jinseob2kim / jstable

Compare c5bcd88 ... +0 ... 9418241

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 5 files from the diff.
Other files ignored by Codecov
NEWS.md has changed.
NAMESPACE has changed.
DESCRIPTION has changed.
CRAN-RELEASE was deleted.

@@ -40,7 +40,6 @@
Loading
40 40
#' @importFrom survival coxph
41 41
#' @importFrom survey svycoxph
42 42
#' @importFrom stats confint coefficients
43 -
#' @importFrom car Anova
44 43
#' @importFrom utils tail
45 44
46 45
TableSubgroupCox <- function(formula, var_subgroup = NULL, var_cov = NULL, data, time_eventrate = 3 * 365, decimal.hr = 2, decimal.percent = 1, decimal.pvalue = 3){
@@ -127,8 +126,8 @@
Loading
127 126
        model.int <- survival::coxph(as.formula(gsub(xlabel, paste(xlabel, "*", var_subgroup, sep=""), deparse(formula))), data = data.int, weights = get(names(data$allprob)), robust =T)
128 127
        model.int$call$formula <- as.formula(gsub(xlabel, paste(xlabel, "*", var_subgroup, sep=""), deparse(formula)))
129 128
        model.int$call$data <- as.name("data.int")
130 -
        pv_anova <- car::Anova(model.int, test.statistics = "Wald")
131 -
        pv_int <- pv_anova[nrow(pv_anova), 3]
129 +
        pv_anova <- anova(model.int)
130 +
        pv_int <- pv_anova[nrow(pv_anova), 4]
132 131
      }
133 132
      res.kap <- purrr::map(label_val, ~survey::svykm(formula.km, design = subset(data, get(var_subgroup) == . )))
134 133
      mkz <- function(reskap){
@@ -151,8 +150,8 @@
Loading
151 150
      if (length(label_val) > 2){
152 151
        model.int$call$formula <- as.formula(gsub(xlabel, paste(xlabel, "*", var_subgroup, sep=""), deparse(formula)))
153 152
        model.int$call$data <- as.name("data")
154 -
        pv_anova <- car::Anova(model.int, test.statistics = "Wald")
155 -
        pv_int <- round(pv_anova[nrow(pv_anova), 3], decimal.pvalue)
153 +
        pv_anova <- anova(model.int)
154 +
        pv_int <- round(pv_anova[nrow(pv_anova), 4], decimal.pvalue)
156 155
      }
157 156
      res.kap.times <- data %>% filter(!is.na(get(var_subgroup))) %>% group_split(get(var_subgroup)) %>% purrr::map(~survival::survfit(formula.km, data = .)) %>% purrr::map(~summary(., times = time_eventrate, extend = T))
158 157
      prop <- res.kap.times %>% purrr::map(~round(100 * (1 - .[["surv"]]), decimal.percent)) %>% dplyr::bind_cols() %>% t

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 84.65%
Project Totals (13 files) 84.65%
Loading