From 4fd2f6e260f71ad40d899f8046f66ed1f1c57817 Mon Sep 17 00:00:00 2001 From: sbalci Date: Sun, 10 Dec 2023 11:49:48 +0300 Subject: [PATCH] will fix https://github.com/sbalci/jsurvival/issues/2 functions are being updated --- DESCRIPTION | 4 +- R/jjhistostats.b.R | 2 +- R/jjhistostats.h.R | 6 +- R/multisurvival.b.R | 267 ++++++++-------- R/multisurvival.h.R | 32 +- R/survival.b.R | 588 ++++++++++++++++++++++++++++-------- R/survival.h.R | 141 +++++---- jamovi/0000.yaml | 4 +- jamovi/jjhistostats.a.yaml | 2 +- jamovi/multisurvival.r.yaml | 28 +- jamovi/survival.a.yaml | 13 +- jamovi/survival.r.yaml | 144 ++++++--- jamovi/survival.u.yaml | 33 +- man/jjhistostats.Rd | 2 +- man/survival.Rd | 13 +- 15 files changed, 820 insertions(+), 459 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 004141a9..09e6b5ca 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Type: Package Package: ClinicoPath Title: Analysis for Clinicopathological Research -Version: 0.0.2.08 -Date: 2023-12-03 +Version: 0.0.2.12 +Date: 2023-12-07 Authors@R: person(given = "Serdar", family = "Balci", diff --git a/R/jjhistostats.b.R b/R/jjhistostats.b.R index aa6a046b..a48d86d6 100644 --- a/R/jjhistostats.b.R +++ b/R/jjhistostats.b.R @@ -169,7 +169,7 @@ jjhistostatsClass <- if (requireNamespace('jmvcore')) x = !!dep, binwidth = binwidth, - # bar.measure = barmeasure, ---- + # bar.measure = barmeasure, # xlab = NULL, # title = NULL, # subtitle = NULL, diff --git a/R/jjhistostats.h.R b/R/jjhistostats.h.R index 1d5452b7..5a7a6907 100644 --- a/R/jjhistostats.h.R +++ b/R/jjhistostats.h.R @@ -8,7 +8,7 @@ jjhistostatsOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas initialize = function( dep = NULL, grvar = NULL, - excl = TRUE, + excl = FALSE, typestatistics = "parametric", centralityparameter = "mean", centralityline = TRUE, @@ -55,7 +55,7 @@ jjhistostatsOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas private$..excl <- jmvcore::OptionBool$new( "excl", excl, - default=TRUE) + default=FALSE) private$..typestatistics <- jmvcore::OptionList$new( "typestatistics", typestatistics, @@ -339,7 +339,7 @@ jjhistostats <- function( data, dep, grvar, - excl = TRUE, + excl = FALSE, typestatistics = "parametric", centralityparameter = "mean", centralityline = TRUE, diff --git a/R/multisurvival.b.R b/R/multisurvival.b.R index 101cfd03..d602f418 100644 --- a/R/multisurvival.b.R +++ b/R/multisurvival.b.R @@ -9,62 +9,62 @@ multisurvivalClass <- if (requireNamespace('jmvcore')) inherit = multisurvivalBase, private = list( - .todo = function() { - # If no variable selected Initial Message ---- - - if ( - - (is.null(self$options$outcome) && !(self$options$multievent)) || - - (self$options$multievent && (is.null(self$options$dod) && is.null(self$options$dooc) && is.null(self$options$awd) && is.null(self$options$awod))) || - - (is.null(self$options$elapsedtime) && !(self$options$tint)) || - - (self$options$tint && (is.null(self$options$dxdate) || is.null(self$options$fudate))) || - - is.null(self$options$explanatory) - - # || - - # (!is.null(self$options$explanatory) && is.null(self$options$contexpl)) - - - ) - { - # TODO ---- - - todo <- glue::glue( - " -
Welcome to ClinicoPath -

- This tool will help you perform a multivariable survival analysis. -

- Explanatory variables can be categorical (ordinal or nominal) or continuous. -

- Select outcome level from Outcome variable. -

- Outcome Level: if patient is dead or event (recurrence) occured. You may also use advanced outcome options depending on your analysis type. -

- Survival time should be numeric, continuous, and in months. You may also use dates to calculate survival time in advanced elapsed time options. -

- This function uses finalfit, survival, survminer and ggstatsplot packages. Please cite jamovi and the packages as given below. -

- " - ) - # https://finalfit.org/articles/all_tables_examples.html#cox-proportional-hazards-model-survival-time-to-event - - - html <- self$results$todo - html$setContent(todo) - return() - - } else { - if (nrow(self$data) == 0) - stop('Data contains no (complete) rows') - } - - } - , + # .todo = function() { + # # If no variable selected Initial Message ---- + # + # if ( + # + # (is.null(self$options$outcome) && !(self$options$multievent)) || + # + # (self$options$multievent && (is.null(self$options$dod) && is.null(self$options$dooc) && is.null(self$options$awd) && is.null(self$options$awod))) || + # + # (is.null(self$options$elapsedtime) && !(self$options$tint)) || + # + # (self$options$tint && (is.null(self$options$dxdate) || is.null(self$options$fudate))) || + # + # is.null(self$options$explanatory) + # + # # || + # + # # (!is.null(self$options$explanatory) && is.null(self$options$contexpl)) + # + # + # ) + # { + # # TODO ---- + # + # todo <- glue::glue( + # " + #
Welcome to ClinicoPath + #

+ # This tool will help you perform a multivariable survival analysis. + #

+ # Explanatory variables can be categorical (ordinal or nominal) or continuous. + #

+ # Select outcome level from Outcome variable. + #

+ # Outcome Level: if patient is dead or event (recurrence) occured. You may also use advanced outcome options depending on your analysis type. + #

+ # Survival time should be numeric, continuous, and in months. You may also use dates to calculate survival time in advanced elapsed time options. + #

+ # This function uses finalfit, survival, survminer and ggstatsplot packages. Please cite jamovi and the packages as given below. + #

