fixes related to #29

make sure all map_ methods work for when occ_search and occ_data give back > 1 taxa results wasnt working before this fix
ropensci-archive · Mar 20, 2018 · c3bdf1c · c3bdf1c
1 parent e69ca3d
commit c3bdf1c
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Showing 15 changed files with 145 additions and 37 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -4,7 +4,7 @@ Description: Utilities for visualizing species occurrence data. Includes
     functions to visualize occurrence data from 'spocc', 'rgbif',
     and other packages. Mapping options included for base R plots, 'ggplot2',
     'ggmap', 'leaflet' and 'GitHub' 'gists'.
-Version: 0.3.6.9210
+Version: 0.3.6.9410
 License: MIT + file LICENSE
 Authors@R: person("Scott", "Chamberlain", role = c("aut", "cre"),
     email = "[email protected]", comment = c(ORCID = "0000-0003-1444-9135"))
@@ -22,7 +22,8 @@ Imports:
     rworldmap,
     RColorBrewer,
     jsonlite,
-    gistr
+    gistr,
+    data.table
 Suggests:
     testthat,
     ggmap,

diff --git a/Makefile b/Makefile
@@ -40,12 +40,12 @@ README.md: README.Rmd
 	rm -f $@.bak
 
 move:
-		cp inst/vign/mapr_vignette.md vignettes
-		cp -rf inst/vign/img/* vignettes/img/
+	cp inst/vign/mapr_vignette.md vignettes
+	cp -rf inst/vign/img/* vignettes/img/
 
 rmd2md:
-		cd vignettes;\
-		mv mapr_vignette.md mapr_vignette.Rmd
+	cd vignettes;\
+	mv mapr_vignette.md mapr_vignette.Rmd
 
 
 

diff --git a/NAMESPACE b/NAMESPACE
@@ -7,6 +7,7 @@ S3method(map_ggmap,SpatialPointsDataFrame)
 S3method(map_ggmap,data.frame)
 S3method(map_ggmap,default)
 S3method(map_ggmap,gbif)
+S3method(map_ggmap,gbif_data)
 S3method(map_ggmap,occdat)
 S3method(map_ggmap,occdatind)
 S3method(map_ggplot,SpatialPoints)
@@ -22,20 +23,23 @@ S3method(map_gist,SpatialPointsDataFrame)
 S3method(map_gist,data.frame)
 S3method(map_gist,default)
 S3method(map_gist,gbif)
+S3method(map_gist,gbif_data)
 S3method(map_gist,occdat)
 S3method(map_gist,occdatind)
 S3method(map_leaflet,SpatialPoints)
 S3method(map_leaflet,SpatialPointsDataFrame)
 S3method(map_leaflet,data.frame)
 S3method(map_leaflet,default)
 S3method(map_leaflet,gbif)
+S3method(map_leaflet,gbif_data)
 S3method(map_leaflet,occdat)
 S3method(map_leaflet,occdatind)
 S3method(map_plot,SpatialPoints)
 S3method(map_plot,SpatialPointsDataFrame)
 S3method(map_plot,data.frame)
 S3method(map_plot,default)
 S3method(map_plot,gbif)
+S3method(map_plot,gbif_data)
 S3method(map_plot,occdat)
 S3method(map_plot,occdatind)
 export(hull)

diff --git a/R/map_ggmap.R b/R/map_ggmap.R
@@ -41,7 +41,12 @@
 #' res <- occ_data(scientificName = "Puma concolor", limit = 100)
 #' map_ggmap(res)
 #' 
+#' #### many taxa
+#' res <- occ_data(scientificName = c("Puma concolor", "Quercus lobata"), 
+#'    limit = 30)
+#' map_ggmap(res)
 #'
+#' 
 #' ## data.frame
 #' df <- data.frame(name = c('Poa annua', 'Puma concolor', 'Foo bar'),
 #'                  longitude = c(-120, -121, -123),
@@ -93,7 +98,8 @@ map_ggmap.gbif <- function(x, zoom = 3, point_color = "#86161f", color = NULL,
                            size = 3, lon = 'longitude', lat = 'latitude',
                            maptype = "terrain", source = "google", ...) {
   check_inputs(match.call())
-  x <- guess_latlon(x$data, lon = 'decimalLongitude', lat = 'decimalLatitude')
+  x <- if ("data" %in% names(x)) x$data else bdt(lapply(x, function(z) z$data))
+  x <- guess_latlon(x, lon = 'decimalLongitude', lat = 'decimalLatitude')
   map_ggmapper(x, zoom, color, size, maptype, source)
 }
 
