Title: adegenet: adegenet version 2.0.1

Type Software Thibaut Jombart, Zhian N. Kamvar, Roman Luštrik, Klaus Schliep, Vladimir Mikryukov, Brian Knaus (2016): adegenet: adegenet version 2.0.1. Zenodo. Software. https://zenodo.org/record/46188

Authors: Thibaut Jombart (Imperial College London) ; Zhian N. Kamvar (Oregon State University) ; Roman Luštrik (PhD student) ; Klaus Schliep ; Vladimir Mikryukov (IPAE) ; Brian Knaus (USDA-Agricultural Research Service) ;

Links

• Item record in Zenodo
• Digital object URL

Summary

Adegenet version 2.0.1

This version contains a few new features, speedups, and bug fixes

Hs() is now much faster and will scale better for large number of loci

Hs.test() allows for testing differences in expected heterozygosity between two groups of individuals

strata tutorial is now available via adegenetTutorial(which="strata")

repool can now handle objects with no population information, and can return a list of repooled genind (argument 'list' defauling to FALSE)

read.fstat() can now handle missing data coded by any number of "0"

scatter.dapc() function can now label individuals using orditorp() function from vegan package, which takes care of overlapping (See issue #100)

df2genind() is now faster at handling missing data (See issue #114)

the summary method has better formatting

Hs() no longer returns NaN if one locus has not been typed; instead, computations are done using all available loci

adegenetTutorial() now opens up-to-date tutorials

subsetting genlight objects now treats missing data appropriately when given logical, character, or negative subscripts. (See issue #83)

fixed occasional spurious warning about duplicated individual labels in df2genind()

fixed issues with mis-placed missing data in df2genind() when samples were labeled with numbers (See issue #96)

frequencies can now be obtained from P/A genpop objects (See issue #105)

Windows no longer throws an error with as.genlight() (See issue #109)

read.genpop() now returns individual names (See issue #117)

More information

• DOI: 10.5281/zenodo.46188

Dates

• Publication date: 2016
• Issued: February 17, 2016

Rights

• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

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