Commit ⋅ jinseob2kim/jsmodule

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@@ -44,6 +44,7 @@

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#' @param default.unires Set default independent variables using univariate analysis.
#' @param limit.unires Change to default.unires = F if number of independent variables > limit.unires, Default: 20
#' @param id.cluster reactive cluster variable if marginal cox model, Default: NULL
#' @param ties.coxph 'coxph' ties option, one of 'efron', 'breslow', 'exact', default: 'erfon'
#' @return Shiny modulde server for Cox's model.
#' @details Shiny modulde server for Cox's model.
#' @examples

@@ -80,7 +81,7 @@

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#' @importFrom purrr map_lgl
#' @importFrom survival cluster coxph Surv

coxModule <- function(input, output, session, data, data_label, data_varStruct = NULL, nfactor.limit = 10, design.survey = NULL, default.unires = T, limit.unires = 20, id.cluster = NULL) {
coxModule <- function(input, output, session, data, data_label, data_varStruct = NULL, nfactor.limit = 10, design.survey = NULL, default.unires = T, limit.unires = 20, id.cluster = NULL, ties.coxph = "efron") {

  ## To remove NOTE.
  data.cox.step <- level <- val_label <- variable <- NULL

@@ -205,10 +206,10 @@

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                          function(v){
                            if (is.null(id.cluster)){
                              forms <- as.formula(paste("survival::Surv(", input$time_cox, ",", input$event_cox, ") ~ ", v, sep = ""))
                              coef <- tryCatch(summary(survival::coxph(forms, data = data.cox))$coefficients, error = function(e){return(NULL)})
                              coef <- tryCatch(summary(survival::coxph(forms, data = data.cox, ties = ties.coxph))$coefficients, error = function(e){return(NULL)})
                            } else{
                              forms <- as.formula(paste("survival::Surv(", input$time_cox, ",", input$event_cox, ") ~ ", v, " + cluster(", id.cluster(), ")", sep = ""))
                              coef <- tryCatch(summary(survival::coxph(forms, data = data.cox, robust = T))$coefficients, error = function(e){return(NULL)})
                              coef <- tryCatch(summary(survival::coxph(forms, data = data.cox, robust = T, ties = ties.coxph))$coefficients, error = function(e){return(NULL)})
                            }
                            sigOK <- ifelse(is.null(coef), F, !all(coef[, "Pr(>|z|)"] > 0.05))
                            return(sigOK)

@@ -382,9 +383,9 @@

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    if (is.null(design.survey)){
      if (is.null(id.cluster)){
        cc <- substitute(survival::coxph(.form, data= data.cox, model = T), list(.form= form.cox()))
        cc <- substitute(survival::coxph(.form, data= data.cox, model = T, ties = .ties), list(.form= form.cox(), .ties = ties.coxph))
      } else{
        cc <- substitute(survival::coxph(.form, data= data.cox, model = T, robust = T), list(.form= form.cox()))
        cc <- substitute(survival::coxph(.form, data= data.cox, model = T, robust = T, ties = .ties), list(.form= form.cox(), .ties = ties.coxph))
      }
      res.cox <- eval(cc)
      if (input$step_check == T){

@@ -399,9 +400,9 @@

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        data.cox.step <<- data.cox[complete.cases(data.cox[, .SD, .SDcols = c(input$time_cox, input$event_cox, input$indep_cox)])]

        if (is.null(id.cluster)){
          cc.step <- substitute(survival::coxph(.form, data= data.cox.step, model = T), list(.form= form.cox()))
          cc.step <- substitute(survival::coxph(.form, data= data.cox.step, model = T, ties = .ties), list(.form= form.cox(), .ties = ties.coxph))
        } else{
          cc.step <- substitute(survival::coxph(.form, data= data.cox.step, model = T, robust = T), list(.form= form.cox()))
          cc.step <- substitute(survival::coxph(.form, data= data.cox.step, model = T, robust = T, ties = .ties), list(.form= form.cox(), .ties = ties.coxph))
        }

        res.cox <- stats::step(eval(cc.step), direction = input$step_direction, scope = list(upper = scope[[1]], lower = scope[[2]]))

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R	6,483	411	0	6,072	6.34%
Project Totals (19 files)	6,483	411	0	6,072	6.34%

