Genepop

Package ‘genepop’
January 20, 2023

Type Package
Title Population Genetic Data Analysis Using Genepop
Version 1.2.2
Date 2023-01-19
Maintainer François Rousset <francois.rousset@umontpellier.fr>
Description Makes the Genepop software available in R. This software implements a mixture of tradi-
tional population genetic methods and some more focused developments: it computes ex-
act tests for Hardy-Weinberg equilibrium, for population differentiation and for genotypic dise-
quilibrium among pairs of loci; it computes estimates of F-statistics, null allele frequencies, al-
lele size-based statistics for microsatellites, etc.; and it performs analyses of isolation by dis-
tance from pairwise comparisons of individuals or population samples.
License CeCILL-2
Encoding UTF-8
Imports Rcpp (>= 0.12.10), stringr
LinkingTo Rcpp, RcppProgress
Suggests testthat, knitr, shiny
Config/build/clean-inst-doc false
RoxygenNote 7.2.3
ByteCompile true
URL https://www.r-project.org,
https://kimura.univ-montp2.fr/~rousset/Genepop.htm
NeedsCompilation yes
Author François Rousset [aut, cre, cph]
(<https://orcid.org/0000-0003-4670-0371>),
Jimmy Lopez [ctb],
Alexandre Genin [ctb],
Khalid Belkhir [ctb]
Repository CRAN
Date/Publication 2023-01-19 23:30:17 UTC
1
2 genepop-package
R topics documented:
genepop-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
basic_info . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
clean_workdir . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Contingency-test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
conversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Differentiation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Fst . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
genedivFis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
genepopExample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
GUI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Hardy-Weinberg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
IBD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Linkage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
manipulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Nm_private . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
nulls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
setMantelSeed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
setRandomSeed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
set_restriction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Index 19
genepop-package Population genetic analyses using the Genepop software
Description
A distribution of the Genepop software as an R package. The included C++ sources are suitable for
compilation as a stand-alone executable. A shiny interface is also included. Genepop performs three
main tasks: it computes exact tests for Hardy-Weinberg equilibrium (test_HW), for population
differentiation (test_diff) and for genotypic disequilibrium among pairs of loci (test_LD); it
computes estimates of F-statistics (Fst), null allele frequencies (nulls), allele size-based statistics
for microsatellites, etc., and of number of immigrants by Barton & Slatkin’s (1986) private allele
method (Nm_private); It performs analyses of isolation by distance from pairwise comparisons of
individuals or groups (ibd), including confidence intervals for "neighborhood size". It also provides
various data conversion and manipulation utilities.
Author(s)
R package originally developed by Jimmy Lopez and Khalid Belkhir from the C++ sources of the
Genepop executable version 4.6 (2016; Rousset 2008).
genepop-package 3
References
Main reference for current maintained version of Genepop:
Rousset, F. (2008). Genepop’007: a complete reimplementation of the Genepop software for Win-
dows and Linux. Mol. Ecol. Res. 8: 103-106.
Original Genepop publication:
Raymond, M. & Rousset, F., 1995b. GENEPOP Version 1.2: population genetics software for exact
tests and ecumenicism. J. Hered. 86: 248-249.
Methods implemented in Genepop:
Barton, N. H. & Slatkin, M., 1986. A quasi-equilibrium theory of the distribution of rare alleles in
a subdivided population. Heredity 56: 409-415.
Brookfield, J. F. Y., 1996. A simple new method for estimating null allele frequency from heterozy-
gote deficiency. Mol. Ecol. 5: 453-455.
Goudet, J., Raymond, M., de Meeus, T. & Rousset, F., 1996. Testing differentiation in diploid
populations. Genetics 144: 1931-1938.
Guo, S. W. & Thompson, E. A., 1992. Performing the exact test of Hardy-Weinberg proportion for
multiple alleles. Biometrics 48: 361-372.
Kalinowski, S. T. & Taper, M. L., 2006. Maximum likelihood estimation of the frequency of null
alleles at microsatellite loci. Conserv. Genetics 7:991-995.
Louis, E. J. & Dempster, E. R., 1987. An exact test for Hardy-Weinberg and multiple alleles.
Biometrics 43: 805-811.
Mantel, N., 1967. The detection of disease clustering and a generalized regression approach. Cancer