+ # " + # ) + # # https://finalfit.org/articles/all_tables_examples.html#cox-proportional-hazards-model-survival-time-to-event + # + # + # html <- self$results$todo + # html$setContent(todo) + # # return() + # + # } else { + # if (nrow(self$data) == 0) + # stop('Data contains no (complete) rows') + # } + # + # } + # , .cleandata = function() { @@ -81,6 +81,7 @@ multisurvivalClass <- if (requireNamespace('jmvcore')) elapsedtime <- self$options$elapsedtime outcome <- self$options$outcome explanatory <- self$options$explanatory + contexpl <- self$options$contexpl outcomeLevel <- self$options$outcomeLevel tint <- self$options$tint @@ -285,26 +286,35 @@ multisurvivalClass <- if (requireNamespace('jmvcore')) myfactors <- c(myexplanatory, mycontexpl) + self$results$mydataview$setContent( + list( + head(mydata, n = 10), + myexplanatory = myexplanatory, + mycontexpl = mycontexpl, + myfactors = myfactors + ) + ) - # Add Redefined Outcome to Data ---- - if (self$options$multievent) { + # Add Redefined Outcome to Data ---- - if (self$options$outcomeredifened && - self$results$outcomeredifened$isNotFilled()) { - self$results$outcomeredifened$setValues(mydata[["myoutcome"]]) - } - } + # if (self$options$multievent) { + # + # if (self$options$outcomeredifened && + # self$results$outcomeredifened$isNotFilled()) { + # self$results$outcomeredifened$setValues(mydata[["myoutcome"]]) + # } + # } # Add Calculated Time to Data ---- - if (self$options$tint) { - - if (self$options$calculatedtime && - self$results$calculatedtime$isNotFilled()) { - self$results$calculatedtime$setValues(mydata[["mytime"]]) - } - } + # if (self$options$tint) { + # + # if (self$options$calculatedtime && + # self$results$calculatedtime$isNotFilled()) { + # self$results$calculatedtime$setValues(mydata[["mytime"]]) + # } + # } @@ -332,7 +342,11 @@ multisurvivalClass <- if (requireNamespace('jmvcore')) mydata <- jmvcore::select(df = mydata, columnNames = c("mytime", "myoutcome", myfactors)) - + # self$results$mydataview$setContent( + # list( + # head(mydata, n = 30) + # ) + # ) # naOmit ---- @@ -355,24 +369,24 @@ multisurvivalClass <- if (requireNamespace('jmvcore')) # Errors ---- - if ( - - (is.null(self$options$outcome) && !(self$options$multievent)) || - - (self$options$multievent && (is.null(self$options$dod) && is.null(self$options$dooc) && is.null(self$options$awd) && is.null(self$options$awod))) || - - (self$options$tint && (is.null(self$options$dxdate) || is.null(self$options$fudate))) || - - is.null(self$options$explanatory) - - # || - # - # (!is.null(self$options$explanatory) && is.null(self$options$contexpl)) - - ) { - private$.todo() - return() - } + # if ( + # + # (is.null(self$options$outcome) && !(self$options$multievent)) || + # + # (self$options$multievent && (is.null(self$options$dod) && is.null(self$options$dooc) && is.null(self$options$awd) && is.null(self$options$awod))) || + # + # (self$options$tint && (is.null(self$options$dxdate) || is.null(self$options$fudate))) || + # + # is.null(self$options$explanatory) + # + # # + # # + # # (!is.null(self$options$explanatory) && is.null(self$options$contexpl)) + # + # ) { + # private$.todo() + # # return() + # } if (nrow(self$data) == 0) stop('Data contains no (complete) rows') @@ -384,6 +398,9 @@ multisurvivalClass <- if (requireNamespace('jmvcore')) mydata <- cleaneddata$mydata + + + # Cox ---- private$.cox(mydata) @@ -396,7 +413,7 @@ multisurvivalClass <- if (requireNamespace('jmvcore')) # ) - # # Prepare Data For Plots ---- + # Prepare Data For Plots ---- image <- self$results$plot @@ -406,8 +423,8 @@ multisurvivalClass <- if (requireNamespace('jmvcore')) image3$setState(mydata) - image4 <- self$results$plot4 - image4$setState(mydata) + # image4 <- self$results$plot4 + # image4$setState(mydata) # imageKM <- self$results$plotKM @@ -827,39 +844,39 @@ multisurvivalClass <- if (requireNamespace('jmvcore')) - # coxzph plot ---- - , - .plot4 = function(image4, ggtheme, theme, ...) { - - plotData <- image4$state - - formula2 <- - jmvcore::constructFormula(terms = c(self$options$explanatory, self$options$contexpl)) - - formula3 <- - paste("survival::Surv(mytime, myoutcome) ~ ", formula2) - - formula3 <- as.formula(formula3) - - cox_model <- - survival::coxph(formula = formula3, - data = plotData) - - - - cox_zph_fit <- survival::cox.zph(cox_model) - - - # plot all variables - plot4 <- survminer::ggcoxzph(cox_zph_fit) - - - # print plot ---- - - print(plot4) - TRUE - - } + # # coxzph plot ---- + # , + # .plot4 = function(image4, ggtheme, theme, ...) { + # + # plotData <- image4$state + # + # formula2 <- + # jmvcore::constructFormula(terms = c(self$options$explanatory, self$options$contexpl)) + # + # formula3 <- + # paste("survival::Surv(mytime, myoutcome) ~ ", formula2) + # + # formula3 <- as.formula(formula3) + # + # cox_model <- + # survival::coxph(formula = formula3, + # data = plotData) + # + # + # + # cox_zph_fit <- survival::cox.zph(cox_model) + # + # + # # plot all variables + # plot4 <- survminer::ggcoxzph(cox_zph_fit) + # + # + # # print plot ---- + # + # print(plot4) + # TRUE + # + # } diff --git a/R/multisurvival.h.R b/R/multisurvival.h.R index 6a144ece..ed621c54 100644 --- a/R/multisurvival.h.R +++ b/R/multisurvival.h.R @@ -221,11 +221,11 @@ multisurvivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cla inherit = jmvcore::Group, active = list( todo = function() private$.items[["todo"]], + mydataview = function() private$.items[["mydataview"]], text = function() private$.items[["text"]], text2 = function() private$.items[["text2"]], plot = function() private$.items[["plot"]], - plot3 = function() private$.items[["plot3"]], - plot4 = function() private$.items[["plot4"]]), + plot3 = function() private$.items[["plot3"]]), private = list(), public=list( initialize=function(options) { @@ -261,8 +261,11 @@ multisurvivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cla "fudate", "dxdate", "tint", - "multievent", - "adjexplanatory"))) + "multievent"))) + self$add(jmvcore::Preformatted$new( + options=options, + name="mydataview", + title="mydataview")) self$add(jmvcore::Html$new( options=options, name="text", @@ -277,8 +280,7 @@ multisurvivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cla "fudate", "dxdate", "tint", - "multievent", - "adjexplanatory"))) + "multievent"))) self$add(jmvcore::Html$new( options=options, name="text2", @@ -293,8 +295,7 @@ multisurvivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cla "fudate", "dxdate", "tint", - "multievent", - "adjexplanatory"))) + "multievent"))) self$add(jmvcore::Image$new( options=options, name="plot", @@ -316,8 +317,7 @@ multisurvivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cla "fudate", "dxdate", "tint", - "multievent", - "adjexplanatory"))) + "multievent"))) self$add(jmvcore::Image$new( options=options, name="plot3", @@ -339,15 +339,7 @@ multisurvivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cla "fudate", "dxdate", "tint", - "multievent", - "adjexplanatory"))) - self$add(jmvcore::Image$new( - options=options, - name="plot4", - title="coxzph Plot", - width=800, - height=600, - renderFun=".plot4"))})) + "multievent")))})) multisurvivalBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "multisurvivalBase", @@ -402,11 +394,11 @@ multisurvivalBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( #' @return A results object containing: #' \tabular{llllll}{ #' \code{results$todo} \tab \tab \tab \tab \tab a html \cr +#' \code{results$mydataview} \tab \tab \tab \tab \tab a preformatted \cr #' \code{results$text} \tab \tab \tab \tab \tab a html \cr #' \code{results$text2} \tab \tab \tab \tab \tab a html \cr #' \code{results$plot} \tab \tab \tab \tab \tab an image \cr #' \code{results$plot3} \tab \tab \tab \tab \tab an image \cr -#' \code{results$plot4} \tab \tab \tab \tab \tab an image \cr #' } #' #' @export diff --git a/R/survival.b.R b/R/survival.b.R index 3af2d0ed..437569ad 100644 --- a/R/survival.b.R +++ b/R/survival.b.R @@ -9,72 +9,169 @@ survivalClass <- if (requireNamespace('jmvcore')) "survivalClass", inherit = survivalBase, private = list( + + + + .init = function() { - if (self$options$sas) { + + + + if(self$options$ph_cox) { # Disable tables - self$results$medianSummary$setVisible(FALSE) - self$results$medianTable$setVisible(FALSE) - self$results$coxSummary$setVisible(FALSE) - self$results$coxTable$setVisible(FALSE) - self$results$tCoxtext2$setVisible(FALSE) - self$results$survTableSummary$setVisible(FALSE) - self$results$survTable$setVisible(FALSE) - self$results$pairwiseSummary$setVisible(FALSE) - self$results$pairwiseTable$setVisible(FALSE) + self$results$cox_ph$setVisible(TRUE) } + # if (self$options$sas) { + # # Disable tables + # self$results$medianSummary$setVisible(FALSE) + # self$results$medianTable$setVisible(FALSE) + # self$results$coxSummary$setVisible(FALSE) + # self$results$coxTable$setVisible(FALSE) + # self$results$tCoxtext2$setVisible(FALSE) + # self$results$survTableSummary$setVisible(FALSE) + # self$results$survTable$setVisible(FALSE) + # self$results$pairwiseSummary$setVisible(FALSE) + # self$results$pairwiseTable$setVisible(FALSE) + # } + } + , - .todo = function() { - if ((is.null(self$options$outcome) && !(self$options$multievent)) || - (self$options$multievent && - ( - is.null(self$options$dod) && - is.null(self$options$dooc) && - is.null(self$options$awd) && is.null(self$options$awod) - )) || - (self$options$tint && - ( - is.null(self$options$dxdate) || is.null(self$options$fudate) - )) || - ((is.null(self$options$explanatory)) || (is.null(self$explanatory$sas)))) { - - todo <- glue::glue( - " -
Welcome to ClinicoPath -

