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fixes dependencies and lower bounded Bayesian tests with -Inf prior #127

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fixes dependencies and lower bounded Bayesian tests with -Inf prior #127

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17c8a0e
fix dependencies
FBartos Oct 30, 2024
711ef49
fix dependencies (forgotten var)
FBartos Oct 30, 2024
3a222c5
fix numerical integration error for extreme bounds
FBartos Oct 30, 2024
f0876f9
renv stuff
FBartos Oct 30, 2024
fa179c5
GroupTitles + Bayesian logo
FBartos Oct 30, 2024
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2 changes: 2 additions & 0 deletions .Rbuildignore
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
^renv$
^renv\.lock$
^.*\.Rproj$
^\.Rproj\.user$
^\.travis\.yml$
1 change: 1 addition & 0 deletions .Rprofile
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@@ -0,0 +1 @@
source("renv/activate.R")
45 changes: 32 additions & 13 deletions R/commonequivalencefunctions.R
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Expand Up @@ -31,12 +31,9 @@ gettextf <- function(fmt, ..., domain = NULL) {

if (is.null(jaspResults[["equivalencePriorPosteriorContainer"]])) {
equivalencePriorPosteriorContainer <- createJaspContainer(title = gettext("Equivalence Prior and Posterior"))
equivalencePriorPosteriorContainer$dependOn(c("priorandposterior", "missingValues", "priorWidth",
"effectSizeStandardized", "equivalenceRegion", "lower", "upper",
"region", "lowerbound", "upperbound", "lower_max", "upper_min", "prior",
"informative", "informativeCauchyLocation", "informativeCauchyScale",
"informativeNormalMean", "informativeNormalStd", "informativeTLocation",
"informativeTScale", "informativeTDf", "priorandposteriorAdditionalInfo"))
equivalencePriorPosteriorContainer$dependOn(c("priorandposterior", "priorandposteriorAdditionalInfo", "missingValues",
,
.equivalencePriorDependencies))
jaspResults[["equivalencePriorPosteriorContainer"]] <- equivalencePriorPosteriorContainer
} else {
equivalencePriorPosteriorContainer <- jaspResults[["equivalencePriorPosteriorContainer"]]
Expand Down Expand Up @@ -512,19 +509,28 @@ gettextf <- function(fmt, ..., domain = NULL) {

# Step 1: Density in the range of the prior
integralEquivalencePrior <- pnorm(options$upperbound, prior.mean, sqrt(prior.variance)) - pnorm(options$lowerbound, prior.mean, sqrt(prior.variance))

errorEquivalencePrior <- 0

integralNonequivalencePrior <- 1 - integralEquivalencePrior

# Step 2: Density in the equivalence range of the posterior
upperbound <- .equivalence_cdf_normal(x = options$upperbound, t, n1, n2, independentSamples,
prior.mean = prior.mean, prior.variance = prior.variance)
if (options$upperbound == Inf) {
upperbound <- list(value = 1, abs.error = 0)
} else {
upperbound <- .equivalence_cdf_normal(x = options$upperbound, t, n1, n2, independentSamples,
prior.mean = prior.mean, prior.variance = prior.variance)
}

if (options$lowerbound == -Inf) {
lowerbound <- list(value = 0, abs.error = 0)
} else {
lowerbound <- .equivalence_cdf_normal(x = options$lowerbound, t, n1, n2, independentSamples,
prior.mean = prior.mean, prior.variance = prior.variance)
}

lowerbound <- .equivalence_cdf_normal(x = options$lowerbound, t, n1, n2, independentSamples,
prior.mean = prior.mean, prior.variance = prior.variance)

errorEquivalencePosterior <- upperbound$abs.error + lowerbound$abs.error
errorEquivalencePosterior <- upperbound$abs.error + lowerbound$abs.error
integralEquivalencePosterior <- upperbound$value - lowerbound$value

# to prevent numerical integration error (value < error)
Expand Down Expand Up @@ -660,7 +666,7 @@ gettextf <- function(fmt, ..., domain = NULL) {

