issue #1272

vincentarelbundock · Dec 11, 2024 · c828f45 · c828f45
1 parent 7129130
commit c828f45
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Showing 4 changed files with 9 additions and 14 deletions.
diff --git a/R/ci.R b/R/ci.R
@@ -5,7 +5,6 @@ get_ci <- function(
     draws = NULL,
     vcov = TRUE,
     null_hypothesis = 0,
-    p_adjust = NULL,
     model = NULL,
     ...) {
 
@@ -61,8 +60,7 @@ get_ci <- function(
                    p_overwrite
 
     ci_overwrite <- !"conf.low" %in% colnames(x) &&
-                    "std.error" %in% colnames(x) &&
-                    is.null(p_adjust)
+                    "std.error" %in% colnames(x)
 
     if (z_overwrite) {
         x[["statistic"]] <- (x[["estimate"]] - null_hypothesis) / x[["std.error"]]
@@ -83,10 +81,6 @@ get_ci <- function(
         x[["conf.low"]] <- x[["estimate"]] - critical * x[["std.error"]]
         x[["conf.high"]] <- x[["estimate"]] + critical * x[["std.error"]]
     }
-
-    if (!is.null(p_adjust) && "p.value" %in% colnames(x)) {
-        x$p.value <- stats::p.adjust(x$p.value, method = p_adjust)
-    }
 
     # s-value
     if ("p.value" %in% colnames(x)) {

diff --git a/R/sanity.R b/R/sanity.R
@@ -1,10 +1,3 @@
-sanity_equivalence_p_adjust <- function(equivalence, p_adjust) {
-    if (!is.null(equivalence) && !is.null(p_adjust)) {
-        insight::format_error("The `equivalence` and `p_adjust` arguments cannot be used together.")
-    }
-    checkmate::assert_choice(p_adjust, choices = stats::p.adjust.methods, null.ok = TRUE)
-}
-
 
 sanity_df <- function(df, x) {
     checkmate::assert(

diff --git a/R/sanity_dots.R b/R/sanity_dots.R
@@ -43,6 +43,9 @@ sanity_dots <- function(model, calling_function = NULL, ...) {
     # flexsurv
     valid[["flexsurvreg"]] <- c("times", "p", "start")
 
+    # survival
+    valid[["survreg"]] <- c("p")
+
     # WeightIt models
     valid[["ordinal_weightit"]] <- valid[["multinom_weightit"]] <- "values"
 

diff --git a/inst/tinytest/test-pkg-survival.R b/inst/tinytest/test-pkg-survival.R
@@ -133,6 +133,11 @@ expect_equivalent(e0$estimate, e3$estimate)
 
 
 
+# Issue #1272
+fit <- survreg(Surv(time, status) ~ ph.ecog + age + sex, lung,dist="weibull")
+p1 <- avg_predictions(fit, variables = "sex", type = "quantile", p = 0.5)
+p2 <- avg_predictions(fit, variables = "sex", type = "quantile", p = 0.1)
+expect_true(all(p1$estimate > p2$estimate))