- Only implement non-parametric bootstrap for censored data.

poissonconsulting · Sep 23, 2024 · d187237 · d187237
1 parent 763fa04
commit d187237
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Showing 5 changed files with 12 additions and 12 deletions.
diff --git a/R/hcp.R b/R/hcp.R
@@ -316,9 +316,9 @@ hcp_weighted <- function(hcp, level, samples, min_pboot) {
   weighted <- .weighted_fitdists(x)
   unequal <- .unequal_fitdists(x)
   estimates <- .list_estimates(x, all_estimates = FALSE)
-
-  if (parametric && ci && identical(censoring, c(NA_real_, NA_real_))) {
-    wrn("Parametric CIs cannot be calculated for inconsistently censored data.")
+  
+  if (parametric && ci && !identical(censoring, c(0, Inf))) {
+    wrn("Parametric CIs cannot be calculated for censored data.")
     ci <- FALSE
   }
 

diff --git a/tests/testthat/_snaps/hc/fullyleft.csv b/tests/testthat/_snaps/hc/fullyleft.csv
@@ -1,2 +1,2 @@
 dist,proportion,est,se,lcl,ucl,wt,method,nboot,pboot,samples
-average,0.05,0.0276014,0,0.0457722,0.0457722,1,parametric,10,1,numeric(0)
+average,0.05,0.0276014,NA,NA,NA,1,parametric,0,NA,numeric(0)
diff --git a/tests/testthat/_snaps/hc/partialeftfull.csv b/tests/testthat/_snaps/hc/partialeftfull.csv
@@ -1,2 +1,2 @@
 dist,proportion,est,se,lcl,ucl,wt,method,nboot,pboot,samples
-lnorm,0.05,1.83148,0.798458,0.945173,3.2476,1,parametric,10,1,numeric(0)
+lnorm,0.05,1.83148,NA,NA,NA,1,parametric,0,NA,numeric(0)
diff --git a/tests/testthat/test-hc.R b/tests/testthat/test-hc.R
@@ -265,7 +265,7 @@ test_that("ssd_hc doesn't calculate cis with inconsistent censoring", {
   set.seed(10)
   expect_warning(
     hc <- ssd_hc(fits, ci = TRUE, nboot = 10),
-    "^Parametric CIs cannot be calculated for inconsistently censored data[.]$"
+    "^Parametric CIs cannot be calculated for censored data[.]$"
   )
   expect_identical(hc$se, NA_real_)
 })
@@ -276,7 +276,8 @@ test_that("ssd_hc works with fully left censored data", {
   data$Conc <- 0
   fits <- ssd_fit_dists(data, right = "Conc2", dists = c("lnorm", "llogis"))
   set.seed(10)
-  hc <- ssd_hc(fits, ci = TRUE, nboot = 10, ci_method = "weighted_arithmetic")
+  expect_warning(hc <- ssd_hc(fits, ci = TRUE, nboot = 10, ci_method = "weighted_arithmetic"),
+                 "^Parametric CIs cannot be calculated for censored data[.]$")
   expect_snapshot_data(hc, "fullyleft")
 })
 
@@ -288,7 +289,7 @@ test_that("ssd_hc warns with partially left censored data", {
   set.seed(100)
   fits <- ssd_fit_dists(data, dists = "lnorm", right = "right")
   expect_warning(hc <- ssd_hc(fits, ci = TRUE, nboot = 10, average = FALSE),
-                 "Parametric CIs cannot be calculated for inconsistently censored data\\.")
+                 "Parametric CIs cannot be calculated for censored data\\.")
   expect_snapshot_data(hc, "partialeft")
 })
 
@@ -302,7 +303,6 @@ test_that("ssd_hc works with fully left censored data", {
   fits <- ssd_fit_dists(data, dists = "lnorm", right = "right")
   hc <- ssd_hc(fits, ci = TRUE, nboot = 10, average = FALSE)
   expect_snapshot_data(hc, "partialeftfull")
-  expect_gt(hc$ucl, hc$est)
 })
 
 test_that("ssd_hc works with partially left censored data non-parametric", {
@@ -325,7 +325,7 @@ test_that("ssd_hc not work partially censored even if all same left", {
   set.seed(10)
   expect_warning(
     hc <- ssd_hc(fits, ci = TRUE, nboot = 10),
-    "^Parametric CIs cannot be calculated for inconsistently censored data[.]$"
+    "^Parametric CIs cannot be calculated for censored data[.]$"
   )
 })
 
@@ -338,7 +338,7 @@ test_that("ssd_hc doesn't works with inconsisently censored data", {
   set.seed(10)
   expect_warning(
     hc <- ssd_hc(fits, ci = TRUE, nboot = 10),
-    "^Parametric CIs cannot be calculated for inconsistently censored data[.]$"
+    "^Parametric CIs cannot be calculated for censored data[.]$"
   )
 })
 

diff --git a/tests/testthat/test-hp.R b/tests/testthat/test-hp.R
@@ -158,7 +158,7 @@ test_that("ssd_hp doesn't calculate cis with inconsistent censoring", {
   set.seed(10)
   expect_warning(
     hp <- ssd_hp(fits, 1, ci = TRUE, nboot = 10),
-    "^Parametric CIs cannot be calculated for inconsistently censored data[.]$"
+    "^Parametric CIs cannot be calculated for censored data[.]$"
   )
   expect_identical(hp$se, NA_real_)
 })