Deprecated functions from package pedantics.

The functions listed below are deprecated and are available for backward compatibility only. They might be defunct in a future version When possible, alternative functions with similar functionality are also mentioned.

Usage

makemakePedigreeFactor(id, sire, dam, key = NULL)

makePedigreeNumeric(id, sire, dam, missingVal = NA)

drawPedigree(
  Ped,
  cohorts = NULL,
  sex = NULL,
  dat = NULL,
  dots = "n",
  plotfull = "y",
  writeCohortLabels = "n",
  links = "all",
  sexInd = c(0, 1),
  dotSize = 0.001,
  dataDots = "n",
  dataDots.cex = 2,
  cohortLabs.cex = 1,
  retain = "informative",
  focal = NULL,
  sexColours = c("red", "blue"),
  ...
)

fixPedigree(ped, dat = NULL)

genomesim(
  pedigree,
  founders = NULL,
  positions = NULL,
  initHe = NULL,
  mutationType = NULL,
  mutationRate = NULL,
  phenotyped = NULL,
  founderHaplotypes = NULL,
  genotyped = NULL,
  returnG = "n",
  initFreqs = NULL
)

microsim(
  pedigree,
  genFreqs = NULL,
  genotypesSample = NULL,
  knownGenotypes = NULL,
  records = NULL,
  eRate1 = 0,
  eRate2 = 0,
  eRate3 = 0
)

pedigreeStat()

pedStatSummary()

phensim(
  pedigree,
  traits = 1,
  randomA = NULL,
  randomE = NULL,
  parentalA = NULL,
  parentalE = NULL,
  sampled = NULL,
  records = NULL,
  returnAllEffects = FALSE
)

Value

dependant on the deprecated function see pedantics help for details

makePedigreeFactor

the function is now a special case of the convert_ped function when type is factor

makePedigreeNumeric

the function is now a special case of the convert_ped function when type is numeric

drawPedigree

the function has just been renamed with no other changes for the moment, but will soon be replace by "ggpedigree" function

fixPedigree

the function has just been renamed with no other changes for the moment

genomesim

the function has just been renamed with no other changes for the moment

microsim

the function has just been renamed with no other changes for the moment

pedigreeStats

the function has been simplified but only the functionality are still available via ped_stats and its summary and plot methods

pedStatSummary

the function has been simplified but only the functionality are still available via ped_stats and its summary and plot methods

phensim

the function has just been renamed with no other changes for the moment