} else if (options[["informativeStandardizedEffectSize"]] == "normal") {

bfObject <- .equivalence_bf_normal(t = tValue,
bfObject <- .equivalence_bf_normal(t = tValue,
n1 = n1,
n2 = n2,
independentSamples = !paired && !is.null(y),
Expand Down Expand Up @@ -1189,3 +1195,16 @@ gettextf <- function(fmt, ..., domain = NULL) {
exitAnalysisIfErrors = TRUE)
}
}

.equivalenceRegionDependencies <- c(
"equivalenceRegion",
"lowerbound", "upperbound",
"lower_max", "upper_min"
)
.equivalencePriorDependencies <- c(
"effectSize", "effectSizeStandardized", "defaultStandardizedEffectSize", "informativeStandardizedEffectSize",
"priorWidth",
"informativeCauchyLocation", "informativeCauchyScale",
"informativeNormalMean", "informativeNormalStd",
"informativeTLocation", "informativeTScale", "informativeTDf"
)
22 changes: 5 additions & 17 deletions R/equivalencebayesianindependentsamplesttest.R
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Expand Up @@ -125,11 +125,7 @@ EquivalenceBayesianIndependentSamplesTTest <- function(jaspResults, dataset, opt

# Save results to state
jaspResults[["stateEquivalenceBayesianIndTTestResults"]] <- createJaspState(results)
jaspResults[["stateEquivalenceBayesianIndTTestResults"]]$dependOn(c("variables", "groupingVariable", "equivalenceRegion", "lower", "upper",
"region", "lowerbound", "upperbound", "lower_max", "upper_min", "prior", "missingValues",
"informative", "informativeCauchyLocation", "informativeCauchyScale",
"informativeNormalMean", "informativeNormalStd", "informativeTLocation",
"informativeTScale", "informativeTDf"))
jaspResults[["stateEquivalenceBayesianIndTTestResults"]]$dependOn(c("variables", "groupingVariable", "missingValues", .equivalenceRegionDependencies, .equivalencePriorDependencies))

return(results)
}
Expand All @@ -138,11 +134,7 @@ EquivalenceBayesianIndependentSamplesTTest <- function(jaspResults, dataset, opt

# Create table
equivalenceBayesianIndTTestTable <- createJaspTable(title = gettext("Equivalence Bayesian Independent Samples T-Test"))
equivalenceBayesianIndTTestTable$dependOn(c("variables", "groupingVariable", "priorWidth",
"effectSizeStandardized", "equivalenceRegion", "lower", "upper", "region", "lowerbound", "upperbound",
"lower_max", "upper_min", "informative", "informativeCauchyLocation", "informativeCauchyScale",
"informativeNormalMean", "informativeNormalStd", "informativeTLocation",
"informativeTScale", "informativeTDf"))
equivalenceBayesianIndTTestTable$dependOn(c("variables", "groupingVariable", "missingValues", .equivalenceRegionDependencies, .equivalencePriorDependencies))

# Add Columns to table
equivalenceBayesianIndTTestTable$addColumnInfo(name = "variable", title = " ", type = "string", combine = TRUE)
Expand All @@ -154,8 +146,8 @@ EquivalenceBayesianIndependentSamplesTTest <- function(jaspResults, dataset, opt

if (ready)
equivalenceBayesianIndTTestTable$setExpectedSize(length(options$variables))
message <- gettextf("I ranges from %1$s to %2$s",

message <- gettextf("I ranges from %1$s to %2$s",
ifelse(options$lowerbound == -Inf, "-\u221E", options$lowerbound),
ifelse(options$upperbound == Inf, "\u221E", options$upperbound))
equivalenceBayesianIndTTestTable$addFootnote(message)
Expand Down Expand Up @@ -290,11 +282,7 @@ EquivalenceBayesianIndependentSamplesTTest <- function(jaspResults, dataset, opt

