#' Get the direct ancestors of selected animals
#'
## Copyright(c) 2017-2020 R. Mark Sharp
## This file is part of nprcgenekeepr
#' Gets direct ancestors from labkey \code{study} schema and \code{demographics}
#' table.
#'
#' @return A data.frame with pedigree structure having all of the direct
#' ancestors for the Ids provided.
#'
#' @examples
#' \donttest{
#' library(nprcgenekeepr)
#' ## Have to a vector of focal animals
#' focalAnimals <- c("1X2701", "1X0101")
#' suppressWarnings(getLkDirectRelatives(ids = focalAnimals))
#' }
#'
#' @param ids character vector with Ids.
#' @param unrelatedParents logical vector when \code{FALSE} the unrelated
#' parents of offspring do not get a record as an ego; when \code{TRUE}
#' a place holder record where parent (\code{sire},
#' \code{dam}) IDs are set to \code{NA}.
#'
#' @import futile.logger
#' @importFrom stringi stri_c
#' @export
getLkDirectRelatives <- function(ids, unrelatedParents = FALSE) {
siteInfo <- getSiteInfo()
colSet <- siteInfo$lkPedColumns
source <- " generated by getDemographics in getLkDirectRelatives: "
pedSourceDf <- tryCatch(getDemographics(colSelect = colSet),
warning = function(cond) {
flog.debug(stri_c("Warning", source, cond),
name = "nprcgenekeepr")
return(NULL)},
error = function(cond) {
flog.debug(stri_c("Error", source, cond),
name = "nprcgenekeepr")
return(NULL)}
)
if (is.null(pedSourceDf))
return(NULL)
names(pedSourceDf) <- siteInfo$mapPedColumns
parents <- ids
offspring <- ids
len <- length(parents)
relativesDf <- pedSourceDf[pedSourceDf$id %in% ids, ]
while (len > 0) {
parents <- getParents(pedSourceDf, parents)
offspring <- getOffspring(pedSourceDf, offspring)
len <- length(parents) + length(offspring)
if (len > 0) {
if (length(parents) > 0) {
relativesDf <- rbind(relativesDf,
pedSourceDf[pedSourceDf$id %in% parents, ],
stringsAsFactors = FALSE)
}
if (length(offspring) > 0) {
relativesDf <- rbind(relativesDf,
pedSourceDf[pedSourceDf$id %in% offspring, ],
stringsAsFactors = FALSE)
}
relativesDf <- relativesDf[!duplicated(relativesDf$id), ]
}
}
unrelated <- unique(c(
relativesDf$sire[!relativesDf$sire %in% relativesDf$id],
relativesDf$dam[!relativesDf$dam %in% relativesDf$id]))
addIdRecords(ids = unrelated, fullPed = pedSourceDf, partialPed = relativesDf)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.