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breedr

An R package for analyzing and visualizing pedigrees

Package Contents:

  • nameR() - A helper function that attempts to standardize names with pesky inconsistencies
  • plotigree() - Quick assembly of pedigrees plots
  • breedr_f() - Calculates Wright's F statistic from pedigree data
  • breedr_COP() - Computes a Coefficient of Parentage matrix from pedigree data
  • replace_name() - A function that replaces names using a key. Helpful when going from selection numbers to cultivar names (similar to Excel's vlookup function).
  • habsburg - A small set of pedigree data from an infamously inbred royal family...
  • xplotter() - An interactive GUI for crossing simulations

Installation Instructions

Simply run the following two lines of code in an R session

install.packages("devtools")
devtools::install_github("mchizk1/breedr")

breedr input format - the Habsburg Dynasty example

Once upon a time, in a far away land, there lived a king who was very inbred. Run the following to see an example of the simple 3-column format required for breedr datasets. Column 1 - individual ID Column 2 - female parent ID Column 3 - male parent ID

library(breedr)
head(habsburg)

Plotigree() Demonstration

The plotigree() function uses the DiagrammeR package to make dynamic flowchart representations of family tree plots.

The "FULL" (default) method displays the entire tree with color coding for parental sex:

plotigree(habsburg, "charles the bewitched", orientation = "LR")

FULL

The "CA" method displays a similar tree, but is consolidated by common ancestry. Common ancestors are highlighted in yellow:

plotigree(habsburg, "charles the bewitched", method = "CA")

CA

Inbreeding and Kinship Statistics

To calculate the inbreeding coefficients (F) of all unique individuals in a dataset, run this:

breedr_F(habsburg)

And for a kinship matrix (coefficients of parentage), run this (this one can take a while):

breedr_COP(habsburg)