.massPriorPosteriorIndpTTestTable <- function(jaspResults, dataset, options, equivalenceBayesianIndTTestResults, ready) {
equivalenceMassTable <- createJaspTable(title = gettext("Prior and Posterior Mass Table"))
equivalenceMassTable$dependOn(c("variables", "groupingVariable", "priorWidth", "lower", "upper", "region",
"effectSizeStandardized", "equivalenceRegion", "lowerbound", "upperbound", "lower_max", "upper_min",
"informative", "informativeCauchyLocation", "informativeCauchyScale",
"informativeNormalMean", "informativeNormalStd", "informativeTLocation",
"informativeTScale", "informativeTDf"))
equivalenceMassTable$dependOn(c("variables", "groupingVariable", "missingValues", .equivalenceRegionDependencies, .equivalencePriorDependencies))

equivalenceMassTable$addColumnInfo(name = "variable", title = " ", type = "string", combine = TRUE)
equivalenceMassTable$addColumnInfo(name = "section", title = gettext("Section"), type = "string")
Expand Down
18 changes: 4 additions & 14 deletions R/equivalencebayesianonesamplettest.R
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Expand Up @@ -112,21 +112,15 @@ EquivalenceBayesianOneSampleTTest <- function(jaspResults, dataset, options) {

# Save results to state
jaspResults[["stateEquivalenceBayesianOneTTestResults"]] <- createJaspState(results)
jaspResults[["stateEquivalenceBayesianOneTTestResults"]]$dependOn(c("variables", "mu", "equivalenceRegion", "lower", "upper", "region", "lowerbound", "upperbound", "lower_max", "upper_min",
"priorWidth", "effectSizeStandardized","informative", "informativeCauchyLocation", "informativeCauchyScale",
"informativeNormalMean", "informativeNormalStd", "informativeTLocation",
"informativeTScale", "informativeTDf", "missingValues"))
jaspResults[["stateEquivalenceBayesianOneTTestResults"]]$dependOn(c("variables", "groupingVariable", "missingValues", "mu", .equivalenceRegionDependencies, .equivalencePriorDependencies))
return(results)
}

.equivalenceBayesianOneTTestTableMain <- function(jaspResults, dataset, options, equivalenceBayesianOneTTestResults, ready) {

# Create table
equivalenceBayesianOneTTestTable <- createJaspTable(title = gettext("Equivalence Bayesian One Sample T-Test"))
equivalenceBayesianOneTTestTable$dependOn(c("variables", "mu", "equivalenceRegion", "priorWidth", "lower", "upper", "region", "lowerbound", "upperbound", "lower_max", "upper_min",
"effectSizeStandardized","informative", "informativeCauchyLocation", "informativeCauchyScale",
"informativeNormalMean", "informativeNormalStd", "informativeTLocation",
"informativeTScale", "informativeTDf", "missingValues"))
equivalenceBayesianOneTTestTable$dependOn(c("variables", "groupingVariable", "missingValues", "mu", .equivalenceRegionDependencies, .equivalencePriorDependencies))
equivalenceBayesianOneTTestTable$showSpecifiedColumnsOnly <- TRUE

# Add Columns to table
Expand All @@ -138,7 +132,7 @@ EquivalenceBayesianOneSampleTTest <- function(jaspResults, dataset, options) {
if (ready)
equivalenceBayesianOneTTestTable$setExpectedSize(length(options$variables))

message <- gettextf("I ranges from %1$s to %2$s",
message <- gettextf("I ranges from %1$s to %2$s",
ifelse(options$lowerbound == -Inf, "-\u221E", options$lowerbound),
ifelse(options$upperbound == Inf, "\u221E", options$upperbound))
equivalenceBayesianOneTTestTable$addFootnote(message)
Expand Down Expand Up @@ -241,11 +235,7 @@ EquivalenceBayesianOneSampleTTest <- function(jaspResults, dataset, options) {
.massPriorPosteriorOneTTestTable <- function(jaspResults, dataset, options, equivalenceBayesianOneTTestResults, ready) {

equivalenceMassTable <- createJaspTable(title = gettext("Prior and Posterior Mass Table"))
equivalenceMassTable$dependOn(c("variables", "priorWidth", "mu", "lower", "upper", "region",
"effectSizeStandardized", "equivalenceRegion", "lowerbound", "upperbound", "lower_max", "upper_min",
"informative", "informativeCauchyLocation", "informativeCauchyScale",
"informativeNormalMean", "informativeNormalStd", "informativeTLocation",
"informativeTScale", "informativeTDf"))
equivalenceMassTable$dependOn(c("variables", "mu", "groupingVariable", "missingValues", .equivalenceRegionDependencies, .equivalencePriorDependencies))