@@ -102,7 +108,8 @@ map_ggmap.gbif_data <- function(x, zoom = 3, point_color = "#86161f", color = NU
                            size = 3, lon = 'longitude', lat = 'latitude',
                            maptype = "terrain", source = "google", ...) {
   check_inputs(match.call())
-  x <- guess_latlon(x$data, lon = 'decimalLongitude', lat = 'decimalLatitude')
+  x <- if ("data" %in% names(x)) x$data else bdt(lapply(x, function(z) z$data))
+  x <- guess_latlon(x, lon = 'decimalLongitude', lat = 'decimalLatitude')
   map_ggmapper(x, zoom, color, size, maptype, source)
 }
 

diff --git a/R/map_ggplot.R b/R/map_ggplot.R
@@ -48,6 +48,11 @@
 #' res <- occ_data(scientificName = "Puma concolor", limit = 100)
 #' map_ggplot(res)
 #' 
+#' #### many taxa
+#' res <- occ_data(scientificName = c("Puma concolor", "Quercus lobata"), 
+#'    limit = 30)
+#' map_ggplot(res)
+#' 
 #' ### add a convex hull
 #' map_ggplot(res) + hull()
 #' 
@@ -96,7 +101,8 @@ map_ggplot.gbif <- function(x, map = "world", point_color = "#86161f",
                             color = NULL, size = 3, lon = 'longitude',
                             lat = 'latitude', ...) {
   check_inputs(match.call())
-  make_amap(dat_cleaner(x$data, lon = 'decimalLongitude',
+  x <- if ("data" %in% names(x)) x$data else bdt(lapply(x, function(z) z$data))
+  make_amap(dat_cleaner(x, lon = 'decimalLongitude',
                         lat = 'decimalLatitude'), map, color, size)
 }
 
@@ -105,7 +111,8 @@ map_ggplot.gbif_data <- function(x, map = "world", point_color = "#86161f",
                             color = NULL, size = 3, lon = 'longitude',
                             lat = 'latitude', ...) {
   check_inputs(match.call())
-  make_amap(dat_cleaner(x$data, lon = 'decimalLongitude',
+  x <- if ("data" %in% names(x)) x$data else bdt(lapply(x, function(z) z$data))
+  make_amap(dat_cleaner(x, lon = 'decimalLongitude',
                         lat = 'decimalLatitude'), map, color, size)
 }
 

diff --git a/R/map_gist.R b/R/map_gist.R
@@ -41,6 +41,13 @@
 #' ### occ_data() output
 #' res <- occ_data(scientificName = "Puma concolor", limit = 100)
 #' map_gist(res)
+#' 
+#' #### many taxa
+#' res <- occ_data(scientificName = c("Puma concolor", "Quercus lobata"), 
+#'    limit = 30)
+#' res
+#' map_gist(res)
+#' 
 #'
 #' ## data.frame
 #' df <- data.frame(name = c('Poa annua', 'Puma concolor', 'Foo bar'),
@@ -77,7 +84,7 @@ map_gist.occdatind <- function(x, description = "", public = TRUE,
 #' @export
 map_gist.gbif <- function(x, description = "", public = TRUE, browse = TRUE,
                           lon = 'longitude', lat = 'latitude', ...) {
-  x <- x$data
+  x <- if ("data" %in% names(x)) x$data else bdt(lapply(x, function(z) z$data))
   x <- re_name(x, c('decimalLatitude' = 'latitude'))
   x <- re_name(x, c('decimalLongitude' = 'longitude'))
   map_gister(x, description, public, browse, ...)
@@ -86,7 +93,7 @@ map_gist.gbif <- function(x, description = "", public = TRUE, browse = TRUE,
 #' @export
 map_gist.gbif_data <- function(x, description = "", public = TRUE, browse = TRUE,
                           lon = 'longitude', lat = 'latitude', ...) {
-  x <- x$data
+  x <- if ("data" %in% names(x)) x$data else bdt(lapply(x, function(z) z$data))
   x <- re_name(x, c('decimalLatitude' = 'latitude'))
   x <- re_name(x, c('decimalLongitude' = 'longitude'))
   map_gister(x, description, public, browse, ...)

