Inbreeding-Purging Estimation in Pedigreed Populations

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Documentation for package ‘purgeR’ version 1.8

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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purgeR-package	purgeR: Estimation of inbreeding-purging genetic parameters in pedigreed populations
ancestors	Individuals to be evaluated in purging analyses
arrui	Arrui pedigree
atlas	Cuvier's gazelle pedigree
check_ancestors	Check ancestor individuals
check_basic	Check basic
check_bool	Check if a variable is boolean or not
check_col	Check that optional column is included
check_d	Check purging coefficient
check_df	Check pedigree class
check_Fcol	Check columns with inbreeding values
check_index	Check individual index
check_int	Check if a variable is a positive integer or not
check_length	Check if a variable has length >1
check_na	Check if a vector contains NA values
check_names	Check that mandatory column names are included
check_Ne	Check Ne
check_not_col	Check if optional column is included
check_nrows	Check observed and expected number of rows
check_order	Check individual order
check_reference	Check columns with reference individuals
check_repeat_id	Check repeated ids
check_target	Check columns with reference individuals
check_tcol	Check columns with generation numbers
check_types	Check that mandatory column names are of type int
check_zero_id	Check individuals named zero
dama	Dama gazelle pedigree
darwin	Darwin/Wedgwood pedigree
delta_Fi	Individual inbreeding variation
dorcas	Dorcas gazelle pedigree
exp_F	Expected inbreeding coefficient
exp_Fa	Expected ancestral inbreeding coefficient
exp_g	Expected purged inbreeding coefficient
F	Inbreeding coefficient
Fa	Ancestral inbreeding coefficient
Fij_core	Partial inbreeding coefficient (core function)
Fij_core_i_cpp	Partial inbreeding coefficient (core function)
g	Purged inbreeding coefficient
hwd	Deviation from Hardy-Weinberg equilibrium
idx_ancestors	Index ancestors
ip_F	Inbreeding coefficient
ip_Fa	Ancestral inbreeding coefficient
ip_Fij	Partial inbreeding coefficient
ip_g	Purged inbreeding coefficient
ip_op	Opportunity of purging
map_ancestors	Map ancestors
Ne_delta	Realized effective population size (mean)
op	Opportunity of purging
ped_clean	Remove individuals not used for purging analyses
ped_graph	Input for igraph
ped_maternal	Maternal effects
ped_rename	Rename individuals in a pedigree from 1 to N
ped_sort	Sort individuals (with ancestors on top of descendants)
ped_sort_i	Sorting steps
pop_hwd	Deviation from Hardy-Weinberg equilibrium
pop_Na	Population founders and ancestors
pop_Nae	Population founders and ancestors
pop_Nancestors	Population founders and ancestors
pop_Ne	Effective population size
pop_Nf	Population founders and ancestors
pop_Nfe	Population founders and ancestors
pop_Ng	Population founders and ancestors
pop_t	Number of equivalent complete generations
purgeR	purgeR: Estimation of inbreeding-purging genetic parameters in pedigreed populations
reproductive_value	Reproductive value
sample_allele	Sample dam or sire inherited allele
search_ancestors	Search and individuals' ancestors
se_Ne_delta	Realized effective population size (mean)
sort_step	Sorting steps
w_grandoffspring	Grandoffspring
w_offspring	Offspring
w_reproductive_value	Reproductive value