Global functions | |
---|---|
+.coalmodelpart | Man page |
.onLoad | Source code |
activate_ms | Man page Source code |
activate_msms | Man page Source code |
activate_scrm | Man page Source code |
activate_seqgen | Man page Source code |
add_to_model | Source code |
add_to_model.default | Source code |
add_to_model.feature | Source code |
add_to_model.locus | Source code |
add_to_model.named_par | Source code |
add_to_model.parameter | Source code |
add_to_model.partial_model | Source code |
add_to_model.sumstat | Source code |
add_to_model.variation_par | Source code |
add_variation | Source code |
as.matrix.segsites | Source code |
as.segsites | Man page Source code |
as.segsites.GENOME | Man page Source code |
as.segsites.default | Source code |
as.segsites.list | Source code |
cache | Source code |
calc_four_gamete_stat | Source code |
calc_jsfs | Man page Source code |
calc_mcmf | Source code |
calc_nucleotide_div | Source code |
calc_sumstats | Source code |
calc_sumstats_from_data | Man page Source code |
calc_sumstats_from_sim | Source code |
check_model | Man page Source code |
coal_model | Man page Source code |
coala | Man page |
coala-package | Man page |
coalmodelpart | Man page |
combine_results | Source code |
conv_for_trios | Source code |
conv_middle_to_trio_pos | Source code |
conv_to_ms_arg | Man page Source code |
conv_to_ms_arg.default | Man page Source code |
conv_to_ms_arg.files_feat | Man page |
conv_to_ms_arg.growth | Man page Source code |
conv_to_ms_arg.ign_singletons | Man page |
conv_to_ms_arg.migration | Man page Source code |
conv_to_ms_arg.mutation | Man page Source code |
conv_to_ms_arg.outgroup | Man page Source code |
conv_to_ms_arg.pop_merge | Man page Source code |
conv_to_ms_arg.recombination | Man page Source code |
conv_to_ms_arg.sample | Man page Source code |
conv_to_ms_arg.seg_sites_feat | Man page Source code |
conv_to_ms_arg.selection | Man page Source code |
conv_to_ms_arg.size_change | Man page Source code |
conv_to_ms_arg.trees_feat | Man page Source code |
conv_to_ms_arg.unphased | Man page |
conv_to_ms_output | Source code |
conv_to_msms_arg | Source code |
conv_to_msms_arg.default | Man page Source code |
conv_to_msms_arg.files_feat | Man page |
conv_to_msms_arg.growth | Man page |
conv_to_msms_arg.ign_singletons | Man page |
conv_to_msms_arg.migration | Man page |
conv_to_msms_arg.mutation | Man page |
conv_to_msms_arg.outgroup | Man page Source code |
conv_to_msms_arg.pop_merge | Man page |
conv_to_msms_arg.recombination | Man page |
conv_to_msms_arg.sample | Man page |
conv_to_msms_arg.seg_sites_feat | Man page |
conv_to_msms_arg.selection | Man page Source code |
conv_to_msms_arg.size_change | Man page |
conv_to_msms_arg.trees_feat | Man page |
conv_to_msms_arg.unphased | Man page |
conv_to_scrm_arg | Source code |
conv_to_scrm_arg.default | Man page Source code |
conv_to_scrm_arg.files_feat | Man page |
conv_to_scrm_arg.growth | Man page |
conv_to_scrm_arg.ign_singletons | Man page |
conv_to_scrm_arg.migration | Man page |
conv_to_scrm_arg.mutation | Man page Source code |
conv_to_scrm_arg.outgroup | Man page Source code |
conv_to_scrm_arg.pop_merge | Man page |
conv_to_scrm_arg.recombination | Man page |
conv_to_scrm_arg.sample | Man page |
conv_to_scrm_arg.seg_sites_feat | Man page |
conv_to_scrm_arg.selection | Man page |
conv_to_scrm_arg.size_change | Man page |
conv_to_scrm_arg.trees_feat | Man page |
conv_to_scrm_arg.unphased | Man page |
conv_to_seqgen_arg | Source code |
conv_to_seqgen_arg.default | Man page Source code |
conv_to_seqgen_arg.files_feat | Man page |
conv_to_seqgen_arg.growth | Man page |
conv_to_seqgen_arg.ign_singletons | Man page |
conv_to_seqgen_arg.migration | Man page |
conv_to_seqgen_arg.mutation | Man page Source code |
conv_to_seqgen_arg.outgroup | Man page |
conv_to_seqgen_arg.pop_merge | Man page |
conv_to_seqgen_arg.recombination | Man page |
conv_to_seqgen_arg.sample | Man page Source code |
conv_to_seqgen_arg.seg_sites_feat | Man page |
conv_to_seqgen_arg.selection | Man page |
conv_to_seqgen_arg.size_change | Man page |
conv_to_seqgen_arg.trees_feat | Man page Source code |
conv_to_seqgen_arg.unphased | Man page |
create_abc_param | Man page Source code |
create_abc_sumstat | Man page Source code |
create_empty_segsites | Source code |
create_group_model | Source code |
create_locus_trio | Man page Source code |
create_par_env | Source code |
create_popgenome_test_data | Source code |
create_segsites | Man page Source code |
create_sim_task | Source code |
create_sumstat_container | Source code |
create_test_segsites | Source code |
create_zero_frac_func | Source code |
dim.segsites | Source code |
feat_growth | Man page Source code |
