Package index • visPedigree

Core Functions

Main tools for processing and visualizing animal pedigrees.

tidyped(): Tidy and prepare a pedigree using graph theory
as_tidyped(): Restore the tidyped class to a manipulated pedigree
is_tidyped(): Test if an object is a tidyped
has_inbreeding(): Check whether a tidyped object contains inbreeding coefficients
has_candidates(): Check whether a tidyped object contains candidate flags
visped(): Visualize a tidy pedigree
splitped(): Split Pedigree into Disconnected Groups

Tools for computing and analyzing genetic relationship matrices.

pedmat(): Genetic Relationship Matrices and Inbreeding Coefficients
expand_pedmat(): Expand a Compact Pedigree Matrix to Full Dimensions
query_relationship(): Query Relationship Coefficients from a Pedigree Matrix
vismat(): Visualize Relationship Matrices

Functions for genealogical and genetic computations.

inbreed(): Calculate inbreeding coefficients
pedancestry(): Calculate Ancestry Proportions
pedcontrib(): Calculate Founder and Ancestor Contributions
pedecg(): Calculate Equi-Generate Coefficient
pedfclass(): Summarize Inbreeding Levels
pedgenint(): Calculate Generation Intervals
pedhalflife() print(<pedhalflife>) plot(<pedhalflife>): Calculate Information-Theoretic Diversity Half-Life
pediv(): Calculate Genetic Diversity Indicators
pedmat(): Genetic Relationship Matrices and Inbreeding Coefficients
pedmeta(): Access pedigree metadata from a tidyped object
pedne(): Calculate Effective Population Size
pedpartial(): Calculate Partial Inbreeding
pedrel(): Calculate Mean Relationship or Coancestry Within Groups
pedstats(): Pedigree Statistics
pedsubpop(): Pedigree Subpopulations

Built-in pedigree examples for testing and demonstration.

Generic methods for ‘tidyped’ and ‘pedmat’ objects.

`[`(<tidyped>): Subset a tidyped object
pedhalflife() print(<pedhalflife>) plot(<pedhalflife>): Calculate Information-Theoretic Diversity Half-Life
plot(<tidyped>): Plot a tidy pedigree
summary(<tidyped>): Summary method for tidyped objects
summary_pedmat(): Summary Statistics for Pedigree Matrices
print(<pedcontrib>): Print Founder and Ancestor Contributions
print(<pediv>): Print Genetic Diversity Summary
print(<pedstats>): Print Pedigree Statistics
print(<summary.tidyped>): Print method for summary.tidyped
print(<tidyped>): Print method for tidyped pedigree