hierfstat

Estimation and Tests of Hierarchical F-Statistics

v0.5-11 · May 5, 2022 · GPL (>= 2)

Description

Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution(1998), 52:950). Tests via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G (Goudet et al. (1996) <https://academic.oup.com/genetics/article/144/4/1933/6017091>). Estimates genetic diversity statistics for haploid and diploid genetic datasets in various formats, including inbreeding and coancestry coefficients, and population specific F-statistics following Weir and Goudet (2017) <https://academic.oup.com/genetics/article/206/4/2085/6072590>.

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14 NOTE

Show all 14 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	NOTE	151.6s
r-devel-linux-x86_64-debian-gcc	NOTE	104.1s
r-devel-linux-x86_64-fedora-clang	NOTE	232.9s
r-devel-linux-x86_64-fedora-gcc	NOTE	239.9s
r-devel-macos-arm64	NOTE	41s
r-devel-windows-x86_64	NOTE	180s
r-oldrel-macos-arm64	NOTE
r-oldrel-macos-x86_64	NOTE	116s
r-oldrel-windows-x86_64	NOTE	228s
r-patched-linux-x86_64	NOTE	143.2s
r-release-linux-x86_64	NOTE	139.3s
r-release-macos-arm64	NOTE
r-release-macos-x86_64	NOTE	147s
r-release-windows-x86_64	NOTE	171s

Check details (14 non-OK)

NOTE r-devel-linux-x86_64-debian-clang

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-devel-linux-x86_64-debian-gcc

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-devel-linux-x86_64-fedora-clang

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-devel-linux-x86_64-fedora-gcc

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

Check History

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

NOTE r-devel-linux-x86_64-debian-clang

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-devel-linux-x86_64-debian-gcc

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-devel-linux-x86_64-fedora-clang

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-devel-linux-x86_64-fedora-gcc

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

Reverse Dependencies (8)

imports

GenomeAdmixR dartR.sim graph4lg wingen

suggests

adegenet dartR dartR.base tidypopgen

Dependency Network

Version History

new 0.5-11 Mar 10, 2026

updated 0.5-11 ← 0.5-10 diff May 5, 2022

updated 0.5-10 ← 0.5-7 diff Nov 16, 2021

updated 0.5-7 ← 0.04-22 diff Jul 19, 2020

updated 0.04-22 ← 0.04-14 diff Dec 3, 2015

updated 0.04-14 ← 0.04-10 diff Sep 28, 2014

updated 0.04-10 ← 0.04-6 diff Apr 9, 2013

updated 0.04-6 ← 0.04-4 diff Nov 23, 2011

updated 0.04-4 ← 0.04-3 diff Sep 20, 2006

updated 0.04-3 ← 0.04-2 diff Jul 9, 2006

updated 0.04-2 ← 0.04-1 diff Dec 13, 2005

updated 0.04-1 ← 0.03-3 diff Jun 6, 2005

updated 0.03-3 ← 0.03-1 diff Mar 14, 2005

updated 0.03-1 ← 0.02-2 diff Mar 2, 2005

updated 0.02-2 ← 0.01-4 diff Jan 13, 2005

new 0.01-4 Aug 13, 2004

Maintainer

Jerome Goudet

Dependencies

Depends

R (>= 2.10)

Imports

ade4 adegenet gaston gtools methods

Suggests

ape pegas knitr rmarkdown testthat

Compilation

No compilation needed

First Published

Aug 13, 2004

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