eBirdAnalysis/ebird_pre_processing.R at master · mkmitchell/eBirdAnalysis · GitHub

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library(scales)

############################################################################
# Setup environment and variables
############################################################################
# Variable designiation
# Workspace directory
workspace = "D:/ebird/datadownload"
# Input ArcGIS Model csv file
birdlist = list( "agwtea1",  "ambduc", "amewig", "bargol", "blksco2", "buwtea", "buffle", "canvas", "cintea", "comeid", "comgol", "commer", "kineid", "gadwal", "gresca", "harduc", "hoomer", "lessca", "lotduc", "mallar", "norpin", "norsho", "rebmer", "redhea", "rinduc", "rudduc", "sursco", "whwsco", "wooduc")
for (sp in 1:length(birdlist)) {
#  if (any(c("buffle", "comeid", "kineid", "lotduc") == birdlist[[sp]])){
#    inbird = paste("ebd_",birdlist[[sp]], "_relMay-2017.txt", sep="")
#  } else {
#    inbird = paste("ebd_",birdlist[[sp]], "_relNov-2016.txt", sep="")
#  }
  inbird = paste("ebd_",birdlist[[sp]], "_relAug-2017.txt", sep="")
  bcr = "BCR.csv"
  ############################################################################
  # Read in ebird data (16 species)
  ebird <- read.delim(paste(workspace,inbird,sep="/"), sep="\t", header=TRUE, quote = "", stringsAsFactors = FALSE, na.strings=c(""))
  bcr = read.csv(paste(workspace, bcr, sep="/"), header=TRUE)
  # Join arcData to coverData based on cover_type
  ebird = merge(ebird, bcr, by.x = "BCR.CODE", by.y = "BCR")
  setwd(workspace)

  # Drop extra columns and data
  #ebird = subset(ebird, ebird$COUNTRY_CODE == "US")
  ebird = subset(ebird, ebird$APPROVED == "1")
  ebird$PROJECT.CODE = NULL
  ebird$PROTOCOL.TYPE = NULL
  ebird$SAMPLING.EVENT.IDENTIFIER = NULL
  ebird$FIRST.NAME = NULL
  ebird$LAST.NAME = NULL
  ebird$OBSERVER.ID = NULL
  ebird$BREEDING.BIRD.ATLAS.CODE = NULL
  ebird$GLOBAL.UNIQUE.IDENTIFIER = NULL
  ebird$SUBSPECIES.COMMON.NAME = NULL
  ebird$SUBSPECIES.SCIENTIFIC.NAME = NULL
  ebird$AGE.SEX = NULL
  ebird$COUNTRY = NULL
  ebird$IBA.CODE = NULL
  ebird$SUBNATIONAL1_CODE = NULL
  ebird$SUBNATIONAL2_CODE = NULL
  ebird$ATLAS.BLOCK = NULL
  ebird$LOCALITY = NULL
  ebird$LOCALITY.ID = NULL
  ebird$LOCALITY.TYPE = NULL
  ebird$REVIEWED = NULL
  ebird$REASON = NULL
  ebird$TRIP.COMMENTS = NULL
  ebird$EFFORT.AREA.HA = NULL
  ebird$EFFORT.DISTANCE.KM = NULL
  ebird$SPECIES.COMMENTS = NULL
  ebird$X = NULL
  ebird$APPROVED = NULL
  ebird$TIME.OBSERVATIONS.STARTED = NULL
  ebird$DURATION.MINUTES = NULL
  ebird$NUMBER.OBSERVERS = NULL
  ebird$ALL.SPECIES.REPORTED = NULL
  ebird$GROUP.IDENTIFIER = NULL
  ebird$TAXONOMIC.ORDER = NULL
  ebird$CATEGORY = NULL

  # Set date field and divide up by year, month, week for plotting
  ebird$Date = as.Date(ebird$OBSERVATION.DATE, "%Y-%m-%d")
  ebird$Year = strtoi(format(ebird$Date, "%Y"))
  to.month = function(x) as.integer(format(x, "%m"))
  to.day <- function(x) as.integer(format(x, "%d"))
  ebird$Month = to.month(ebird$Date)
  ebird$Day = to.day(ebird$Date)
  ebird$MonthDay = paste(ebird$Month, ebird$Day, sep="/")
  # Remove years < 2005 and months 6,7,8
  ebird = subset(ebird, ebird$Year > 2000 & ebird$Year <= 2016)
  ebird = subset(ebird, ebird$Month >= 9 | ebird$Month <= 4)

  ebird$Winter = ifelse(ebird$Month <= 4, paste(ebird$Year - 1,ebird$Year, sep = "/"),paste(ebird$Year, ebird$Year + 1, sep = "/"))
  ebird$Week = as.numeric(format(ebird$Date, "%U"))
  ebird = subset(ebird, ebird$Winter != "2000/2001" & ebird$Winter != "2016/2017")

  ebird$OBSERVATION.COUNT = ifelse(ebird$OBSERVATION.COUNT == "X", 1, ebird$OBSERVATION.COUNT)
  ebird$OBSERVATION.COUNT = as.numeric(ebird$OBSERVATION.COUNT)

  write.csv(ebird, file=paste(workspace, "/post/", paste(inbird, "post.csv", sep="_"), sep=""), quote=FALSE, row.names=FALSE)
}