Reference

Using spip and summarizing its output Functions for running a spip simulation, reading its output back into R, and processing the output into pairs of related samples
install_spip()	Download the spip binary and install it where CKMRpop expects it
run_spip()	Run spip in a user-specified directory
slurp_spip()	Read in the pedigree, census, and sampling information from the spip run
compile_related_pairs()	compile pairwise relationships from the samples
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
downsample_pairs()	downsample the number of individuals sampled
Designing spip parameters Functions for obtaining spip parameters desired for simulating given situations
leslie_from_spip()	Return a Leslie-like matrix from the spip parameters
Visualizing simulation results High-level functions for visualizing the results of spip simulations
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
ggplot_census_by_year_age_sex()	Just a simple plot function
plot_conn_comps()	plot the graph showing the connected components
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
uncooked_spaghetti()	Summarise kin-pair information and use it to create uncooked spaghetti plots
Helper functions Low-level functions used in some of the above functions. Most users will typically not interact with these functions directly.
plot_amm_from_matrix()	plot an ancestry matrix (or multiple such matrices) from its (their) matrix form
amm2tibble()	convert an ancestry-matching matrix to a ggplot-able tibble
relationship_zone_perimeters()	Return the perimeters of all the relationship zones
Example package data Package data sets that are used in the examples: either parameter values or examples of spip output.
species_1_life_history	a list of life-history / life-table data for a hypothetical species
species_2_life_history	a list of life-history / life-table data for another 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.
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
growth_0.01_results	The result of running spip with growth 0.01 in the population-growth-with-spip vignette
growth_n0.005_results	The result of running spip with growth -0.005 in the population-growth-with-spip vignette
Helper package data Package data sets that define values used primarily internally in functions or for some external examples
empty_crp	A tibble like that produced by compile_related_pairs(), but with zero rows
example_amms	a list of examples of ancestry-match matrices
half_first_cousin_amm	A half-first cousin ancestry match matrix
necessary_generations	Minimum number of generations for the ancestry match matrix to include relationship types
relationship_zone_names	relationship zone names
relatives_from_ancestry_vectors()	Find relatives amongst samples from their ancestor vectors