Package: twigstats 1.0.1
twigstats: twigstats
This package takes Relate genealogies as input to compute time-stratified f-statistics.
Authors:
twigstats_1.0.1.tar.gz
twigstats_1.0.1.zip(r-4.5)twigstats_1.0.1.zip(r-4.4)twigstats_1.0.1.zip(r-4.3)
twigstats_1.0.1.tgz(r-4.4-x86_64)twigstats_1.0.1.tgz(r-4.4-arm64)twigstats_1.0.1.tgz(r-4.3-x86_64)twigstats_1.0.1.tgz(r-4.3-arm64)
twigstats_1.0.1.tar.gz(r-4.5-noble)twigstats_1.0.1.tar.gz(r-4.4-noble)
twigstats.pdf |twigstats.html✨
twigstats/json (API)
# Install 'twigstats' in R: |
install.packages('twigstats', repos = c('https://leospeidel.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/leospeidel/twigstats/issues
Last updated 9 days agofrom:aeb8552450. Checks:OK: 1 WARNING: 5 ERROR: 3. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 28 2024 |
R-4.5-win-x86_64 | ERROR | Oct 28 2024 |
R-4.5-linux-x86_64 | WARNING | Oct 28 2024 |
R-4.4-win-x86_64 | ERROR | Oct 28 2024 |
R-4.4-mac-x86_64 | WARNING | Oct 28 2024 |
R-4.4-mac-aarch64 | WARNING | Oct 28 2024 |
R-4.3-win-x86_64 | ERROR | Oct 28 2024 |
R-4.3-mac-x86_64 | WARNING | Oct 28 2024 |
R-4.3-mac-aarch64 | WARNING | Oct 28 2024 |
Exports:ExpPaintingProfilef2_blocks_from_Relatef2_blocks_from_RelateAgesf4_ratioFst_blocks_from_RelatejackknifePaintingPaintingNNLSPaintingProfilePaintingProfileRrun_testthat_teststheoretical_zscoreTMRCA_from_RelateTMRCAdist_from_RelateTwigScan
Dependencies:briocallrclicrayondescdiffobjdigestdplyrevaluatefansifsgenericsgluejsonlitelifecyclemagrittrpillarpkgbuildpkgconfigpkgloadpraiseprocessxpsR6RcppRcppArmadillorematch2rlangrprojroottestthattibbletidyselectutf8vctrswaldowithr
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Function to calculate f2 statistics from Relate trees for pairs of populations specified in poplabels. | f2_blocks_from_Relate |
Function to calculate f2 statistics from plink files, ascertained using mutation ages in Relate trees. | f2_blocks_from_RelateAges |
Function implementing the F4-ratio statistic | f4_ratio jackknife |
Function to calculate Fst from Relate trees for pairs of populations specified in poplabels. | Fst_blocks_from_Relate |
Chromosome painting using genealogies. | Painting |
Function to run an NNLS on genome-wide copying proportions to estimate admixture proportions. | PaintingNNLS |
Function to compute genome-wide copying proportions. | PaintingProfile |
Function to compute a theoretical z-score given source split times and admixture proportions. | theoretical_zscore |
Function implementing TwigScan | TwigScan |