Commit 8e54ba17 authored by Corson N. Areshenkoff's avatar Corson N. Areshenkoff

Initial commit

parent 9b49e157
# 2017_smart_metaAnalysis
# smartMetaAnalysis
Data and code for replicating the meta-analysis reported in Smart et al. (2017).
The file 'data/masterSpreadsheet.csv' reports raw outcomes reported by the studies
included in the meta-analysis. The meta-analysis models are located in the 'models'
folder.
Code for replicating the analyses reported in Smart, et al. 2017.
\ No newline at end of file
The script 'runMetaAnalysis.R' runs the complete analysis, from the importing and preparation
of the raw data in 'data/masterSpreadsheet.csv', to the plotting of the fitted model. More
details are found within the '.R' files.
Currently, the code only replicates the cognitive outcome model. Code for the full model
is forthcoming.
## References
Smart, C. M., Karr, J. E., Areshenkoff, C. N., Rabin, L. A., Hudon, C., Gates, N., ... & Hampel, H. (2017). Non-pharmacologic interventions for older adults with subjective cognitive decline: systematic review, meta-analysis, and preliminary recommendations. Neuropsychology Review, 1-13.
library(plyr)
# Load data spreadsheet
raw <- read.table('data/masterSpreadsheet.csv', sep = ',',
header = T, na.strings = 'NR')
# Study info frame
studyInfo <- ddply(raw, c("Author", "Condition"), summarise,
Year = Year[1],
N = Sample.Size[1],
Age = Age[1],
Group.or.Individual = Group.or.Individual[1],
Control.Type = Control[1],
Percent.Male = Percent.Male[1],
Percent.White = Percent.White[1],
MMSE = MMSE[1],
PEDro = PEDro[1],
Treatment.Length = Treatment.Length[1],
Treatment.Frequency = Treatment.Frequency[1],
Session.Duration = Tx.Sesson.Duration[1])
# Compute mean differences
# Note that some studies report both pre- and post-test means,
# while others report pre-test means and mean differences.
# For the former, we compute the differences here.
for (i in 1:dim(raw)[1]){
if (is.na(raw$Mean.Change[i])){
raw$Mean.Change[i] <- raw$Mean.Post[i] - raw$Mean.Pre[i]
}
}
# Comput effect sizes and variances
# For each study, we compute the Morris effect size using
# the control as a baseline.
raw$Effect.Size <- NA
raw$ES.Variance <- NA
numStudies <- length(levels(raw$Author))
studies <- levels(raw$Author)
for (i in 1:numStudies){
dummyStudy <- subset(raw, Author == studies[i])
# Split by condition
numConditions <- length(levels(factor(dummyStudy$Condition))) - 1
treatmentIdx <- which(levels(factor(dummyStudy$Condition)) != 'Control')
conditions <- levels(factor(dummyStudy$Condition))[treatmentIdx]
dummyControl <- subset(dummyStudy, Condition == 'Control')
for (j in 1:numConditions){
# Compute effect size
dummyCondition <- subset(dummyStudy, Condition == conditions[j])
nT <- dummyCondition$Sample.Size
nC <- dummyControl$Sample.Size
cP <- 1 - 3 / ( 4*(nT + nC - 2) - 1 )
SD <- sqrt( ( (nT-1)*dummyCondition$SD.Pre^2 + (nC-1)*dummyControl$SD.Pre^2 ) /
(nT+nC-2))
ES <- cP * ( ( dummyCondition$Mean.Change - dummyControl$Mean.Change ) / SD)
raw$Effect.Size[raw$Author == studies[i] & raw$Condition == conditions[j]] <- ES
# Compute variance
raw$ES.Variance[raw$Author == studies[i] & raw$Condition == conditions[j]] <-
(nT+nC)/(nT*nC) + (ES^2)/(2*(nT + nC - 2))
}
}
# Remove the control studies
maData <- subset(raw, Condition != 'Control')
# Flip effects sizes to that positive is better
maData$Effect.Size <- maData$Effect.Size * maData$Higher.Score.Direction
# Save
write.table(studyInfo, file = 'data/studyInfo.csv',
sep = ',', row.names = F)
write.table(maData, file = 'data/maData.csv',
sep = ',', row.names = F)
# Load sample
load('data/cognitiveModelSamples')
samples = rstan::extract(fit)
# Labels
plotFrame = data.frame(Study = as.character(unique(fitData$Author)),
Mean = colMeans(samples$theta),
Lower = apply(samples$theta, 2, function(x) quantile(x, .025)),
Upper = apply(samples$theta, 2, function(x) quantile(x, .975)))
# We plot the studies in order of their mean effect size,
# so we get the ordering here
idx = order(plotFrame$Mean)
plotFrame = plotFrame[order(plotFrame$Mean),]
