gxeFw {statgenGxE}

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
)

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.

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.

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.

See Also

Other Finlay-Wilkinson: fitted.FW(), plot.FW(), report.FW(), residuals.FW()

Examples

## 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")


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