R/get_obs_inat.R

In rinat: Access iNaturalist data through APIs

#' Primary function to retrive observations from iNaturalist, allows users to search for data, or just filter results by a subset of what is offered by the API
#' @param query Query string for a general search
#' @param quality the quality grade to be used.  Must be either "casual" or "research"  If left blank both will be returned.
#' @param geo flag for returning only results that are georeferenced, TRUE will exclude non-georeferenced results, but they cannot be excluded.
#' @param year return observations only in that year (can only be one year, not a range of years)
#' @param month return observations only by month, must be numeric, 1...12
#' @param day return observations only on a given day of the month,  1...31
#' @param bounds a bounding box of longitude (-180 to 180) and latitude (-90 to 90) to search within.  It is a vector in the form of southern latitude, western longitude, northern latitude, and easter longitude
#' @param maxresults the maximum number of results to return
#' @return a dataframe of the number of observations requestsed
#' @examples \dontrun{
#'   ### Make a standard query
#'   get_obs_inat(query="Monarch Butterfly")
#'   
#'   ##Filter by a bounding box of Northern California
#'   bounds <- c(38.44047,-125,40.86652,-121.837)
#'   get_obs_inat(query="Mule Deer", bounds=bounds)
#' }
#' @import httr plyr
#' @export



get_obs_inat <- function(query=NULL,quality=NULL,geo=NULL,year=NULL,month=NULL,day=NULL,bounds=NULL,maxresults=100) 
{  
  
  ## Parsing and error-handling of input strings
  search <- ""
  if(!is.null(query)){
    search <- paste(search,"&q=",gsub(" ","+",query),sep="")
  }
  
  if(!is.null(quality)){
    if(!sum(grepl(quality,c("casual","research")))){
      stop("Please enter a valid quality flag,'casual' or 'research'.")
    }
    
    search <- paste(search,"&quality_grade=",quality,sep="")
  }
  
  if(!is.null(geo) && geo){
    search <- paste(search,"&has[]=geo",sep="")
  }
  
  if(!is.null(year)){
    if(length(year) > 1){
      stop("you can only filter results by one year, please enter only one value for year")
    }
    search <- paste(search,"&year=",year,sep="")
  }
  
  if(!is.null(month)){
    month <- as.numeric(month)
    if(is.na(month)){
      stop("please enter a month as a number between 1 and 12, not as a word ")
    }
    if(length(month) > 1){
      stop("you can only filter results by one month, please enter only one value for month")
    }
    if(month < 1 || month > 12){ stop("Please enter a valid month between 1 and 12")}
    search <- paste(search,"&month=",month,sep="")
  }
  
  if(!is.null(day)){
    day <- as.numeric(day)
    if(is.na(day)){
      stop("please enter a day as a number between 1 and 31, not as a word ")
    }
    if(length(day) > 1){
      stop("you can only filter results by one day, please enter only one value for day")
    }
    if(day < 1 || day > 31){ stop("Please enter a valid day between 1 and 31")}
    
    search <- paste(search,"&day=",day,sep="")
  }
  
  if(!is.null(bounds)){
    if(length(bounds) != 4){stop("bounding box specifications must have 4 coordinates")}
    search <- paste(search,"&swlat=",bounds[1],"&swlng=",bounds[2],"&nelat=",bounds[3],"&nelng=",bounds[4],sep="")
    
  }
  
  
  
  base_url <- "http://www.inaturalist.org/"
  q_path <- "observations.csv"
  ping_path <- "observations.json"
  ping_query <- paste(search,"&per_page=1&page=1",sep="")
  ### Make the first ping to the server to get the number of results
  ### easier to pull down if you make the query in json, but easier to arrange results
  ### that come down in CSV format
  ping <-  GET(base_url,path = ping_path, query = ping_query)
  total_res <- as.numeric(ping$headers$`x-total-entries`)
  
  if(total_res == 0){
    stop("Your search returned zero results.  Either your species of interest has no records or you entered an invalid search")
  }
  
  
  
    page_query <- paste(search,"&per_page=200&page=1",sep="")
    data <-  GET(base_url,path = q_path, query = page_query)
    data_out <-read.csv(textConnection(content(data)))
  if(maxresults > 200){
      for(i in 2:ceiling(total_res/200)){
        page_query <- paste(search,"&per_page=200&page=",i,sep="")
        data <-  GET(base_url,path = q_path, query = page_query)
        data_out <- rbind(data_out, read.csv(textConnection(content(data))))
      }
    
  }
  
  if(maxresults < dim(data_out)[1]){
    data_out <- data_out[1:maxresults,]
  }
  
  return(data_out)
}