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Rename options for syntax (#102)
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fixes jasp-stats/INTERNAL-jasp#1942
fixes jasp-stats/INTERNAL-jasp#1943
fixes jasp-stats/INTERNAL-jasp#1944
fixes jasp-stats/INTERNAL-jasp#1945
fixes jasp-stats/INTERNAL-jasp#1946
fixes jasp-stats/INTERNAL-jasp#1947
fixes jasp-stats/INTERNAL-jasp#1948
fixes jasp-stats/INTERNAL-jasp#1949
fixes jasp-stats/INTERNAL-jasp#1950
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@Kucharssim
Kucharssim authored Nov 9, 2022
1 parent 0f4b0f4 commit 4a004ea
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Showing 56 changed files with 1,015 additions and 694 deletions.
1 change: 1 addition & 0 deletions .Rbuildignore
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Original file line number Diff line number Diff line change
Expand Up @@ -2,3 +2,4 @@
^renv\.lock$
^.*\.Rproj$
^\.Rproj\.user$
^tests/upgrades$
102 changes: 51 additions & 51 deletions R/abtestbayesian.R
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Original file line number Diff line number Diff line change
Expand Up @@ -36,23 +36,23 @@ ABTestBayesian <- function(jaspResults, dataset = NULL, options) {
.abTestBayesianTableMain(jaspResults, ab_obj, options, ready, position = 1)

### DESCRIPTIVES TABLE ###
if (options$descriptives)
if (options$descriptivesTable)
.abTestBayesianDescriptivesTable(jaspResults, dataset, options, ready, position = 2)

### PRIOR AND POSTERIOR PLOT ###
if (options$plotPriorAndPosterior)
if (options$priorPosteriorPlot)
.abTestPlotPriorPosterior(jaspResults, ab_obj, options, ready, position = 3)

### SEQUENTIAL PLOT ###
if (options$plotSequentialAnalysis)
if (options$bfSequentialPlot)
.abTestPlotSequential(jaspResults, ab_obj, ready, position = 4)

### ROBUSTNESS PLOT ###
if (options$plotRobustness)
if (options$bfRobustnessPlot)
.abTestPlotRobustness(jaspResults, ab_obj, options, ready, position = 5)

### PRIOR PLOT ###
if (options$plotPriorOnly)
if (options$priorPlot)
.abTestPlotPriorOnly(jaspResults, options, position = 6)
}

Expand Down Expand Up @@ -119,11 +119,11 @@ ABTestBayesian <- function(jaspResults, dataset = NULL, options) {
.abTestBayesianFillTableMain <- function(abTestBayesianTable, ab_obj, options) {

# Normalize prior probabilities
sum_logor <- options$orGreaterThan1Prob + options$orLessThan1Prob + options$orEqualTo1Prob + options$orNotEqualTo1Prob
orGreaterThan1Prob <- options$orGreaterThan1Prob / sum_logor
orLessThan1Prob <- options$orLessThan1Prob / sum_logor
orEqualTo1Prob <- options$orEqualTo1Prob / sum_logor
orNotEqualTo1Prob <- options$orNotEqualTo1Prob / sum_logor
sum_logor <- options$priorModelProbabilityGreater + options$priorModelProbabilityLess + options$priorModelProbabilityEqual + options$priorModelProbabilityTwoSided
priorModelProbabilityGreater <- options$priorModelProbabilityGreater / sum_logor
priorModelProbabilityLess <- options$priorModelProbabilityLess / sum_logor
priorModelProbabilityEqual <- options$priorModelProbabilityEqual / sum_logor
priorModelProbabilityTwoSided <- options$priorModelProbabilityTwoSided / sum_logor

if (inherits(ab_obj, "try-error")) {
errorMessage <- as.character(ab_obj)
Expand All @@ -135,43 +135,43 @@ ABTestBayesian <- function(jaspResults, dataset = NULL, options) {
output.rows <- list()
rowCount <- 0

