R syntax workaround for bug in Custom Contrasts in (classical) Linear Mixed Models?

andersony3k

I am attempting a workaround for a current bug in Classical Linear Mixed Models wherein in the number of allowable custom contrasts appears to be arbitrarily limited.

My attempted workaround uses JASP's generated R syntax to try to circumvent the GUI limitation on the number of contrasts. I already have some custom contrasts implemented in the model (using the GUI), but when I look at the generated syntax, I don't see a specification of those custom contrasts, so I can't figure out what part of the code I need to modify/elaborate in order to produce the entire set of desired custom contrasts. (Is the problem that the generated code shows Contrasts = NULL when it should not be NULL?) The generated syntax is shown below.

jaspMixedModels::MixedModelsLMM(

data = NULL,

version = "0.95.5",

formula = `log RT` ~ Congruence * Tempo * Angle + (1 | Participant),

bootstrapSamples = 1000,

contrasts = NULL,

factorContrast = "sum",

fixedEffectEstimate = FALSE,

includeIntercept = TRUE,

interceptTest = FALSE,

marginalMeansCiLevel = 0.95,

marginalMeansComparison = FALSE,

marginalMeansComparisonWith = 0,

marginalMeansContrast = TRUE,

marginalMeansDf = "satterthwaite",

marginalMeansDfEstimated = FALSE,

marginalMeansPAdjustment = "none",

marginalMeansSd = 1,

marginalMeansTerms = ~ Tempo + Congruence,

modelSummary = TRUE,

plotBackgroundColor = "darkgrey",

plotBackgroundData = ~ Participant.nominal,

plotBackgroundElement = "jitter",

plotCiLevel = 0.95,

plotCiType = "model",

plotDodge = 0.3,

plotElementWidth = 1,

plotEstimatesTable = FALSE,

plotHeight = 320,

plotHorizontalAxis = NULL,

plotJitterHeight = 0,

plotJitterWidth = 0.1,

plotLegendPosition = "none",

plotLevelsByColor = FALSE,

plotLevelsByFill = FALSE,

plotLevelsByLinetype = TRUE,

plotLevelsByShape = TRUE,

plotRelativeSizeData = 1,

plotRelativeSizeText = 1.5,

plotSeparateLines = NULL,

plotSeparatePlots = NULL,

plotTheme = "jasp",

plotTransparency = 0.7,

plotWidth = 480,

randomEffectEstimate = FALSE,

seed = 1,

setSeed = TRUE,

testMethod = "parametricBootstrap",

trendsCiLevel = 0.95,

trendsComparison = FALSE,

trendsComparisonWith = 0,

trendsContrast = FALSE,

trendsContrasts = NULL,

trendsDf = "asymptotic",

trendsDfEstimated = FALSE,

trendsPAdjustment = "holm",

trendsSd = 1,

trendsTrendVariable = NULL,

trendsVariables = NULL,

type = "3",

varianceCorrelationEstimate = FALSE,

vovkSellke = FALSE)

patc3

That was a good idea of using the syntax, but I also can't figure out how to make it work. In the meantime here's two options I thought of that you might have thought of already:

1. duplicating the analysis and continuing your contrasts in the second (duplicated) analysis; this is annoying because you get twice the output and also if you change an option in one analysis you need to change it in the second one as well
2. use the R console (which basically defeats the purpose of using JASP), if you want I can try to write you the required syntax to run in the R console

option #1 is clunky and inconvenient but much simpler than option #2 it seems to me

andersony3k

Thanks for the suggestions. I complication of Option 1 is that I would need to specify no correction for familywise error, and then semi-manually adjust the p values afterward.

For now, I think I'll just wait and see if the bug gets fixed soon.

patc3

ah yes you're right didn't think about that. OK, if you change your mind later and want to try the R console I should be able to help