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... better handling of null hypothesis ...
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Brice Maxime Hugues Ozenne committed Feb 13, 2024
1 parent a376fc4 commit 09e1c32
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Showing 2 changed files with 33 additions and 26 deletions.
6 changes: 3 additions & 3 deletions R/S4-BuyseTest-confint.R
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
## Created: maj 19 2018 (23:37)
## Version:
## By: Brice Ozenne
## Update #: 1155
## Update #: 1160
##----------------------------------------------------------------------
##
### Commentary:
Expand Down Expand Up @@ -391,8 +391,8 @@ setMethod(f = "confint",
null <- switch(statistic,
"netBenefit" = 0,
"winRatio" = 1,
"favorable" = 1/2,
"unfavorable" = 1/2)
"favorable" = ifelse(add.halfNeutral,1/2,NA),
"unfavorable" = ifelse(add.halfNeutral,1/2,NA))
}else {
validNumeric(null, valid.length = 1,
refuse.NA = !attr(method.inference,"permutation"),
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53 changes: 30 additions & 23 deletions R/S4-BuyseTest-summary.R
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Original file line number Diff line number Diff line change
Expand Up @@ -140,16 +140,15 @@ setMethod(f = "summary",
min = 1,
max = 9, ## limitation in model.tables
valid.length = 1)
type.display.original <- option$summary.display[[type.display]]
type.display <- paste0("summary",type.display)
type.display.original <- paste0("summary",type.display)
type.display <- option$summary.display[[type.display]]
}else{
validCharacter(type.display,
name1 = "type.display",
valid.values = c("endpoint","restriction","threshold","strata","weight","total","favorable","unfavorable","neutral","uninf","information(%)",
"delta","Delta","Delta(%)",
"p.value","CI","significance"),
valid.length = NULL)
type.display.original <- type.display
}
if(is.null(conf.level)){
conf.level <- option$conf.level
Expand Down Expand Up @@ -181,8 +180,11 @@ setMethod(f = "summary",
attr(conf.level,"warning.permutation") <- FALSE
}
table.print <- model.tables(object, percentage = percentage, statistic = statistic, conf.level = conf.level, strata = strata,
columns = type.display, ...)

columns = union(setdiff(type.display,c("CI","significance")),"null"), ...)
null <- table.print$null
if("null" %in% type.display == FALSE){
table.print$null <- NULL
}
name.print <- names(table.print)
endpoint.restriction.threshold <- attr(table.print,"endpoint")
transform <- attr(table.print,"transform")
Expand All @@ -205,7 +207,7 @@ setMethod(f = "summary",

## ** reformat table
## *** add column with stars
if(("p.value" %in% name.print) && ("significance" %in% type.display.original)){
if(("p.value" %in% name.print) && ("significance" %in% type.display)){
colStars <- sapply(table.print[,"p.value"],function(x){
if(is.na(x)){""}else if(x<0.001){"***"}else if(x<0.01){"**"}else if(x<0.05){"*"}else if(x<0.1){"."}else{""}
})
Expand Down Expand Up @@ -273,7 +275,7 @@ setMethod(f = "summary",
}

## *** merge CI inf and CI sup column
if("CI" %in% type.display.original && "lower.ci" %in% name.print && "upper.ci" %in% name.print){
if("CI" %in% type.display && "lower.ci" %in% name.print && "upper.ci" %in% name.print){
qInf <- round(100*alpha/2, digits = digit[2])
qSup <- round(100*(1-alpha/2), digits = digit[2])
name.ci <- paste0("CI [",qInf,"% ; ",qSup,"%]")
Expand Down Expand Up @@ -301,22 +303,27 @@ setMethod(f = "summary",

## *** display
if(print){
cat(" Generalized pairwise comparisons ",txt.endpoint,txt.strata,"\n\n", sep = "")
if(statistic == "winRatio"){
cat(" - statistic : ",if(any(!is.na(object@restriction))){"restricted "}else{""},"win ratio (delta: endpoint specific, Delta: global) \n",
" - null hypothesis : Delta == 1 \n", sep = "")
}else if(statistic == "netBenefit"){
cat(" - statistic : ",if(any(!is.na(object@restriction))){"restricted "}else{""},"net benefit (delta: endpoint specific, Delta: global) \n",
" - null hypothesis : Delta == 0 \n", sep = "")
}else if(statistic == "favorable"){
cat(" - statistic : ",if(any(!is.na(object@restriction))){"restricted "}else{""},"proportion in favor of treatment (delta: endpoint specific, Delta: global) \n",
" - null hypothesis : Delta == 1/2 \n", sep = "")
}else if(statistic == "favorable"){
cat(" - statistic : ",if(any(!is.na(object@restriction))){"restricted "}else{""},"proportion in favor of control (delta: endpoint specific, Delta: global) \n",
" - null hypothesis : Delta == 1/2 \n", sep = "")
}
if(method.inference != "none"){
cat(" - confidence level: ",1-alpha," \n", sep = "")
cat(" Generalized pairwise comparisons ",txt.endpoint,txt.strata,"\n\n", sep = "")

txt.statistic <- c(" - statistic : ",
ifelse(any(!is.na(object@restriction)),"restricted",""),
switch(statistic,
"winRatio" = ifelse(object@add.halfNeutral,"win odds","win ratio"),
"netBenefit" = "net treatment benefit",
"favorable" = ifelse(object@add.halfNeutral,"proportion in favor of treatment","proportion strictly in favor of treatment"),
"unfavorable" = ifelse(object@add.halfNeutral,"proportion in favor of control","proportion strictly in favor of control")
)
)
cat(paste(txt.statistic, collapse = "")," (delta: endpoint specific, Delta: global) \n")
if(all(is.na(null))){
cat(" - null hypothesis : requires specification of the argument \'null\' \n", sep = "")
table.print$p.value <- NULL
}else{
cat(" - null hypothesis : Delta == ",stats::na.omit(null)[1]," \n", sep = "")
}

if(method.inference != "none"){
cat(" - confidence level: ",1-alpha," \n", sep = "")

if(attr(method.inference,"permutation")){
txt.method <- "permutation test"
Expand Down

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