In pvrqualitasag/PedigreeFromTvdData: Import pedigree data from TVD-Input files

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

require(PedigreeFromTvdData)
require(dplyr)
require(magrittr)

Disclaimer

This document describes a function implementing different functions to check and transform a pedigree. A general description of the strategies is available in a separate vignette on Pedigree Checks - Concepts and Strategies. Further description about the consistency checks implementation is available on Pedigree Checks - Implementations and a description about the transformation implementation is available on Pedigree Transformation - Implementations.

sDataFileErrors <- system.file(file.path("extdata","KLDAT_20170524_AllFehler.txt"), 
                             package = "PedigreeFromTvdData")

(tbl_transform_ped <- build_check_pedigree_from_tvd(ps_tvd_file = sDataFileErrors))

Remaining:

• All dupicate are deleted;

• Parent and offspring birthdates are set to NA, if a parent is not older as offspring;

• Animal sex is set to NA, if the sex is incorrect;

• Animal record is deleted, if his TVD format is incorrect;

• Parent is set to NA, if it's TVD format is incorrect;

• Birthdate is set to NA, if the birthdate format is incorrect.

Time how long is this function running.

sDataFileName <- system.file(file.path("extdata","KLDAT_20170524_10000.txt"), 
                             package = "PedigreeFromTvdData")

(mb.main <- microbenchmark::microbenchmark(
  data.base = PedigreeFromTvdData::build_check_pedigree_from_tvd(ps_tvd_file = sDataFileName,
                                                                 pvec_format = getK11ColPositionVecFromDsch()),
  times = 5, unit = "s"))

Overview of results The following table shows the median times (column MedianTime) in seconds for the function that was used.

vecMethods <- c("PedigreeFromTvdData::build_check_pedigree_from_tvd")
vecMedTimes <- c(mb.main$time[3])
nMinTime <- vecMedTimes[order(vecMedTimes)][1]
dfMedTime <- data.frame(Methode = vecMethods,
                        MedianTime = round(vecMedTimes*10^(-9), digits = 4))
knitr::kable(dfMedTime)

Session Info

sessionInfo()

Latest Update

r paste(Sys.time(),paste0("(", Sys.info()[["user"]],")" ))

pvrqualitasag/PedigreeFromTvdData documentation built on May 29, 2019, 7:50 a.m.