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Updated dichotomous models and added Lee2004
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@kylehamilton
kylehamilton committed May 21, 2021
1 parent 2a0c158 commit b23a658
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Showing 17 changed files with 479 additions and 30 deletions.
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206 changes: 189 additions & 17 deletions R/metadichotomousmodel.b.R
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Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,9 @@ metaDichotomousModelClass <-
private = list(
.run = function() {
ai <- self$options$ai
bi <- self$options$bi
# bi <- self$options$bi
ci <- self$options$ci
di <- self$options$di
# di <- self$options$di
n1i <- self$options$n1i
n2i <- self$options$n2i
moderator <- self$options$moderatorcor
Expand Down Expand Up @@ -45,6 +45,14 @@ metaDichotomousModelClass <-
code = ''
)
}

# ready <- FALSE
# # I really need to think of a better error message this is a place holder until I figure something out
# jmvcore::reject(
# "Incidents, Sample Size, and Study Label fields must be populated to run analysis",
# code = ''
# )
# }
if (is.null(self$options$slab) == TRUE) {
ready <- FALSE
# I really need to think of a better error message this is a place holder until I figure something out
Expand All @@ -63,19 +71,23 @@ metaDichotomousModelClass <-
data <-
data.frame(
ai = self$data[[self$options$ai]],
n1i = self$data[[self$options$n1i]],
# bi = self$data[[self$options$bi]],
ci = self$data[[self$options$ci]],
# di = self$data[[self$options$di]],
n1i = self$data[[self$options$n1i]],
n2i = self$data[[self$options$n2i]],
slab = self$data[[self$options$slab]]
)
data[[ai]] <- jmvcore::toNumeric(data[[ai]])
data[[n1i]] <- jmvcore::toNumeric(data[[n1i]])
# data[[bi]] <- jmvcore::toNumeric(data[[bi]])
data[[ci]] <- jmvcore::toNumeric(data[[ci]])
# data[[di]] <- jmvcore::toNumeric(data[[di]])
data[[n1i]] <- jmvcore::toNumeric(data[[n1i]])
data[[n2i]] <- jmvcore::toNumeric(data[[n2i]])
data$checkG1 <- 0
data$checkG2 <- 0
data$checkG1 <- data$n1i - data$ai
data$checkG2 <- data$n2i - data$ci
data$checkG1 <- 0
data$checkG2 <- 0
data$checkG1 <- data$n1i - data$ai
data$checkG2 <- data$n2i - data$ci
if (data$checkG1 < 0) {
#ready <- FALSE
jmvcore::reject(
Expand All @@ -90,12 +102,14 @@ metaDichotomousModelClass <-
code = ''
)
}
}
}
res <-
metafor::rma(
ai = ai,
n1i = n1i,
# bi = bi,
ci = ci,
# di = di,
n1i = n1i,
n2i = n2i,
method = method2,
measure = mdmseasure,
Expand Down Expand Up @@ -124,8 +138,10 @@ metaDichotomousModelClass <-
slab = self$data[[self$options$slab]]
)
data[[ai]] <- jmvcore::toNumeric(data[[ai]])
data[[n1i]] <- jmvcore::toNumeric(data[[n1i]])
# data[[bi]] <- jmvcore::toNumeric(data[[bi]])
data[[ci]] <- jmvcore::toNumeric(data[[ci]])
# data[[di]] <- jmvcore::toNumeric(data[[di]])
data[[n1i]] <- jmvcore::toNumeric(data[[n1i]])
data[[n2i]] <- jmvcore::toNumeric(data[[n2i]])
data[[moderator]] <- jmvcore::toNumeric(data[[moderator]])
data$checkG1 <- 0
Expand All @@ -149,8 +165,10 @@ metaDichotomousModelClass <-
res <-
metafor::rma(
ai = ai,
n1i = n1i,
#bi = bi,
ci = ci,
#di = di,
n1i = n1i,
n2i = n2i,
mods = moderator,
method = method2,
Expand All @@ -176,8 +194,10 @@ metaDichotomousModelClass <-
slab = self$data[[self$options$slab]]
)
data[[ai]] <- jmvcore::toNumeric(data[[ai]])
data[[n1i]] <- jmvcore::toNumeric(data[[n1i]])
# data[[bi]] <- jmvcore::toNumeric(data[[bi]])
data[[ci]] <- jmvcore::toNumeric(data[[ci]])
# data[[di]] <- jmvcore::toNumeric(data[[di]])
data[[n1i]] <- jmvcore::toNumeric(data[[n1i]])
data[[n2i]] <- jmvcore::toNumeric(data[[n2i]])
data[[moderator]] <- jmvcore::toNumeric(data[[moderator]])
data$checkG1 <- 0
Expand All @@ -201,8 +221,10 @@ metaDichotomousModelClass <-
res <-
metafor::rma(
ai = ai,
n1i = n1i,
# bi = bi,
ci = ci,
# di = di,
n1i = n1i,
n2i = n2i,
mods = ~ factor(moderator),
method = method2,
Expand All @@ -223,7 +245,45 @@ metaDichotomousModelClass <-
# if (is.character(res)== TRUE)
# jmvcore::reject("Check sample size and incident data", code='')

summaryOutputText <- self$results$summaryOutputText
if (self$options$moderatorType == "NON") {

textReport <- reporterMAJOR(res)
outputTextSummary <- textReport[[1]]

}

if (self$options$moderatorType == "CAT") {

outputTextSummary <- "Text reporting does not currently work with moderators"

