pedantics (version 1.01)

pedigreeStats: Calculates a range of statistics of pedigrees.

Description

Statistics are those that will hopefully be useful for describing pedigrees to be used in quantitative genetic analyses of natural populations. This module will be most useful when cohort affinities for all individuals can be provided. All outputs are produced in a numerical form as well as in graphical summaries.

Usage

pedigreeStats(Ped, cohorts = NULL, dat = NULL, 
              retain='informative', graphicalReport = "y",
              includeA=TRUE,lowMem=FALSE,grContrast=FALSE)

Arguments

Ped

A pedigree

cohorts

(Optional) Cohort affinities for members of the pedigree

dat

(Optional) Available data based upon which the pedigree can be pruned for just informative individuals

retain

The default value ('informative') results in pedigree being pruned to only those indivduals who's records contribute to estimation of quantitative genetic parameters with respect to the available data specified in dat. Otherwise, specifying

graphicalReport

Controls whether or not grphical output is produced.

includeA

If TRUE, additive genetic relatedness matrix is returned.

lowMem

If TRUE, then stats based on calculation of A are not performed.

grContrast

If TRUE, then uglier shades of red and blue are used to denote male and female statistics in graphical reports, but these colours provide better contrast in greyscale.

Value

• totalMaternities
  Total number of maternities defined by the pedigree.
• totalPaternities
  Total number of paternities defined by the pedigree.
• totalFullSibs
  Total number of pair-wise full sib relationships defined by the pedigree.
• totalMaternalSibs
  Total number of pair-wise maternal sib relationships defined by the pedigree. To get the number of maternal half sibs, subtract totalFullSibs.
• totalPaternalSibs
  Total number of pair-wise paternal sib relationships defined by the pedigree. To get the number of paternal half sibs, subtract totalFullSibs.
• totalMaternalGrandmothers
  Total number of maternal grandmothers defined by the pedigree.
• totalMaternalGrandfathers
  Total number of maternal grandfathers defined by the pedigree.
• totalPaternalGrandmothers
  Total number of paternal grandmothers defined by the pedigree.
• totalPaternalGrandfathers
  Total number of paternal grandfathers defined by the pedigree.
• pedigreeDepth
  The pedidigree pedth, i.e. maximum number of ancestral generations, for each individual.
• inbreedingCoefficients
  Individual inbreeding coefficients
• maternalSibships
  Sibship size of each individual appearing the the dam column of the pedigree.
• paternalSibships
  Sibship size of each individual appearing the the sire column of the pedigree.
• cumulativeRelatedness
  Proportion of pair-wise relatedness values less than values ranging from 0 to 1.
• relatednessCategories
  Discretized distribution of relatedness.
• analyzedPedigree
  Returns the pedigree.
• sampleSizesByCohort
  (Optional) Numer of individuals belonging to each cohort.
• maternitiesByCohort
  (Optional) Number of assigned maternities by offspring cohort.
• paternitiesByCohort
  (Optional) Number of assigned paternities by offspring cohort.
• fullSibsByCohort
  (Optional) Number of pair-wise full sib relationships by cohort - note the sum of these need not be equal to totalFullSibs in pedigrees of long-lived organisms.
• maternalSibsByCohort
  (Optional) Number of pair-wise maternal sib relationships by cohort - note the sum of these need not be equal to totalMaternalSibs in pedigrees of long-lived organisms.
• paternalSibsByCohort
  (Optional) Number of pair-wise paternal sib relationships by cohort - note the sum of these need not be equal to totalPaternalSibs in pedigrees of long-lived organisms.
• maternalGrandmothersByCohort
  (Optional) Numbers of maternal grandmother assignments by offspring cohort.
• maternalGrandfathersByCohort
  (Optional) Numbers of maternal grandmother assignments by offspring cohort.
• paternalGrandmothersByCohort
  (Optional) Numbers of paternal grandfather assignments by offspring cohort.
• paternalGrandfathersByCohort
  (Optional) Numbers of paternal grandfather assignments by offspring cohort.
• cumulativePedigreeDepth
  (Optional) Distributions of pedigree depth by cohort.
• meanRelatednessAmongCohorts
  (Optional) Mean relatedness among cohorts.
• cohorts
  (Optional) Returns cohort designations.
• Graphical summaries of a number of these summary statistics are printed to the console when code{graphicalReports=='y'}.

References

Morrissey, M.B, and A.J. Wilson, 2009. pedantics, an R package for pedigree-based genetic simulation, and pedigree manipulation, characterisation, and viewing. Molecular Ecology Resources.

See Also

fixPedigree

Examples

data(gryphons)
pedigree<-gryphons[,1:3]

gryphonsPedigreeSummary<-pedigreeStats(pedigree,
                       cohorts=gryphons$cohort,graphicalReport='n')

gryphonsPedigreeSummary$totalMaternities
gryphonsPedigreeSummary$totalPaternities

gryphonsPedigreeSummary$maternitiesByCohort
gryphonsPedigreeSummary$paternitiesByCohort