if (orEqualTo1Prob > 0) {
if (priorModelProbabilityEqual > 0) {
rowCount = rowCount + 1
output.rows[[rowCount]] <- list(
"Models" = gettext("Log odds ratio = 0"),
"BF" = 1.00,
"P(M|data)" = ab_obj$post_prob[["H0"]],
"P(M)" = orEqualTo1Prob
"P(M)" = priorModelProbabilityEqual
)
}

if (orGreaterThan1Prob > 0) {
if (priorModelProbabilityGreater > 0) {
rowCount = rowCount + 1
output.rows[[rowCount]] <- list(
"Models" = gettext("Log odds ratio > 0"),
"BF" = ab_obj$bf[["bfplus0"]],
"P(M|data)" = ab_obj$post_prob[["H+"]],
"P(M)" = orGreaterThan1Prob
"P(M)" = priorModelProbabilityGreater
)
}

if (orLessThan1Prob > 0) {
if (priorModelProbabilityLess > 0) {
rowCount = rowCount + 1
output.rows[[rowCount]] <- list(
"Models" = gettext("Log odds ratio < 0"),
"BF" = ab_obj$bf[["bfminus0"]],
"P(M|data)" = ab_obj$post_prob[["H-"]],
"P(M)" = orLessThan1Prob
"P(M)" = priorModelProbabilityLess
)
}

if (orNotEqualTo1Prob > 0) {
if (priorModelProbabilityTwoSided > 0) {
rowCount = rowCount + 1
output.rows[[rowCount]] <- list(
"Models" = gettextf("Log odds ratio %s 0","\u2260"),
"BF" = ab_obj$bf[["bf10"]],
"P(M|data)" = ab_obj$post_prob[["H1"]],
"P(M)" = orNotEqualTo1Prob
"P(M)" = priorModelProbabilityTwoSided
)
}

Expand Down Expand Up @@ -205,27 +205,27 @@ ABTestBayesian <- function(jaspResults, dataset = NULL, options) {

# we copy dependencies from this state object in a few places, so it must always exist
jaspResults[["model"]] <- createJaspState()
jaspResults[["model"]]$dependOn(c("n1", "y1", "n2", "y2", "normal_mu", "normal_sigma", "orEqualTo1Prob",
"orLessThan1Prob", "orGreaterThan1Prob", "orNotEqualTo1Prob", "numSamples", "setSeed", "seed"))
jaspResults[["model"]]$dependOn(c("n1", "y1", "n2", "y2", "normalPriorMean", "normalPriorSd", "priorModelProbabilityEqual",
"priorModelProbabilityLess", "priorModelProbabilityGreater", "priorModelProbabilityTwoSided", "samples", "setSeed", "seed"))

if (!ready)
return(NULL)

prior_par <- list(mu_psi = options$normal_mu, sigma_psi = options$normal_sigma, mu_beta = 0, sigma_beta = 1)
prior_par <- list(mu_psi = options$normalPriorMean, sigma_psi = options$normalPriorSd, mu_beta = 0, sigma_beta = 1)

# Normalize prior probabilities
sum_logor <- options$orGreaterThan1Prob + options$orLessThan1Prob + options$orEqualTo1Prob + options$orNotEqualTo1Prob
orGreaterThan1Prob <- options$orGreaterThan1Prob / sum_logor
orLessThan1Prob <- options$orLessThan1Prob / sum_logor
orEqualTo1Prob <- options$orEqualTo1Prob / sum_logor
orNotEqualTo1Prob <- options$orNotEqualTo1Prob / sum_logor
sum_logor <- options$priorModelProbabilityGreater + options$priorModelProbabilityLess + options$priorModelProbabilityEqual + options$priorModelProbabilityTwoSided
priorModelProbabilityGreater <- options$priorModelProbabilityGreater / sum_logor
priorModelProbabilityLess <- options$priorModelProbabilityLess / sum_logor
priorModelProbabilityEqual <- options$priorModelProbabilityEqual / sum_logor
priorModelProbabilityTwoSided <- options$priorModelProbabilityTwoSided / sum_logor

prior_prob <- c(orNotEqualTo1Prob, orGreaterThan1Prob, orLessThan1Prob, orEqualTo1Prob)
prior_prob <- c(priorModelProbabilityTwoSided, priorModelProbabilityGreater, priorModelProbabilityLess, priorModelProbabilityEqual)
names(prior_prob) <- c("H1", "H+", "H-", "H0")