- This tool will help you calculate median survivals and 1,3,5-yr survivals for a given fisk factor. -

- Explanatory variable should be categorical (ordinal or nominal). -

- Select outcome level from Outcome variable. -

- Outcome Level: if patient is dead or event (recurrence) occured. You may also use advanced outcome options depending on your analysis type. -

- Survival time should be numeric and continuous. You may also use dates to calculate survival time in advanced elapsed time options. -

- This function uses survival, survminer, and finalfit packages. Please cite jamovi and the packages as given below. -
-
- See details for survival here." - ) - html <- self$results$todo - html$setContent(todo) - } + + + + .getData = function() { + + mydata <- self$data + + mydata$row_names <- rownames(mydata) + + original_names <- names(mydata) + + labels <- setNames(original_names, original_names) + + mydata <- mydata %>% janitor::clean_names() + + corrected_labels <- + setNames(original_names, names(mydata)) + + mydata <- labelled::set_variable_labels(.data = mydata, + .labels = corrected_labels) + + all_labels <- labelled::var_label(mydata) + + + mytime <- + names(all_labels)[all_labels == self$options$elapsedtime] + + myoutcome <- + names(all_labels)[all_labels == self$options$outcome] + + mydxdate <- + names(all_labels)[all_labels == self$options$dxdate] + + myfudate <- + names(all_labels)[all_labels == self$options$fudate] + + myexplanatory <- + names(all_labels)[all_labels == self$options$explanatory] + + return(list( + "mydata_labelled" = mydata + , "mytime_labelled" = mytime + , "myoutcome_labelled" = myoutcome + , "mydxdate_labelled" = mydxdate + , "myfudate_labelled" = myfudate + , "myexplanatory_labelled" = myexplanatory + )) + } + + + # , + # .todo = function() { + # if ( + # (is.null(self$options$outcome) && !(self$options$multievent)) || + + # (self$options$multievent && + # ( + # is.null(self$options$dod) && + # is.null(self$options$dooc) && + # is.null(self$options$awd) && is.null(self$options$awod) + + # ) + # ) || + + # (self$options$tint && + # ( + # is.null(self$options$dxdate) || is.null(self$options$fudate) + # )) || + + # (is.null(self$options$explanatory) + + # # + # # || (is.null(self$explanatory$sas)) + # # + + # ) + # ) { + + # todo <- glue::glue( + # " + #
Welcome to ClinicoPath + #

+ # This tool will help you calculate median survivals and 1,3,5-yr survivals for a given fisk factor. + #

+ # Explanatory variable should be categorical (ordinal or nominal). + #

+ # Select outcome level from Outcome variable. + #

+ # Outcome Level: if patient is dead or event (recurrence) occured. You may also use advanced outcome options depending on your analysis type. + #

+ # Survival time should be numeric and continuous. You may also use dates to calculate survival time in advanced elapsed time options. + #

