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Fit single trial mixed model

Source: R/fitTD.R
fitTD.Rd

Perform REML analysis given a specific experimental design using either SpATS, lme4 or asreml. SpATS is used as a default method when row coordinates (rowCoord) and column coordinates (colCoord) are present, lme4 otherwise. See details for the exact models fitted.

Usage

fitTD(
  TD,
  trials = names(TD),
  design = NULL,
  traits,
  what = c("fixed", "random"),
  covariates = NULL,
  useCheckId = FALSE,
  spatial = FALSE,
  engine = NA,
  control = NULL,
  progress = FALSE,
  ...
)

Arguments

TD

An object of class TD.

trials

A character vector specifying the trials for which the models should be fitted.

design

A character string specifying the experimental design. Either "ibd" (incomplete block design), "res.ibd" (resolvable incomplete block design), "rcbd" (randomized complete block design), "rowcol" (row column design) or "res.rowcol" (resolvable row column design). Can be ignored when the trial design is specified in the meta data (see setMeta).

traits

A character vector specifying the traits for which the models should be fitted.

what

A character vector specifying whether "genotype" should be fitted as fixed or random effect. If not specified, both models are fitted.

covariates

A character vector specifying covariates to be fitted as extra fixed effects in the model.

useCheckId

Should checkId be used as a fixed effect in the model?
If TRUE, TD has to contain a column 'checkId'. Using checkId as fixed effect can only be done when genotype is fitted as a random effect in the model.

spatial

Should spatial models be tried? Spatial models can only be fitted with SpATS and asreml. If SpATS is used for modeling, only spatial models can be fitted and spatial is always set to TRUE. If asreml is used, fitting spatial models is optional.

engine

A character string specifying the name of the mixed modeling engine to use, either "SpATS", "lme4" or "asreml." For spatial models, "SpaTS" is used as default, for other models "lme4".

control

An optional list with control parameters to be passed to the actual fitting functions. Currently nSeg and nestDiv are valid parameters when fitting a model using SpATS. They pass a value to nseg and nest.div in PSANOVA respectively. For nSeg also a named list can be supplied containing values for nSeg per trial.
criterion is a valid parameter when fitting a spatial model using asreml. It may be used to pass a goodness-of-fit criterion for comparing different spatial models. See also in details. Other parameters are ignored.

progress

Should the progress of the modeling be printed. If TRUE, for every trial a line is output indicating the traits fitted for the particular trial.

...

Further arguments to be passed to SpATS, lme4 or asreml.

Value

An object of class STA, a list containing, per trial that has been analyzed, a list of:

mRand

A list of models with fitted with genotype as random effect.

mFix

A list of models fitted with genotype as fixed effect.

TD

An object of class TD containing the data on which mRand and mFix are based.

traits

A character vector indicating the traits for which the models are fitted.

design

A character string containing the design of the trial. (see fitTD for the possible designs).

spatial

A character string indicating the spatial part of the model. FALSE if no spatial design has been used.

engine

A character string containing the engine used for the analysis.

predicted

A character string indicating the variable that has been predicted.

sumTab

A data.frame with a summary table for the spatial models tried when engine = "asreml" and spatial = TRUE

useCheckId

A boolean indicating if checkId was used when fitting the models

Details

The actual model fitted depends on the design. For the supported designs, the following models are used:

DesignCodeModel fitted
incomplete block designibdtrait = subBlock + genotype + \(\epsilon\)
resolvable incomplete block designres.ibdtrait = repId + repId:subBlock + genotype + \(\epsilon\)
randomized complete block designrcbdtrait = repId + genotype + \(\epsilon\)
row column designrowcoltrait = rowId + colId + genotype + \(\epsilon\)
resolvable row column designres.rowcoltrait = repId + repId:rowId + repId:colId + genotype + \(\epsilon\)

In the models above, fixed effects are indicated in italics whereas random effects are indicated in bold. genotype can be fitted as fixed or as random effect depending on the value of the parameter what. Extra fixed effects may be fitted using the parameter covariates.

If SpATS is used as modeling engine, an extra spatial term is always included in the model. This term is constructed using the function PSANOVA from the SpATS package as
PSANOVA(colCoord, rowCoord, nseg = nSeg, nest.div = 2) where
nSeg = (number of columns / 2, number of rows / 2). nseg and nest.div can be modified using the control parameter.

When asreml is used for modeling and spatial is TRUE seven models are fitted with different random terms and covariance structure. The best model is determined based on a goodness-of-fit criterion, either AIC or BIC. This can be set using the control parameter criterion, default is AIC. The fitted random terms depend on the structure of the data. If the trial has a regular structure, i.e. all replicates appear the same amount of times in the trial, the following combinations of random and spatial terms are fitted:

Random partSpatial part
random effects based on designnone
random effects based on designAR1(rowId):colId
random effects based on designrowId:AR1(colId)
random effects based on designAR1(rowId):ar1(colId)
random effects based on design + nuggetAR1(rowId):colId
random effects based on design + nuggetrowId:AR1(colId)
random effects based on design + nuggetAR1(rowId):AR1(colId)

If the design is not regular the following combinations of random and spatial terms are fitted:

Random partSpatial part
random effects based on designnone
random effects based on designexp(rowCoord):colCoord
random effects based on designrowCoord:exp(colCoord)
random effects based on designiexp(rowCoord, colCoord)
random effects based on design + nuggetexp(rowCoord):colCoord
random effects based on design + nuggetrowCoord:exp(colCoord)
random effects based on design + nuggetiexp(rowCoord,colCoord)

References

Maria Xose Rodriguez-Alvarez, Martin P. Boer, Fred A. van Eeuwijk, Paul H.C. Eilers (2017). Correcting for spatial heterogeneity in plant breeding experiments with P-splines. Spatial Statistics doi:10.1016/j.spasta.2017.10.003

Butler, D. G., et al. (2010). Analysis of Mixed Models for S language environments: ASReml-R reference manual. Brisbane, DPI Publications

Douglas Bates, Martin Maechler, Ben Bolker, Steve Walker (2015). Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software, 67(1), 1-48. https://www.jstatsoft.org/article/view/v067i01/0.

Examples

# \donttest{
## Fit model using lme4.
lmeMod <- fitTD(TD = TDHeat05,
                design = "ibd",
                traits = "yield",
                what = "fixed",
                engine = "lme4")

## Summarize results.
summary(lmeMod)
#> Summary statistics 
#> ==================
#> 
#> Summary statistics for yield in HEAT05  
#> 
#>                             yield
#> Number of observations      338.0
#> Number of missing values      0.0
#> Mean                       184.16
#> Median                     179.81
#> Min                         54.58
#> Max                        341.77
#> First quantile             148.56
#> Third quantile             220.50
#> Variance                 2569.229
#> 
#> 
#> Predicted means (BLUEs) 
#> ===============================
#> Best 20 genotypes
#>        BLUEs     SE
#> SB023 302.84 30.194
#> SB025 297.84 30.194
#> SB022 285.13 30.194
#> SB032 280.96 30.194
#> SB011 272.45 30.194
#> SB156 262.77 30.194
#> SB055 253.21 30.194
#> SB020 253.08 30.194
#> SB144 251.55 30.194
#> SB045 250.07 30.194
#> SB054 246.51 30.194
#> SB031 245.69 30.338
#> SB027 244.27 30.194
#> SB128 243.91 30.338
#> SB194 239.22 30.194
#> SB077 238.66 30.194
#> SB093 236.58 30.194
#> SB106 233.86 30.194
#> SB041 232.83 30.194
#> SB143 232.41 30.194

## Create base plots of the results.
plot(lmeMod)


## Create a pdf report summarizing results.
report(lmeMod,
       outfile = tempfile(fileext = ".pdf"),
       what = "fixed")
#> Error in report.STA(lmeMod, outfile = tempfile(fileext = ".pdf"), what = "fixed"): An installation of LaTeX is required to create a pdf report.

## Fit model using SpATS.
spaMod <- fitTD(TD = TDHeat05,
                design = "res.rowcol",
                traits = "yield",
                what = "fixed")
#> Using SpATS for fitting models.
summary(spaMod)
#> Summary statistics 
#> ==================
#> 
#> Summary statistics for yield in HEAT05  
#> 
#>                             yield
#> Number of observations      338.0
#> Number of missing values      0.0
#> Mean                       184.16
#> Median                     179.81
#> Min                         54.58
#> Max                        341.77
#> First quantile             148.56
#> Third quantile             220.50
#> Variance                 2569.229
#> 
#> 
#> Predicted means (BLUEs) 
#> ===============================
#> Best 20 genotypes
#>        BLUEs     SE
#> SB023 285.02 11.120
#> SB025 283.93 11.058
#> SB022 281.90 11.149
#> SB032 278.93 11.100
#> SB011 271.10 11.300
#> SB156 267.22 11.313
#> SB144 265.80 11.391
#> SB031 252.95 11.063
#> SB093 247.71 11.249
#> SB054 247.14 11.463
#> SB055 247.04 11.414
#> SB020 241.19 11.094
#> SB028 239.22 11.212
#> SB128 238.02 11.437
#> SB194 237.85 11.260
#> SB155 236.51 11.268
#> SB143 236.26 11.454
#> SB027 235.38 11.120
#> SB163 234.34 11.146
#> SB181 233.11 11.083

## Create spatial plots of the results.
plot(spaMod, plotType = "spatial")


## Fit model using SpATS.
## Specify the number of segments to use in PSANOVA
spaMod2 <- fitTD(TD = TDHeat05,
                 design = "res.rowcol",
                 traits = "yield",
                 what = "fixed",
                 control = list(nSeg = c(13, 26)))
#> Using SpATS for fitting models.

## Create a pdf report summarizing results.
report(spaMod, outfile = tempfile(fileext = ".pdf"), what = "fixed")
#> Error in report.STA(spaMod, outfile = tempfile(fileext = ".pdf"), what = "fixed"): An installation of LaTeX is required to create a pdf report.

## Fit model using asreml.
if (requireNamespace("asreml", quietly = TRUE)) {
  asrMod <- fitTD(TD = TDHeat05,
                  design = "res.rowcol",
                  traits = "yield",
                  what = "fixed",
                  engine = "asreml")
  summary(asrMod)

  report(asrMod,
         outfile = tempfile(fileext = ".pdf"),
         what = "fixed")
}
# }