Other packages > Find by keyword >

poolfstat  

Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data
View on CRAN: Click here


Download and install poolfstat package within the R console
Install from CRAN:
install.packages("poolfstat")

Install from Github:
library("remotes")
install_github("cran/poolfstat")

Install by package version:
library("remotes")
install_version("poolfstat", "3.0.0")



Attach the package and use:
library("poolfstat")
Maintained by
Mathieu Gautier
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-03-14
Latest Update: 2024-11-23
Description:
Functions for the computation of f- and D-statistics (estimation of 'Fst', Patterson's 'F2', 'F3', 'F3*', 'F4' and D parameters) in population genomics studies from allele count or Pool-Seq read count data and for the fitting, building and visualization of admixture graphs. The package also includes several utilities to manipulate Pool-Seq data stored in standard format (e.g., such as 'vcf' files or 'rsync' files generated by the the 'PoPoolation' software) and perform conversion to alternative format (as used in the 'BayPass' and 'SelEstim' software). As of version 2.0, the package also includes utilities to manipulate standard allele count data (e.g., stored in 'TreeMix', 'BayPass' or 'SelEstim' format).
How to cite:
Mathieu Gautier (2018). poolfstat: Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data. R package version 3.0.0, https://cran.r-project.org/web/packages/poolfstat. Accessed 28 Jun. 2026.
Previous versions and publish date:
0.0.1 (2018-03-14 12:36), 1.0.0 (2018-09-14 21:20), 1.1.0 (2019-06-20 17:00), 1.1.1 (2019-10-22 11:30), 1.2.0 (2020-11-04 17:20), 2.0.0 (2021-05-27 11:20), 2.1.1 (2022-05-02 18:10), 2.1.2 (2023-03-22 23:00), 2.2.0 (2023-09-06 17:50), 3.0.0 (2024-11-23 16:20)
Other packages that cited poolfstat R package
View poolfstat citation profile
Other R packages that poolfstat depends, imports, suggests or enhances
Complete documentation for poolfstat
Functions, R codes and Examples using the poolfstat R package
Some associated functions: add.leaf . bjack_cov . compare.fitted.fstats . compute.f4ratio . compute.fstats . compute.pairwiseFST . computeFST . compute_Ddenom . compute_Ddenom_bjmeans . compute_F2_bjmeans . compute_F3fromF2 . compute_F3fromF2samples . compute_F4DfromF2samples . compute_F4fromF2 . compute_F4fromF2samples . compute_H1 . compute_Q2 . compute_Q_bjmeans . compute_QmatfromF2samples . compute_blockDdenom . countdata-class . countdata.subset . extract_allele_names . extract_nonvscan_counts . extract_vscan_counts . find.tree.popset . find_indelneighbor_idx . fit.graph . fitted.graph-class . fstats-class . generate.graph.params . generate.jackknife.blocks . generateF3names . generateF4names . genobaypass2countdata . genobaypass2pooldata . genoselestim2pooldata . genotreemix2countdata . graph.builder . graph.params-class . graph.params2qpGraphFiles . graph.params2symbolic.fstats . heatmap-pairwisefst-method . is.countdata . is.fitted.graph . is.fstats . is.graph.params . is.pairwisefst . is.pooldata . make.example.files . pairwisefst-class . plot-fitted.graph-method . plot-fstats-method . plot-graph.params-method . plot-pairwisefst-method . plot_fstats . pooldata-class . pooldata.subset . pooldata2diyabc . pooldata2genobaypass . pooldata2genoselestim . poolfstat . poppair_idx . popsync2pooldata . randomallele.pca . rooted.njtree.builder . scan_allele_info . show-countdata-method . show-fitted.graph-method . show-fstats-method . show-graph.params-method . show-pairwisefst-method . show-pooldata-method . vcf2pooldata . 
Some associated R codes: RcppExports.R . add.leaf.R . compare.fitted.fstats.R . compute.F4ratio.R . compute.fstats.R . compute.pairwiseFST.R . computeFST.R . countdata.subset.R . find.tree.popset.R . fit.graph.R . generate.graph.params.R . generate.jacknife.blocks.R . genobaypass2countdata.R . genobaypass2pooldata.R . genoselestim2pooldata.R . genotreemix2countdata.R . graph.builder.R . graph.params2qpGraphFiles.R . graph.params2symbolicfstats.R . is.countdata.R . is.fitted.graph.R . is.graph.params.R . is.pooldata.R . make.example.files.R . outjects.R . plot_fstats.R . pooldata.subset.R . pooldata2diyabc.R . pooldata2genobaypass.R . pooldata2genoselestim.R . poolfstat-package.R . popsync2pooldata.R . randomallele.pca.R . rooted.njtree.builder.R . vcf2pooldata.R .  Full poolfstat package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

EventWinRatios  
Event-Specific Win Ratios for Terminal and Non-Terminal Events
Provides several confidence interval and testing procedures using event-specific win ratios for sem ...
Download / Learn more Package Citations See dependency  
XKCDdata  
Get XKCD Comic Data
Download data from individual XKCD comics, written by Randall Munroe < ...
Download / Learn more Package Citations See dependency  
minimax  
The Minimax Distribution Family
The minimax family of distributions is a two-parameter family like the beta family, but computation ...
Download / Learn more Package Citations See dependency  
geoelectrics  
3D-Visualization of Geoelectric Resistivity Measurement Profiles
Visualizes two-dimensional geoelectric resistivity measurement profiles in three dimensions. ...
Download / Learn more Package Citations See dependency  
Rirt  
Data Analysis and Parameter Estimation Using Item Response Theory
Parameter estimation, computation of probability, information, and (log-)likelihood, and visualizat ...
Download / Learn more Package Citations See dependency  
nlraa  
Nonlinear Regression for Agricultural Applications
Additional nonlinear regression functions using self-start (SS) algorithms. One of the functions is ...
Download / Learn more Package Citations See dependency  

27,653

R Packages

236,180

Dependencies

73,487

Author Associations

27,536

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA