R/bird_wide.focal.r

In pointblue/RMN.functions:

#' @title Creates a subsetted wide data frame for Point Count data
#'
#' @description For the output of bird_wide.data(). This function subsets the wide dataframe by ranch, year and focal species.
#'
#' @param df is a dataframe. Only works with newpc2 created by add.zeros() and it's previous steps.
#' @param transect A ranch code or a list of ranch codes ie."TOKA".
#' @param surveyyear A year or multiple years. ie. c(2016,2018)
#' @param choose_focal_group Three bird focal groups: Grassland, Oak Woodland, and Riparian. Each contain Spp codes that we consider focal species for that habitat type.
#'
#'
#' @return A subsetted wide data frame by focal group
#'
#' @examples bird_wide.focal(newpc2, "TOKA", surveyyear= 2018, choose_focal_group="Grassland")
#'
#' @export bird_wide.focal
#'



bird_wide.focal<-function(df, distance, transect=c(levels(as.factor(df$Transect))), surveyyear=c(levels(as.factor(df$YEAR))), choose_focal_group= c("Grassland", "Oak Woodland", "Riparian")){
  visits<-bird_visits(df, distance = distance, transect = transect, surveyyear = surveyyear)

  data<-subset(df, subset = df$Distance.Bin <= distance)
  data$Distance.Bin.ID<-as.factor(data$Distance.Bin.ID)
  data = subset(data, Transect %in% transect)
  data = subset(data, YEAR %in% surveyyear)
  df2<-data


  species2<-aggregate(df2$Count,list(df2$Spp , df2$Transect, df2$YEAR, df2$Point),sum)
  names(species2)<-c("Spp", "Transect", "YEAR", "POINT","COUNT")
  species2$PointYear<-as.factor(paste(species2$POINT,species2$YEAR, sep=""))

  species<-left_join(species2, visits, by="PointYear")

  df3<-add.zeros.noCount(species)


  df4<-reshape(df3, v.names="ABUNDANCE", idvar="PointYear",timevar="Spp", direction="wide")

  JustSpp<-substr(names(df4[,6:ncol(df4)]),11,14)
  colnames(df4)[6:ncol(df4)] <- JustSpp

  first<-df4[,1:5]
  second<-df4[,6:length(df4[1,])]
  second<-second[,order(colnames(second))]
  df5<-as.data.frame(cbind(first,second))

  data = subset(data, Transect %in% transect)
  data = subset(data, YEAR %in% surveyyear)
  df5 = subset(df5, df5$YEAR %in% surveyyear)
  df<-df5

  #subset grassland birds, Ferruginous Hawk, Grasshopper Sparrow , Mountain Plover, Northern Harrier,White-tailed Kite, Western Meadowlark

  grassland<-df[,c(1:5)]
  if("MOPL" %in% colnames(df)){grassland6<-select(df, MOPL)
  grassland<-bind_cols(grassland, grassland6)}else{df<-df}
  if("GRSP" %in% colnames(df)){grassland2<-select(df, GRSP)
  grassland<-bind_cols(grassland, grassland2)}else{df<-df}
  if("SAVS" %in% colnames(df)){grassland3<-select(df, SAVS)
  grassland<-bind_cols(grassland, grassland3)}else{df<-df}
  if("WEME" %in% colnames(df)){grassland8<-select(df, WEME)
  grassland<-bind_cols(grassland, grassland8)}else{df<-df}
  if("LOSH" %in% colnames(df)){grassland4<-select(df, LOSH)
  grassland<-bind_cols(grassland, grassland4)}else{df<-df}
  if("FEHA" %in% colnames(df)){grassland5<-select(df, FEHA)
  grassland<-bind_cols(grassland, grassland5)}else{df<-df}
  if("WTKI" %in% colnames(df)){grassland7<-select(df, WTKI)
  grassland<-bind_cols(grassland, grassland7)}else{df<-df}
  if("NOHA" %in% colnames(df)){grassland9<-select(df, NOHA)
  grassland<-bind_cols(grassland, grassland9)}else{df<-df}
  if("BUOW" %in% colnames(df)){grassland10<-select(df, BUOW)
  grassland<-bind_cols(grassland, grassland10)}else{df<-df}
  if("AMKE" %in% colnames(df)){grassland11<-select(df, AMKE)
  grassland<-bind_cols(grassland, grassland11)}else{df<-df}