feat_ignore_singletons | Man page Source code |
feat_migration | Man page Source code |
feat_mutation | Man page Source code |
feat_outgroup | Man page Source code |
feat_pop_merge | Man page Source code |
feat_recombination | Man page Source code |
feat_sample | Man page Source code |
feat_selection | Man page Source code |
feat_size_change | Man page Source code |
feat_unphased | Man page Source code |
fill_cmd_template | Source code |
generate_sim_tasks | Source code |
generate_tree_model | Source code |
generate_trio_trees | Source code |
get_cmd | Source code |
get_feature_unphased | Source code |
get_features | Man page Source code |
get_id | Source code |
get_loci | Source code |
get_locus_group | Source code |
get_locus_group_number | Source code |
get_locus_length | Man page Source code |
get_locus_length_matrix | Man page Source code |
get_locus_number | Man page Source code |
get_outgroup | Man page Source code |
get_outgroup_size | Man page Source code |
get_par_names | Source code |
get_parameter | Man page Source code |
get_parameter_table | Man page Source code |
get_ploidy | Source code |
get_population_individuals | Man page Source code |
get_populations | Man page Source code |
get_positions | Man page Source code |
get_sample_size | Man page Source code |
get_samples_per_ind | Source code |
get_simulator | Source code |
get_snp_positions | Source code |
get_snps | Man page Source code |
get_summary_statistics | Man page Source code |
get_trio_locus | Man page Source code |
has_ign_singletons | Source code |
has_ms | Source code |
has_msms | Source code |
has_omega | Source code |
has_seqgen | Source code |
has_trios | Source code |
has_variation | Source code |
ignore_par | Source code |
is.feature | Source code |
is.locus | Source code |
is.model | Source code |
is.named_par | Source code |
is.par | Source code |
is.par_variation | Source code |
is.prior_par | Source code |
is.ranged_par | Source code |
is.sum_stat | Source code |
is_feat_mutation | Source code |
is_feat_outgroup | Source code |
is_feat_sample | Source code |
is_feat_unphased | Source code |
is_partial_model | Source code |
is_segsites | Man page Source code |
is_simulation_task | Source code |
is_simulator | Source code |
is_unphased | Source code |
list_simulators | Man page Source code |
loci | Man page |
locus | Man page |
locus_averaged | Man page Source code |
locus_single | Man page Source code |
locus_trio | Man page Source code |
model_gtr | Source code |
model_hky | Source code |
model_theta_tau | Source code |
model_trios | Source code |
par_const | Man page Source code |
par_eval_func | Source code |
par_expr | Man page Source code |
par_named | Man page Source code |
par_print_func | Source code |
par_prior | Man page Source code |
par_range | Man page Source code |
par_variation | Man page Source code |
par_zero_inflation | Man page Source code |
parameter | Man page |
parse_ms_output | Source code |
parse_ms_positions | Source code |
parse_seqgen_output | Source code |
prepare_pars | Source code |
print.coalmodel | Source code |
print.partial_model | Source code |
print.segsites | Source code |
print_model_part | Source code |
print_par | Source code |
read_cache | Source code |
reduce_sim_tasks | Source code |
register_simulator | Source code |
remove_singletons | Source code |
require_package | Source code |
requires_files | Source code |
requires_segsites | Source code |
requires_trees | Source code |
reset_cache | Source code |
sample_par_priors | Source code |
sample_seed | Source code |
scale_model | Man page Source code |
search_executable | Man page Source code |
segsites | Man page |
select_simprog | Source code |
set_positions | Man page Source code |
set_trio_locus | Man page Source code |
sg_generate_opts | Source code |
simulate.coalmodel | Man page Source code |
simulator_ms | Man page |
simulator_msms | Man page |
simulator_scrm | Man page |
simulator_seqgen | Man page |
sumstat_class | Man page |
sumstat_dna | Man page Source code |
sumstat_file | Man page Source code |
sumstat_four_gamete | Man page Source code |
sumstat_ihh | Man page Source code |
sumstat_jsfs | Man page Source code |
sumstat_mcmf | Man page Source code |
sumstat_nucleotide_div | Man page Source code |
sumstat_omega | Man page Source code |
sumstat_seg_sites | Man page Source code |
sumstat_sfs | Man page Source code |
sumstat_tajimas_d | Man page Source code |
sumstat_trees | Man page Source code |
tempfile | Source code |
test_model | Source code |
test_simulator | Source code |
unphase_segsites | Source code |
variation | Source code |
zero_inflate | Source code |
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