Merge pull request #35 from LDalby/use-json-endpoint-in-get-inat-proj

Use json endpoint in get_inat_project

DESCRIPTION

@@ -14,6 +14,6 @@ Imports:
     jsonlite,
     ggplot2,
     maps
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.1
 Suggests: knitr, rmarkdown, testthat
 VignetteBuilder: knitr

NAMESPACE

@@ -1,3 +1,4 @@
+# Generated by roxygen2: do not edit by hand
 
 export(get_inat_obs)
 export(get_inat_obs_id)
@@ -11,4 +12,3 @@ import(httr)
 import(jsonlite)
 import(maps)
 import(plyr)
-importFrom("utils", "read.csv")

R/get_inat_obs_project.R

@@ -1,31 +1,30 @@
 #' Download observations or info from a project
-#'@description retrieve observations from a particular iNaturalist project.  This function can be used to get either observations or information from a project by project name or ID
+#'@description retrieve observations from a particular iNaturalist project. This function can be used to get either observations or information from a project by project name or ID
 #'@param grpid Name of the group as an iNaturalist slug or group id
-#'@param type Either "observations" or "info"  Observations returns all observations, and "info" returns project details similar to what you can find on a project webpage.
-#'@param raw True or False.  If TRUE and searching for project info, returns the raw output of parsed JSON for that project.  Otherwise just some basic information is returned as a list
+#'@param type character Either "observations" or "info"  Observations returns all observations, and "info" returns project details similar to what you can find on a project webpage.
+#'@param raw logical TRUE or FALSE. If TRUE and searching for project info, returns the raw output of parsed JSON for that project. Otherwise just some basic information is returned as a list
 #'@details An iNaturalist slug is usually the project as single string with words seperated by hyphens. For instance, the project "State Flowers of the United States" has a slug of "state-flowers-of-the-united-states-eol-collection".  This can be extracted from the URL for the project usually. The state flowers project has the following URL http://www.inaturalist.org/projects/state-flowers-of-the-united-states-eol-collection
 #'
 #'@examples \dontrun{
 #'  get_inat_obs_project(354, type = "observations")
-#'  get_inat_obs_project("crows-in-vermont", type="info",raw=FALSE) 
+#'  get_inat_obs_project("crows-in-vermont", type="info",raw=FALSE)
 #'}
 #'@import httr jsonlite
 #'@export
 
-get_inat_obs_project <- function(grpid,type = c("observations","info"), raw = F){
+get_inat_obs_project <- function(grpid, type = c("observations", "info"), raw = FALSE){
   argstring = switch(match.arg(type),
-         observations = "obs",
-         info = "info")
-  url= paste("http://www.inaturalist.org/projects/",grpid,".json",sep="")
-  xx = fromJSON(content(GET(url),as="text"))
-  recs =xx$project_observations_count
- 
+                     observations = "obs",
+                     info = "info")
+  url <- paste0("http://www.inaturalist.org/projects/",grpid,".json")
+  xx <- fromJSON(content(GET(url), as = "text"))
+  recs <- xx$project_observations_count
+
   ### Error handling for empty projects
-  dat = NULL
+  dat <- NULL
   if(is.null(recs))(return(dat))
-  cat(paste(recs," Records\n0"))
-
-
+  cat(paste(recs," Records\n"))
+
   if(argstring == "info"){
     output <- list()
     output[["title"]] <- xx$title
@@ -40,20 +39,40 @@ get_inat_obs_project <- function(grpid,type = c("observations","info"), raw = F)
     if(raw){
       output[["raw"]] <- xx
     }
-
-
     return(output)
-  } else if(argstring == "obs"){
-
-  if (recs %% 100 == 0){loopval<-recs %/% 100}
-  else{loopval <-(recs %/% 100)+1}
-  for(i in 1:loopval){
-    url1=paste("http://www.inaturalist.org/observations/project/",grpid,".csv?page=",i,"&per_page=100",sep="")
-    cat(paste("-",i*100,sep=""))
-    newdat=read.csv(url1,stringsAsFactors = FALSE)
-    dat=rbind(dat,newdat)
   }
-  return(dat)
-}
-
+  else if (argstring == "obs") {
+    per_page <- 200
+    if (recs %% per_page == 0) {
+      loopval <- recs %/% per_page
+    }
+    if (recs >= 10000) {
+      cat(
+        "Number of observations in project greater than current API limit\nreturning the first 10000\n"
+      )
+      loopval <- 10000 / per_page
+    }
+    else {
+      loopval <- (recs %/% per_page) + 1
+    }
+    obs_list <- vector("list", loopval)
+    for (i in 1:loopval) {
+      url1 <-
+        paste0(
+          "http://www.inaturalist.org/observations/project/", grpid,
+          ".json?page=", i,
+          "&per_page=", per_page
+        )
+      if (i == 1) {
+        cat(paste0("0-", per_page))
+      }
+      if (i > 1) {
+        cat(paste0("-", i * per_page))
+      }
+      obs_list[[i]] <-
+        fromJSON(content(GET(url1), as = "text"), flatten = TRUE)
+    }
+    project_obs <- do.call("rbind", obs_list)
+    return(project_obs)
+  }
 }

README.Rmd

@@ -174,12 +174,12 @@ print(place_counts$most_species[1:10,])
 
 
 
-## Mapping.
+## Mapping
 
 Basic maps can be created as well to quickly visualize search results.  Maps can either be plotted automatically `plot = TRUE` or simply return a ggplot2 object with `plot = FALSE`.  This works well with single species data, but more complicated plots are best made from scratch.
 
 
-```{r fig.width=7,fig.height=4}
+```{r fig.width=7, fig.height=4, fig.retina=3}
 library(ggplot2)
 
 ## Map salamanders in the genuse Ambystoma