corehunter: Multi-Purpose Core Subset Selection

Core Hunter is a tool to sample diverse, representative subsets from large germplasm collections, with minimum redundancy. Such so-called core collections have applications in plant breeding and genetic resource management in general. Core Hunter can construct cores based on genetic marker data, phenotypic traits or precomputed distance matrices, optimizing one of many provided evaluation measures depending on the precise purpose of the core (e.g. high diversity, representativeness, or allelic richness). In addition, multiple measures can be simultaneously optimized as part of a weighted index to bring the different perspectives closer together. The Core Hunter library is implemented in Java 8 as an open source project (see <http://www.corehunter.org>).

Install the latest version of this package by entering the following in R:
install.packages("corehunter")
AuthorHerman De Beukelaer [aut, cre], Guy Davenport [aut], Veerle Fack [ths]
Date of publication2017-02-20 19:15:04
MaintainerHerman De Beukelaer <herman.debeukelaer@gmail.com>
LicenseMIT + file LICENSE
Version3.1.0

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Files

inst
inst/java
inst/java/slf4j-nop-1.7.21.jar
inst/java/corehunter-3.1.0.jar
inst/java/LICENSE
inst/java/NOTICE
inst/extdata
inst/extdata/phenotypes.csv
inst/extdata/genotypes.csv
inst/extdata/distances.csv
inst/extdata/genotypes-frequency.csv
inst/extdata/genotypes-biparental.csv
tests
tests/test.R
tests/testthat
tests/testthat/testUtils.R
tests/testthat/data
tests/testthat/data/phenotypes-unknown-type.csv
tests/testthat/data/genotypes-small.csv
tests/testthat/data/genotypes-bi-small.csv
tests/testthat/data/genotypes-freq-small.csv
tests/testthat/data/phenotypes-small.csv
tests/testthat/data/distances-small.txt
tests/testthat/data/phenotypes-no-types.csv
tests/testthat/testAnalysis.R tests/testthat/testExecution.R tests/testthat/testData.R
NAMESPACE
NEWS.md
R
R/execution.R R/analysis.R R/java.R R/data.R R/corehunter.R R/zzz.R
README.md
MD5
java
java/README.txt
DESCRIPTION
man
man/sampleCore.Rd man/exampleData.Rd man/distances.Rd man/objective.Rd man/genotypes.Rd man/phenotypes.Rd man/coreHunterData.Rd man/getAlleleFrequencies.Rd man/read.autodelim.Rd man/wrapData.Rd man/evaluateCore.Rd man/getNormalizationRanges.Rd man/corehunter.Rd man/setRange.Rd
LICENSE

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.