.setSeedJASP(options)
ab <- try(abtest::ab_test(data = dataset, prior_par = prior_par, prior_prob = prior_prob,
posterior = TRUE, nsamples = options$numSamples))
posterior = TRUE, nsamples = options$samples))

jaspResults[["model"]]$object <- ab

Expand All @@ -240,7 +240,7 @@ ABTestBayesian <- function(jaspResults, dataset = NULL, options) {

abTestBayesianDescriptivesTable <- createJaspTable(title = gettext("Descriptives"))

abTestBayesianDescriptivesTable$dependOn(c("n1", "y1", "n2", "y2", "descriptives"))
abTestBayesianDescriptivesTable$dependOn(c("n1", "y1", "n2", "y2", "descriptivesTable"))
abTestBayesianDescriptivesTable$position <- position

abTestBayesianDescriptivesTable$addColumnInfo(name = "group", title = "", type = "string")
Expand Down Expand Up @@ -279,7 +279,7 @@ ABTestBayesian <- function(jaspResults, dataset = NULL, options) {
.abTestPlotPriorPosterior <- function(jaspResults, ab_obj, options, ready, position) {

abTestPriorAndPosteriorPlot <- createJaspPlot(title = gettext("Prior and Posterior"), width = 530, height = 400)
abTestPriorAndPosteriorPlot$dependOn(c("n1", "y1", "n2", "y2", "normal_mu", "normal_sigma", "numSamples", "plotPosteriorType", "plotPriorAndPosterior",
abTestPriorAndPosteriorPlot$dependOn(c("n1", "y1", "n2", "y2", "normalPriorMean", "normalPriorSd", "samples", "priorPosteriorPlotType", "priorPosteriorPlot",
"setSeed", "seed"))
abTestPriorAndPosteriorPlot$position <- position

Expand All @@ -288,7 +288,7 @@ ABTestBayesian <- function(jaspResults, dataset = NULL, options) {
if (!ready)
return()

abTestPriorAndPosteriorPlot$plotObject <- .plotPosterior.abTest(ab_obj, options$plotPosteriorType)
abTestPriorAndPosteriorPlot$plotObject <- .plotPosterior.abTest(ab_obj, options$priorPosteriorPlotType)
}


Expand All @@ -300,11 +300,11 @@ ABTestBayesian <- function(jaspResults, dataset = NULL, options) {
# posteriorPlotType
what <- switch(
posteriorPlotType,
"LogOddsRatio" = "logor",
"OddsRatio" = "or",
"RelativeRisk" = "rrisk",
"AbsoluteRisk" = "arisk",
"p1&p2" = "p1p2"
"logOddsRatio" = "logor",
"oddsRatio" = "or",
"relativeRisk" = "rrisk",
"absoluteRisk" = "arisk",
"p1P2" = "p1p2"
)

plotFunc <- function() {
Expand All @@ -318,7 +318,7 @@ ABTestBayesian <- function(jaspResults, dataset = NULL, options) {
.abTestPlotSequential <- function(jaspResults, ab_obj, ready, position) {

abTestSequentialPlot <- createJaspPlot(title = gettext("Sequential Analysis"), width = 530, height = 400)
abTestSequentialPlot$dependOn(options = "plotSequentialAnalysis", optionsFromObject = jaspResults[["model"]])
abTestSequentialPlot$dependOn(options = "bfSequentialPlot", optionsFromObject = jaspResults[["model"]])
abTestSequentialPlot$position <- position

jaspResults[["abTestSequentialPlot"]] <- abTestSequentialPlot
Expand All @@ -338,7 +338,7 @@ ABTestBayesian <- function(jaspResults, dataset = NULL, options) {
.abTestPlotRobustness <- function(jaspResults, ab_obj, options, ready, position) {

abTestRobustnessPlot <- createJaspPlot(title = gettext("Bayes Factor Robustness Check"), width = 530, height = 400)
abTestRobustnessPlot$dependOn(c("n1", "y1", "n2", "y2", "normal_mu", "normal_sigma", "mu_stepsize", "sigma_stepsize", "mu_stepsize_lower", "mu_stepsize_upper", "sigma_stepsize_lower", "sigma_stepsize_upper", "plotRobustnessBFType", "numSamples", "plotRobustness", "setSeed", "seed"))
abTestRobustnessPlot$dependOn(c("n1", "y1", "n2", "y2", "normalPriorMean", "normalPriorSd", "bfRobustnessPlotStepsPriorMean", "bfRobustnessPlotStepsPriorSd", "bfRobustnessPlotLowerPriorMean", "bfRobustnessPlotUpperPriorMean", "bfRobustnessPlotLowerPriorSd", "bfRobustnessPlotUpperPriorSd", "bfRobustnessPlotType", "samples", "bfRobustnessPlot", "setSeed", "seed"))
abTestRobustnessPlot$position <- position

jaspResults[["abTestRobustnessPlot"]] <- abTestRobustnessPlot
Expand All @@ -354,18 +354,18 @@ ABTestBayesian <- function(jaspResults, dataset = NULL, options) {
# Args:
# ab_obj: ab test object

mu_range = c(options$mu_stepsize_lower, options$mu_stepsize_upper)
sigma_range = c(options$sigma_stepsize_lower, options$sigma_stepsize_upper)
mu_range = c(options$bfRobustnessPlotLowerPriorMean, options$bfRobustnessPlotUpperPriorMean)
sigma_range = c(options$bfRobustnessPlotLowerPriorSd, options$bfRobustnessPlotUpperPriorSd)

plotFunc <- function() {

abtest::plot_robustness(
x = ab_obj,
mu_steps = options$mu_stepsize,
sigma_steps = options$sigma_stepsize,
mu_steps = options$bfRobustnessPlotStepsPriorMean,
sigma_steps = options$bfRobustnessPlotStepsPriorSd,
mu_range = mu_range,
sigma_range = sigma_range,
bftype = options$plotRobustnessBFType
bftype = options$bfRobustnessPlotType
)
}

Expand All @@ -376,7 +376,7 @@ ABTestBayesian <- function(jaspResults, dataset = NULL, options) {
.abTestPlotPriorOnly <- function(jaspResults, options, position) {

abTestPriorPlot <- createJaspPlot(title = gettext("Prior"), width = 530, height = 400)
abTestPriorPlot$dependOn(c("normal_mu", "normal_sigma", "plotPriorType", "plotPriorOnly"))
abTestPriorPlot$dependOn(c("normalPriorMean", "normalPriorSd", "priorPlotType", "priorPlot"))
abTestPriorPlot$position <- position

jaspResults[["abTestPriorPlot"]] <- abTestPriorPlot
Expand All @@ -391,15 +391,15 @@ ABTestBayesian <- function(jaspResults, dataset = NULL, options) {
# Args:
# options

prior_par <- list(mu_psi = options$normal_mu, sigma_psi = options$normal_sigma, mu_beta = 0, sigma_beta = 1)
prior_par <- list(mu_psi = options$normalPriorMean, sigma_psi = options$normalPriorSd, mu_beta = 0, sigma_beta = 1)

what <- switch(
options$plotPriorType,
"LogOddsRatio" = "logor",
"OddsRatio" = "or",
"RelativeRisk" = "rrisk",
"AbsoluteRisk" = "arisk",
"p1&p2" = "p1p2",
options$priorPlotType,
"logOddsRatio" = "logor",
"oddsRatio" = "or",
"relativeRisk" = "rrisk",
"absoluteRisk" = "arisk",
"p1P2" = "p1p2",
"p1" = "p1",
"p2" = "p2"
)
Expand Down
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