Files in eriqande/CKMRpop
Forward-in-Time Simulation and Tallying of Pairwise Relationships
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.gitignore
CKMRpop.Rproj
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md
R/RcppExports.R
R/amm2tibble.R
R/anc_match_masks.R
R/ancestor_abbrvs.R
R/cat_dom_relat.R
R/compile_related_pairs.R
R/count_and_plot_ancestry_matrices.R
R/count_and_plot_mate_distribution.R
R/data.R
R/downsample_pairs.R
R/find_ancestors_and_relatives_of_samples.R
R/gg_add_generation_bands.R
R/gg_add_zone_perimeters.R
R/ggplot_census_by_year_age_sex.R
R/import.R
R/install_spip.R
R/leslie_from_spip.R
R/plot_amm_from_matrix.R
R/plot_conn_comps.R
R/prepare_for_dfs.R
R/recapture_pairs.R
R/relationship_zone_perimeters.R
R/relatives_from_ancestry_vectors.R
R/relpair_conn_comps.R
R/run_spip.R
R/slurp_spip.R
R/spip_binary.R
R/spip_binary_path.R
R/spip_exists.R
R/spip_help.R
R/spip_help_full.R
R/summarize_offspring_and_mate_numbers.R
R/summarize_survival_from_census.R
R/uncooked_spaghetti.R
README.Rmd
README.md
README_files/figure-gfm/unnamed-chunk-10-1.png
README_files/figure-gfm/unnamed-chunk-11-1.png
README_files/figure-gfm/unnamed-chunk-13-1.png
README_files/figure-gfm/unnamed-chunk-14-1.png
README_files/figure-gfm/unnamed-chunk-15-1.png
README_files/figure-gfm/unnamed-chunk-18-1.png
README_files/figure-gfm/unnamed-chunk-24-1.png
README_files/figure-gfm/unnamed-chunk-25-1.png
README_files/figure-gfm/unnamed-chunk-27-1.png
README_files/figure-gfm/unnamed-chunk-28-1.png
README_files/figure-gfm/unnamed-chunk-34-1.png
README_files/figure-gfm/unnamed-chunk-7-1.png
TODO.md
_pkgdown.yml
cluster-run-one-big-kelp-rf-pop/census.pdf
cluster-run-one-big-kelp-rf-pop/crel.rds
cluster-run-one-big-kelp-rf-pop/relat_counts.rds
cluster-run-one-big-kelp-rf-pop/samples.rds
cluster_runs/.gitignore
cluster_runs/array-script.sh
cluster_runs/array_jobs.tsv
cluster_runs/devise-runs.R
cluster_runs/line-assign.sh
cluster_runs/species_2_run_script.R
cluster_runs/summarize-results.R
cran-comments.md
data/empty_crp.rda
data/example_amms.rda
data/growth_0.01_results.rda
data/growth_n0.005_results.rda
data/half_first_cousin_amm.rda
data/necessary_generations.rda
data/relationship_zone_names.rda
data/species_1_life_history.rda
data/species_1_slurped_results.rda
data/species_1_slurped_results_100_loci.rda
data/species_1_slurped_results_1gen.rda
data/species_2_life_history.rda
data/three_pops_no_mig_slurped_results.rda
data/three_pops_with_mig_slurped_results.rda
development/.gitignore
development/001-species_2_simulation.Rmd
development/002-Bayesian-inference-from-species-2-simulations.Rmd
development/003-package-dependencies-graph.R
development/004-bayes-inf-with-5K-samples.Rmd
development/005-kelp-rockfish-like-simulations.Rmd
development/006-one-big-kelp-rockfish-pop-for-cluster.R
development/007-kelp-rockfish-rushed-analyses.Rmd
development/008-bayes-inf-with-sampled-8-year-olds.R
development/inputs/002/kelp_areas_and_adults.csv