  oak<-df[,c(1:5)]
  if("ACWO" %in% colnames(df)){oak1<-select(df, ACWO)
  oak<-bind_cols(oak, oak1)}else{df<-df}
  if("NUWO" %in% colnames(df)){oak2<-select(df, NUWO)
  oak<-bind_cols(oak, oak2)}else{df<-df}
  if("ATFL" %in% colnames(df)){oak3<-select(df, ATFL)
  oak<-bind_cols(oak, oak3)}else{df<-df}
  if("WBNU" %in% colnames(df)){oak4<-select(df, WBNU)
  oak<-bind_cols(oak, oak4)}else{df<-df}
  if("WEBL" %in% colnames(df)){oak5<-select(df, WEBL)
  oak<-bind_cols(oak, oak5)}else{df<-df}
  if("OATI" %in% colnames(df)){oak6<-select(df, OATI)
  oak<-bind_cols(oak, oak6)}else{df<-df}
  if("EUST" %in% colnames(df)){oak7<-select(df, EUST)
  oak<-bind_cols(oak, oak7)}else{df<-df}
  if("YBMA" %in% colnames(df)){oak8<-select(df, YBMA)
  oak<-bind_cols(oak, oak8)}else{df<-df}
  if("HUVI" %in% colnames(df)){oak9<-select(df, HUVI)
  oak<-bind_cols(oak, oak9)}else{df<-df}
  if("BEWR" %in% colnames(df)){oak10<-select(df, BEWR)
  oak<-bind_cols(oak, oak10)}else{df<-df}
  if("BLGR" %in% colnames(df)){oak11<-select(df, BLGR)
  oak<-bind_cols(oak, oak10)}else{df<-df}
  if("CALT" %in% colnames(df)){oak12<-select(df, CALT)
  oak<-bind_cols(oak, oak12)}else{df<-df}
  if("CASJ" %in% colnames(df)){oak13<-select(df, CASJ)
  oak<-bind_cols(oak, oak13)}else{df<-df}
  if("LASP" %in% colnames(df)){oak14<-select(df, LASP)
  oak<-bind_cols(oak, oak14)}else{df<-df}
  if("CAQU" %in% colnames(df)){oak15<-select(df, CAQU)
  oak<-bind_cols(oak, oak15)}else{df<-df}

  riparian<-df[,c(1:5)]
  if("ATFL" %in% colnames(df)){riparian1<-select(df, ATFL)
  riparian<-bind_cols(riparian, riparian1)}else{df<-df}
  if("NOFL" %in% colnames(df)){riparian2<-select(df, NOFL)
  riparian<-bind_cols(riparian, riparian2)}else{df<-df}
  if("NUWO" %in% colnames(df)){riparian3<-select(df, NUWO)
  riparian<-bind_cols(riparian, riparian3)}else{df<-df}
  if("LAZB" %in% colnames(df)){riparian4<-select(df, LAZB)
  riparian<-bind_cols(riparian, riparian4)}else{df<-df}
  if("BEWR" %in% colnames(df)){riparian5<-select(df, BEWR)
  riparian<-bind_cols(riparian, riparian5)}else{df<-df}
  if("SPTO" %in% colnames(df)){riparian6<-select(df, SPTO)
  riparian<-bind_cols(riparian, riparian6)}else{df<-df}
  if("YEWA" %in% colnames(df)){riparian7<-select(df, YEWA)
  riparian<-bind_cols(riparian, riparian7)}else{df<-df}
  if("COYE" %in% colnames(df)){riparian8<-select(df, COYE)
  riparian<-bind_cols(riparian, riparian8)}else{df<-df}
  if("YBCH" %in% colnames(df)){riparian9<-select(df, YBCH)
  riparian<-bind_cols(riparian, riparian9)}else{df<-df}
  if("SOSP" %in% colnames(df)){riparian10<-select(df, SOSP)
  riparian<-bind_cols(riparian, riparian10)}else{df<-df}
  if("BHGR" %in% colnames(df)){riparian11<-select(df, BHGR)
  riparian<-bind_cols(riparian, riparian11)}else{df<-df}
  if("BLGR" %in% colnames(df)){riparian12<-select(df, BLGR)
  riparian<-bind_cols(riparian, riparian12)}else{df<-df}
  if("BUOR" %in% colnames(df)){riparian13<-select(df, BUOR)
  riparian<-bind_cols(riparian, riparian13)}else{df<-df}
  if("WAVI" %in% colnames(df)){riparian14<-select(df, WAVI)
  riparian<-bind_cols(riparian, riparian14)}else{df<-df}

  if(("Grassland" %in% choose_focal_group)){df<-grassland}
  if(("Oak Woodland" %in% choose_focal_group)){df<-oak}
  if(("Riparian" %in% choose_focal_group)){df<-riparian }

  df$Richness<-rowSums(df[,6:ncol(df)] != 0)

###########################NEED TO FIX THIS FUNCTION. Currently not filtering properly.
  return(df)
}