## The rest of the columns in the table.
tabletext <- cbind(c("Study", "\n", as.character(plotFrame$Study), '\n', 'Overall\n', ''))
pdf("plots/cognitive_forestPlot.pdf",
width = 6, height = 5)
forestplot(labeltext = tabletext, graph.pos=2,
mean=c(NA, NA, c(plotFrame$Mean, NA, mean(samples$mu), NA)),
lower = c(NA, NA, plotFrame$Lower, NA, quantile(samples$mu, .025), NA),
upper=c(NA, NA, plotFrame$Upper, NA, quantile(samples$mu, .975), NA),
title = "",
xlab = "Effect Size",
hrzl_lines = list("2" = gpar(lwd=2, col="#99999922")),
col=fpColors(box = "black", lines = "black", zero = "gray50"),
zero = 0, cex = 0.9, lineheight = "auto",
colgap = unit(6,"mm"), cex.lab = 1.5,
lwd.ci = 2, ci.vertices = F, grid = T,
txt_gp = fpTxtGp(ticks = gpar(cex=1),
xlab = gpar(cex=1)))
dev.off()
maData = read.table('data/maData.csv', sep = ',', header = T)
# Load data
fitData <- maData[maData$Method == 'Cognitive' &
maData$Condition == 'Cognitive',]
fitData$Author <- factor(fitData$Author,
levels = unique(as.character(fitData$Author)))
# Prepare data for Stan
stanData <- list(N = dim(fitData)[1],
K = length(levels(fitData$Author)),
Y = fitData$Effect.Size,
V = fitData$ES.Variance,
Study = as.numeric(fitData$Author))
# Fit model
fit = stan(file = 'models/maModel.stan',
data = stanData)
save(fit, file = 'data/cognitiveModelSamples')
\ No newline at end of file
Author,Year,Condition,Control,Group.or.Individual,Sample Size,Age,Percent.Male,Percent.White,MMSE,PEDro,Treatment.Length,Tx.Sesson.Duration,Treatment.Frequency,Measure.Name,Method,Constructs,Higher.Score.Direction,Mean.Pre,SD.Pre,Mean.Post,SD.Post,Mean.Change
Barnes et al.,2013,Combined,Active Control,Group,32,74.8,37.5,65.6,NR,9,12,1,3,"Rey Auditory Verbal Learning Test, # words learned",Cognitive,COG - memory,1,41.2,10.2,NR,NR,-0.04
Barnes et al.,2013,Combined,Active Control,Group,32,74.8,37.5,65.6,NR,9,12,1,3,"Rey Auditory Verbal Learning Test, # words recalled",Cognitive,COG - memory,1,7.1,2.9,NR,NR,-0.07
Barnes et al.,2013,Combined,Active Control,Group,32,74.8,37.5,65.6,NR,9,12,1,3,"verbal fluency, letter",Cognitive,COG - exec fx,1,12.8,4.6,NR,NR,0.22
Barnes et al.,2013,Combined,Active Control,Group,32,74.8,37.5,65.6,NR,9,12,1,3,"verbal fluency, category",Cognitive,COG - language,1,18.6,4.4,NR,NR,0.18
Barnes et al.,2013,Combined,Active Control,Group,32,74.8,37.5,65.6,NR,9,12,1,3,Digit Symbol Substitution Test,Cognitive,COG - attention,1,56.6,11,NR,NR,0.08
Barnes et al.,2013,Combined,Active Control,Group,32,74.8,37.5,65.6,NR,9,12,1,3,Trails A,Cognitive,COG - attention,-1,44.4,14.8,NR,NR,-0.36
Barnes et al.,2013,Combined,Active Control,Group,32,74.8,37.5,65.6,NR,9,12,1,3,Trails B,Cognitive,COG - exec fx,-1,87.6,31.1,NR,NR,-0.25
Barnes et al.,2013,Combined,Active Control,Group,32,74.8,37.5,65.6,NR,9,12,1,3,"Eriksen Flanker Test, congruent reaction time",Cognitive,COG - exec fx,-1,659.2,136.5,NR,NR,-0.33
Barnes et al.,2013,Combined,Active Control,Group,32,74.8,37.5,65.6,NR,9,12,1,3,"Eriksen Flanker Test, incongruent reaction time",Cognitive,COG - exec fx,-1,732.6,147.7,NR,NR,-0.33
Barnes et al.,2013,Combined,Active Control,Group,32,74.8,37.5,65.6,NR,9,12,1,3,"Useful Field of View, processing speed",Cognitive,COG - attention,-1,34.6,35.6,NR,NR,-0.39
Barnes et al.,2013,Combined,Active Control,Group,32,74.8,37.5,65.6,NR,9,12,1,3,"Useful Field of View, divided attention",Cognitive,COG - attention,-1,117,124.3,NR,NR,-0.62
Barnes et al.,2013,Combined,Active Control,Group,32,74.8,37.5,65.6,NR,9,12,1,3,"Useful Field of View, selective attention",Cognitive,COG - attention,-1,234.3,107.5,NR,NR,-0.71
Barnes et al.,2013,Cognitive,Active Control,Group,31,73.8,41.9,71,NR,9,12,1,3,"Rey Auditory Verbal Learning Test, # words learned",Cognitive,COG - memory,1,40,9.9,NR,NR,0.13
Barnes et al.,2013,Cognitive,Active Control,Group,31,73.8,41.9,71,NR,9,12,1,3,"Rey Auditory Verbal Learning Test, # words recalled",Cognitive,COG - memory,1,7.2,4.1,NR,NR,-0.1
