Forward-in-Time Simulation and Tallying of Pairwise
Relationships
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Documentation for package ‘CKMRpop’ version 0.1.3
Help Pages
| amm2tibble | convert an ancestry-matching matrix to a ggplot-able tibble |
| 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 make a plot |
| count_and_plot_mate_distribution | Count and plot the number of mates each individuals has produced offspring with |
| downsample_pairs | downsample the number of individuals sampled |
| example_amms | a list of examples of ancestry-match matrices |
| 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 it |
| leslie_from_spip | Return a Leslie-like matrix from the spip parameters |
| plot_amm_from_matrix | plot an ancestry matrix (or multiple such matrices) from its (their) matrix form |
| plot_conn_comps | plot the graph showing the connected components |
| relationship_zone_names | relationship zone names |
| relationship_zone_perimeters | Return the perimeters of all the relationship zones |
| run_spip | Run spip in a user-specified directory |
| slurp_spip | Read in the pedigree, census, and sampling information from the spip run |
| species_1_life_history | a list of life-history / life-table data for a hypothetical species |
| species_1_slurped_results | The result of running spip in the species_1_simulation vignette. |
| species_1_slurped_results_100_loci | The result of running spip in the species_1_simulation vignette with 100 loci. |
| species_1_slurped_results_1gen | The result of running spip in the species_1_simulation vignette and slurping out with num_generations = 1. |
| species_2_life_history | a list of life-history / life-table data for another hypothetical species |
| 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 of mates |
| summarize_survival_from_census | Summarize annual sex-and-age-specific survival rates from the census information |
| three_pops_no_mig_slurped_results | The result of running spip and slurping the output in the three population case with no migration |
| three_pops_with_mig_slurped_results | The result of running spip and slurping the output in the three population case with migration |
| uncooked_spaghetti | Summarise kin-pair information and use it to create uncooked spaghetti plots |