API for coala
A Framework for Coalescent Simulation

Global functions
+.coalmodelpart Man page
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
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
onLoad 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
coala documentation built on Nov. 17, 2017, 8:17 a.m.