diff --git a/R/map_leaflet.R b/R/map_leaflet.R
@@ -47,6 +47,13 @@
 #' ### occ_data() output
 #' res <- occ_data(scientificName = "Puma concolor", limit = 100)
 #' map_leaflet(res)
+#' 
+#' #### many taxa
+#' res <- occ_data(scientificName = c("Puma concolor", "Quercus lobata"), 
+#'    limit = 30)
+#' res
+#' map_leaflet(res)
+#' 
 #'
 #' ## data.frame
 #' df <- data.frame(name = c('Poa annua', 'Puma concolor'),
@@ -99,8 +106,9 @@ map_leaflet.SpatialPointsDataFrame <- function(x, lon = 'longitude',
 #' @export
 map_leaflet.gbif <- function(x, lon = 'longitude', lat = 'latitude',
                              color = NULL, size = 13, ...) {
+  x <- if ("data" %in% names(x)) x$data else bdt(lapply(x, function(z) z$data))
   make_map_ll(
-    dat_cleaner(x$data, lon = 'decimalLongitude', lat = 'decimalLatitude'),
+    dat_cleaner(x, lon = 'decimalLongitude', lat = 'decimalLatitude'),
     color = color,
     size = size
   )
@@ -109,8 +117,9 @@ map_leaflet.gbif <- function(x, lon = 'longitude', lat = 'latitude',
 #' @export
 map_leaflet.gbif_data <- function(x, lon = 'longitude', lat = 'latitude',
                              color = NULL, size = 13, ...) {
+  x <- if ("data" %in% names(x)) x$data else bdt(lapply(x, function(z) z$data))
   make_map_ll(
-    dat_cleaner(x$data, lon = 'decimalLongitude', lat = 'decimalLatitude'),
+    dat_cleaner(x, lon = 'decimalLongitude', lat = 'decimalLatitude'),
     color = color,
     size = size
   )

diff --git a/R/map_plot.R b/R/map_plot.R
@@ -40,6 +40,12 @@
 #' ### occ_data() output
 #' res <- occ_data(scientificName = "Puma concolor", limit = 100)
 #' map_plot(res)
+#' #### many taxa
+#' res <- occ_data(scientificName = c("Puma concolor", "Quercus lobata"), 
+#'    limit = 30)
+#' res
+#' map_plot(res)
+#' 
 #'
 #' ## data.frame
 #' df <- data.frame(
@@ -104,7 +110,7 @@ map_plot.occdatind <- function(x, lon = 'longitude', lat = 'latitude',
 #' @export
 map_plot.gbif <- function(x, lon = 'longitude', lat = 'latitude', color = NULL,
                           size = 1, pch = 16, hull = FALSE, ...) {
-  df <- x$data
+  df <- if ("data" %in% names(x)) x$data else bdt(lapply(x, function(z) z$data))
   df <- guess_latlon(df)
   df <- df[stats::complete.cases(df$latitude, df$longitude), ]
   df <- df[df$longitude != 0, ]
@@ -116,7 +122,7 @@ map_plot.gbif <- function(x, lon = 'longitude', lat = 'latitude', color = NULL,
 #' @export
 map_plot.gbif_data <- function(x, lon = 'longitude', lat = 'latitude', color = NULL,
                           size = 1, pch = 16, hull = FALSE, ...) {
-  df <- x$data
+  df <- if ("data" %in% names(x)) x$data else bdt(lapply(x, function(z) z$data))
   df <- guess_latlon(df)
   df <- df[stats::complete.cases(df$latitude, df$longitude), ]
   df <- df[df$longitude != 0, ]

diff --git a/R/zzz.r b/R/zzz.r
@@ -28,3 +28,9 @@ check_inputs <- function(x) {
          call. = FALSE)
   }
 }
+
+bdt <- function(x) {
+  (bb <- data.table::setDF(
+    data.table::rbindlist(x, fill = TRUE, use.names = TRUE)
+  ))
+}
diff --git a/man/map_ggmap.Rd b/man/map_ggmap.Rd
diff --git a/man/map_ggplot.Rd b/man/map_ggplot.Rd
diff --git a/man/map_gist.Rd b/man/map_gist.Rd