Package: CKMRpop 0.1.3.9999

CKMRpop: Forward-in-Time Simulation and Tallying of Pairwise Relationships

Provides an R wrapper around the program 'spip' (<https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1471-8286.2005.00884.x>), a C program for the simulation of pedigrees within age-structured populations with user-specified life histories. Also includes a variety of functions to parse 'spip' output to compile information about related pairs amongst simulated, sampled individuals, to assess the feasibility and potential accuracy of close-kin mark-recapture (CKMR). Full documentation and vignettes are mirrored at <https://eriqande.github.io/CKMRpop/index.html> and can be read online there.

Authors:Eric C. Anderson [aut, cre]

CKMRpop_0.1.3.9999.tar.gz
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CKMRpop.pdf |CKMRpop.html✨
CKMRpop/json (API)
NEWS

# Install 'CKMRpop' in R:
install.packages('CKMRpop', repos = c('https://eriqande.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/eriqande/ckmrpop/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

noaa-omics-software

5.26 score 3 stars 24 scripts 740 downloads 28 exports 63 dependencies

Last updated 12 months agofrom:710484f926. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-win-x86_64OKNov 22 2024
R-4.5-linux-x86_64OKNov 22 2024
R-4.4-win-x86_64OKNov 22 2024
R-4.4-mac-x86_64OKNov 22 2024
R-4.4-mac-aarch64OKNov 22 2024
R-4.3-win-x86_64OKNov 22 2024
R-4.3-mac-x86_64OKNov 22 2024
R-4.3-mac-aarch64OKNov 22 2024

Exports:%>%amm2tibbleanc_match_masksancestor_abbrvscat_dom_relatcompile_related_pairscount_and_plot_ancestry_matricescount_and_plot_mate_distributiondownsample_pairsfind_ancestors_and_relatives_of_samplesggplot_census_by_year_age_sexinstall_spipleslie_from_spipplot_amm_from_matrixplot_conn_compsprepare_for_dfsprimary_ancestor_pairsrcpp_ancestors_and_relativesrelationship_zone_perimetersrelatives_from_ancestry_vectorsrun_spipslurp_spipspip_existsspip_helpspip_help_fullsummarize_offspring_and_mate_numberssummarize_survival_from_censusuncooked_spaghetti

Dependencies:bitbit64cachemclicliprcolorspacecpp11crayondplyrfansifarverfastmapgenericsggforceggplot2ggraphggrepelgluegraphlayoutsgridExtragtablehmsigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmunsellnlmepillarpkgconfigpolyclipprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloRcppEigenreadrrlangscalesstringistringrsystemfontstibbletidygraphtidyrtidyselecttweenrtzdbutf8vctrsviridisviridisLitevroomwithr

A Simple Example With Migration

Eric C. Anderson

Rendered fromsimple-example-with-migration.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2023-02-21
Started: 2021-06-10

About spip

Eric C. Anderson

Rendered fromabout_spip.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2021-06-10
Started: 2021-04-28

population-growth-with-spip

Rendered frompopulation-growth-with-spip.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2023-12-04
Started: 2023-12-04

Simulation from species 1 life history

Rendered fromspecies_1_simulation.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2023-02-21
Started: 2020-11-16

Using Other Simulation Programs with CKMRpop

Eric C. Anderson

Rendered fromusing-other-simulation-programs.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2023-02-21
Started: 2021-08-20

Readme and manuals

Help Manual

Help pageTopics
convert an ancestry-matching matrix to a ggplot-able tibbleamm2tibble
compile pairwise relationships from the samplescompile_related_pairs
Count up the number of different kinds of related pairs and make a plotcount_and_plot_ancestry_matrices
Count and plot the number of mates each individuals has produced offspring withcount_and_plot_mate_distribution
downsample the number of individuals sampleddownsample_pairs
A tibble like that produced by 'compile_related_pairs()', but with zero rowsempty_crp
a list of examples of ancestry-match matricesexample_amms
Just a simple plot functionggplot_census_by_year_age_sex
The result of running spip with growth 0.01 in the population-growth-with-spip vignettegrowth_0.01_results
The result of running spip with growth -0.005 in the population-growth-with-spip vignettegrowth_n0.005_results
A half-first cousin ancestry match matrixhalf_first_cousin_amm
Download the spip binary and install it where CKMRpop expects itinstall_spip
Return a Leslie-like matrix from the spip parametersleslie_from_spip
Minimum number of generations for the ancestry match matrix to include relationship typesnecessary_generations
plot an ancestry matrix (or multiple such matrices) from its (their) matrix formplot_amm_from_matrix
plot the graph showing the connected componentsplot_conn_comps
relationship zone namesrelationship_zone_names
Return the perimeters of all the relationship zonesrelationship_zone_perimeters
Find relatives amongst samples from their ancestor vectorsrelatives_from_ancestry_vectors
Run spip in a user-specified directoryrun_spip
Read in the pedigree, census, and sampling information from the spip runslurp_spip
a list of life-history / life-table data for a hypothetical speciesspecies_1_life_history
The result of running spip in the species_1_simulation vignette.species_1_slurped_results
The result of running spip in the species_1_simulation vignette with 100 loci.species_1_slurped_results_100_loci
The result of running spip in the species_1_simulation vignette and slurping out with num_generations = 1.species_1_slurped_results_1gen
a list of life-history / life-table data for another hypothetical speciesspecies_2_life_history
return TRUE if spip exists where it should be installed.spip_exists
print the abbreviated usage information from spipspip_help
print the full usage information from spipspip_help_full
Summarize the distribution of number of offspring and number of matessummarize_offspring_and_mate_numbers
Summarize annual sex-and-age-specific survival rates from the census informationsummarize_survival_from_census
The result of running spip and slurping the output in the three population case with no migrationthree_pops_no_mig_slurped_results
The result of running spip and slurping the output in the three population case with migrationthree_pops_with_mig_slurped_results
Summarise kin-pair information and use it to create uncooked spaghetti plotsuncooked_spaghetti