R/alleleDataValidityCheck.R

In ndukler/phyloGLM: Tests for signals of variable rates of evolution between gene classes and lineages for probabalistic alleles

#' @description  Validity checker for alleleData-class
alleleDataValidityCheck <- function(object) {
  errors <- c()
  if (class(object@tree) != "phylo") {
    errors <- c(errors, "Tree must be of class phylo")
  }
  ## Check that there are a minimum of two alleles
  if (object@nAlleles <= 1) {
    errors <- c(errors, "Less than two alleles per species")
  }
  ## Check that tree is unrooted
  # if(ape::is.rooted(object@tree)){
  #   errors=c(errors,c("Tree must be unrooted."))
  # }
  ## Check that tree is post-ordered
  if (any(object@tree$edge != ape::reorder.phylo(object@tree, "postorder")$edge)) {
    errors <- c(errors, c("Tree must be sorted in post-order travel order."))
  }
  ## Check that the number of sites are correct
  # if(nrow(object@data)!=object@nSites){
  #   errors=c(errors,c("Incorrect number of sites"))
  # }
  
  ## Check that all of the columns in site info are either numeric, factors, or integers
  if(!all(sapply(object@siteInfo,class) %in% c("numeric","factor","integer","logical"))){
    stop("All siteInfo columns must be either numeric, logical, or factors.")
  }
  
  ## Check that there are the same number of rows in the siteInfo data.frame as there are rows in the data
  if (length(errors) == 0) TRUE else errors
}