PhillRob

rbind.keep.columns <- function(x, y) {
    x.dif <- setdiff(colnames(x), colnames(y))
    y.dif <- setdiff(colnames(y), colnames(x))
     x[, c(as.character(y.dif))] <- NA
     y[, c(as.character(x.dif))] <- NA
     return(rbind(x, y))
}

PhillRob

reverseGeo <- function(latlng) {
    require("XML")
    require("httr")
    latlng <- as.numeric(latlng)
    latlngStr <- gsub(" ", "%20", paste(round(latlng, 2), collapse = ","))
    url <- "http://maps.google.com"
    path <- "/maps/api/geocode/xml"
    query <- list(sensor = "false", latlng = latlngStr)
    response <- GET(url, path = path, query = query)
    if (response$status != 200) {

PhillRob

# Matching point records to polygones boundaries of a country, state or
# region polygones for regions of NZ
require(maptools)
library(maps)
library(SDMTools)
# obtain lon/lat boundaries for north and south island of NZ
nz.n.poly <- cbind(map("nz", regions = "North.Island")$x, map("nz", regions = "North.Island")$y)
nz.s.poly <- cbind(map("nz", regions = "South.Island")$x, map("nz", regions = "South.Island")$y)

# match to points where d[(6:5)] are the columns of a dataframe containing lon/lat data

PhillRob

stratifiedDT <- function(indt, group, size, select = NULL, 
                         replace = FALSE, keep.rownames = FALSE,
                         bothSets = FALSE) {
  require(data.table)
  if (is.numeric(group)) group <- names(indt)[group]
  if (!is.data.table(indt)) indt <- as.data.table(
    indt, keep.rownames = keep.rownames)
  if (is.null(select)) {
    indt <- indt
  } else {

PhillRob

nat.year.nzpcn <- function(x) {
    sp <- getURL(paste0("http://nzpcn.org.nz/flora_details.aspx?ID=", x))
    if (length(grep("Error: Cannot find species with ID =", sp))) {
        return("Not_found")
    } else {
        flush.console()
        sp.st <- unlist(gregexpr(pattern = "<title>", sp, ignore.case = F, 
                                 fixed = T))
        sp.end <- unlist(gregexpr(pattern = " | New Zealand Plant Conservation Network", 
                                  sp, ignore.case = F, fixed = T))

PhillRob

getGeoCode <- function(gcStr, countryID)  {
    #library("RJSONIO") #Load Library
    print(gcStr)
    apik<-"AIzaSyCAaXX1jrJoD19uHBUnL97xpegOUxsDeSw"
    apik1<-"AIzaSyA1rQIGrUfizL6E4mE22RhUh_X5saYPMU0"
    gcStr <- gsub(' ','%20',gcStr) #Encode URL Parameters
    #Open Connection
    data.json <- fromJSON(paste(getURL(paste('https://maps.google.com/maps/api/geocode/json?sensor=false&address=',gcStr, '&components=country:',countryID,sep=""))))
    #'&key=',apik1
    #Flatten the received JSON

PhillRob

get.eol.trait <- function(sp,trait)
{
    if (length(trait)==0)
    {
        print("need trait")
        stop()
    }
    library("reol"); library("traits"); library("dplyr")
    pages<-DownloadSearchedTaxa(sp, to.file=F, MyKey=NULL, verbose=TRUE)
    pages1<-as.numeric(gsub("eol","",colnames(as.data.frame(pages))))

PhillRob

isgg<- function(x) {
    species<-gsub(" ","+",x)
    sp <- getURL(paste0("http://www.issg.org/database/species/search.asp?sts=sss&st=sss&fr=1&x=16&y=13&sn=", species,"&rn=&hci=-1&ei=-1&lang=EN"))
  
    if (length(grep("No invasive species currently recorded",sp))) {
        return("Not_found")
    } else {return("Found")}
}

PhillRob

disp.sp <- function(x) {
  print(x)
  x.genus <- unlist( strsplit(x," "))[1]
  x.species <- unlist( strsplit(x," "))[2]
  sp.test <- getURL(paste0("http://data.kew.org/sid/SidServlet?Clade=&Order=&Family=&APG=off&Genus=", x.genus,"&Species=",x.species,"&StorBehav=0&DsFlag=on"))
  
  if (grepl("0 records found.", sp.test)) 
    {
    #return("Not_found")
    results<-c(x,"Not_found")

PhillRob

ha <- function(x){
    x$Lat<-(as.numeric(paste(x$Lat)))
    x$Lon<-(as.numeric(paste(x$Lon)))
    pre<-x[(x[,17]==0),]
    post<-x[(x[,17]==1),]
    if(nrow(pre)<2| nrow(post)<2){results<-paste("not enought records per phase")}else{
    early <- x[(which.min(x$Year)),]
    e1 <- early[1,]
    predist<-apply(pre, 1, function(x) distHaversine(as.numeric(e1[4:3]),as.numeric(x[4:3]), r=6378137))
    postdist<-apply(post, 1, function(x) distHaversine(as.numeric(e1[4:3]),as.numeric(x[4:3]), r=6378137))