Barnes et al.,2013,Cognitive,Active Control,Group,31,73.8,41.9,71,NR,9,12,1,3,"verbal fluency, letter",Cognitive,COG - exec fx,1,12.6,4,NR,NR,0.24
Barnes et al.,2013,Cognitive,Active Control,Group,31,73.8,41.9,71,NR,9,12,1,3,"verbal fluency, category",Cognitive,COG - language,1,17.2,5.4,NR,NR,0.22
Barnes et al.,2013,Cognitive,Active Control,Group,31,73.8,41.9,71,NR,9,12,1,3,Digit Symbol Substitution Test,Cognitive,COG - attention,1,54.8,14.6,NR,NR,0.27
Barnes et al.,2013,Cognitive,Active Control,Group,31,73.8,41.9,71,NR,9,12,1,3,Trails A,Cognitive,COG - attention,-1,36.5,17.1,NR,NR,-0.03
Barnes et al.,2013,Cognitive,Active Control,Group,31,73.8,41.9,71,NR,9,12,1,3,Trails B,Cognitive,COG - exec fx,-1,94.7,46.4,NR,NR,0.13
Barnes et al.,2013,Cognitive,Active Control,Group,31,73.8,41.9,71,NR,9,12,1,3,"Eriksen Flanker Test, congruent reaction time",Cognitive,COG - exec fx,-1,612.8,116.1,NR,NR,-0.17
Barnes et al.,2013,Cognitive,Active Control,Group,31,73.8,41.9,71,NR,9,12,1,3,"Eriksen Flanker Test, incongruent reaction time",Cognitive,COG - exec fx,-1,700.4,151,NR,NR,-0.15
Barnes et al.,2013,Cognitive,Active Control,Group,31,73.8,41.9,71,NR,9,12,1,3,"Useful Field of View, processing speed",Cognitive,COG - attention,-1,34.9,33.3,NR,NR,-0.17
Barnes et al.,2013,Cognitive,Active Control,Group,31,73.8,41.9,71,NR,9,12,1,3,"Useful Field of View, divided attention",Cognitive,COG - attention,-1,118.4,116,NR,NR,-0.6
Barnes et al.,2013,Cognitive,Active Control,Group,31,73.8,41.9,71,NR,9,12,1,3,"Useful Field of View, selective attention",Cognitive,COG - attention,-1,228.8,116.8,NR,NR,-0.34
Barnes et al.,2013,Exercise,Active Control,Group,31,71.1,32.3,54.8,NR,9,12,1,3,"Rey Auditory Verbal Learning Test, # words learned",Cognitive,COG - memory,1,41.5,9,NR,NR,0.14
Barnes et al.,2013,Exercise,Active Control,Group,31,71.1,32.3,54.8,NR,9,12,1,3,"Rey Auditory Verbal Learning Test, # words recalled",Cognitive,COG - memory,1,8.3,2.8,NR,NR,0.02
Barnes et al.,2013,Exercise,Active Control,Group,31,71.1,32.3,54.8,NR,9,12,1,3,"verbal fluency, letter",Cognitive,COG - exec fx,1,12.4,5.3,NR,NR,0.08
Barnes et al.,2013,Exercise,Active Control,Group,31,71.1,32.3,54.8,NR,9,12,1,3,"verbal fluency, category",Cognitive,COG - language,1,18.3,5.1,NR,NR,-0.07
Barnes et al.,2013,Exercise,Active Control,Group,31,71.1,32.3,54.8,NR,9,12,1,3,Digit Symbol Substitution Test,Cognitive,COG - attention,1,58.1,13.9,NR,NR,0.19
Barnes et al.,2013,Exercise,Active Control,Group,31,71.1,32.3,54.8,NR,9,12,1,3,Trails A,Cognitive,COG - attention,-1,37.2,14.5,NR,NR,-0.12
Barnes et al.,2013,Exercise,Active Control,Group,31,71.1,32.3,54.8,NR,9,12,1,3,Trails B,Cognitive,COG - exec fx,-1,102.9,56.9,NR,NR,-0.18
Barnes et al.,2013,Exercise,Active Control,Group,31,71.1,32.3,54.8,NR,9,12,1,3,"Eriksen Flanker Test, congruent reaction time",Cognitive,COG - exec fx,-1,600.8,153.7,NR,NR,0.01
Barnes et al.,2013,Exercise,Active Control,Group,31,71.1,32.3,54.8,NR,9,12,1,3,"Eriksen Flanker Test, incongruent reaction time",Cognitive,COG - exec fx,-1,685.2,115.7,NR,NR,-0.07
Barnes et al.,2013,Exercise,Active Control,Group,31,71.1,32.3,54.8,NR,9,12,1,3,"Useful Field of View, processing speed",Cognitive,COG - attention,-1,36.5,49.3,NR,NR,-0.04
Barnes et al.,2013,Exercise,Active Control,Group,31,71.1,32.3,54.8,NR,9,12,1,3,"Useful Field of View, divided attention",Cognitive,COG - attention,-1,129.3,137.1,NR,NR,-0.17
Barnes et al.,2013,Exercise,Active Control,Group,31,71.1,32.3,54.8,NR,9,12,1,3,"Useful Field of View, selective attention",Cognitive,COG - attention,-1,217.3,99.6,NR,NR,-0.14
Barnes et al.,2013,Control,Active Control,Group,32,73.9,37.5,68.8,NR,9,12,1,3,"Rey Auditory Verbal Learning Test, # words learned",Cognitive,COG - memory,1,41,8.9,NR,NR,0.33
Barnes et al.,2013,Control,Active Control,Group,32,73.9,37.5,68.8,NR,9,12,1,3,"Rey Auditory Verbal Learning Test, # words recalled",Cognitive,COG - memory,1,7.3,2.6,NR,NR,0.01
Barnes et al.,2013,Control,Active Control,Group,32,73.9,37.5,68.8,NR,9,12,1,3,"verbal fluency, letter",Cognitive,COG - exec fx,1,12.8,3.7,NR,NR,-0.05
