# Forward-in-Time Simulation and Tallying of Pairwise Relationships

## Documentation for package ‘CKMRpop’ version 0.1.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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