pedtricks package

Functions for sensitivity and power analysis, for calculating statistics describing pedigrees from wild populations, and for visualizing pedigrees.

This package is essentially a reboot of the now archived pedantics package. We took the pedantics package, removed the dependencies on archived packages (MasterBayes), renamed some functions and removed 2 (fpederr() and rpederr()).

Installation

Install with

remotes::install_github(
  "JulienGAMartin/pedtricks"
)

Changes from pedantics

see the News page of pedtricks website for the list of all the changes

speed

Code has been optimized to run faster (over 200 times faster on example pedigree for ped_stats from >160s to <1s)

Defunct functions

• rpederr() and fpederr() have been removed from the package.

The questions about rates of pedigree error typically encountered, and their effects on inference of elementary QG parameters are basically settled (Charmantier & Réale 2005, Morrissey et al. 2007, Firth et al. 2015, Bourret & Garant 2017), and outstanding questions will not plausibly be supported by these functions or any straightforward modifications thereof.

functions structure changes

• pedigreeStats() and pedStatSummary() have been replaced by ped_stats() with a summary() and plot() methods to simplify the workflow and allow to get the plots without running the statistics each time
• makePedigreeFactor() and makePedigreeNumeric() have been combined in convert_ped() which convert a pedigree to numeric or factor

functions renamed

• fixPedigree() is now fix_ped()
• genomesim(), microsim() and phensim() have been renamed as genome_sim(), micro_sim() and phen_sim()

new functions

• ggpedigreedraw pedigrees ggplot style
• draw_pedA graphical representation of the relatedness matrix

future for 1.0.0

• replace drawPedigree by ggpedigree
• reimplement all plot methods from ped_stats using ggplot
• add a plotting function for relatedness matrices
• …

References

Bourret, A., and D. Garant. 2017. An assessment of the reliability of quantitative genetics estimates in study systems with high rate of extra pair paternity and low recruitment. Heredity 118: 229-38.

Charmantier, A., and D. Réale. 2005. How do misassigned paternities affect estimation of heritability in the wild? Molecular Ecology 14: 2839-50

Firth, J.A. J.D. Hadfield, A.W. Santure, J. Slate and B.C. Sheldon. 2015. The influence of non-random extra pair paternity on heritability estimates derived from wild pedigrees. Evolution 69: 1336-44.

Morrissey, M.B., A.J. Wilson, J.M. Pemberton, and M.M. Ferguson. 2007. A framework for power and sensitivity analysis for quantitative genetic studies of natural populations, and a case study in Soay sheep (Ovis aries). Journal of Evolutionary Biology 20: 2309-21.