R/URsum.R

Defines functions URsum

Documented in URsum

#' Sum of all Use Reports (UR) for all species
#'
#' Calculates the sum of all ethnobotany use reports (UR) for all species, a common metric for ethnobotany studies.
#' @usage URsum(data)
#' 
#' @references  
#' Prance, G. T., W. Balee, B. M. Boom, and R. L. Carneiro. 1987. “Quantitative Ethnobotany and the Case for Conservation in Amazonia.” Conservation Biology 1 (4): 296–310.
#' 
#' @param data is an ethnobotany data set with column 1 'informant' and 2 'sp_name' as row identifiers of informants and of species names respectively.
#' The rest of the columns are the identified ethnobotany use categories. The data should be populated with counts of uses per person (should be 0 or 1 values).
#' 
#' @keywords arith math logic methods misc survey
#'
#' @return Single value sum of all ethnobotany use reports (UR) for all species in the data.
#' 
#' @section Warning:
#' 
#' Identification for informants and species must be listed by the names 'informant' and 'sp_name' respectively in the data set.
#' The rest of the columns should all represent separate identified ethnobotany use categories. These data should be populated with counts of uses per informant (should be 0 or 1 values).
#' 
#' @importFrom dplyr select
#'
#' @examples
#' 
#' #Use built-in ethnobotany data example
#' URsum(ethnobotanydata)
#' 
#' #Generate random dataset of three informants uses for four species
#' 
#' eb_data <- data.frame(replicate(10,sample(0:1,20,rep=TRUE)))
#' names(eb_data) <- gsub(x = names(eb_data), pattern = "X", replacement = "Use_")  
#' eb_data$informant <- sample(c('User_1', 'User_2', 'User_3'), 20, replace=TRUE)
#' eb_data$sp_name <- sample(c('sp_1', 'sp_2', 'sp_3', 'sp_4'), 20, replace=TRUE)
#' 
#' URsum(eb_data)
#' 
#' @export URsum
#' 
URsum <- function(data) {
  
  #Add error stops ####
  #Check that packages are loaded
    {
  if (!requireNamespace("dplyr", quietly = TRUE)) {
    stop("Package \"dplyr\" needed for this function to work. Please install it.",
         call. = FALSE)
  }

    }# end package check
    
    ## Check that use categories are greater than zero
    if (!any(sum(dplyr::select(data, -informant, -sp_name)>0))){
      warning("The sum of all UR is not greater than zero. Perhaps not all uses have values or are not numeric.")
      data<-data[stats::complete.cases(data), ]
    }
    
    ## Use 'complete.cases' from stats to get to the collection of obs without NA
    if (any(is.na(data))) {
      warning("Some of your observations included \"NA\" and were removed. Consider using \"0\" instead.")
      data<-data[stats::complete.cases(data), ]
    }#end error stops
  
  # Set the variables to NULL first, appeasing R CMD check
  URsum <- informant <- sp_name <- NULL 
  
  #Calculate sum of UR
  URsum <-  sum(dplyr::select(data, -informant, -sp_name))
  
  URsum
}
CWWhitney/ethnobotanyR documentation built on May 1, 2023, 10:13 a.m.