detectExptDesigns: "Detect" experimental designs

In wolfemd/genomicMateSelectR: Genomic Mate Selection

"Detect" experimental designs

Description

After cleaning up cassavabase trial data, the next step is to run some ad hoc code that checks the experimental design of each trial. If you are absolutely certain of the usage of the design variables in your dataset, you might not need this step.

Usage

detectExptDesigns(indata)

Arguments

indata

Details

Returns the input data.frame with two new columns indicating TRUE/FALSE, for each trial (location-year-studyName), whether the trial replicate / repInTrial columns indicates CompleteBlocks and if the blockInRep / blockNumber contains IncompleteBlocks.

Examples of reasons to do the step below:

• Some trials appear to be complete blocked designs and the blockNumber is used instead of replicate, which is what most use.

• Some complete block designs have nested, incomplete sub-blocks, others simply copy the "replicate" variable into the "blockNumber variable"

• Some trials have only incomplete blocks but the incomplete block info might be in the replicate and/or the blockNumber column

One reason it might be important to get this right is that the variance among complete blocks might not be the same among incomplete blocks. If we treat a mixture of complete and incomplete blocks as part of the same random-effect (replicated-within-trial), we assume they have the same variance.

NOTICE: This function is part of a family of functions ("cassavabase_pheno_pipeline") developed as part of the NextGen Cassava Breeding Project genomic selection pipeline. For some examples of their useage:

• IITA_2021GS (should be first use of this package)

• NRCRI_2021GS

• TARI_2020GS

• IITA_2020GS

Value

Returns the input data.frame with two new columns indicating TRUE/FALSE, for each trial (location-year-studyName), whether the trial replicate / repInTrial columns indicates CompleteBlocks and if the blockInRep / blockNumber contains IncompleteBlocks.

See Also

Other cassavabase_pheno_pipeline: calcPropMissing(), curateTrialOneTrait(), curateTrialsByTrait(), fitMultiTrialModel(), makeTrialTypeVar(), nestByTrials(), nestDesignsDetectedByTraits(), nestForMultiTrialAnalysis(), nestTrialsByTrait(), readDBdata(), renameAndSelectCols()

wolfemd/genomicMateSelectR documentation built on July 1, 2022, 10:42 p.m.