Barnes et al.,2013,Control,Active Control,Group,32,73.9,37.5,68.8,NR,9,12,1,3,"verbal fluency, category",Cognitive,COG - language,1,18.9,5.1,NR,NR,0.06
Barnes et al.,2013,Control,Active Control,Group,32,73.9,37.5,68.8,NR,9,12,1,3,Digit Symbol Substitution Test,Cognitive,COG - attention,1,55.7,13.9,NR,NR,0.15
Barnes et al.,2013,Control,Active Control,Group,32,73.9,37.5,68.8,NR,9,12,1,3,Trails A,Cognitive,COG - attention,-1,41.6,15.3,NR,NR,-0.36
Barnes et al.,2013,Control,Active Control,Group,32,73.9,37.5,68.8,NR,9,12,1,3,Trails B,Cognitive,COG - exec fx,-1,100.9,47.6,NR,NR,-0.22
Barnes et al.,2013,Control,Active Control,Group,32,73.9,37.5,68.8,NR,9,12,1,3,"Eriksen Flanker Test, congruent reaction time",Cognitive,COG - exec fx,-1,622.2,113,NR,NR,-0.17
Barnes et al.,2013,Control,Active Control,Group,32,73.9,37.5,68.8,NR,9,12,1,3,"Eriksen Flanker Test, incongruent reaction time",Cognitive,COG - exec fx,-1,691.1,135.8,NR,NR,-0.12
Barnes et al.,2013,Control,Active Control,Group,32,73.9,37.5,68.8,NR,9,12,1,3,"Useful Field of View, processing speed",Cognitive,COG - attention,-1,33.7,39.7,NR,NR,-0.23
Barnes et al.,2013,Control,Active Control,Group,32,73.9,37.5,68.8,NR,9,12,1,3,"Useful Field of View, divided attention",Cognitive,COG - attention,-1,115.5,116.1,NR,NR,-0.13
Barnes et al.,2013,Control,Active Control,Group,32,73.9,37.5,68.8,NR,9,12,1,3,"Useful Field of View, selective attention",Cognitive,COG - attention,-1,238.9,107.8,NR,NR,-0.18
Fabre et al.,1999,Exercise,NR,Group,8,65.4,25,100,NR,6,8,1,2,Wechsler Memory Scale - Memory Quotient,Cognitive,COG - memory,1,102.4,14.9,NR,NR,8.704
Fabre et al.,2001,Cognitive,NR,Group,8,67.5,12.5,100,NR,6,8,1.5,1,Wechsler Memory Scale - Memory Quotient,Cognitive,COG - memory,1,110.7,7.3,NR,NR,8.1918
Fabre et al.,2003,Combined,NR,Group,8,64.9,12.5,100,NR,6,8,2.5,3,Wechsler Memory Scale - Memory Quotient,Cognitive,COG - memory,1,101.9,6.5,NR,NR,9.3748
Fabre et al.,2005,Control,NR,Group,8,65.7,12.5,100,NR,6,8,NR,NR,Wechsler Memory Scale - Memory Quotient,Cognitive,COG - memory,1,108.6,12.7,NR,NR,1
Lautenschlager et al.,2008,Exercise,Active Control,Individual,85,68.7,48.2,NR,NR,8,24,0.833,3,Total Alzheimer Disease Assessment Scale-Cog,Cognitive,COG - global,-1,7,1.8,NR,NR,-0.04
Lautenschlager et al.,2008,Exercise,Active Control,Individual,85,68.7,48.2,NR,NR,8,24,0.833,3,Consortium to Establish a Registry for Alzheimer’s Disease (CERAD) - word list immediate recall,Cognitive,COG - memory,1,17.4,4.7,NR,NR,1.19
Lautenschlager et al.,2008,Exercise,Active Control,Individual,85,68.7,48.2,NR,NR,8,24,0.833,3,Consortium to Establish a Registry for Alzheimer’s Disease (CERAD) - word list delayed recall,Cognitive,COG - memory,1,5.5,2.4,NR,NR,-0.02
Lautenschlager et al.,2008,Exercise,Active Control,Individual,85,68.7,48.2,NR,NR,8,24,0.833,3,Digit symbol coding,Cognitive,COG - attention,1,53.4,14.1,NR,NR,3.02
Lautenschlager et al.,2008,Exercise,Active Control,Individual,85,68.7,48.2,NR,NR,8,24,0.833,3,DKEFS verbal fluency,Cognitive,COG - exec fx,1,39.5,13.1,NR,NR,1.42
Lautenschlager et al.,2008,Exercise,Active Control,Individual,85,68.7,48.2,NR,NR,8,24,0.833,3,Clinical Dementia Rating - Sum of boxes,Questionnaire,SELF-REPORT - Cog,-1,1,0.7,NR,NR,-0.2
Lautenschlager et al.,2008,Exercise,Active Control,Individual,85,68.7,48.2,NR,NR,8,24,0.833,3,Beck Depression Inventory,Questionnaire,SELF-REPORT - Non-Cog,-1,4.1,2.8,NR,NR,-0.51
Lautenschlager et al.,2008,Exercise,Active Control,Individual,85,68.7,48.2,NR,NR,8,24,0.833,3,Physical Component Summary (PCS) - SF-36,Questionnaire,SELF-REPORT - Non-Cog,1,49.4,8.7,NR,NR,-4.69
Lautenschlager et al.,2008,Exercise,Active Control,Individual,85,68.7,48.2,NR,NR,8,24,0.833,3,Mental Component Summary (MCS) - SF-36,Questionnaire,SELF-REPORT - Non-Cog,1,48.1,5.5,NR,NR,2.74
Lautenschlager et al.,2008,Control,Active Control,Individual,85,68.6,50.6,NR,NR,8,24,NR,NR,Total Alzheimer Disease Assessment Scale-Cog,Cognitive,COG - global,-1,7,1.7,NR,NR,-0.73