}

if (self$options$moderatorType == "CON") {

outputTextSummary <- "Text reporting does not currently work with moderators"

}


summaryOutputText$setContent(outputTextSummary)

### Second part
summaryOutputText2 <- self$results$summaryOutputText2

if (self$options$moderatorType == "NON") {

outputTextSummary2 <- textReport[[2]]

}
if (self$options$moderatorType == "CAT" ||
self$options$moderatorType == "CON") {

outputTextSummary2 <- " "
}


summaryOutputText2$setContent(outputTextSummary2)

#Pub Bias
failsafePB <-
Expand Down Expand Up @@ -471,11 +531,106 @@ metaDichotomousModelClass <-
# `self$options` contains the options
# `self$results` contains the results object (to populate)

# image <- self$results$plot
# imageFUN <- self$results$funplot
#
# image$setState(res)
# imageFUN$setState(res)

#Forest Plots
image <- self$results$plot

forestSmall <- self$results$plot
forestMedium <- self$results$plotMed
forestLarge <- self$results$plotLarge
forestSmallWide <- self$results$plotSmallWide
forestMediumWide <- self$results$plotMedWide
forestLargeWide <- self$results$plotLargeWide

forestSmall$setState(res)
forestMedium$setState(res)
forestLarge$setState(res)
forestSmallWide$setState(res)
forestMediumWide$setState(res)
forestLargeWide$setState(res)

## Funnel
imageFUN <- self$results$funplot

image$setState(res)
imageFUN$setState(res)
funPlot <- self$results$funplot
funPlotMed <- self$results$funplotMed
funPlotLarge <- self$results$funplotLarge

funPlot$setState(res)
funPlotMed$setState(res)
funPlotLarge$setState(res)

#Forest Plot Size
if (self$options$forestPlotSize == "SMALL") {
forestSmall$setVisible(visible = TRUE)
forestMedium$setVisible(visible = FALSE)
forestLarge$setVisible(visible = FALSE)
forestSmallWide$setVisible(visible = FALSE)
forestMediumWide$setVisible(visible = FALSE)
forestLargeWide$setVisible(visible = FALSE)
}
if (self$options$forestPlotSize == "MEDIUM") {
forestSmall$setVisible(visible = FALSE)
forestMedium$setVisible(visible = TRUE)
forestLarge$setVisible(visible = FALSE)
forestSmallWide$setVisible(visible = FALSE)
forestMediumWide$setVisible(visible = FALSE)
forestLargeWide$setVisible(visible = FALSE)
}
if (self$options$forestPlotSize == "LARGE") {
forestSmall$setVisible(visible = FALSE)
forestMedium$setVisible(visible = FALSE)
forestLarge$setVisible(visible = TRUE)
forestSmallWide$setVisible(visible = FALSE)
forestMediumWide$setVisible(visible = FALSE)
forestLargeWide$setVisible(visible = FALSE)
}
if (self$options$forestPlotSize == "SMALLWIDE") {
forestSmall$setVisible(visible = FALSE)
forestMedium$setVisible(visible = FALSE)
forestLarge$setVisible(visible = FALSE)
forestSmallWide$setVisible(visible = TRUE)
forestMediumWide$setVisible(visible = FALSE)
forestLargeWide$setVisible(visible = FALSE)
}
if (self$options$forestPlotSize == "MEDIUMWIDE") {
forestSmall$setVisible(visible = FALSE)
forestMedium$setVisible(visible = FALSE)
forestLarge$setVisible(visible = FALSE)
forestSmallWide$setVisible(visible = FALSE)
forestMediumWide$setVisible(visible = TRUE)
forestLargeWide$setVisible(visible = FALSE)
}
if (self$options$forestPlotSize == "LARGEWIDE") {
forestSmall$setVisible(visible = FALSE)
forestMedium$setVisible(visible = FALSE)
forestLarge$setVisible(visible = FALSE)
forestSmallWide$setVisible(visible = FALSE)
forestMediumWide$setVisible(visible = FALSE)
forestLargeWide$setVisible(visible = TRUE)
}

#Funnel Plot Size
if (self$options$funnelPlotSize == "SMALL") {
funPlot$setVisible(visible = TRUE)
funPlotMed$setVisible(visible = FALSE)
funPlotLarge$setVisible(visible = FALSE)
}
if (self$options$funnelPlotSize == "MEDIUM") {
funPlot$setVisible(visible = FALSE)
funPlotMed$setVisible(visible = TRUE)
funPlotLarge$setVisible(visible = FALSE)
}
if (self$options$funnelPlotSize == "LARGE") {
funPlot$setVisible(visible = FALSE)
funPlotMed$setVisible(visible = FALSE)
funPlotLarge$setVisible(visible = TRUE)
}

# }}))
#}
Expand Down Expand Up @@ -521,7 +676,18 @@ metaDichotomousModelClass <-
steps = steps,
pch = pch
)
plotMed <- plot
plotLarge <- plot
plotSmallWide <- plot
plotMedWide <- plot
plotLargeWide <- plot

print(plot)
print(plotMed)
print(plotLarge)
print(plotSmallWide)
print(plotMedWide)
print(plotLargeWide)
TRUE
}
},
Expand Down Expand Up @@ -573,7 +739,13 @@ metaDichotomousModelClass <-

}
}
print(plotFUN)
funplot <- plotFUN
funplotMed <- plotFUN
funplotLarge <- plotFUN

print(funplot)
print(funplotMed)
print(funplotLarge)
TRUE
}
}
Expand Down
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