R/bird_species.list.r

In weverkaj/RMN: Tools for the Rangeland Monitoring Network

#' @title Create Species List with common names
#'
#' @description Takes bird data that has been prepared by bird_prepare function and bird_species.common function to create a bird list that can be controlled by transect and surveyyear.
#'
#' @param df A data frame object. Only will take species2 which is created by:  bird_species.common(). See that function for 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)
#'
#' @return A data frame that summerises counts of each bird species per year.
#'
#' @examples data = bird_species.list(species2, "TOKA", 2016)
#'
#' @export bird_species.list
#'

bird_species.list<-function(df,transect=c(levels(as.factor(df$Transect))), surveyyear=c(levels(as.factor(df$YEAR)))){
  df = subset(df, Transect %in% transect)
  df = subset(df, YEAR %in% surveyyear)

  species3<-aggregate(df$COUNT, by=list(Spp=df$Common.Name), FUN=sum)
  names(species3)<-c("Spp", "COUNT")
  species3<-arrange(species3, desc(COUNT))
  df<-species3
  return(df)
}