Lautenschlager et al.,2008,Control,Active Control,Individual,85,68.6,50.6,NR,NR,8,24,NR,NR,Consortium to Establish a Registry for Alzheimer’s Disease (CERAD) - word list immediate recall,Cognitive,COG - memory,1,18.4,4.9,NR,NR,1.56
Lautenschlager et al.,2008,Control,Active Control,Individual,85,68.6,50.6,NR,NR,8,24,NR,NR,Consortium to Establish a Registry for Alzheimer’s Disease (CERAD) - word list delayed recall,Cognitive,COG - memory,1,5.8,2.6,NR,NR,0.76
Lautenschlager et al.,2008,Control,Active Control,Individual,85,68.6,50.6,NR,NR,8,24,NR,NR,Digit symbol coding,Cognitive,COG - attention,1,54.2,15.1,NR,NR,3.72
Lautenschlager et al.,2008,Control,Active Control,Individual,85,68.6,50.6,NR,NR,8,24,NR,NR,DKEFS verbal fluency,Cognitive,COG - exec fx,1,37.8,11.5,NR,NR,1.9
Lautenschlager et al.,2008,Control,Active Control,Individual,85,68.6,50.6,NR,NR,8,24,NR,NR,Clinical Dementia Rating - Sum of boxes,Questionnaire,SELF-REPORT - Cog,-1,1,0.7,NR,NR,-0.33
Lautenschlager et al.,2008,Control,Active Control,Individual,85,68.6,50.6,NR,NR,8,24,NR,NR,Beck Depression Inventory,Questionnaire,SELF-REPORT - Non-Cog,-1,3.6,3.5,NR,NR,-0.46
Lautenschlager et al.,2008,Control,Active Control,Individual,85,68.6,50.6,NR,NR,8,24,NR,NR,Physical Component Summary (PCS) - SF-36,Questionnaire,SELF-REPORT - Non-Cog,1,48.5,9.4,NR,NR,-4.85
Lautenschlager et al.,2008,Control,Active Control,Individual,85,68.6,50.6,NR,NR,8,24,NR,NR,Mental Component Summary (MCS) - SF-36,Questionnaire,SELF-REPORT - Non-Cog,1,48.4,7,NR,NR,4.58
Hoogenhout et al.,2012,Cognitive,Waitlist Control,Group,24,66,0,100,29.24,7,4,1.5,2,Maastricht Metacognition Inventory (MMI) - Ability,Questionnaire,SELF-REPORT - Cog,-1,46.83,9.44,45.5,10.07,NR
Hoogenhout et al.,2012,Cognitive,Waitlist Control,Group,24,66,0,100,29.24,7,4,1.5,2,Maastricht Metacognition Inventory (MMI) - Affect,Questionnaire,SELF-REPORT - Non-Cog,-1,30.5,6.65,28.04,7.93,NR
Hoogenhout et al.,2012,Cognitive,Waitlist Control,Group,24,66,0,100,29.24,7,4,1.5,2,Maastricht Metacognition Inventory (MMI) - Control,Questionnaire,SELF-REPORT - Cog,-1,12.13,2.91,11.58,3.73,NR
Hoogenhout et al.,2012,Cognitive,Waitlist Control,Group,24,66,0,100,29.24,7,4,1.5,2,Maastricht Metacognition Inventory (MMI) - Strategy,Questionnaire,SELF-REPORT - Cog,-1,42.58,4.13,43.71,4.23,NR
Hoogenhout et al.,2012,Cognitive,Waitlist Control,Group,24,66,0,100,29.24,7,4,1.5,2,Memory Quotient (MQ),Cognitive,COG - memory,1,109.2,14.62,117.3,15.32,NR
Hoogenhout et al.,2012,Cognitive,Waitlist Control,Group,24,66,0,100,29.24,7,4,1.5,2,Executive functioning and Speed Quotient (ESQ),Cognitive,COG - global,1,108.04,6.8,106.97,7.34,NR
Hoogenhout et al.,2012,Cognitive,Waitlist Control,Group,24,66,0,100,29.24,7,4,1.5,2,Psychological Well-being Quotient (PWQ),Questionnaire,SELF-REPORT - Non-Cog,1,103.72,14.93,104.43,13.15,NR
Hoogenhout et al.,2012,Control,Waitlist Control,Individual,26,66.1,0,100,29.11,7,NR,NR,NR,Maastricht Metacognition Inventory (MMI),Questionnaire,SELF-REPORT - Cog,-1,50.12,10.61,49.92,11.37,NR
Hoogenhout et al.,2012,Control,Waitlist Control,Individual,26,66.1,0,100,29.11,7,NR,NR,NR,Maastricht Metacognition Inventory (MMI) - Affect,Questionnaire,SELF-REPORT - Non-Cog,-1,32.81,8.51,33.04,9.08,NR
Hoogenhout et al.,2012,Control,Waitlist Control,Individual,26,66.1,0,100,29.11,7,NR,NR,NR,Maastricht Metacognition Inventory (MMI) - Control,Questionnaire,SELF-REPORT - Cog,-1,13.77,4.11,13.12,3.89,NR
Hoogenhout et al.,2012,Control,Waitlist Control,Individual,26,66.1,0,100,29.11,7,NR,NR,NR,Maastricht Metacognition Inventory (MMI) - Strategy,Questionnaire,SELF-REPORT - Non-Cog,-1,43.65,4.84,43.5,3.81,NR
Hoogenhout et al.,2012,Control,Waitlist Control,Individual,26,66.1,0,100,29.11,7,NR,NR,NR,Memory Quotient (MQ),Cognitive,COG - memory,1,102.86,16.23,105.63,17.8,NR
Hoogenhout et al.,2012,Control,Waitlist Control,Individual,26,66.1,0,100,29.11,7,NR,NR,NR,Executive functioning and Speed Quotient (ESQ),Cognitive,COG - global,1,105.37,12.91,107.05,9.83,NR
