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 <email@example.com>|
|License||MIT + file LICENSE|
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.