development/species_2_run_script.R
extras/gawk.exe
figure_creation/spip-time-periods-explained/latex-table.txt
figure_creation/spip-time-periods-explained/make_matrix-crop.pdf
figure_creation/spip-time-periods-explained/make_matrix.aux
figure_creation/spip-time-periods-explained/make_matrix.log
figure_creation/spip-time-periods-explained/make_matrix.pdf
figure_creation/spip-time-periods-explained/make_matrix.synctex.gz
figure_creation/spip-time-periods-explained/make_matrix.tex
figure_creation/spip-time-periods-explained/matrix-latexit.pdf
figure_creation/spip-time-periods-explained/mig-outs-latexit.pdf
figure_creation/spip-time-periods-explained/mig-pools.tex
figure_creation/spip-time-periods-explained/spip-periods-with-migration.svg
figure_creation/spip-time-periods-explained/spip-periods-with-sampling.svg
figure_creation/spip-time-periods-explained/spip-periods.svg
inst/SLiM/slim-example-1.slim
inst/SLiM/slim-example-2.slim
inst/shell/single_pass_cps.awk
man/amm2tibble.Rd
man/anc_match_masks.Rd
man/ancestor_abbrvs.Rd
man/ancestor_vectors_cpp.Rd
man/basic_amm_plot.Rd
man/cat_dom_relat.Rd
man/compile_related_pairs.Rd
man/count_and_plot_ancestry_matrices.Rd
man/count_and_plot_mate_distribution.Rd
man/downsample_pairs.Rd
man/empty_crp.Rd
man/example_amms.Rd
man/figures/CKMRpop-sticker.png
man/figures/slim1_num_offs_plot.png
man/figures/spip-periods-with-migration.svg
man/figures/spip-periods-with-sampling.svg
man/figures/spip-periods.svg
man/find_ancestors_and_relatives_of_samples.Rd
man/gg_add_generation_bands.Rd
man/gg_add_zone_perimeters.Rd
man/ggplot_census_by_year_age_sex.Rd
man/growth_0.01_results.Rd
man/growth_n0.005_results.Rd
man/half_first_cousin_amm.Rd
man/install_spip.Rd
man/int_pow2.Rd
man/leslie_from_spip.Rd
man/necessary_generations.Rd
man/pipe.Rd
man/plot_amm_from_matrix.Rd
man/plot_conn_comps.Rd
man/prepare_for_dfs.Rd
man/primary_ancestor_pairs.Rd
man/rcpp_ancestors_and_relatives.Rd
man/recapture_pairs.Rd
man/relationship_zone_names.Rd
man/relationship_zone_perimeters.Rd
man/relatives_from_ancestry_vectors.Rd
man/relpair_conn_comps.Rd
man/run_spip.Rd
man/search_down.Rd
man/search_up.Rd
man/slurp_spip.Rd
man/species_1_life_history.Rd
man/species_1_slurped_results.Rd
man/species_1_slurped_results_100_loci.Rd
man/species_1_slurped_results_1gen.Rd
man/species_2_life_history.Rd
man/spip_binary.Rd
man/spip_binary_path.Rd
man/spip_exists.Rd
man/spip_help.Rd
man/spip_help_full.Rd
man/summarize_offspring_and_mate_numbers.Rd
man/summarize_survival_from_census.Rd
man/three_pops_no_mig_slurped_results.Rd
man/three_pops_with_mig_slurped_results.Rd
man/uncooked_spaghetti.Rd
references.bib
src/RcppExports.cpp
src/dfs_find_sampled_relatives.cpp
src/primary_ancestor_pairs.cpp
src/rcpp_test.cpp
vignettes/.gitignore
vignettes/about_spip.Rmd
vignettes/population-growth-with-spip.Rmd
vignettes/references.bib
vignettes/simple-example-with-migration.Rmd
vignettes/species_1_simulation.Rmd
vignettes/using-other-simulation-programs.Rmd
