Overview | Choosing Runs, Batches, Monte Carlo Replicates, and Species | Conversion Helpers | create_cdmat() | cdmetapop_to_gene() | Output Data Frames | Population Summary Plots | Initial Population Size | Sex Counts | Mature Counts | Births | Myy Ratio | Patch Abundance from summary_popAllTime.csv | Allelic Richness and Heterozygosity from summary_popAllTime.csv | Class Summary Plots | Age Class Counts | Age Plus One | Disease State Summaries | Default State Names | Custom State and Scenario Names | Cumulative State | Individual File Summaries | Age Histogram | Size Histogram | Size by Age | Hindex Histogram | Movement Distance Histogram | Movement Over Time | Individual-Level Genetics | Allele Frequencies by Patch | Heterozygosity by Patch | Pairwise FST | Patch Maps from Individual Files | All Individuals | One Disease State | Faceted by Disease State | Allele Frequency Map | Heterozygosity Map | Older Summary Helpers | age_structure_proportions() | Interactive and External-Run Functions | launch_cdmetapop() | Template Editors
Package: cdmetapopR 1.0.0
Dominique Alò
cdmetapopR: Utility Functions for 'CDMetaPOP'
Provides a set of helper functions to launch, analyze, and visualize the output files of 'CDMetaPOP' <https://computationalecologylab.github.io/cdmetapop_web/>.
Authors:
cdmetapopR_1.0.0.tar.gz
cdmetapopR_1.0.0.tar.gz(r-4.7-any)cdmetapopR_1.0.0.tar.gz(r-4.6-any)
cdmetapopR_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cdmetapopR/json (API)
| # Install 'cdmetapopR' in R: |
| install.packages('cdmetapopR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:f8488854a0. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 403 | ||
| source / vignettes | OK | 364 | ||
| linux-release-x86_64 | OK | 394 | ||
| wasm-release | OK | 201 |
Exports:age_structure_proportionsallele_frequencies_indcdmetapop_to_genecreate_cdmatheterozygosity_indlaunch_cdmetapopmake_classvarsmake_patchvarsmake_popvarsmake_runvarspairwise_fst_indsummary_classsummary_dataframesummary_diseasesummary_indsummary_patch_mapsummary_pop
Dependencies:abindade4adegenetapebase64encbootbslibcachemclassclassIntcliclustercommonmarkcpp11DBIdeldirdigestdplyre1071ecodistfarverfastmapfontawesomeforeignfsgastongdistancegenericsggplot2gluegoftestgraph4lggtablegtoolshierfstathtmltoolshttpuvigraphisobandjquerylibjsonliteKernSmoothlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimenlmeotelpegaspermutepillarpixmappkgconfigplyrpolyclippolysatpopprprogressrpromisesproxypurrrR6rappdirsrasterrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRdpackreshape2rlangrparts2S7sassscalessegmentedseqinrsfshinyshinyBSsourcetoolsspspatstat.dataspatstat.explorespatstat.geomspatstat.linnetspatstat.modelspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrtensorterratibbletidyrtidyselectunitsutf8vctrsveganviridisLitewithrwkxtable
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Determine the proportions of the age structure of the population | age_structure_proportions |
| Plot Individual-Level Allele Frequencies | allele_frequencies_ind |
| Convert CDMetaPOP data to GENEPOP or GENALEX format | cdmetapop_to_gene |
| Create cost distance matrix for CDMetaPOP simulation | create_cdmat |
| Plot Individual-Level Heterozygosity | heterozygosity_ind |
| Function to facilitate the running of CDMetaPOP software from R | launch_cdmetapop |
| Build ClassVars File from Template | make_classvars |
| Build PatchVars File from Template | make_patchvars |
| Build PopVars File from Template | make_popvars |
| Build RunVars File from Template | make_runvars |
| Plot Pairwise FST Between Individual Groups | pairwise_fst_ind |
| Plot CDMetaPOP Class Summary Dynamics | summary_class |
| Return CDMetaPOP Output Data as Data Frames | summary_dataframe |
| Summarize CDMetaPOP Disease States | summary_disease |
| Plot CDMetaPOP Individual File Summaries | summary_ind |
| Map CDMetaPOP Patch Abundance | summary_patch_map |
| Plot CDMetaPOP Population Summary Dynamics | summary_pop |
