Man pages for CKMRpop
Forward-in-Time Simulation and Tallying of Pairwise Relationships
| amm2tibble | convert an ancestry-matching matrix to a ggplot-able tibble |
| ancestor_abbrvs | Return a string of ancestor abbreviations in the order of the... |
| ancestor_vectors_cpp | Function to make a vector of all the ancestors of an... |
| anc_match_masks | Return ancestry-matrix-zone masks for different relationship... |
| basic_amm_plot | here is a function to plot a basic ancestry match matrix |
| cat_dom_relat | Categorize the dominant relationship from an ancestry match... |
| compile_related_pairs | compile pairwise relationships from the samples |
| count_and_plot_ancestry_matrices | Count up the number of different kinds of related pairs and... |
| count_and_plot_mate_distribution | Count and plot the number of mates each individuals has... |
| downsample_pairs | downsample the number of individuals sampled |
| example_amms | a list of examples of ancestry-match matrices |
| find_ancestors_and_relatives_of_samples | Find ancestors and relative of each sampled member of a... |
| gg_add_generation_bands | Add bands of transparent colors to denote generations on... |
| gg_add_zone_perimeters | Add perimeters around the relationship zones |
| ggplot_census_by_year_age_sex | Just a simple plot function |
| half_first_cousin_amm | A half-first cousin ancestry match matrix |
| install_spip | Download the spip binary and install it where CKMRpop expects... |
| int_pow2 | Exponentiation function for integer arguments |
| leslie_from_spip | Return a Leslie-like matrix from the spip parameters |
| pipe | Pipe operator |
| plot_amm_from_matrix | plot an ancestry matrix (or multiple such matrices) from its... |
| plot_conn_comps | plot the graph showing the connected components |
| prepare_for_dfs | Prepare input for the DFS relative-finding algorithm |
| primary_ancestor_pairs | Return a list of the indices of the primary shared ancestors |
| rcpp_ancestors_and_relatives | function to test and use DFS stuff |
| recapture_pairs | Return the recaptures from amongst the samples |
| relationship_zone_names | relationship zone names |
| relationship_zone_perimeters | Return the perimeters of all the relationship zones |
| relpair_conn_comps | Find connected components amongst the related pairs |
| run_spip | Run spip in a user-specified directory |
| search_down | Depth first search down the pedigree to N generations. |
| search_up | Depth first search up the pedigree to N generations. |
| slurp_spip | Read in the pedigree, census, and sampling information from... |
| species_1_life_history | a list of life-history / life-table data for a hypothetical... |
| species_1_slurped_results | The result of running spip in the species_1_simulation... |
| species_1_slurped_results_100_loci | The result of running spip in the species_1_simulation... |
| species_1_slurped_results_1gen | The result of running spip in the species_1_simulation... |
| species_2_life_history | a list of life-history / life-table data for another... |
| spip_binary | file path to be used in a call to spip |
| spip_binary_path | return the path where spip should be in the R system paths |
| spip_exists | return TRUE if spip exists where it should be installed. |
| spip_help | print the abbreviated usage information from spip |
| spip_help_full | print the full usage information from spip |
| summarize_offspring_and_mate_numbers | Summarize the distribution of number of offspring and number... |
| summarize_survival_from_census | Summarize annual sex-and-age-specific survival rates from the... |
| three_pops_no_mig_slurped_results | The result of running spip and slurping the output in the... |
| three_pops_with_mig_slurped_results | The result of running spip and slurping the output in the... |
| uncooked_spaghetti | Summarise kin-pair information and use it to create uncooked... |
