Man pages for purgeR
Inbreeding-Purging Estimation 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_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_Nancestors | Population founders and ancestors |
| pop_Ne | Effective population size |
| pop_t | Number of equivalent complete generations |
| purgeR | purgeR: Estimation of inbreeding-purging genetic parameters... |
| reproductive_value | Reproductive value |
| sample_allele | Sample dam or sire inherited allele |
| search_ancestors | Search and individuals' ancestors |
| w_grandoffspring | Grandoffspring |
| w_offspring | Offspring |
| w_reproductive_value | Reproductive value |
