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# Pastes: Three level Random-Intercepts Model
# http://xxm.times.uh.edu/learn-xxm/lme4-example-pastes/
libraries <- rownames(installed.packages())
if (!("lme4" %in% libraries)) stop("SKIP")
library(testthat)
library(lme4)
library(OpenMx)
(fm01 <- lmer(strength ~ 1 + (1 | sample) + (1 | batch), REML = FALSE, Pastes))
batch <- mxModel(
'batch', type="RAM",
latentVars = c('batch'),
mxData(data.frame(batch=unique(Pastes$batch)), 'raw', primaryKey='batch'),
mxPath('batch', arrows=2, values=1))
sample <- mxModel(
'sample', type="RAM", batch,
latentVars = c('sample'),
mxData(as.data.frame(Pastes[!duplicated(Pastes$sample), c('batch','sample')]),
'raw', primaryKey='sample'),
mxPath('sample', arrows=2, values=1),
mxPath('batch.batch', 'sample', values=1, free=FALSE, joinKey='batch'))
strength <- mxModel(
'strength', type='RAM', sample,
manifestVars = c('strength'),
mxData(Pastes, 'raw'),
mxPath('one', 'strength'),
mxPath('strength', arrows=2, values=1),
mxPath('sample.sample', 'strength', free=FALSE, values=1, joinKey="sample"))
strength <- mxRun(strength)
omxCheckCloseEnough(strength$output$fit, 247.9945, 1e-2)
omxCheckCloseEnough(logLik(fm01), logLik(strength), 1e-6)
# --------
Pastes$strength = ifelse(Pastes$strength < 60, 1, 0)
Pastes$strength = mxFactor(Pastes$strength, levels = c(0, 1))
ordStrength <- mxModel(
strength,
mxData(Pastes, 'raw'),
mxThreshold('strength', nThresh = 1, values = 1))
expect_error(mxRun(ordStrength),
"Ordinal indicators are not supported in multilevel")
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