gxeFw function

Finlay-Wilkinson analysis

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

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.

Returns

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.

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"))

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()