Hoogenhout et al.,2012,Control,Waitlist Control,Individual,26,66.1,0,100,29.11,7,NR,NR,NR,Psychological Well-being Quotient (PWQ),Questionnaire,SELF-REPORT - Non-Cog,1,96.57,16.31,97.93,15.46,NR
Kwok et al.,2013,Cognitive,Active Control,Group,86,77.41,12.8,0,25.74,3,8,1,1,Chinese version of the Mattis Dementia Rating Scale (CDRS),Cognitive,COG - global,1,145.68,14.42,157.92,8.19,12.24
Kwok et al.,2013,Cognitive,Active Control,Group,86,77.41,12.8,0,25.74,3,8,1,1,Subdomain,Cognitive,COG - attention,1,33.11,2.82,34.64,1.88,1.52
Kwok et al.,2013,Cognitive,Active Control,Group,86,77.41,12.8,0,25.74,3,8,1,1,Subdomain,Cognitive,COG - exec fx,1,43.88,6.03,46.2,4.59,2.33
Kwok et al.,2013,Cognitive,Active Control,Group,86,77.41,12.8,0,25.74,3,8,1,1,Subdomain,Cognitive,COG - visuospatial,1,5.17,1.32,5.38,1.23,0.21
Kwok et al.,2013,Cognitive,Active Control,Group,86,77.41,12.8,0,25.74,3,8,1,1,Subdomain,Cognitive,COG - exec fx,1,27.56,5.8,33.21,2.83,5.65
Kwok et al.,2013,Cognitive,Active Control,Group,86,77.41,12.8,0,25.74,3,8,1,1,Subdomain,Cognitive,COG - memory,1,29.45,3.69,31.71,2.67,2.26
Kwok et al.,2013,Cognitive,Active Control,Group,86,77.41,12.8,0,25.74,3,8,1,1,12-item Short-Form Health Survey total (SF12),Questionnaire,SELF-REPORT - Non-Cog,1,88.62,13.88,96.44,13.67,7.82
Kwok et al.,2013,Cognitive,Active Control,Group,86,77.41,12.8,0,25.74,3,8,1,1,Subdomain,Questionnaire,SELF-REPORT - Non-Cog,1,38.95,10.29,39.23,11.28,0.28
Kwok et al.,2013,Cognitive,Active Control,Group,86,77.41,12.8,0,25.74,3,8,1,1,Subdomain,Questionnaire,SELF-REPORT - Non-Cog,1,49.66,11.54,57.2,9.23,7.54
Kwok et al.,2013,Control,Active Control,Group,90,73.5,16.7,0,26.09,3,8,NR,NR,Chinese version of the Mattis Dementia Rating Scale (CDRS),Cognitive,COG - global,1,152.8,10.73,157.17,8.23,4.37
Kwok et al.,2013,Control,Active Control,Group,90,73.5,16.7,0,26.09,3,8,NR,NR,Subdomain,Cognitive,COG - attention,1,34,2.84,34.56,1.81,0.56
Kwok et al.,2013,Control,Active Control,Group,90,73.5,16.7,0,26.09,3,8,NR,NR,Subdomain,Cognitive,COG - exec fx,1,45.76,4.84,46.39,3.95,0.63
Kwok et al.,2013,Control,Active Control,Group,90,73.5,16.7,0,26.09,3,8,NR,NR,Subdomain,Cognitive,COG - visuospatial ,1,5.53,0.95,5.3,1.25,-0.23
Kwok et al.,2013,Control,Active Control,Group,90,73.5,16.7,0,26.09,3,8,NR,NR,Subdomain,Cognitive,COG - exec fx,1,31.62,3.92,33.71,3.42,2.09
Kwok et al.,2013,Control,Active Control,Group,90,73.5,16.7,0,26.09,3,8,NR,NR,Subdomain,Cognitive,COG - memory,1,30.06,3.52,31.38,2.59,1.78
Kwok et al.,2013,Control,Active Control,Group,90,73.5,16.7,0,26.09,3,8,NR,NR,12-item Short-Form Health Survey total (SF12),Questionnaire,SELF-REPORT - Non-Cog,1,94.24,14.66,97.42,14.25,3.18
Kwok et al.,2013,Control,Active Control,Group,90,73.5,16.7,0,26.09,3,8,NR,NR,Subdomain,Questionnaire,SELF-REPORT - Non-Cog,1,42.76,10.03,42.85,9.23,0.09
Kwok et al.,2013,Control,Active Control,Group,90,73.5,16.7,0,26.09,3,8,NR,NR,Subdomain,Questionnaire,SELF-REPORT - Non-Cog,1,51.48,11.14,54.56,9.02,3.08
Tsai et al.,2008,Cognitive,Active Control,Group,14,69.4,NR,0,26.71,2,5,2,2,Alzheimer Disease Assessment Scale-Cog,Cognitive,COG - global,-1,7.88,3.15,3.2,1.65,NR
Tsai et al.,2008,Cognitive,Active Control,Group,14,69.4,NR,0,26.71,2,5,2,2,Mini Mental State Examination,Cognitive,COG - global,1,26.71,1.85,28.64,1.21,NR
Tsai et al.,2008,Cognitive,Active Control,Group,14,69.4,NR,0,26.71,2,5,2,2,Selective reminding test,Cognitive,COG - memory,1,8.42,2.68,9.71,3.33,NR
Tsai et al.,2008,Cognitive,Active Control,Group,14,69.4,NR,0,26.71,2,5,2,2,Clock drawing test,Cognitive,COG - exec fx,1,16,0,15.42,1.34,NR
Tsai et al.,2008,Control,Active Control,Group,11,69.4,NR,0,25.54,2,8,1.5,1,Alzheimer Disease Assessment Scale-Cog,Cognitive,COG - global,-1,6.76,3.92,3.91,1.73,NR
Tsai et al.,2008,Control,Active Control,Group,11,69.4,NR,0,25.54,2,8,1.5,1,Mini Mental State Examination,Cognitive,COG - global,1,25.54,2.76,28.54,1.12,NR
Tsai et al.,2008,Control,Active Control,Group,11,69.4,NR,0,25.54,2,8,1.5,1,Selective reminding test,Cognitive,COG - memory,1,10,1.51,10,1.73,NR
