R/cdb_compare.R

In Rcompadre: Utilities for using the 'COM(P)ADRE' Matrix Model Database

#' Compare two versions or subsets of a COM(P)ADRE database
#'
#' Prints a summary of the differences between two CompadreDB objects, including
#' the number of species, studies, and matrices in each. If argument
#' \code{verbose == TRUE}, additionally prints a list of the species and studies
#' that are present in one database but not the other.
#'
#' @param cdb1,cdb2 CompadreDB objects to compare
#' @param verbose Logical argument indicating whether or not to return lots of
#'   detail
#'
#' @return NULL. Output is printed rather than returned.
#'
#' @author Owen R. Jones <jones@@biology.sdu.dk>
#'
#' @family data checking
#'
#' @examples
#' Compadre1 <- subset(Compadre, Continent == "Asia")
#' Compadre2 <- subset(Compadre, Continent == "Africa")
#'
#' cdb_compare(Compadre1, Compadre2)
#'
#' @export cdb_compare
cdb_compare <- function(cdb1, cdb2, verbose = FALSE) {
  if (!inherits(cdb1, "CompadreDB") || !inherits(cdb2, "CompadreDB")) {
    stop("cdbs must be of class CompadreDB. See function as_cdb")
  }

  # Quick summary
  cat("Quick Summary...\n\n")

  # File 1
  cat(paste0(
    "cdb1 contains data for:\n",
    NumberStudies(cdb1), " source papers\n",
    NumberAcceptedSpecies(cdb1), " accepted species\n",
    NumberMatrices(cdb1), " matrices\n\n"
  ))

  # File 2
  cat(paste0(
    "cdb2 contains data for:\n",
    NumberStudies(cdb2), " source papers\n",
    NumberAcceptedSpecies(cdb2), " accepted species\n",
    NumberMatrices(cdb2), " matrices\n\n"
  ))

  if (verbose == TRUE) {
    cat("Detailed summary...\n\n")

    # Accepted species in File 1 that are not in File 2
    sp1 <- unique(cdb1$SpeciesAccepted)
    sp2 <- unique(cdb2$SpeciesAccepted)

    cat("Species in cdb1 not in cdb2:\n")
    print(sp1[which(!sp1 %in% sp2)])

    cat("Species in cdb2 not in cdb1:\n")
    print(sp2[which(!sp2 %in% sp1)])

    uniqueSource1 <- unique(paste0(
      cdb1$Authors, " (",
      cdb1$YearPublication, ") ",
      cdb1$Journal
    ))

    uniqueSource2 <- unique(paste0(
      cdb2$Authors, " (",
      cdb2$YearPublication, ") ",
      cdb2$Journal
    ))

    cat("\n\nSource papers in cdb2 not in cdb1\n")
    print(sort(uniqueSource2[which(!uniqueSource2 %in% uniqueSource1)]))

    cat("\n\nSource papers in cdb1 not in cdb2\n")
    print(sort(uniqueSource1[which(!uniqueSource1 %in% uniqueSource2)]))

    cat("See the User Guide for definitions\n")
  }
}