Research 27: 209-220.
Michalakis, Y. & Excoffier, L., 1996. A generic estimation of population subdivision using dis-
tances between alleles with special interest to microsatellite loci. Genetics 142: 1061-1064.
Raymond, M. & Rousset, F., 1995a. An exact test for population differentiation.Evolution 49:
1283-1286.
Robertson, A. & Hill, W. G., 1984. Deviations from Hardy-Weinberg proportions: sampling vari-
ances and use in estimation of inbreeding coefficients. Genetics 107: 703-718.
Rousset, F., 1996. Equilibrium values of measures of population subdivision for stepwise mutation
processes. Genetics 142: 1357-1362.
Rousset, F., 1997. Genetic differentiation and estimation of gene flow from F-statistics under isola-
tion by distance. Genetics 145: 1219-1228.
Rousset, F., 2000. Genetic differentiation between individuals. J. Evol. Biol. 13:58-62.
Rousset, F. & Raymond, M., 1995. Testing heterozygote excess and deficiency. Genetics 140:
1413-1419.
Watts, P. C., Rousset, F., Saccheri, I. J., Leblois, R., Kemp, S. J. & Thompson, D. J., 2007. Compat-
ible genetic and ecological estimates of dispersal rates in insect (Coenagrion mercuriale: Odonata:
Zygoptera) populations: analysis of ’neighbourhood size’ using a more precise estimator. Mol.
Ecol. 16: 737-751.
Weir, B. S., 1996. Genetic Data Analysis II. Sinauer, Sunderland, Mass.
Weir, B. S. & Cockerham, C. C., 1984. Estimating F-statistics for the analysis of population struc-
ture. Evolution 38: 1358-1370.
4 clean_workdir
basic_info Allele and genotype frequencies
Description
Allele and genotype frequencies per locus and per sample. See this section of the Genepop exe-
cutable documentation for more information on the statistical methods.
Usage
basic_info(inputFile, outputFile = "", verbose = interactive())
Arguments
inputFile The path of the input file, in Genepop format
outputFile character: The path of the output file
verbose logical: whether to print some information
Value
The path of the output file is returned invisibly.
Examples
locinfile <- genepopExample('sample.txt')
basic_info(locinfile,'sample.txt.INF')
if ( ! interactive()) clean_workdir(otherfiles='sample.txt')
clean_workdir Removing files created by Genepop
Description
This removes “temporary files” created by Genepop, but also output files, so it should be used only
when one no longer needs the latter files. This function asumes that the input file name contains
only alphanumeric, dot, or underscore characters.
Usage
clean_workdir(
otherfiles = NULL,
path = ".",
suffixes = c("GRA", "ISO", "MIG", "PRI", "DAT", "DG", "DIV", "D", "DIS", "FST", "NUL",
"RHO", "2G2", "G", "GE", "GE2", "INF", "MSD", "TAB", "ST2"),
in. = TRUE,
cmdline = TRUE
)
Contingency-test 5
Arguments
otherfiles Character vector(s): one or more names of files to be removed and not matched
by the other arguments (such as the input file, or some output files not identified
by their suffix, as shown in the Example).
path character vector: path from where files should be removed.
suffixes Character vector(s): suffixes of files to be removed (useful for output files with
readily identifiable suffixes).
in. boolean: whether to remove the fichier.in file created by Genepop.
cmdline boolean: whether to remove the cmdline.txt file created by Genepop.
Examples
# Removing files possibly written by other examples in the documentation:
clean_workdir(otherfiles=c("sample.txt", "Dsample.txt", "w2.txt",
"PEL1600withCoord.txt", "Rhesus.txt", "structest.txt"))
Contingency-test Exact test on a single contingency table
Description
Performs an exact conditional contingency-table test. There are many other ways of doing this in R
but this function replicates the functionality of earlier genepop code analysing a contingency table
provided in a file with ad hoc format. See this section of the Genepop executable documentation
for more information on the statistical methods.
Usage
struc(
inputFile,
settingsFile = "",
dememorization = 10000,
batches = 100,
iterations = 5000,
verbose = interactive()
)
Arguments
inputFile character: The path of the input file. This file should be in an ad hoc format
settingsFile character: The path of the settings file
dememorization integer: length of dememorization step of Markov chain algorithm
batches integer: Number of batches
iterations integer: Iterations per batch
6 conversion
Value
Examples
locinfile <- genepopExample('structest.txt')
struc(locinfile)
if ( ! interactive()) clean_workdir(otherfiles='structest.txt')
conversion File conversions
Description
Converts input files from genepop format to some other formats (some maybe only of historical
interest): Fstat, two Biosys formats. and linkdos. See this section of the Genepop executable
documentation for more information on the statistical methods.
Usage
conversion(inputFile, format, outputFile = "", verbose = interactive())
Arguments