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205	206		function(v){
206	207		if (is.null(id.cluster)){
207	208		forms <- as.formula(paste("survival::Surv(", input$time_cox, ",", input$event_cox, ") ~ ", v, sep = ""))
208		-	coef <- tryCatch(summary(survival::coxph(forms, data = data.cox))$coefficients, error = function(e){return(NULL)})
	209	+	coef <- tryCatch(summary(survival::coxph(forms, data = data.cox, ties = ties.coxph))$coefficients, error = function(e){return(NULL)})
209	210		} else{
210	211		forms <- as.formula(paste("survival::Surv(", input$time_cox, ",", input$event_cox, ") ~ ", v, " + cluster(", id.cluster(), ")", sep = ""))
211		-	coef <- tryCatch(summary(survival::coxph(forms, data = data.cox, robust = T))$coefficients, error = function(e){return(NULL)})
	212	+	coef <- tryCatch(summary(survival::coxph(forms, data = data.cox, robust = T, ties = ties.coxph))$coefficients, error = function(e){return(NULL)})
212	213		}
213	214		sigOK <- ifelse(is.null(coef), F, !all(coef[, "Pr(>\|z\|)"] > 0.05))
214	215		return(sigOK)

382	383
383	384		if (is.null(design.survey)){
384	385		if (is.null(id.cluster)){
385		-	cc <- substitute(survival::coxph(.form, data= data.cox, model = T), list(.form= form.cox()))
	386	+	cc <- substitute(survival::coxph(.form, data= data.cox, model = T, ties = .ties), list(.form= form.cox(), .ties = ties.coxph))
386	387		} else{
387		-	cc <- substitute(survival::coxph(.form, data= data.cox, model = T, robust = T), list(.form= form.cox()))
	388	+	cc <- substitute(survival::coxph(.form, data= data.cox, model = T, robust = T, ties = .ties), list(.form= form.cox(), .ties = ties.coxph))
388	389		}
389	390		res.cox <- eval(cc)
390	391		if (input$step_check == T){

399	400		data.cox.step <<- data.cox[complete.cases(data.cox[, .SD, .SDcols = c(input$time_cox, input$event_cox, input$indep_cox)])]
400	401
401	402		if (is.null(id.cluster)){
402		-	cc.step <- substitute(survival::coxph(.form, data= data.cox.step, model = T), list(.form= form.cox()))
	403	+	cc.step <- substitute(survival::coxph(.form, data= data.cox.step, model = T, ties = .ties), list(.form= form.cox(), .ties = ties.coxph))
403	404		} else{
404		-	cc.step <- substitute(survival::coxph(.form, data= data.cox.step, model = T, robust = T), list(.form= form.cox()))
	405	+	cc.step <- substitute(survival::coxph(.form, data= data.cox.step, model = T, robust = T, ties = .ties), list(.form= form.cox(), .ties = ties.coxph))
405	406		}
406	407
407	408		res.cox <- stats::step(eval(cc.step), direction = input$step_direction, scope = list(upper = scope[[1]], lower = scope[[2]]))

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44	44		#' @param default.unires Set default independent variables using univariate analysis.
45	45		#' @param limit.unires Change to default.unires = F if number of independent variables > limit.unires, Default: 20
46	46		#' @param id.cluster reactive cluster variable if marginal cox model, Default: NULL
	47	+	#' @param ties.coxph 'coxph' ties option, one of 'efron', 'breslow', 'exact', default: 'erfon'
47	48		#' @return Shiny modulde server for Cox's model.
48	49		#' @details Shiny modulde server for Cox's model.
49	50		#' @examples

80	81		#' @importFrom purrr map_lgl
81	82		#' @importFrom survival cluster coxph Surv
82	83
83		-	coxModule <- function(input, output, session, data, data_label, data_varStruct = NULL, nfactor.limit = 10, design.survey = NULL, default.unires = T, limit.unires = 20, id.cluster = NULL) {
	84	+	coxModule <- function(input, output, session, data, data_label, data_varStruct = NULL, nfactor.limit = 10, design.survey = NULL, default.unires = T, limit.unires = 20, id.cluster = NULL, ties.coxph = "efron") {
84	85
85	86		## To remove NOTE.
86	87		data.cox.step <- level <- val_label <- variable <- NULL

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