corehunter: Multi-Purpose Core Subset Selection

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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>).

Author
Herman De Beukelaer [aut, cre], Guy Davenport [aut], Veerle Fack [ths]
Date of publication
2016-10-04 16:13:09
Maintainer
Herman De Beukelaer <herman.debeukelaer@gmail.com>
License
MIT + file LICENSE
Version
3.0.1

View on CRAN

Man pages

corehunter
Core Hunter 3
coreHunterData
Initialize Core Hunter data.
distances
Create Core Hunter distance data from matrix or file.
evaluateCore
Evaluate a core collection using the specified objective.
exampleData
Example dataset with 218 individuals.
genotypes
Create Core Hunter genotype data from data frame, matrix or...
getAlleleFrequencies
Get Allele frequency matrix.
getNormalizationRanges
Determine normalization ranges of all objectives in a...
objective
Create Core Hunter objective.
phenotypes
Create Core Hunter phenotype data from data frame or file.
read.autodelim
Read delimited file.
sampleCore
Sample a core collection from the given data.
setRange
Set the normalization range of the given objective.
wrapData
Wrap distances, genotypes or phenotypes in Core Hunter data.

Files in this package

corehunter
corehunter/inst
corehunter/inst/java
corehunter/inst/java/slf4j-nop-1.7.21.jar
corehunter/inst/java/corehunter-3.0.0.jar
corehunter/inst/java/LICENSE
corehunter/inst/java/NOTICE
corehunter/inst/extdata
corehunter/inst/extdata/phenotypes.csv
corehunter/inst/extdata/genotypes.csv
corehunter/inst/extdata/distances.csv
corehunter/inst/extdata/genotypes-frequency.csv
corehunter/inst/extdata/genotypes-biparental.csv
corehunter/tests
corehunter/tests/test.R
corehunter/tests/testthat
corehunter/tests/testthat/testUtils.R
corehunter/tests/testthat/data
corehunter/tests/testthat/data/phenotypes-unknown-type.csv
corehunter/tests/testthat/data/genotypes-small.csv
corehunter/tests/testthat/data/phenotypes-small.csv
corehunter/tests/testthat/data/distances-small.txt
corehunter/tests/testthat/data/phenotypes-no-types.csv
corehunter/tests/testthat/testAnalysis.R
corehunter/tests/testthat/testExecution.R
corehunter/tests/testthat/testData.R
corehunter/NAMESPACE
corehunter/NEWS.md
corehunter/R
corehunter/R/execution.R
corehunter/R/analysis.R
corehunter/R/java.R
corehunter/R/data.R
corehunter/R/corehunter.R
corehunter/R/zzz.R
corehunter/README.md
corehunter/MD5
corehunter/java
corehunter/java/README.txt
corehunter/DESCRIPTION
corehunter/man
corehunter/man/sampleCore.Rd
corehunter/man/exampleData.Rd
corehunter/man/distances.Rd
corehunter/man/objective.Rd
corehunter/man/genotypes.Rd
corehunter/man/phenotypes.Rd
corehunter/man/coreHunterData.Rd
corehunter/man/getAlleleFrequencies.Rd
corehunter/man/read.autodelim.Rd
corehunter/man/wrapData.Rd
corehunter/man/evaluateCore.Rd
corehunter/man/getNormalizationRanges.Rd
corehunter/man/corehunter.Rd
corehunter/man/setRange.Rd
corehunter/LICENSE