+ # This function uses survival, survminer, and finalfit packages. Please cite jamovi and the packages as given below. + #
+ #
+ # See details for survival here." + # ) + + # html <- self$results$todo + # html$setContent(todo) + + # } + + # } + + + + + # Define Survival Time ---- , .definemytime = function() { - mydata <- self$data + # mydata <- self$data + + # Read Labelled Data ---- + + labelled_data <- private$.getData() + + mydata <- labelled_data$mydata_labelled + mytime_labelled <- labelled_data$mytime_labelled + # myoutcome_labelled <- labelled_data$myoutcome_labelled + mydxdate_labelled <- labelled_data$mydxdate_labelled + myfudate_labelled <- labelled_data$myfudate_labelled + # myexplanatory_labelled <- labelled_data$myexplanatory_labelled tint <- self$options$tint @@ -84,15 +181,16 @@ survivalClass <- if (requireNamespace('jmvcore')) # mydata[[self$options$elapsedtime]] <- jmvcore::toNumeric(mydata[[self$options$elapsedtime]]) - mydata[["mytime"]] <- - jmvcore::toNumeric(mydata[[self$options$elapsedtime]]) + mydata[["mytime"]] <- + jmvcore::toNumeric(mydata[[mytime_labelled]]) + } else if (tint) { # Time Interval ---- - dxdate <- self$options$dxdate - fudate <- self$options$fudate + dxdate <- mydxdate_labelled # self$options$dxdate + fudate <- myfudate_labelled #self$options$fudate timetypedata <- self$options$timetypedata @@ -150,34 +248,68 @@ survivalClass <- if (requireNamespace('jmvcore')) } - return(mydata[["mytime"]]) + df_time <- mydata %>% jmvcore::select(c("row_names", "mytime")) - } - # Add Calculated Time to Data ---- - , - .mytimetodata = function() { - mycalculatedtime <- private$.definemytime() + return(df_time) - if (self$options$calculatedtime && - self$results$calculatedtime$isNotFilled()) { - self$results$calculatedtime$setValues(mycalculatedtime) - } } + # # Add Calculated Time to Data ---- + # , + # .mytimetodata = function() { + # mycalculatedtime <- private$.definemytime() + + # if (self$options$calculatedtime && + # self$results$calculatedtime$isNotFilled()) { + # self$results$calculatedtime$setValues(mycalculatedtime) + # } + + # } + # Define Outcome ---- , .definemyoutcome = function() { - mydata <- self$data + + + labelled_data <- private$.getData() + + mydata <- labelled_data$mydata_labelled + # mytime_labelled <- labelled_data$mytime_labelled + myoutcome_labelled <- labelled_data$myoutcome_labelled + # mydxdate_labelled <- labelled_data$mydxdate_labelled + # myfudate_labelled <- labelled_data$myfudate_labelled + # myexplanatory_labelled <- labelled_data$myexplanatory_labelled + + # self$results$mydataview$setContent( + # list( + # mydata_labelled = mydata_labelled, + # mytime_labelled = mytime_labelled, + # myoutcome_labelled = myoutcome_labelled, + # mydxdate_labelled = mydxdate_labelled, + # myfudate_labelled = myfudate_labelled, + # myexplanatory_labelled = myexplanatory_labelled + # ) + # ) + + + + # mydata <- mydata_labelled #self$data contin <- c("integer", "numeric", "double") outcomeLevel <- self$options$outcomeLevel multievent <- self$options$multievent - outcome1 <- self$options$outcome - outcome1 <- self$data[[outcome1]] + + + # outcome1 <- self$options$outcome + # outcome1 <- self$data[[outcome1]] + outcome1 <- mydata[[myoutcome_labelled]] + + + if (!multievent) { if (inherits(outcome1, contin)) { @@ -192,8 +324,8 @@ survivalClass <- if (requireNamespace('jmvcore')) } - mydata[["myoutcome"]] <- - mydata[[self$options$outcome]] + mydata[["myoutcome"]] <- mydata[[myoutcome_labelled]] + # mydata[[self$options$outcome]] } else if (inherits(outcome1, "factor")) { mydata[["myoutcome"]] <- @@ -262,23 +394,25 @@ survivalClass <- if (requireNamespace('jmvcore')) } + df_outcome <- mydata %>% jmvcore::select(c("row_names", "myoutcome")) + - return(mydata[["myoutcome"]]) + return(df_outcome) } # Add Redefined Outcome to Data ---- - , - .myoutcometodata = function() { - mydefinedoutcome <- private$.definemyoutcome() + # , + # .myoutcometodata = function() { + # mydefinedoutcome <- private$.definemyoutcome() - if (self$options$outcomeredifened && - self$results$outcomeredifened$isNotFilled()) { - self$results$outcomeredifened$setValues(mydefinedoutcome) - } + # if (self$options$outcomeredifened && + # self$results$outcomeredifened$isNotFilled()) { + # self$results$outcomeredifened$setValues(mydefinedoutcome) + # } - } + # } @@ -286,22 +420,45 @@ survivalClass <- if (requireNamespace('jmvcore')) # Define Factor ---- , + .definemyfactor = function() { - mydata <- self$data + # mydata <- self$data - expl <- self$options$explanatory + # expl <- self$options$explanatory + + + labelled_data <- private$.getData() - mydata[["myfactor"]] <- mydata[[expl]] + mydata_labelled <- labelled_data$mydata_labelled + mytime_labelled <- labelled_data$mytime_labelled + myoutcome_labelled <- labelled_data$myoutcome_labelled + mydxdate_labelled <- labelled_data$mydxdate_labelled + myfudate_labelled <- labelled_data$myfudate_labelled + myexplanatory_labelled <- labelled_data$myexplanatory_labelled - # single arm ---- - sas <- self$options$sas + mydata <- mydata_labelled - if (sas) { - mydata[["myfactor"]] <- "1" - } + # mydata[["myfactor"]] <- mydata[[expl]] + + + mydata[["myfactor"]] <- mydata[[myexplanatory_labelled]] + + # # single arm ---- + # + # sas <- self$options$sas + # + # if (sas) { + # mydata[["myfactor"]] <- "1" + # } + # + # return(mydata[["myfactor"]]) + + + df_factor <- mydata %>% jmvcore::select(c("row_names","myfactor")) + + return(df_factor) - return(mydata[["myfactor"]]) } @@ -309,13 +466,45 @@ survivalClass <- if (requireNamespace('jmvcore')) # Clean Data For Analysis ---- , .cleandata = function() { + + labelled_data <- private$.getData() + + mydata_labelled <- labelled_data$mydata_labelled + mytime_labelled <- labelled_data$mytime_labelled + myoutcome_labelled <- labelled_data$myoutcome_labelled + mydxdate_labelled <- labelled_data$mydxdate_labelled + myfudate_labelled <- labelled_data$myfudate_labelled + myexplanatory_labelled <- labelled_data$myexplanatory_labelled + + + + + + + + time <- private$.definemytime() outcome <- private$.definemyoutcome() factor <- private$.definemyfactor() - cleanData <- data.frame("mytime" = time, - "myoutcome" = outcome, - "factor" = factor) + + + + + cleanData <- dplyr::left_join(time, outcome, by = "row_names") %>% + dplyr::left_join(factor, by = "row_names") + # %>% + # dplyr::select(-row_names) + + + + + + + + # data.frame("mytime" = time, + # "myoutcome" = outcome, + # "factor" = factor) # Landmark ---- # https://www.emilyzabor.com/tutorials/survival_analysis_in_r_tutorial.html#landmark_method @@ -342,23 +531,36 @@ survivalClass <- if (requireNamespace('jmvcore')) if (!self$options$tint && !is.null(self$options$elapsedtime)) { - name1time <- jmvcore::composeTerm(self$options$elapsedtime) + name1time <- mytime_labelled + # jmvcore::composeTerm(self$options$elapsedtime) } - name2outcome <- - jmvcore::composeTerm(self$options$outcome) + name2outcome <- myoutcome_labelled + # jmvcore::composeTerm(self$options$outcome) - if (self$options$sas) { - name3explanatory <- "SingleArm" - } + # if (self$options$sas) { + # name3explanatory <- "SingleArm" + # } - if (!self$options$sas && - !is.null(self$options$explanatory)) { - name3explanatory <- jmvcore::composeTerm(self$options$explanatory) - } + if ( + # !self$options$sas && + !is.null(self$options$explanatory) + ) { + name3explanatory <- myexplanatory_labelled + # jmvcore::composeTerm(self$options$explanatory) + } + + cleanData <- cleanData %>% + dplyr::rename( + !!name1time := mytime, + !!name2outcome := myoutcome, + !!name3explanatory := myfactor + ) + + - names(cleanData) <- - c(name1time, name2outcome, name3explanatory) + # names(cleanData) <- + # c(name1time, name2outcome, name3explanatory) # naOmit ---- @@ -447,11 +649,25 @@ survivalClass <- if (requireNamespace('jmvcore')) if (nrow(self$data) == 0) stop('Data contains no (complete) rows') + + labelled_data <- private$.getData() + + mydata_labelled <- labelled_data$mydata_labelled + mytime_labelled <- labelled_data$mytime_labelled + myoutcome_labelled <- labelled_data$myoutcome_labelled + mydxdate_labelled <- labelled_data$mydxdate_labelled + myfudate_labelled <- labelled_data$myfudate_labelled + myexplanatory_labelled <- labelled_data$myexplanatory_labelled + + + + + # Add Calculated Time to Data ---- - if (self$options$tint) { - private$.mytimetodata() - } + # if (self$options$tint) { + # private$.mytimetodata() + # } # mycalculatedtime <- private$.definemytime() # @@ -461,31 +677,76 @@ survivalClass <- if (requireNamespace('jmvcore')) # Add Redefined Outcome to Data ---- - if (self$options$multievent) { - private$.myoutcometodata() - } + # if (self$options$multievent) { + # private$.myoutcometodata() + # } # Get Clean Data ---- results <- private$.cleandata() + + self$results$mydataview$setContent( + list( + mydata_labelled = head(mydata_labelled), + mytime_labelled = mytime_labelled, + myoutcome_labelled = myoutcome_labelled, + mydxdate_labelled = mydxdate_labelled, + myfudate_labelled = myfudate_labelled, + myexplanatory_labelled = myexplanatory_labelled, + # time = head(time), + # outcome = head(outcome), + # factor = head(factor), + results = head(results) + ) + ) + + + + + + + + # Run Analysis ---- - if (!self$options$sas) { + # if (!self$options$sas) { # Median Survival ---- private$.medianSurv(results) # Cox ---- private$.cox(results) # Survival Table ---- private$.survTable(results) - } + # } # Pairwise ---- - if (self$options$pw && !self$options$sas) { + if (self$options$pw + # && !self$options$sas + ) { private$.pairwise(results) } + + + + + + + + + + + + + + + + + + + + } @@ -707,6 +968,56 @@ survivalClass <- if (requireNamespace('jmvcore')) self$results$coxSummary$setContent(coxSummary) + # Proportional Hazards Assumption ---- + + if (self$options$ph_cox) { + + # self$results$mydataview$setContent( + # list( + # mydata = head(mydata), + # # mydata_labelled = head(mydata_labelled), + # # mytime_labelled = mytime_labelled, + # # myoutcome_labelled = myoutcome_labelled, + # # mydxdate_labelled = mydxdate_labelled, + # # myfudate_labelled = myfudate_labelled, + # # myexplanatory_labelled = myexplanatory_labelled, + # # time = head(time), + # # outcome = head(outcome), + # # factor = head(factor), + # results = head(results) + # ) + # ) + + + + + + + mydata[[mytime]] <- jmvcore::toNumeric(mydata[[mytime]]) + + + formula <- + paste('survival::Surv(', + mytime, + ',', + myoutcome, + ') ~ ', + myfactor) + + formula <- as.formula(formula) + + + + cox_model <- survival::coxph(formula, data = mydata) + + zph <- survival::cox.zph(cox_model) + + self$results$cox_ph$setContent(print(zph)) + + image7 <- self$results$plot7 + image7$setState(zph) + + } } @@ -935,11 +1246,11 @@ survivalClass <- if (requireNamespace('jmvcore')) title2 <- as.character(myfactor) - sas <- self$options$sas - - if (sas) { - title2 <- "Overall" - } + # sas <- self$options$sas + # + # if (sas) { + # title2 <- "Overall" + # } plot <- plotData %>% @@ -1004,11 +1315,11 @@ survivalClass <- if (requireNamespace('jmvcore')) title2 <- as.character(myfactor) - sas <- self$options$sas - - if (sas) { - title2 <- "Overall" - } + # sas <- self$options$sas + # + # if (sas) { + # title2 <- "Overall" + # } plot2 <- plotData %>% finalfit::surv_plot( @@ -1070,11 +1381,11 @@ survivalClass <- if (requireNamespace('jmvcore')) title2 <- as.character(myfactor) - sas <- self$options$sas - - if (sas) { - title2 <- "Overall" - } + # sas <- self$options$sas + # + # if (sas) { + # title2 <- "Overall" + # } plot3 <- plotData %>% @@ -1131,11 +1442,11 @@ survivalClass <- if (requireNamespace('jmvcore')) title2 <- as.character(myfactor) - sas <- self$options$sas - - if (sas) { - title2 <- "Overall" - } + # sas <- self$options$sas + # + # if (sas) { + # title2 <- "Overall" + # } myformula <- @@ -1169,5 +1480,26 @@ survivalClass <- if (requireNamespace('jmvcore')) } + # cox.zph ---- + , + .plot7 = function(image7, ggtheme, theme, ...) { + + ph_cox <- self$options$ph_cox + + if (!ph_cox) + return() + + zph <- image7$state + + plot7 <- plot(zph) + + print(plot7) + TRUE + + } + + + + ) ) diff --git a/R/survival.h.R b/R/survival.h.R index f8b9ca79..2594a0fc 100644 --- a/R/survival.h.R +++ b/R/survival.h.R @@ -25,6 +25,7 @@ survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( landmark = 3, pw = FALSE, padjustmethod = "holm", + ph_cox = FALSE, sc = FALSE, kmunicate = FALSE, ce = FALSE, @@ -35,8 +36,7 @@ survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( ci95 = FALSE, risktable = FALSE, censored = FALSE, - pplot = TRUE, - sas = FALSE, ...) { + pplot = TRUE, ...) { super$initialize( package="ClinicoPath", @@ -160,6 +160,10 @@ survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "fdr", "none"), default="holm") + private$..ph_cox <- jmvcore::OptionBool$new( + "ph_cox", + ph_cox, + default=FALSE) private$..sc <- jmvcore::OptionBool$new( "sc", sc, @@ -204,10 +208,6 @@ survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "pplot", pplot, default=TRUE) - private$..sas <- jmvcore::OptionBool$new( - "sas", - sas, - default=FALSE) self$.addOption(private$..elapsedtime) self$.addOption(private$..tint) @@ -228,6 +228,7 @@ survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( self$.addOption(private$..landmark) self$.addOption(private$..pw) self$.addOption(private$..padjustmethod) + self$.addOption(private$..ph_cox) self$.addOption(private$..sc) self$.addOption(private$..kmunicate) self$.addOption(private$..ce) @@ -239,7 +240,6 @@ survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( self$.addOption(private$..risktable) self$.addOption(private$..censored) self$.addOption(private$..pplot) - self$.addOption(private$..sas) }), active = list( elapsedtime = function() private$..elapsedtime$value, @@ -261,6 +261,7 @@ survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( landmark = function() private$..landmark$value, pw = function() private$..pw$value, padjustmethod = function() private$..padjustmethod$value, + ph_cox = function() private$..ph_cox$value, sc = function() private$..sc$value, kmunicate = function() private$..kmunicate$value, ce = function() private$..ce$value, @@ -271,8 +272,7 @@ survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( ci95 = function() private$..ci95$value, risktable = function() private$..risktable$value, censored = function() private$..censored$value, - pplot = function() private$..pplot$value, - sas = function() private$..sas$value), + pplot = function() private$..pplot$value), private = list( ..elapsedtime = NA, ..tint = NA, @@ -293,6 +293,7 @@ survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( ..landmark = NA, ..pw = NA, ..padjustmethod = NA, + ..ph_cox = NA, ..sc = NA, ..kmunicate = NA, ..ce = NA, @@ -303,8 +304,7 @@ survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( ..ci95 = NA, ..risktable = NA, ..censored = NA, - ..pplot = NA, - ..sas = NA) + ..pplot = NA) ) survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( @@ -313,11 +313,14 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( active = list( subtitle = function() private$.items[["subtitle"]], todo = function() private$.items[["todo"]], + mydataview = function() private$.items[["mydataview"]], medianSummary = function() private$.items[["medianSummary"]], medianTable = function() private$.items[["medianTable"]], coxSummary = function() private$.items[["coxSummary"]], coxTable = function() private$.items[["coxTable"]], tCoxtext2 = function() private$.items[["tCoxtext2"]], + cox_ph = function() private$.items[["cox_ph"]], + plot7 = function() private$.items[["plot7"]], survTableSummary = function() private$.items[["survTableSummary"]], survTable = function() private$.items[["survTable"]], pairwiseSummary = function() private$.items[["pairwiseSummary"]], @@ -325,9 +328,7 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( plot = function() private$.items[["plot"]], plot2 = function() private$.items[["plot2"]], plot3 = function() private$.items[["plot3"]], - plot6 = function() private$.items[["plot6"]], - calculatedtime = function() private$.items[["calculatedtime"]], - outcomeredifened = function() private$.items[["outcomeredifened"]]), + plot6 = function() private$.items[["plot6"]]), private = list(), public=list( initialize=function(options) { @@ -360,11 +361,14 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "dxdate", "tint", "multievent"))) + self$add(jmvcore::Preformatted$new( + options=options, + name="mydataview", + title="mydataview")) self$add(jmvcore::Preformatted$new( options=options, name="medianSummary", title="`Median Survival Summary and Table - ${explanatory}`", - visible="(!sas)", clearWith=list( "explanatory", "outcome", @@ -413,8 +417,7 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( `name`="x0_95ucl", `title`="Upper", `superTitle`="95% Confidence Interval", - `type`="number", - `visible`="(!sas)")), + `type`="number")), clearWith=list( "explanatory", "outcome", @@ -428,7 +431,6 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( options=options, name="coxSummary", title="`Cox Regression Summary and Table - ${explanatory}`", - visible="(!sas)", clearWith=list( "explanatory", "outcome", @@ -459,8 +461,7 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( list( `name`="HR_univariable", `title`="HR (Univariable)", - `type`="text", - `visible`="(!sas)")), + `type`="text")), clearWith=list( "explanatory", "outcome", @@ -484,13 +485,46 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "dxdate", "tint", "multievent", - "contexpl"), - visible="(!sas)")) + "contexpl"))) + self$add(jmvcore::Preformatted$new( + options=options, + name="cox_ph", + title="Proportional Hazards Assumption", + clearWith=list( + "explanatory", + "outcome", + "outcomeLevel", + "overalltime", + "fudate", + "dxdate", + "tint", + "multievent", + "contexpl"))) + self$add(jmvcore::Image$new( + options=options, + name="plot7", + title="`Proportional Hazards Assumption - ${explanatory}`", + width=600, + height=450, + renderFun=".plot7", + visible="(ph_cox)", + requiresData=TRUE, + clearWith=list( + "ph_cox", + "endplot", + "byplot", + "explanatory", + "outcome", + "outcomeLevel", + "overalltime", + "fudate", + "dxdate", + "tint", + "multievent"))) self$add(jmvcore::Preformatted$new( options=options, name="survTableSummary", title="`1, 3, 5-yr Survival Summary and Table - ${explanatory}`", - visible="(!sas)", clearWith=list( "explanatory", "outcome", @@ -539,7 +573,6 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( `superTitle`="95% Confidence Interval", `type`="number", `format`="pc")), - visible="(!sas)", clearWith=list( "explanatory", "outcome", @@ -563,7 +596,7 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "dxdate", "tint", "multievent"), - visible="(pw && !sas)")) + visible="(pw)")) self$add(jmvcore::Table$new( options=options, name="pairwiseTable", @@ -583,7 +616,7 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( `title`="p-value", `type`="number", `format`="zto,pvalue")), - visible="(pw && !sas)", + visible="(pw)", clearWith=list( "pw", "explanatory", @@ -609,7 +642,6 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "sc", "endplot", "byplot", - "sas", "ci95", "risktable", "censored", @@ -635,7 +667,6 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "ce", "endplot", "byplot", - "sas", "ci95", "risktable", "censored", @@ -660,7 +691,6 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "ch", "endplot", "byplot", - "sas", "ci95", "risktable", "censored", @@ -685,7 +715,6 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "kmunicate", "endplot", "byplot", - "sas", "explanatory", "outcome", "outcomeLevel", @@ -696,42 +725,7 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "multievent"), refs=list( "KMunicate", - "KMunicate2"))) - self$add(jmvcore::Output$new( - options=options, - name="calculatedtime", - title="Add Calculated Time to Data", - varTitle="`Calculated Time - from ${ dxdate } to { fudate }`", - varDescription="Calculated Time from given Dates", - clearWith=list( - "tint", - "dxdate", - "fudate", - "explanatory", - "outcome", - "outcomeLevel", - "overalltime", - "fudate", - "dxdate", - "tint", - "multievent"))) - self$add(jmvcore::Output$new( - options=options, - name="outcomeredifened", - title="Add Redefined Outcome to Data", - varTitle="`Redefined Outcome - from ${ outcome } for analysis { analysistype }`", - varDescription="Redefined Outcome from Outcome based on Analysis Type", - clearWith=list( - "outcome", - "analysistype", - "multievent", - "explanatory", - "outcomeLevel", - "overalltime", - "fudate", - "dxdate", - "tint", - "multievent")))})) + "KMunicate2")))})) survivalBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "survivalBase", @@ -781,6 +775,7 @@ survivalBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( #' @param landmark . #' @param pw . #' @param padjustmethod . +#' @param ph_cox . #' @param sc . #' @param kmunicate . #' @param ce . @@ -792,16 +787,18 @@ survivalBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( #' @param risktable . #' @param censored . #' @param pplot . -#' @param sas . #' @return A results object containing: #' \tabular{llllll}{ #' \code{results$subtitle} \tab \tab \tab \tab \tab a preformatted \cr #' \code{results$todo} \tab \tab \tab \tab \tab a html \cr +#' \code{results$mydataview} \tab \tab \tab \tab \tab a preformatted \cr #' \code{results$medianSummary} \tab \tab \tab \tab \tab a preformatted \cr #' \code{results$medianTable} \tab \tab \tab \tab \tab a table \cr #' \code{results$coxSummary} \tab \tab \tab \tab \tab a preformatted \cr #' \code{results$coxTable} \tab \tab \tab \tab \tab a table \cr #' \code{results$tCoxtext2} \tab \tab \tab \tab \tab a html \cr +#' \code{results$cox_ph} \tab \tab \tab \tab \tab a preformatted \cr +#' \code{results$plot7} \tab \tab \tab \tab \tab an image \cr #' \code{results$survTableSummary} \tab \tab \tab \tab \tab a preformatted \cr #' \code{results$survTable} \tab \tab \tab \tab \tab a table \cr #' \code{results$pairwiseSummary} \tab \tab \tab \tab \tab a preformatted \cr @@ -810,8 +807,6 @@ survivalBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( #' \code{results$plot2} \tab \tab \tab \tab \tab an image \cr #' \code{results$plot3} \tab \tab \tab \tab \tab an image \cr #' \code{results$plot6} \tab \tab \tab \tab \tab an image \cr -#' \code{results$calculatedtime} \tab \tab \tab \tab \tab an output \cr -#' \code{results$outcomeredifened} \tab \tab \tab \tab \tab an output \cr #' } #' #' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example: @@ -842,6 +837,7 @@ survival <- function( landmark = 3, pw = FALSE, padjustmethod = "holm", + ph_cox = FALSE, sc = FALSE, kmunicate = FALSE, ce = FALSE, @@ -852,8 +848,7 @@ survival <- function( ci95 = FALSE, risktable = FALSE, censored = FALSE, - pplot = TRUE, - sas = FALSE) { + pplot = TRUE) { if ( ! requireNamespace("jmvcore", quietly=TRUE)) stop("survival requires jmvcore to be installed (restart may be required)") @@ -894,6 +889,7 @@ survival <- function( landmark = landmark, pw = pw, padjustmethod = padjustmethod, + ph_cox = ph_cox, sc = sc, kmunicate = kmunicate, ce = ce, @@ -904,8 +900,7 @@ survival <- function( ci95 = ci95, risktable = risktable, censored = censored, - pplot = pplot, - sas = sas) + pplot = pplot) analysis <- survivalClass$new( options = options, diff --git a/jamovi/0000.yaml b/jamovi/0000.yaml index 50e1fea9..49516632 100644 --- a/jamovi/0000.yaml +++ b/jamovi/0000.yaml @@ -1,12 +1,12 @@ --- title: Common Analysis for Clinicopathological Research name: ClinicoPath -version: 0.0.2.08 +version: 0.0.2.12 jms: '1.0' authors: - Serdar Balci maintainer: Serdar Balci -date: '2023-12-03' +date: '2023-12-07' type: R description: >- ClinicoPath help researchers to generate natural language summaries of their diff --git a/jamovi/jjhistostats.a.yaml b/jamovi/jjhistostats.a.yaml index e6a50131..7cc4cc42 100644 --- a/jamovi/jjhistostats.a.yaml +++ b/jamovi/jjhistostats.a.yaml @@ -41,7 +41,7 @@ options: - name: excl title: Exclude Missing (NA) type: Bool - default: true + default: false diff --git a/jamovi/multisurvival.r.yaml b/jamovi/multisurvival.r.yaml index df09d67b..cb4a3553 100644 --- a/jamovi/multisurvival.r.yaml +++ b/jamovi/multisurvival.r.yaml @@ -33,13 +33,13 @@ items: - dxdate - tint - multievent - - adjexplanatory + # - adjexplanatory - # - name: mydataview - # title: mydataview - # type: Preformatted + - name: mydataview + title: mydataview + type: Preformatted # - name: text3 @@ -63,7 +63,7 @@ items: - dxdate - tint - multievent - - adjexplanatory + # - adjexplanatory - name: text2 title: '' @@ -79,7 +79,7 @@ items: - dxdate - tint - multievent - - adjexplanatory + # - adjexplanatory - name: plot @@ -103,7 +103,7 @@ items: - dxdate - tint - multievent - - adjexplanatory + # - adjexplanatory # - name: plot2 # title: Hazards Regression Plot @@ -144,16 +144,16 @@ items: - dxdate - tint - multievent - - adjexplanatory + # - adjexplanatory - - name: plot4 - title: coxzph Plot - type: Image - width: 800 - height: 600 - renderFun: .plot4 + # - name: plot4 + # title: coxzph Plot + # type: Image + # width: 800 + # height: 600 + # renderFun: .plot4 diff --git a/jamovi/survival.a.yaml b/jamovi/survival.a.yaml index 008097b1..0d99fbd4 100644 --- a/jamovi/survival.a.yaml +++ b/jamovi/survival.a.yaml @@ -209,6 +209,11 @@ options: + - name: ph_cox + title: Proportional Hazards Assumption + type: Bool + default: false + - name: sc title: Survival Plot type: Bool @@ -270,10 +275,10 @@ options: default: true - - name: sas - title: Single Arm Survival - type: Bool - default: false + # - name: sas + # title: Single Arm Survival + # type: Bool + # default: false ... diff --git a/jamovi/survival.r.yaml b/jamovi/survival.r.yaml index e865b614..ec37977c 100644 --- a/jamovi/survival.r.yaml +++ b/jamovi/survival.r.yaml @@ -26,9 +26,9 @@ items: - multievent - # - name: mydataview - # title: mydataview - # type: Preformatted + - name: mydataview + title: mydataview + type: Preformatted # - name: medianSummary2 @@ -41,7 +41,7 @@ items: # title: Median Survival Summary and Table title: '`Median Survival Summary and Table - ${explanatory}`' type: Preformatted - visible: (!sas) + # visible: (!sas) clearWith: - explanatory - outcome @@ -93,7 +93,7 @@ items: title: "Upper" superTitle: '95% Confidence Interval' type: number - visible: (!sas) + # visible: (!sas) clearWith: - explanatory - outcome @@ -109,7 +109,7 @@ items: # title: Cox Regression Summary and Table title: '`Cox Regression Summary and Table - ${explanatory}`' type: Preformatted - visible: (!sas) + # visible: (!sas) clearWith: - explanatory - outcome @@ -140,7 +140,7 @@ items: - name: 'HR_univariable' title: "HR (Univariable)" type: text - visible: (!sas) + # visible: (!sas) # - name: 'HR_multivariable' # title: "HR (Multivariable)" # type: text @@ -170,14 +170,53 @@ items: - tint - multievent - contexpl - visible: (!sas) + # visible: (!sas) + + + + - name: cox_ph + title: 'Proportional Hazards Assumption' + type: Preformatted + clearWith: + - explanatory + - outcome + - outcomeLevel + - overalltime + - fudate + - dxdate + - tint + - multievent + - contexpl + + + + - name: plot7 + title: '`Proportional Hazards Assumption - ${explanatory}`' + type: Image + width: 600 + height: 450 + renderFun: .plot7 + visible: (ph_cox) + requiresData: true + clearWith: + - ph_cox + - endplot + - byplot + - explanatory + - outcome + - outcomeLevel + - overalltime + - fudate + - dxdate + - tint + - multievent - name: survTableSummary # title: '1, 3, 5-yr Survival Summary and Table' title: '`1, 3, 5-yr Survival Summary and Table - ${explanatory}`' type: Preformatted - visible: (!sas) + # visible: (!sas) clearWith: - explanatory - outcome @@ -223,7 +262,7 @@ items: superTitle: '95% Confidence Interval' type: number format: pc - visible: (!sas) + # visible: (!sas) clearWith: - explanatory - outcome @@ -251,7 +290,7 @@ items: - dxdate - tint - multievent - visible: (pw && !sas) + visible: (pw) # && !sas) @@ -270,7 +309,7 @@ items: title: p-value type: number format: zto,pvalue - visible: (pw && !sas) + visible: (pw) # && !sas) clearWith: - pw - explanatory @@ -299,7 +338,6 @@ items: - sc - endplot - byplot - - sas - ci95 - risktable - censored @@ -312,6 +350,7 @@ items: - tint - multievent - pplot + # - sas @@ -328,7 +367,6 @@ items: - ce - endplot - byplot - - sas - ci95 - risktable - censored @@ -340,6 +378,7 @@ items: - dxdate - tint - multievent + # - sas @@ -356,7 +395,6 @@ items: - ch - endplot - byplot - - sas - ci95 - risktable - censored @@ -368,6 +406,7 @@ items: - dxdate - tint - multievent + # - sas @@ -383,7 +422,6 @@ items: - kmunicate - endplot - byplot - - sas - explanatory - outcome - outcomeLevel @@ -392,47 +430,55 @@ items: - dxdate - tint - multievent + # - sas refs: - KMunicate - KMunicate2 - - name: calculatedtime - title: Add Calculated Time to Data - type: Output - varTitle: '`Calculated Time - from ${ dxdate } to { fudate }`' - varDescription: Calculated Time from given Dates - clearWith: - - tint - - dxdate - - fudate - - explanatory - - outcome - - outcomeLevel - - overalltime - - fudate - - dxdate - - tint - - multievent - - name: outcomeredifened - title: Add Redefined Outcome to Data - type: Output - varTitle: '`Redefined Outcome - from ${ outcome } for analysis { analysistype }`' - varDescription: Redefined Outcome from Outcome based on Analysis Type - clearWith: - - outcome - - analysistype - - multievent - - explanatory - - outcomeLevel - - overalltime - - fudate - - dxdate - - tint - - multievent + + + + + # - name: calculatedtime + # title: Add Calculated Time to Data + # type: Output + # varTitle: '`Calculated Time - from ${ dxdate } to { fudate }`' + # varDescription: Calculated Time from given Dates + # clearWith: + # - tint + # - dxdate + # - fudate + # - explanatory + # - outcome + # - outcomeLevel + # - overalltime + # - fudate + # - dxdate + # - tint + # - multievent + + + + # - name: outcomeredifened + # title: Add Redefined Outcome to Data + # type: Output + # varTitle: '`Redefined Outcome - from ${ outcome } for analysis { analysistype }`' + # varDescription: Redefined Outcome from Outcome based on Analysis Type + # clearWith: + # - outcome + # - analysistype + # - multievent + # - explanatory + # - outcomeLevel + # - overalltime + # - fudate + # - dxdate + # - tint + # - multievent refs: - finalfit diff --git a/jamovi/survival.u.yaml b/jamovi/survival.u.yaml index 5b013a64..a1a4da7d 100644 --- a/jamovi/survival.u.yaml +++ b/jamovi/survival.u.yaml @@ -133,16 +133,6 @@ children: - type: ComboBox name: analysistype enable: (outcome && multievent) - - type: CollapseBox - label: Single Arm Survival - collapsed: true - children: - - type: Label - label: Single Arm Survival - fitToGrid: true - children: - - type: CheckBox - name: sas - type: CollapseBox label: Pairwise Comparisons collapsed: true @@ -169,6 +159,8 @@ children: - type: LayoutBox fitToGrid: true children: + - type: CheckBox + name: ph_cox - type: CheckBox name: sc - type: CheckBox @@ -197,6 +189,7 @@ children: name: censored - type: CheckBox name: pplot + - type: CollapseBox label: Survival Tables collapsed: true @@ -208,23 +201,3 @@ children: name: cutp format: string width: large - # - type: CollapseBox - # label: Save Converted Variables to Data - # collapsed: true - # children: - # - type: Label - # label: Add Calculated Time to Your Data - # fitToGrid: true - # children: - # - type: Output - # name: calculatedtime - # enable: (tint) - # fitToGrid: true - # - type: Label - # label: Add Redefined Outcome to Data - # fitToGrid: true - # children: - # - type: Output - # name: outcomeredifened - # enable: (multievent) - # fitToGrid: true diff --git a/man/jjhistostats.Rd b/man/jjhistostats.Rd index b4aa7330..17a8d48e 100644 --- a/man/jjhistostats.Rd +++ b/man/jjhistostats.Rd @@ -8,7 +8,7 @@ jjhistostats( data, dep, grvar, - excl = TRUE, + excl = FALSE, typestatistics = "parametric", centralityparameter = "mean", centralityline = TRUE, diff --git a/man/survival.Rd b/man/survival.Rd index 65483c2e..e0e7e41b 100644 --- a/man/survival.Rd +++ b/man/survival.Rd @@ -25,6 +25,7 @@ survival( landmark = 3, pw = FALSE, padjustmethod = "holm", + ph_cox = FALSE, sc = FALSE, kmunicate = FALSE, ce = FALSE, @@ -35,8 +36,7 @@ survival( ci95 = FALSE, risktable = FALSE, censored = FALSE, - pplot = TRUE, - sas = FALSE + pplot = TRUE ) } \arguments{ @@ -80,6 +80,8 @@ survival( \item{padjustmethod}{.} +\item{ph_cox}{.} + \item{sc}{.} \item{kmunicate}{.} @@ -101,19 +103,20 @@ survival( \item{censored}{.} \item{pplot}{.} - -\item{sas}{.} } \value{ A results object containing: \tabular{llllll}{ \code{results$subtitle} \tab \tab \tab \tab \tab a preformatted \cr \code{results$todo} \tab \tab \tab \tab \tab a html \cr +\code{results$mydataview} \tab \tab \tab \tab \tab a preformatted \cr \code{results$medianSummary} \tab \tab \tab \tab \tab a preformatted \cr \code{results$medianTable} \tab \tab \tab \tab \tab a table \cr \code{results$coxSummary} \tab \tab \tab \tab \tab a preformatted \cr \code{results$coxTable} \tab \tab \tab \tab \tab a table \cr \code{results$tCoxtext2} \tab \tab \tab \tab \tab a html \cr +\code{results$cox_ph} \tab \tab \tab \tab \tab a preformatted \cr +\code{results$plot7} \tab \tab \tab \tab \tab an image \cr \code{results$survTableSummary} \tab \tab \tab \tab \tab a preformatted \cr \code{results$survTable} \tab \tab \tab \tab \tab a table \cr \code{results$pairwiseSummary} \tab \tab \tab \tab \tab a preformatted \cr @@ -122,8 +125,6 @@ A results object containing: \code{results$plot2} \tab \tab \tab \tab \tab an image \cr \code{results$plot3} \tab \tab \tab \tab \tab an image \cr \code{results$plot6} \tab \tab \tab \tab \tab an image \cr -\code{results$calculatedtime} \tab \tab \tab \tab \tab an output \cr -\code{results$outcomeredifened} \tab \tab \tab \tab \tab an output \cr } Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example: