jinseob2kim / jsmodule

Compare 960cb8d ... +0 ... f621609

No flags found

Use flags to group coverage reports by test type, project and/or folders.
Then setup custom commit statuses and notifications for each flag.

e.g., #unittest #integration

#production #enterprise

#frontend #backend

Learn more about Codecov Flags here.

Showing 1 of 4 files from the diff.
Other files ignored by Codecov
NEWS.md has changed.
DESCRIPTION has changed.
man/coxModule.Rd has changed.

@@ -44,6 +44,7 @@
Loading
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
@@ -80,7 +81,7 @@
Loading
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
@@ -205,10 +206,10 @@
Loading
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)
@@ -382,9 +383,9 @@
Loading
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$step_check == T){
@@ -399,9 +400,9 @@
Loading
399 400
        data.cox.step <<- data.cox[complete.cases(data.cox[, .SD, .SDcols = c(input$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]]))

Everything is accounted for!

No changes detected that need to be reviewed.
What changes does Codecov check for?
Lines, not adjusted in diff, that have changed coverage data.
Files that introduced coverage data that had none before.
Files that have missing coverage data that once were tracked.
Files Coverage
R 6.34%
Project Totals (19 files) 6.34%
Loading