#'
 #' @export
 #'
 plot_dendrogram <- function(table,

R/plot_table.R

@@ -15,9 +15,19 @@ NULL
 #' @return Plot package characteristics from the sdmverse table using ggplot.
 #'
 #' @examples
-#' \dontrun{
-#' prep_table() %>%
-#'   plot_table()
+#' \donttest{
+#' library(dplyr)
+#' d <- prep_table(where = "online") %>%
+#'   filter(
+#'     name != "rgbif",
+#'     name != "ibis.iSDM",
+#'     name != "dismo"
+#'   ) %>%
+#'   select(
+#'     -mod_mechanistic,
+#'     -mod_multispecies
+#'   )
+#' plot_table(d, remove_empty_cats = TRUE)
 #' }
 #'
 #' @export

R/prep_table.R

@@ -14,7 +14,17 @@ NULL
 #'
 #' @examples
 #' \donttest{
-#' prep_table()
+#' library(dplyr)
+#' d <- prep_table(where = "online") %>%
+#'   filter(
+#'     name != "rgbif",
+#'     name != "ibis.iSDM",
+#'     name != "dismo"
+#'   ) %>%
+#'   select(
+#'     -mod_mechanistic,
+#'     -mod_multispecies
+#'   )
 #' }
 #'
 #' @export

inst/app/rsconnect/shinyapps.io/sylvainschmitt/smdverse.dcf

@@ -5,5 +5,5 @@ account: sylvainschmitt
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 8255748
-bundleId: 9038005
+bundleId: 9168398
 url: https://sylvainschmitt.shinyapps.io/smdverse/

inst/app/server.R

@@ -95,9 +95,7 @@ shinyServer(function(input, output) {
         )
       )
   })
-  output$table <- DT::renderDataTable(
-    {
-      tab()
-    },
-  )
+  output$table <- DT::renderDataTable({
+    tab()
+  }, )
 })