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 |