fix #29 support output of rgbif::occ_data in map functions, bump dev …

…version

.Rbuildignore

@@ -20,4 +20,4 @@ gistmap*
 ^CONDUCT\.md$
 ^cran-comments\.md$
 ^codemeta\.json$
-.github
+\.github

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: 0.3.5.9210
+Version: 0.3.6.9210
 License: MIT + file LICENSE
 Authors@R: person("Scott", "Chamberlain", role = c("aut", "cre"),
     email = "[email protected]", comment = c(ORCID = "0000-0003-1444-9135"))

NAMESPACE

@@ -45,6 +45,7 @@ export(map_gist)
 export(map_leaflet)
 export(map_plot)
 export(occ2sp)
+export(style_geojson)
 import(leaflet)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,element_blank)

R/map_ggmap.R

@@ -33,8 +33,14 @@
 #'
 #' ## rgbif
 #' library("rgbif")
+#' ### occ_search() output
 #' res <- occ_search(scientificName = "Puma concolor", limit = 100)
 #' map_ggmap(res)
+#' 
+#' ### occ_data() output
+#' res <- occ_data(scientificName = "Puma concolor", limit = 100)
+#' map_ggmap(res)
+#' 
 #'
 #' ## data.frame
 #' df <- data.frame(name = c('Poa annua', 'Puma concolor', 'Foo bar'),
@@ -91,6 +97,15 @@ map_ggmap.gbif <- function(x, zoom = 3, point_color = "#86161f", color = NULL,
   map_ggmapper(x, zoom, color, size, maptype, source)
 }
 
+#' @export
+map_ggmap.gbif_data <- 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')
+  map_ggmapper(x, zoom, color, size, maptype, source)
+}
+
 #' @export
 map_ggmap.data.frame <- function(x, zoom = 3, point_color = "#86161f",
                                  color = NULL, size = 3, lon = 'longitude',

R/map_gist.R

@@ -34,8 +34,13 @@
 #'
 #' ## rgbif
 #' library("rgbif")
+#' ### occ_search() output
 #' res <- occ_search(scientificName = "Puma concolor", limit = 100)
 #' map_gist(res)
+#' 
+#' ### occ_data() output
+#' res <- occ_data(scientificName = "Puma concolor", limit = 100)
+#' map_gist(res)
 #'
 #' ## data.frame
 #' df <- data.frame(name = c('Poa annua', 'Puma concolor', 'Foo bar'),
@@ -78,6 +83,15 @@ map_gist.gbif <- function(x, description = "", public = TRUE, browse = TRUE,
   map_gister(x, description, public, browse, ...)
 }
 
+#' @export
+map_gist.gbif_data <- function(x, description = "", public = TRUE, browse = TRUE,
+                          lon = 'longitude', lat = 'latitude', ...) {
+  x <- x$data
+  x <- re_name(x, c('decimalLatitude' = 'latitude'))
+  x <- re_name(x, c('decimalLongitude' = 'longitude'))
+  map_gister(x, description, public, browse, ...)
+}
+
 #' @export
 map_gist.data.frame <- function(x, description = "", public = TRUE,
                                 browse = TRUE, lon = 'longitude',

R/map_leaflet.R

@@ -36,12 +36,17 @@
 #'
 #' ## SpatialPointsDataFrame class
 #' library("rgbif")
+#' ### occ_search() output
 #' res <- occ_search(scientificName = "Puma concolor", limit = 100)
 #' x <- res$data
 #' library("sp")
 #' x <- x[stats::complete.cases(x$decimalLatitude, x$decimalLongitude), ]
 #' coordinates(x) <- ~decimalLongitude+decimalLatitude
 #' map_leaflet(x)
+#' 
+#' ### occ_data() output
+#' res <- occ_data(scientificName = "Puma concolor", limit = 100)
+#' map_leaflet(res)
 #'
 #' ## data.frame
 #' df <- data.frame(name = c('Poa annua', 'Puma concolor'),
@@ -101,6 +106,16 @@ map_leaflet.gbif <- function(x, lon = 'longitude', lat = 'latitude',
   )
 }
 
+#' @export
+map_leaflet.gbif_data <- function(x, lon = 'longitude', lat = 'latitude',
+                             color = NULL, size = 13, ...) {
+  make_map_ll(
+    dat_cleaner(x$data, lon = 'decimalLongitude', lat = 'decimalLatitude'),
+    color = color,
+    size = size
+  )
+}
+
 #' @export
 map_leaflet.data.frame <- function(x, lon = 'longitude', lat = 'latitude',
                                    color = NULL, size = 13, ...) {

R/map_plot.R

@@ -32,9 +32,14 @@
 #'
 #' ## rgbif
 #' library("rgbif")
+#' ### occ_search() output
 #' res <- occ_search(scientificName = "Puma concolor", limit = 100)
 #' map_plot(res)
 #' map_plot(res, hull = TRUE)
+#' 
+#' ### occ_data() output
+#' res <- occ_data(scientificName = "Puma concolor", limit = 100)
+#' map_plot(res)
 #'
 #' ## data.frame
 #' df <- data.frame(
@@ -108,6 +113,18 @@ map_plot.gbif <- function(x, lon = 'longitude', lat = 'latitude', color = NULL,
   plot_er(df, size, hull, ...)
 }
 
+#' @export
+map_plot.gbif_data <- function(x, lon = 'longitude', lat = 'latitude', color = NULL,
+                          size = 1, pch = 16, hull = FALSE, ...) {
+  df <- x$data
+  df <- guess_latlon(df)
+  df <- df[stats::complete.cases(df$latitude, df$longitude), ]
+  df <- df[df$longitude != 0, ]
+  df <- check_colors(df, color)
+  sp::coordinates(df) <- ~longitude + latitude
+  plot_er(df, size, hull, ...)
+}
+
 #' @export
 map_plot.data.frame <- function(x, lon = 'longitude', lat = 'latitude',
                                 color = NULL, size = 1, pch = 16,

man-roxygen/args.R

@@ -1,9 +1,11 @@
 #' @param x The data. An object of class \code{occdat}, \code{occdatind},
-#' \code{gbif}, \code{SpatialPoints}, \code{SpatialPointsDataFrame}, or
-#' \code{data.frame}. The package \pkg{spocc} needed for
+#' \code{gbif}, \code{gbif_data}, \code{SpatialPoints}, 
+#' \code{SpatialPointsDataFrame}, or \code{data.frame}. The package 
+#' \pkg{spocc} needed for
 #' the first two, and \pkg{rgbif} needed for the third. When \code{data.frame}
 #' input, any number of columns allowed, but with at least the following:
 #' name (the taxonomic name), latitude (in dec. deg.), longitude (in dec. deg.)
 #' @param lon,lat (character) Longitude and latitude variable names. Ignored
-#' unless \code{data.frame} input to \code{x} parameter. We attempt to guess, but
-#' if nothing close, we stop. Default: \code{longitude} and \code{latitude}
+#' unless \code{data.frame} input to \code{x} parameter. We attempt to guess, 
+#' but if nothing close, we stop. Default: \code{longitude} and 
+#' \code{latitude}