R: Inbreeding-Purging Estimation in Pedigreed Populations

# Inbreeding-Purging Estimation in Pedigreed Populations

## Documentation for package ‘purgeR’ version 1.8.3

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

## Help Pages

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_B | Check B
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_F | Check inbreeding coefficient
check_Fcol | Check columns with inbreeding values
check_h | Check dominance degree
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_null | Check if a value is NULL
check_order | Check individual order
check_reference | Check columns with reference individuals
check_repeat_id | Check repeated ids
check_s | Check selection coefficient
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_u | Check u
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