gxeFw: Finlay-Wilkinson analysis

Description

This function performs a Finlay-Wilkinson analysis of data classified by two factors.

Usage

gxeFw(
  TD,
  trials = names(TD),
  trait,
  maxIter = 15,
  tol = 0.001,
  sorted = c("descending", "ascending", "none"),
  genotypes = NULL,
  useWt = FALSE
)

Value

An object of class FW, a list containing:

estimates

A data.frame containing the estimated values, with the following columns:

genotype: The name of the genotype.
sens: The estimate of the sensitivity.
se_sens: The standard error of the estimate of the sensitivity.
genMean: The estimate of the genotypic mean.
se_genMean: The standard error of the estimate of the genotypic mean.
MSdeviation: The mean square deviation about the line fitted to each genotype
rank: The rank of the genotype based on its sensitivity.

anova

A data.frame containing anova scores of the FW analysis.

envEffs

A data.frame containing the environmental effects, with the following columns:

trial: The name of the trial.
envEff: The estimate of the environment effect.
se_envEff: The standard error of the estimate of the environment effect.
envMean: The estimate of the environment mean.
rank: The rank of the trial based on its mean.

TD

The object of class TD on which the analysis was performed.

fittedGeno

A numerical vector containing the fitted values for the genotypes.

trait

A character string containing the analyzed trait.

nGeno

A numerical value containing the number of genotypes in the analysis.

nEnv

A numerical value containing the number of environments in the analysis.

tol

A numerical value containing the tolerance used during the analysis.

iter

A numerical value containing the number of iterations for the analysis to converge.

Arguments

TD: An object of class TD.
trials: A character string specifying the trials to be analyzed. If not supplied, all trials are used in the analysis.
trait: A character string specifying the trait to be analyzed.
maxIter: An integer specifying the maximum number of iterations in the algorithm.
tol: A positive numerical value specifying convergence tolerance of the algorithm.
sorted: A character string specifying the sorting order of the estimated values in the output.
genotypes: An optional character string containing the genotypes to which the analysis should be restricted. If NULL, all genotypes are used.
useWt: Should weighting be used when modeling? Requires a column wt in TD.

References

Finlay, K.W. & Wilkinson, G.N. (1963). The analysis of adaptation in a plant-breeding programme. Australian Journal of Agricultural Research, 14, 742-754.

Examples

Run this code

## Run Finlay-Wilkinson analysis on TDMaize.
geFW <- gxeFw(TDMaize, trait = "yld")

## Summarize results.
summary(geFW)

## Create a scatterplot of the results.
plot(geFW, plotType = "scatter")

# \donttest{
## Create a report summarizing the results.
report(geFW, outfile = tempfile(fileext = ".pdf"))
# }