allocc: Allocation accesions

In ccChooser: Developing a core collections

Description

This function determining the numbers of entries from each cluster (from entire collection) included in a core collection.

Usage

allocc(x, groups, fraction = 0.1, method = "Pro")

Arguments

x	data frame including name of acessions, number of groups and value for quantitaive traits (phenotypic data)
groups	defining column where present number of groups (clusters)
fraction	defining size of core collections, as fraction of accesions from entire collection
method	string defining the allocation method. The four methods implemented are "Pro" (propotional) , "Log" (logarytmic), "D2" (D2 alocation method) and "D3" (D3 alocation method)

Details

Four allocation methods were used in this function. Two of these methods based on the group size, are commonly known as the proportional (Pro) and logarithmic (Log) methods. Franco et al. (2005) proposed allocation methods for determining the number of accessions taken from a group based on the mean of the Gower's distance between accessions within the group. The respective allocation methods suggested by Franco et al. (2005) are called as D2 and D3. The first, D2, allocation method determines that the size of the sample to be drawn from each group should be proportional to the mean squared Euclidean distance between the accessions within that group and size group. The D3 allocation method based on proportional to the mean squared Euclidean distance between the accessions within that group and logarithm from size of the group.

Value

Return a matrix of groups and numbers accesions including in core collection.

Author(s)

Marcin Studnicki and Konrad Debski

References

For information about the allocation method for developing core collection, see:

van Hintum Th., Brown A., Spillane C., Hodgkin T. 2000. Core collections of plant genetic resources. IPGRI Technical Bulletin No. 3. IPGRI, Rome

Franco J., Crossa J., Taba S., Shands H. 2005. A sampling strategy for conserving genetic diversity when forming core subsets. Crop Sci. 45:1035-1044

Studnicki, M., Madry, W., Kociuba, W. 2010. The efficiency and effectiveness of sampling strategies used to develop a core collection for the Polish spring triticale (Triticosecale Wittm.) germplasm resources. Communications in Biometry and Crop Science 5 (2), 127-137

Examples

data(dactylis_EC)
allocc(dactylis_EC, dactylis_EC$UPGMA)
allocc(dactylis_EC, dactylis_EC$UPGMA, fraction = 0.15, method = 'D2')

ccChooser documentation built on May 1, 2019, 10:56 p.m.