extract: Extract statistics from Fitted Models

Description

This function is deprecated. Use extractSTA for extracting results from fitted models.

Usage

extract(
  STA,
  trials = names(STA),
  traits = NULL,
  what = "all",
  keep = NULL,
  restoreColNames = FALSE
)

Value

A list with, per trial for which statistics have been extracted, a list of those statistics.

Arguments

STA: An object of class STA.
trials: A character vector of trials for which the statistics should be computed. If not supplied, statistics are computed for all trials that have been modeled.
traits: A character vector of traits for which the statistics should be computed. If not supplied, statistics are computed for all traits that have been modeled.
what: A character vector indicating which statistics should be computed. Most statistics are available for all models, some only for models fitted using a certain engine. If this is the case, this is indicated in the list with options in details.
If what = "all", all available statistics are computed.
keep: A character vector of column(s) in the object of class TD used for modeling. These columns will be kept as output when computing fitted values, residuals, standardized residuals and rMeans. Columns can also be kept when computing (se)BLUEs and (se)BLUPs but only if the column to keep contains unique values for the modeled variables, i.e. a column repId with several different values per genotype cannot be kept.
restoreColNames: Should the original column names be restored in the output of the extracted data?

Details

Possible options for what are:

F - BLUEs: Best Lineair Unbiased Estimators.
F - seBLUES: Standard errors of the BLUEs.
R - BLUPs: Best Lineair Unbiased Predictors.
R - seBLUPs: Standard errors of the BLUPs.
F - ue: Unit errors - only for lme4 and asreml.
R - heritability: Heritability.
F - varCompF: Variance components for model with genotype as fixed component.
R - varCompR: Variance components for model with genotype as random component.
R - varGen: Genetic variance component(s).
R - varErr: Residual variance component(s) - only for lme4 and asreml.
R - varSpat: Spatial variance components - only for SpATS.
F - fitted: Fitted values for the model with genotype as fixed component.
F - residF: Residuals for the model with genotype as fixed component.
F - stdResF: Standardized residuals for the model with genotype as fixed component
R - rMeans: Fitted values for the model with genotype as random component.
R - ranEf: Random genetic effects.
F - residR: Residuals for the model with genotype as random component.
F - stdResR: Standardized residuals for the model with genotype as random component
F - wald: Results of the wald test - only for lme4 and asreml.
F - CV: Coefficient of variation - only for lme4 and asreml.
F - rDfF: Residual degrees of freedom for the model with genotype as fixed component.
R - rDfR: Residual degrees of freedom for the model with genotype as random component.
R - effDim: Effective dimensions - only for SpATS.
R - ratEffDim: Ratio's of the effective dimensions - only for SpATS.
F - sed: Standard error of difference - only for asreml.
F - lsd: Least significant difference - only for asreml.
all: All available statistics.

Description

Usage

Value

Arguments

Details

See Also