From a907706845b1e415d198de967e147183ba002e45 Mon Sep 17 00:00:00 2001
From: Scott Chamberlain <myrmecocystus@gmail.com>
Date: Sun, 5 Jul 2015 15:32:39 -0700
Subject: [PATCH] changed occ_to_sp to occ2sp

---
 NAMESPACE                       |  2 +-
 R/map_gist.R                    |  6 +-----
 R/occ2sp.R                      | 20 +++++++++-----------
 man/{occ_to_sp.Rd => occ2sp.Rd} | 21 ++++++++++-----------
 4 files changed, 21 insertions(+), 28 deletions(-)
 rename man/{occ_to_sp.Rd => occ2sp.Rd} (60%)

diff --git a/NAMESPACE b/NAMESPACE
index 6707d80..100f08f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -9,7 +9,7 @@ export(map_ggplot)
 export(map_gist)
 export(map_leaflet)
 export(map_plot)
-export(occ_to_sp)
+export(occ2sp)
 export(palettes)
 export(spocc_rcharts_togeojson)
 export(style_geojson)
diff --git a/R/map_gist.R b/R/map_gist.R
index 4b4fb70..bdfe710 100644
--- a/R/map_gist.R
+++ b/R/map_gist.R
@@ -33,11 +33,7 @@
 
 map_gist <- function(data, description = "", public = TRUE, browse = TRUE, ...) {
   stopifnot(is(data, "occdatind") | is(data, "occdat"))
-  data <- if (is(data, "occdatind")) {
-    do.call(rbind, data$data)
-  } else {
-    occ2df(data)
-  }
+  data <- occ2df(data)
   datgeojson <- style_geojson(input = data, var = "name", ...)
   file <- tempfile(fileext = ".csv")
   write.csv(datgeojson, file)
diff --git a/R/occ2sp.R b/R/occ2sp.R
index 487a428..fb09db4 100644
--- a/R/occ2sp.R
+++ b/R/occ2sp.R
@@ -1,9 +1,9 @@
-#' Create a spatial points dataframe from a spocc search.
+#' Create a spatial points dataframe from a spocc search
 #'
 #' @importFrom sp SpatialPoints SpatialPointsDataFrame plot
 #' @export
 #'
-#' @param occObj The resuslts of a spocc search called by occ()
+#' @param x The resuslts of a spocc search called by occ()
 #' @param coord_string A valid EPGS cooridate string from the sp package, the default is WSGS 84
 #' @param just_coords Return data frame with specios names and provenance or just a spatial points
 #' object, which is the default.
@@ -18,18 +18,16 @@
 #' library("maptools")
 #' library("spocc")
 #' data(wrld_simpl)
-#' plot(wrld_simpl[wrld_simpl$NAME == "United States", ],xlim=c(-70,-60))
-#' out <- occ(query = "Accipiter striatus", from = c("inat","gbif"))
-#' sp_points <- occ_to_sp(out, just_coords=TRUE)
-#' points(sp_points,col=2)
+#' plot(wrld_simpl[wrld_simpl$NAME == "United States", ], xlim = c(-70, -60))
+#' out <- occ(query = "Accipiter striatus", from = c("ecoengine", "gbif"), limit = 50)
+#' sp_points <- occ2sp(out, just_coords = TRUE)
+#' points(sp_points, col = 2)
 #' }
-
-occ_to_sp <- function(occObj, coord_string = "+proj=longlat +datum=WGS84", just_coords = FALSE){
-
-  points <- occ2df(occObj)
+occ2sp <- function(x, coord_string = "+proj=longlat +datum=WGS84", just_coords = FALSE) {
+  points <- occ2df(x)
 
   # remove NA rows
-  points <- points[complete.cases(points),]
+  points <- points[complete.cases(points), ]
 
   # check valid coords
   index <- 1:dim(points)[1]
diff --git a/man/occ_to_sp.Rd b/man/occ2sp.Rd
similarity index 60%
rename from man/occ_to_sp.Rd
rename to man/occ2sp.Rd
index a5f6bbb..b752fe7 100644
--- a/man/occ_to_sp.Rd
+++ b/man/occ2sp.Rd
@@ -1,14 +1,13 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/occ2sp.R
-\name{occ_to_sp}
-\alias{occ_to_sp}
-\title{Create a spatial points dataframe from a spocc search.}
+\name{occ2sp}
+\alias{occ2sp}
+\title{Create a spatial points dataframe from a spocc search}
 \usage{
-occ_to_sp(occObj, coord_string = "+proj=longlat +datum=WGS84",
-  just_coords = FALSE)
+occ2sp(x, coord_string = "+proj=longlat +datum=WGS84", just_coords = FALSE)
 }
 \arguments{
-\item{occObj}{The resuslts of a spocc search called by occ()}
+\item{x}{The resuslts of a spocc search called by occ()}
 
 \item{coord_string}{A valid EPGS cooridate string from the sp package, the default is WSGS 84}
 
@@ -16,7 +15,7 @@ occ_to_sp(occObj, coord_string = "+proj=longlat +datum=WGS84",
 object, which is the default.}
 }
 \description{
-Create a spatial points dataframe from a spocc search.
+Create a spatial points dataframe from a spocc search
 }
 \details{
 This function will return either a spatial points dataframe or spatial points object.
@@ -30,10 +29,10 @@ data sources. More coordinate system codes can be found at the EPGS registry:
 library("maptools")
 library("spocc")
 data(wrld_simpl)
-plot(wrld_simpl[wrld_simpl$NAME == "United States", ],xlim=c(-70,-60))
-out <- occ(query = "Accipiter striatus", from = c("inat","gbif"))
-sp_points <- occ_to_sp(out, just_coords=TRUE)
-points(sp_points,col=2)
+plot(wrld_simpl[wrld_simpl$NAME == "United States", ], xlim = c(-70, -60))
+out <- occ(query = "Accipiter striatus", from = c("ecoengine", "gbif"), limit = 50)
+sp_points <- occ2sp(out, just_coords = TRUE)
+points(sp_points, col = 2)
 }
 }