equivalenceMassTable$addColumnInfo(name = "variable", title = " ", type = "string", combine = TRUE)
equivalenceMassTable$addColumnInfo(name = "section", title = gettext("Section"), type = "string")
Expand Down
19 changes: 5 additions & 14 deletions R/equivalencebayesianpairedsamplesttest.R
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Expand Up @@ -121,10 +121,7 @@ EquivalenceBayesianPairedSamplesTTest <- function(jaspResults, dataset, options)

# Save results to state
jaspResults[["stateEquivalenceBayesianPairedTTestResults"]] <- createJaspState(results)
jaspResults[["stateEquivalenceBayesianPairedTTestResults"]]$dependOn(c("pairs", "equivalenceRegion", "missingValues", "lower", "upper", "region", "lowerbound", "upperbound", "lower_max", "upper_min",
"priorWidth", "effectSizeStandardized","informative", "informativeCauchyLocation", "informativeCauchyScale",
"informativeNormalMean", "informativeNormalStd", "informativeTLocation",
"informativeTScale", "informativeTDf"))
jaspResults[["stateEquivalenceBayesianPairedTTestResults"]]$dependOn(c("pairs", "missingValues", .equivalenceRegionDependencies, .equivalencePriorDependencies))
return(results)
}

Expand All @@ -134,10 +131,7 @@ EquivalenceBayesianPairedSamplesTTest <- function(jaspResults, dataset, options)

# Create table
equivalenceBayesianPairedTTestTable <- createJaspTable(title = gettext("Equivalence Bayesian Paired Samples T-Test"))
equivalenceBayesianPairedTTestTable$dependOn(c("pairs", "equivalenceRegion", "lower", "upper", "region", "lowerbound", "upperbound", "lower_max", "upper_min",
"priorWidth", "effectSizeStandardized","informative", "informativeCauchyLocation", "informativeCauchyScale",
"informativeNormalMean", "informativeNormalStd", "informativeTLocation",
"informativeTScale", "informativeTDf"))
equivalenceBayesianPairedTTestTable$dependOn(c("pairs", "missingValues", .equivalenceRegionDependencies, .equivalencePriorDependencies))
equivalenceBayesianPairedTTestTable$showSpecifiedColumnsOnly <- TRUE

# Add Columns to table
Expand All @@ -151,8 +145,8 @@ EquivalenceBayesianPairedSamplesTTest <- function(jaspResults, dataset, options)
if (ready)
equivalenceBayesianPairedTTestTable$setExpectedSize(length(options$pairs))

message <- gettextf("I ranges from %1$s to %2$s",
ifelse(options$lowerbound == -Inf, "-\u221E", options$lowerbound),
message <- gettextf("I ranges from %1$s to %2$s",
ifelse(options$lowerbound == -Inf, "-\u221E", options$lowerbound),
ifelse(options$upperbound == Inf, "\u221E", options$upperbound))
equivalenceBayesianPairedTTestTable$addFootnote(message)

Expand Down Expand Up @@ -268,10 +262,7 @@ EquivalenceBayesianPairedSamplesTTest <- function(jaspResults, dataset, options)

# Create table
equivalenceMassPairedTTestTable <- createJaspTable(title = gettext("Equivalence Mass Table"))
equivalenceMassPairedTTestTable$dependOn(c("pairs", "equivalenceRegion", "priorWidth", "effectSizeStandardized","informative", "lower", "upper", "region",
"informativeCauchyLocation", "informativeCauchyScale", "lowerbound", "upperbound", "lower_max", "upper_min",
"informativeNormalMean", "informativeNormalStd", "informativeTLocation",
"informativeTScale", "informativeTDf"))
equivalenceMassPairedTTestTable$dependOn(c("pairs", "missingValues", .equivalenceRegionDependencies, .equivalencePriorDependencies))
equivalenceMassPairedTTestTable$showSpecifiedColumnsOnly <- TRUE

# Add Columns to table
Expand Down
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