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purgeR (version 1.8.2)

Inbreeding-Purging Estimation in Pedigreed Populations

Description

Inbreeding-purging analysis of pedigreed populations, including the computation of the inbreeding coefficient, partial, ancestral and purged inbreeding coefficients, and measures of the opportunity of purging related to the individual reduction of inbreeding load. In addition, functions to calculate the effective population size and other parameters relevant to population genetics are included. See López-Cortegano E. (2021) .

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Version

Install

install.packages('purgeR')

Monthly Downloads

276

Version

1.8.2

License

GPL-2

Maintainer

Eugenio L<c3><b3>pez-Cortegano

Last Published

November 28th, 2023

Functions in purgeR (1.8.2)

check_reference

Check columns with reference individuals
dorcas

Dorcas gazelle pedigree
check_repeat_id

Check repeated ids
darwin

Darwin/Wedgwood pedigree
delta_Fi

Individual inbreeding variation
check_not_col

Check if optional column is included
check_names

Check that mandatory column names are included
map_ancestors

Map ancestors
op

Opportunity of purging
check_int

Check if a variable is a positive integer or not
check_tcol

Check columns with generation numbers
idx_ancestors

Index ancestors
check_index

Check individual index
check_types

Check that mandatory column names are of type int
ancestors

Individuals to be evaluated in purging analyses
purgeR

purgeR: Estimation of inbreeding-purging genetic parameters in pedigreed populations
ip_F

Inbreeding coefficient
reproductive_value

Reproductive value
pop_hwd

Deviation from Hardy-Weinberg equilibrium
pop_t

Number of equivalent complete generations
check_zero_id

Check individuals named zero
dama

Dama gazelle pedigree
exp_F

Expected inbreeding coefficient
ped_sort

Sort individuals (with ancestors on top of descendants)
ip_Fa

Ancestral inbreeding coefficient
ped_sort_i

Sorting steps
ip_Fij

Partial inbreeding coefficient
ped_rename

Rename individuals in a pedigree from 1 to N
ped_maternal

Maternal effects
hwd

Deviation from Hardy-Weinberg equilibrium
sample_allele

Sample dam or sire inherited allele
check_bool

Check if a variable is boolean or not
g

Purged inbreeding coefficient
w_grandoffspring

Grandoffspring
w_reproductive_value

Reproductive value
w_offspring

Offspring
search_ancestors

Search and individuals' ancestors
ip_g

Purged inbreeding coefficient
ped_clean

Remove individuals not used for purging analyses
check_order

Check individual order
exp_g

Expected purged inbreeding coefficient
check_nrows

Check observed and expected number of rows
exp_Fa

Expected ancestral inbreeding coefficient
check_col

Check that optional column is included
ip_op

Opportunity of purging
pop_Nancestors

Population founders and ancestors
pop_Ne

Effective population size
ped_graph

Input for igraph
arrui

Arrui pedigree
check_Fcol

Check columns with inbreeding values
Ne_delta

Realized effective population size (mean)
Fij_core

Partial inbreeding coefficient (core function)
Fa

Ancestral inbreeding coefficient
F

Inbreeding coefficient
Fij_core_i_cpp

Partial inbreeding coefficient (core function)
check_Ne

Check Ne
check_length

Check if a variable has length >1
atlas

Cuvier's gazelle pedigree
check_df

Check pedigree class
check_d

Check purging coefficient
check_na

Check if a vector contains NA values
check_ancestors

Check ancestor individuals
check_basic

Check basic