format Character string: must be one of 'Fstat', 'BiosysL', 'BiosysN', or 'Linkdos'
Value
Examples
conversion(locinfile, format='Fstat', 'sample.txt.DAT')
Differentiation 7
Differentiation Tests of genic and genotypic differentiation
Description
Exact conditional contingency-table tests for genic or genotypic differentiation. A single test for all
populations, or distinct tests for all pairs of populations, may be computed. See this section of the
Genepop executable documentation for more information on the statistical methods.
Usage
test_diff(
inputFile,
genic = TRUE,
pairs = FALSE,
outputFile = "",
settingsFile = "",
batches = 100,
iterations = 5000,
)
Arguments
genic logical: whether to perform genic or genotypic tests
pairs logical: whether to test differentiation between all pairs of ppulation, or to per-
form a single global test
Value
Examples
test_diff(locinfile,outputFile='sample.txt.GE')
8 Fst
Fst Fst (or rho_ST) estimation
Description
Evaluates Fst or related measures based on allele sizes, for all populations of for all pairs of pop-
ulations. See this section of the Genepop executable documentation for more information on the
statistical methods.
Usage
Fst(
inputFile,
sizes = FALSE,
pairs = FALSE,
outputFile = "",
dataType = "Diploid",
)
Arguments

sizes logical: whether to estimate allele-size based statistics, or identity-based Fst
pairs whether to estimate differentiation between all pairs of populations, or to com-
pute a global estimate for all populations
dataType character: The haploid and diploid data
Value
Examples
Fst(locinfile, outputFile= 'sample.txt.DIV')
genedivFis 9
genedivFis Gene diversities and Fis (or rho_IS)
Description
Evaluates Fis and gene diversities, or related measures based on allele sizes. See this section of the
Genepop executable documentation for more information on the identity-based statistical methods,
and this one for allele-size based ones.
Usage
genedivFis(
inputFile,
sizes = FALSE,
outputFile = "",
)
Arguments

sizes logical: whether to compute statistics based on allele size, or not.
Value
Examples

genedivFis(locinfile,outputFile = 'sample.txt.DIV')
10 GUI
genepopExample Copy an example file from the Genepop package distribution
Description
This function is used to copy an example file to the user’s directory. It should not be used when
analysing one’s own data!
Usage
genepopExample(filename)
Arguments
filename The name of an example file from the Genepop distribution.
Value
Returns the filename
GUI Call an experimental GUI for Genepop
Description
Call an experimental GUI for Genepop
Usage
GUI()
Value
The return value of a ‘shiny::runApp()‘ call.

Hardy-Weinberg 11
Hardy-Weinberg Tests of Hardy-Weinberg genotypic proportions
Description
Compute variants of the exact conditional test for Hardy-Weinberg genotypic proportions. The
tests differ by their test statistics. HWtable_analysis handles a single table of genotype counts,
and test_HW requires a standard genepop input file. See this section of the Genepop-executable
Usage
test_HW(
inputFile,
which = "Proba",
outputFile = "",
settingsFile = "",
enumeration = FALSE,
batches = 20,
iterations = 5000,
)
HWtable_analysis(
inputFile,
which = "Proba",
settingsFile = "",
enumeration = FALSE,
batches = 20,
iterations = 5000,
)
Arguments
inputFile character: The path of the input file. For test_HW, this file should be in Genepop
format. For HWtable_analysis, it should be in ad hoc format illustrated by
sample file Rhesus.txt used in the Examples section, and further detailed in
this section of the Genepop-executable documentation.
which character: 'Proba', 'excess', and 'deficit' to perform the probability test,
score test for excess, and score tests for deficit, respectively, in each popula-
tion and for each locus. test_HW additionally handles 'global excess' and
'global deficit' for global tests for all loci and/or all populations, and HWtable_analysis
additionally handles 'Fis' to report basic information (allele frequencies and
Fis).
12 IBD

enumeration logical: whether to compute the complete enumeration test for samples with less
than 5 alleles
Value
Examples
test_HW(locinfile, which='deficit', 'sample.txt.D')
# Example in Guo & Thompson 1992 Table 5
locinfile <- genepopExample('Rhesus.txt')
outfile <- HWtable_analysis(locinfile,which='Proba',batches = 1000,iterations = 1000)
readLines(outfile)[21]
#clean_workdir(otherfiles='Rhesus.txt')
IBD Isolation by distance
Description
Estimates isolation by distance by regression of genetic distance to geographical distance. See
this section of the Genepop executable documentation for more information on individual-based
analyses and this one for group-based analyses.
Usage
ibd(
inputFile,
outputFile = "",
settingsFile = "",
statistic = "F/(1-F)",
geographicScale = "2D",
CIcoverage = 0.95,
testPoint = 0,
minimalDistance = 1e-04,
maximalDistance = 1e+09,
IBD 13
mantelPermutations = 1000,
mantelRankTest = FALSE,
bootstrapMethod = "ABC",
bootstrapNsim = 999,
)
Arguments
dataType character: 'haploid' or 'diploid'
statistic character: The pairwise genetic distance, either 'a' or 'e' for diploid individual
data, 'a-like' for haploid individual data, and 'F/(1-F)' or 'SingleGeneDiv'
for group data (haploid or diploid)
geographicScale
character: gives either the scale transformation 'Log' or 'Linear' for geo-
graphic distances, or the shape of the habitat '2D' or '1D'
CIcoverage numeric: The coverage probability of confidence intervals
testPoint numeric: Given value of the slope to be tested
minimalDistance
numeric: The minimal geographic distance
maximalDistance
numeric: The maximal geographic distance
mantelPermutations
numeric: The number of permutations may be specified
mantelRankTest logical: whether to use ranks in the Mantel test
bootstrapMethod
character: which bootstrap method to use (one of "ABC", "BC" or "BCa").
bootstrapNsim integer: the number of bootstrap simulations to use (has no effect if method is
"ABC").
Value
Examples
## Not run:
locinfile <- genepopExample('w2.txt')
outfile <- ibd(locinfile,'w2.txt.ISO', geographicScale = 'Log', statistic='e')
if ( ! interactive()) clean_workdir(otherfiles='w2.txt')
locinfile <- genepopExample('PEL1600withCoord.txt')

14 Linkage
outfile <- ibd(locinfile,'PEL1600withCoord.ISO', statistic = 'SingleGeneDiv',

geographicScale = '1D')
if ( ! interactive()) clean_workdir(otherfiles='PEL1600withCoord.txt')
## End(Not run)
Linkage Tables and exact test for genotypic linkage disequilibrium
Description
Exact test for each pair of loci in each population. See this section of the Genepop executable
Usage
test_LD(
inputFile,
outputFile = "",
settingsFile = "",
batches = 100,
iterations = 5000,
)
write_LD_tables(inputFile, outputFile = "", verbose = interactive())
Arguments

Value

manipulation 15
Examples
## Not run: # 'dontrun' only because a bit too slow for CRAN checks
test_LD(locinfile,'sample.txt.DIS')
## End(Not run)
write_LD_tables(locinfile,'sample.txt.TAB')
manipulation Various data manipulation utilities
Description
Various procedures described in the linked sections of the Genepop executable documentation:
diploidize haploid data, relabel_alleles, sample_haploid, and pop_to_indiv. The latter procedure
converts population samples (several individuals in each population) to individual data. The names
given to the individuals in the new file created (names which are to be interpreted as coordinates
in a spatial analysis) may be the population coordinates (given as the name of the last individual in
the original data file), or each individual’s coordinates (given as the name of each individual in the
original data file).
Usage
diploidize(inputFile, outputFile = "", verbose = interactive())
relabel_alleles(inputFile, outputFile = "", verbose = interactive())
pop_to_indiv(inputFile, coordinates, outputFile = "", verbose = interactive())
sample_haploid(inputFile, outputFile = "", verbose = interactive())
Arguments
coordinates character: either 'population' (to use population coordinates) or any other
charater string (to use individual coordinates).
Examples
outfile <- diploidize(inputFile = locinfile,outputFile="Dsample.txt")
if ( ! interactive()) clean_workdir(c("sample.txt", "Dsample.txt"))
16 nulls
Nm_private Private allele method
Description
Estimation of Nm by private allele method of Slatkin and Barton. See this section of the Genepop
executable documentation for more information on the statistical methods.
Usage
Nm_private(
inputFile,
outputFile = "",
)
Arguments
Value
Examples
Nm_private(locinfile,'sample.txt.PRI')
nulls Estimation of allele frequencies under genotyping failure.
Description
Estimates allele frequencies (and failure rate if relevant) under dfferent assumptions: maximum
likelihood assuming that there is null allele (default method), maximum likelihood assuming that
apparent nulls are technical failures independent of genotype ('ApparentNulls'), and Brookfield’s
(1996) estimator ('B96'). See this section of the Genepop executable documentation for more
information on the statistical methods. Genepop takes the allele with the highest number for a given
locus across all populations as the null allele. For example, if you have 4 alleles plus a null allele, a
null homozygote individual should be indicated as e.g. 0505 or 9999 in the input file.
setMantelSeed 17
Usage
nulls(
inputFile,
outputFile = "",
settingsFile = "",
nullAlleleMethod = "",
CIcoverage = 0.95,
)
Arguments

nullAlleleMethod
character: 'ApparentNulls', 'B96' or anything else (default method).
CIcoverage numeric: The coverage probability of confidence interval
Value
setMantelSeed Set random generator seed for Mantel test
Description
Set random generator seed for Mantel test
Usage
setMantelSeed(seed)
Arguments
seed integer: the new seed

18 set_restriction
setRandomSeed Set random generator seed (except for Mantel test)
Description
Set random generator seed (except for Mantel test)
Usage
setRandomSeed(seed)
Arguments
seed integer: the new seed
set_restriction Programming utilities
Description
getVersion returns the version number of the C++ code (the same number that identifies the C++
executable). set_restriction(TRUE) sets the maximum number of populations and of loci to 300.
Usage
set_restriction(set = FALSE)
getVersion()
Arguments
set logical: whether to set restrictions on number of populations and of loci
Index
∗ package setMantelSeed, 17
genepop-package, 2 setRandomSeed, 18
struc (Contingency-test), 5
basic_info, 4
test_diff, 2
clean_workdir, 4 test_diff (Differentiation), 7
Contingency-test, 5 test_HW, 2
conversion, 2, 6 test_HW (Hardy-Weinberg), 11
test_LD, 2
Differentiation, 7 test_LD (Linkage), 14
diploidize (manipulation), 15
write_LD_tables (Linkage), 14
Fst, 2, 8
genedivFis, 9
genepop (genepop-package), 2
genepop-package, 2
genepop-utils (set_restriction), 18
genepopExample, 10
getVersion (set_restriction), 18
GUI, 10
Hardy-Weinberg, 11
HWtable_analysis (Hardy-Weinberg), 11
IBD, 12
ibd, 2
ibd (IBD), 12
Linkage, 14
manipulation, 2, 15
Nm_private, 2, 16
nulls, 2, 16
pop_to_indiv (manipulation), 15
relabel_alleles (manipulation), 15
sample_haploid (manipulation), 15
set_restriction, 18
19

Genepop

Uploaded by

Copyright:

Available Formats

Genepop

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Genepop

Uploaded by

Copyright:

Available Formats

Package ‘genepop’

January 20, 2023

genepop-package Population genetic analyses using the Genepop software

basic_info Allele and genotype frequencies

clean_workdir Removing files created by Genepop

Contingency-test Exact test on a single contingency table

The path of the output file is returned invisibly.

conversion File conversions

conversion(inputFile, format, outputFile = "", verbose = interactive())

inputFile The path of the input file, in Genepop format

The path of the output file is returned invisibly.

Differentiation Tests of genic and genotypic differentiation

Fst Fst (or rho_ST) estimation

inputFile The path of the input file, in Genepop format

The path of the output file is returned invisibly.

genedivFis Gene diversities and Fis (or rho_IS)

inputFile The path of the input file, in Genepop format

The path of the output file is returned invisibly.

locinfile <- genepopExample('sample.txt')

genepopExample Copy an example file from the Genepop package distribution

filename The name of an example file from the Genepop distribution.

Returns the filename

GUI Call an experimental GUI for Genepop

Call an experimental GUI for Genepop

The return value of a ‘shiny::runApp()‘ call.

Hardy-Weinberg Tests of Hardy-Weinberg genotypic proportions

outputFile character: The path of the output file

IBD Isolation by distance

locinfile <- genepopExample('PEL1600withCoord.txt')

outfile <- ibd(locinfile,'PEL1600withCoord.ISO', statistic = 'SingleGeneDiv',

Linkage Tables and exact test for genotypic linkage disequilibrium

write_LD_tables(inputFile, outputFile = "", verbose = interactive())

inputFile The path of the input file, in Genepop format

The path of the output file is returned invisibly.

manipulation Various data manipulation utilities

relabel_alleles(inputFile, outputFile = "", verbose = interactive())

pop_to_indiv(inputFile, coordinates, outputFile = "", verbose = interactive())

sample_haploid(inputFile, outputFile = "", verbose = interactive())

Nm_private Private allele method

nulls Estimation of allele frequencies under genotyping failure.

inputFile The path of the input file, in Genepop format

The path of the output file is returned invisibly.

setMantelSeed Set random generator seed for Mantel test

Set random generator seed for Mantel test

seed integer: the new seed

setRandomSeed Set random generator seed (except for Mantel test)

set_restriction Programming utilities

You might also like

Pfad - The Proxy pFad of © 2024 Garber Painting. All rights reserved.