Description
Core Collection.
Description
Create a custom sized Core Collection based on a distance matrix and applying the A-NE (accession nearest entry), E-NE (entry nearest entry) or E-E (entry entry) method as introduced in Jansen and van Hintum (2007) <doi:10.1007/s00122-006-0433-9> and further elaborated on in Odong, T.L. (2012) <https://edepot.wur.nl/212422>. Optionally a list of preselected accessions to be included into the core can be set. For each accession in the computed core, if available nearby accessions are retrievable that can be used as an alternative.
README.md
coreCollection
R package for creating a core collection based on the provided distanceMatrix, required size of the core n and optionally a set of preselected accessions to be included into the core.
Based on a provided distanceMatrix and required number n of accessions within the core, a random set of accessions is created, implicitly dividing the full population into initial groups based on the nearest randomly chosen random accession. If a set of preselected accessions is provided, this initial division is adjusted using the adjustedGroupMethod. Then, using the coreSelectMethod in the algorithm, the core accessions within these groups are calculated, resulting in the final core collection.
Usage
CoreCollection(
distanceMatrix,
n,
preselected = c(),
coreSelectMethod = "A-NE",
adjustedGroupMethod = "split",
algorithm = "randomDescent",
seed = NULL
)
Arguments
| argument | description |
|---|---|
| distanceMatrix | A distance matrix; can be either a matrix or a dist |
| n | The number of items in the core |
| preselected | An optional list of preselected accessions to be included in the core collection; the provided accessions should occur in the labels or rownames of the provided distanceMatrix |
| coreSelectMethod | The method for computing core accessions within the groups: A-NE (accession nearest entry), E-NE (entry nearest entry) or E-E (entry entry) |
| adjustedGroupMethod | The method to handle adjusting groups when multiple preselected accessions occur within a single group: split to just split the initial groups with multiple accessions or recompute to recompute the division of accessions over the groups. |
| algorithm | Algorithm applied to compute a solution: currently, only randomDescent is available |
| seed | The seed used when generating the core collection. If no seed is provided, a random seed is chosen and each time the recompute() method is called on the object, a new seed will be used. |