Philipp R PhillRob
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PhillRob
/ rbind.keep.columns
Last active
August 29, 2015 14:24
rbind data frames with miss matching columns
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| 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
Last active
August 29, 2015 14:24
use google API to get match lon/lat data to country and state
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| 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$status != 200) { |
PhillRob
/ point.2.poly
Last active
August 29, 2015 14:24
match point data to country/state/region boundary polygon
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| # Matching point records to polygones boundaries of a country, state or | |
| # region polygones for regions of NZ | |
| require(maptools) | |
| library(maps) | |
| library(SDMTools) | |
| # obtain lon/lat boundaries for north and south island of NZ | |
| nz.n.poly <- cbind(map("nz", regions = "North.Island")$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.R
Last active
August 29, 2015 14:27
— forked from mrdwab/stratifiedDT.R
Attempt to rewrite stratified for `data.table`. The `data.frame` version can be found at https://gist.github.com/mrdwab/6424112
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| 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.R
Last active
September 1, 2015 11:44
this runs through nzpcn.org.nz and gets native range and naturalised year. used to run: w<-matrix(rep(1:7700)) test <- sapply(w, function(x) nat.year.nzpcn(x))
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| 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.R
Last active
September 17, 2015 08:21
long/lat data from location description
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| 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.R
Last active
September 24, 2015 06:58
returns the first 8 trait values for any given species in EOL relying on the reol, traints and dplyr packages.
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| 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
/ issg-check.R
Last active
October 21, 2015 10:28
checks if species is included in issg.org
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| 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
/ kew.sid.scraping.R
Last active
December 31, 2015 07:24
scraping for dispersal data on the kew/sid website.
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| 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
/ harvesine.dist.R
Created
January 2, 2016 05:50
test the distance between two strata within a species.
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| 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)) |
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