Package: corehunter 3.2.3
Herman De Beukelaer
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>).
Authors:
corehunter_3.2.3.tar.gz
corehunter_3.2.3.tar.gz(r-4.5-noble)corehunter_3.2.3.tar.gz(r-4.4-noble)
corehunter_3.2.3.tgz(r-4.4-emscripten)corehunter_3.2.3.tgz(r-4.3-emscripten)
corehunter.pdf |corehunter.html✨
corehunter/json (API)
NEWS
| # Install 'corehunter' in R: |
| install.packages('corehunter', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 1 years agofrom:c24611caf5. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 26 2024 |
| R-4.5-linux | OK | Oct 26 2024 |
Exports:coreHunterDatadistancesevaluateCoreexampleDatagenotypesgetAlleleFrequenciesgetNormalizationRangesobjectivephenotypesread.autodelimsampleCoresetRange
Dependencies:naturalsortrJava
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Initialize Core Hunter data. | coreHunterData |
| Create Core Hunter distance data from matrix or file. | distances |
| Evaluate a core collection using the specified objective. | evaluateCore |
| Small example dataset with 218 individuals. | exampleData |
| Create Core Hunter genotype data from data frame, matrix or file. | genotypes |
| Get Allele frequency matrix. | getAlleleFrequencies |
| Determine normalization ranges of all objectives in a multi-objective configuration. | getNormalizationRanges |
| Create Core Hunter objective. | objective |
| Create Core Hunter phenotype data from data frame or file. | phenotypes |
| Read delimited file. | read.autodelim |
| Sample a core collection. | sampleCore |
| Set the normalization range of the given objective. | setRange |
| Wrap distances, genotypes or phenotypes in Core Hunter data. | wrapData |