Tsai et al.,2008,Control,Active Control,Group,11,69.4,NR,0,25.54,2,8,1.5,1,Clock drawing test,Cognitive,COG - exec fx,1,14.27,2.332,16,0,NR
Cohen-Mansfield et al.,2015,Cognitive,Waitlist Control,Group,15,72.8,40,NR,27.93,5,10,NR,NR,Global Cognitive Score,Cognitive,COG - global,1,97.71,8.44,101.98,7.77,NR
Cohen-Mansfield et al.,2015,Cognitive,Waitlist Control,Group,15,72.8,40,NR,27.93,5,10,NR,NR,UCLA Loneliness Scale,Questionnaire,SELF-REPORT - Non-Cog,1,3.11,0.68,3.37,0.58,NR
Cohen-Mansfield et al.,2015,Cognitive,Waitlist Control,Group,15,72.8,40,NR,27.93,5,10,NR,NR,Impact of Health Problems,Questionnaire,SELF-REPORT - Non-Cog,-1,1.75,0.75,1.92,0.79,NR
Cohen-Mansfield et al.,2015,Control,Waitlist Control,Group,14,73.8,21.5,NR,28.8,5,10,NR,NR,Global Cognitive Score,Cognitive,COG - global,1,100.51,8.91,100.57,9.06,NR
Cohen-Mansfield et al.,2015,Control,Waitlist Control,Group,14,73.8,21.5,NR,28.8,5,10,NR,NR,UCLA Loneliness Scale,Questionnaire,SELF-REPORT - Non-Cog,1,3.22,0.54,3.17,0.62,NR
Cohen-Mansfield et al.,2015,Control,Waitlist Control,Group,14,73.8,21.5,NR,28.8,5,10,NR,NR,Impact of Health Problems,Questionnaire,SELF-REPORT - Non-Cog,-1,1.64,0.56,1.82,0.48,NR
Fairchild & Scogin,2010,Cognitive,Active Control,NR,28,73.45,17.86,85.71,NR,5,6,45,1,Immediate recall on Names and Faces Task,Cognitive,COG - memory,1,2.93,2.37,5.96,2.95,NR
Fairchild & Scogin,2010,Cognitive,Active Control,NR,28,73.45,17.86,85.71,NR,5,6,45,1,Delayed recall on Names and Faces task,Cognitive,COG - memory,1,2.04,2.42,4.96,2.94,NR
Fairchild & Scogin,2010,Cognitive,Active Control,NR,28,73.45,17.86,85.71,NR,5,6,45,1,Multifactorial Memory Questionnaire -contentment scale,Questionnaire,SELF-REPORT - Cog,1,39.5,12,47.75,8.7,NR
Fairchild & Scogin,2010,Cognitive,Active Control,NR,28,73.45,17.86,85.71,NR,5,6,45,1,Multifactorial Memory Questionnaire-abilities scale,Questionnaire,SELF-REPORT - Cog,1,42.43,10.28,50.14,9.95,NR
Fairchild & Scogin,2010,Cognitive,Active Control,NR,28,73.45,17.86,85.71,NR,5,6,45,1,Multifactorial Memory Questionnaire-strategies scale,Questionnaire,SELF-REPORT - Cog,1,35.39,11.49,39.86,13.41,NR
Fairchild & Scogin,2010,Cognitive,Active Control,NR,28,73.45,17.86,85.71,NR,5,6,45,1,Object misplacement task - do you know where it is?,Questionnaire,SELF-REPORT - Cog,1,0.96,0.09,0.98,0.06,NR
Fairchild & Scogin,2010,Cognitive,Active Control,NR,28,73.45,17.86,85.71,NR,5,6,45,1,Object misplacement task - have you misplaced it recently?,Questionnaire,SELF-REPORT - Cog,-1,0.84,0.22,0.94,0.11,NR
Fairchild & Scogin,2010,Cognitive,Active Control,NR,28,73.45,17.86,85.71,NR,5,6,45,1,Positive and Negative Affect Schedule (PANAS) - Positive affect,Questionnaire,SELF-REPORT - Non-Cog,1,32.46,7.04,33.71,4.78,NR
Fairchild & Scogin,2010,Cognitive,Active Control,NR,28,73.45,17.86,85.71,NR,5,6,45,1,Positive and Negative Affect Schedule (PANAS) - Negative affect,Questionnaire,SELF-REPORT - Non-Cog,-1,16.86,6.4,16.89,6.6,NR
Fairchild & Scogin,2010,Control,Active Control,NR,25,71.24,20,68,NR,5,6,0.17,0.33,Immediate recall on Names and Faces Task,Cognitive,COG - memory,1,1.72,1.46,2.12,1.67,NR
Fairchild & Scogin,2010,Control,Active Control,NR,25,71.24,20,68,NR,5,6,0.17,0.33,Delayed recall on Names and Faces task,Cognitive,COG - memory,1,1.2,1.29,1.68,1.38,NR
Fairchild & Scogin,2010,Control,Active Control,NR,25,71.24,20,68,NR,5,6,0.17,0.33,Multifactorial Memory Questionnaire -contentment scale,Questionnaire,SELF-REPORT - Cog,1,41.16,11.59,39.48,13.86,NR
Fairchild & Scogin,2010,Control,Active Control,NR,25,71.24,20,68,NR,5,6,0.17,0.33,Multifactorial Memory Questionnaire-abilities scale,Questionnaire,SELF-REPORT - Cog,1,48.56,13.5,49.44,12.85,NR
Fairchild & Scogin,2010,Control,Active Control,NR,25,71.24,20,68,NR,5,6,0.17,0.33,Multifactorial Memory Questionnaire-strategies scale,Questionnaire,SELF-REPORT - Cog,1,30.24,11.42,29.12,13.86,NR
Fairchild & Scogin,2010,Control,Active Control,NR,25,71.24,20,68,NR,5,6,0.17,0.33,Object misplacement task - do you know where it is?,Questionnaire,SELF-REPORT - Cog,1,0.91,0.17,0.88,0.18,NR
