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pedtricks (version 0.4.2)

makemakePedigreeFactor: Deprecated functions from package pedantics.

Description

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
)

Arguments

Value

dependant on the deprecated function see pedantics help for details

<code>makePedigreeFactor</code>

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

<code>makePedigreeNumeric</code>

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

<code>drawPedigree</code>

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

<code>fixPedigree</code>

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

<code>genomesim</code>

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

<code>microsim</code>

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

<code>pedigreeStats</code>

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

<code>pedStatSummary</code>

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

<code>phensim</code>

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