Why use mmod (or what's wrong with GST?) | Which statistic should I use? | Which statistics can mmod not calculate | An Example - differentiation in the nancycats data
Package: mmod 1.3.3
mmod: Modern Measures of Population Differentiation
Provides functions for measuring population divergence from genotypic data.
Authors:
mmod_1.3.3.tar.gz
mmod_1.3.3.zip(r-4.7)mmod_1.3.3.zip(r-4.6)mmod_1.3.3.zip(r-4.5)
mmod_1.3.3.tgz(r-4.6-any)mmod_1.3.3.tgz(r-4.5-any)
mmod_1.3.3.tar.gz(r-4.7-any)mmod_1.3.3.tar.gz(r-4.6-any)
mmod_1.3.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mmod/json (API)
| # Install 'mmod' in R: |
| install.packages('mmod', repos = c('https://dwinter.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/dwinter/mmod/issues
Last updated from:035cd562ee. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 193 | ||
| source / vignettes | OK | 240 | ||
| linux-release-x86_64 | OK | 202 | ||
| macos-release-arm64 | OK | 147 | ||
| macos-oldrel-arm64 | OK | 191 | ||
| windows-devel | OK | 145 | ||
| windows-release | OK | 129 | ||
| windows-oldrel | OK | 114 | ||
| wasm-release | OK | 152 |
Exports:as.genind.DNAbinchao_bootstrapD_Jostdiff_statsdiff_testdist.codomGst_HedrickGst_Neiharmonic_meanjacknife_populationspairwise_Dpairwise_Gst_Hedrickpairwise_Gst_NeiPhi_st_Meirmansrgenotypessummarise_bootstrap
Dependencies:ade4adegenetapebase64encbootbslibcachemcliclustercommonmarkcpp11digestdplyrfarverfastmapfontawesomefsgenericsggplot2gluegtablehtmltoolshttpuvigraphisobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimenlmeotelpegaspermutepillarpixmappkgconfigplyrpromisesR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangS7sassscalessegmentedseqinrshinysourcetoolsspstringistringrtibbletidyselectutf8vctrsveganviridisLitewithrxtable
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| as.genind.DNAbin | as.genind.DNAbin |
| Produce bootstrap samples from each subpopulation of a genind object | chao_bootstrap |
| Calculate Jost's D | D_Jost |
| Calculate differentiation statistics for a genind object | diff_stats |
| An exact test of population differentiation for genind objects | diff_test |
| Calculate distance between individual for co-dominant locus | dist.codom |
| Calculate Nei's Gst using estimators for Hs and Ht | Gst_Hedrick |
| Calculate Nei's Gst using estimators for Hs and Ht | Gst_Nei |
| Harmonic mean | harmonic_mean |
| Create jacknife samples of a genind object by population | jacknife_populations |
| Modern Measures of Differentiation | mmod-package mmod |
| Calculates pairwise values of Jost's D | pairwise_D |
| Calculates pairwise values of Hedrick's G'st | pairwise_Gst_Hedrick |
| Calculates pairwise values of Nei's Gst | pairwise_Gst_Nei |
| Calculate Phi_st from a genind object | Phi_st_Meirmans |
| Randomly create genotypes | rgenotypes |
| Apply a differentiation statistic to a bootstrap sample | summarise_bootstrap |