Fairchild & Scogin,2010,Control,Active Control,NR,25,71.24,20,68,NR,5,6,0.17,0.33,Object misplacement task - have you misplaced it recently?,Questionnaire,SELF-REPORT - Cog,-1,0.86,0.18,0.83,0.22,NR
Fairchild & Scogin,2010,Control,Active Control,NR,25,71.24,20,68,NR,5,6,0.17,0.33,Positive and Negative Affect Schedule (PANAS) - Positive affect,Questionnaire,SELF-REPORT - Non-Cog,1,33.64,9.89,32.12,7.83,NR
Fairchild & Scogin,2010,Control,Active Control,NR,25,71.24,20,68,NR,5,6,0.17,0.33,Positive and Negative Affect Schedule (PANAS) - Negative affect,Questionnaire,SELF-REPORT - Non-Cog,-1,17.48,7.23,16.16,6.26,NR
Smart et al.,2016,Cognitive,Active Control,Group,8,69.6,26.67,91.7,28,9,8,2,1,Cognitive Complaints Index,Questionnaire,SELF-REPORT - Cog,-1,27.13,12.61,26,12.46,NR
Smart et al.,2016,Cognitive,Active Control,Group,8,69.6,26.67,91.7,28,9,8,2,1,Five-Facet Mindfulness Questionnaire,Questionnaire,SELF-REPORT - Non-Cog,1,78.75,12.51,80.63,11.02,NR
Smart et al.,2016,Cognitive,Active Control,Group,8,69.6,26.67,91.7,28,9,8,2,1,Go/No-go - RT Mean,Cognitive,COG - exec fx,-1,388.14,52.16,372.4,31.78,NR
Smart et al.,2016,Cognitive,Active Control,Group,8,69.6,26.67,91.7,28,9,8,2,1,Go/No-go - Proportion Accuracy,Cognitive,COG - exec fx,1,0.9,0.03,0.92,0.04,NR
Smart et al.,2016,Cognitive,Active Control,Group,8,69.6,26.67,91.7,28,9,8,2,1,Go/No-go - RT Intra-Individual Variability,Cognitive,COG - exec fx,-1,9.55,1.98,8.89,1.95,NR
Smart et al.,2016,Control,Active Control,Group,7,69.6,26.67,91.7,28,9,5,2,1,Cognitive Complaints Index,Questionnaire,SELF-REPORT - Cog,-1,31.17,8.98,28,10.08,NR
Smart et al.,2016,Control,Active Control,Group,7,69.6,26.67,91.7,28,9,5,2,1,Five-Facet Mindfulness Questionnaire,Questionnaire,SELF-REPORT - Non-Cog,1,83.17,14.96,87.17,17.26,NR
Smart et al.,2016,Control,Active Control,Group,7,69.6,26.67,91.7,28,9,5,2,1,Go/No-go - RT Mean,Cognitive,COG - exec fx,-1,351.79,26.6,350.97,18.63,NR
Smart et al.,2016,Control,Active Control,Group,7,69.6,26.67,91.7,28,9,5,2,1,Go/No-go - Proportion Accuracy,Cognitive,COG - exec fx,1,0.88,0.04,0.89,0.04,NR
Smart et al.,2016,Control,Active Control,Group,7,69.6,26.67,91.7,28,9,5,2,1,Go/No-go - RT Intra-Individual Variability,Cognitive,COG - exec fx,-1,9.05,2.23,9.51,1.93,NR
data {
int<lower=0> N; // Number of effect sizes
int<lower=0> K; // Number of Studies
vector[N] Y; // Effect sizes
vector<lower=0>[N] V; // Variance of ES
int<lower=0> Study[N]; // Study indicator
}
parameters {
vector[K] theta_dummy; // Study effects
vector[N] d_dummy; // True effects
vector<lower=0>[K] sigma; // Study level variance
real mu; // Mean effect size
real<lower=0> tau; // Between study variance
}
transformed parameters {
vector[K] theta;
vector[N] d;
for (i in 1:K){
theta[i] = mu + theta_dummy[i] * tau;
}
for (i in 1:N){
d[i] = theta[Study[i]] + d_dummy[i] * sigma[Study[i]];
}
}
model {
// Model
for (i in 1:N){
Y[i] ~ normal(d[i], sqrt(V[i]));
}
d_dummy ~ normal(0,1);
theta_dummy ~ normal(0,1);
// Prior
mu ~ normal(0, 1);
tau ~ student_t(3, 0, 0.5);
sigma ~ inv_gamma(3, 0.5);
}
\ No newline at end of file
Github doesn't like empty folders
library(rstan)
library(forestplot)
library(plyr)
# Load raw data and calculate effect sizes
# The script generates two spreadsheets in the 'data/' folder
# maData.csv: Contains effect sizes and associated information
# for each outcome in each study.
# studyInfo.csv: Contains information about each study
source('cleanData.R')
rm(list = ls())
# Fit the model for the cognitive outcomes
# This script imports maData.csv and fits the meta-analysis
# model described in Smart et al. (2017) using the model code
# in 'models/maModel.stan'. The fitted model is saved in
# 'data/cognitiveModelSamples'
source('cognitiveModelFit.R')
# Finally, create a forest plot of the posterior means and
# 95% posterior intervals. The plot is saved as
# 'plots/cognitive_forestPlot.pdf'
source('cognitiveForestPlot.R')
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment