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# Penicillin: Random-Intercept, Cross-Classified model
# http://xxm.times.uh.edu/learn-xxm/penicillin/
libraries <- rownames(installed.packages())
if (!("lme4" %in% libraries)) stop("SKIP")
library(lme4)
library(OpenMx)
plateModel <- mxModel(
'plateModel', type="RAM",
latentVars = c('plate'),
mxData(data.frame(plate=unique(Penicillin$plate)), 'raw', primaryKey='plate'),
mxPath('plate', arrows=2, values=1))
sampleModel <- mxModel(
'sampleModel', type="RAM",
latentVars = c('sample'),
mxData(data.frame(sample=unique(Penicillin$sample)), 'raw', primaryKey='sample'),
mxPath('sample', arrows=2, values=1))
diameterModel <- mxModel(
'diameterModel', type="RAM", plateModel, sampleModel,
manifestVars='diameter',
mxData(Penicillin, 'raw'),
mxPath('one', 'diameter'),
mxPath('diameter', arrows=2, values=1),
mxPath('plateModel.plate', 'diameter', free=FALSE, values=1, joinKey='plate'),
mxPath('sampleModel.sample', 'diameter', free=FALSE, values=1, joinKey='sample'))
diameterModel <- mxRun(diameterModel)
(fm03.1 <- lmer(diameter ~ 1 + (1 | plate) + (1 | sample), REML = FALSE, Penicillin))
omxCheckCloseEnough(logLik(diameterModel), logLik(fm03.1), 1e-5)
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