Merge pull request #355 from poissonconsulting/dev

- set default min_pboot to 0.95 for all functions.
bcgov · Mar 21, 2024 · dd06e91 · dd06e91
2 parents 1ca1321 + 78636e3
commit dd06e91
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Showing 12 changed files with 18 additions and 18 deletions.
diff --git a/R/bcanz.R b/R/bcanz.R
@@ -68,7 +68,7 @@ ssd_fit_bcanz <- function(data, left = "Conc", dists = ssd_dists_bcanz()) {
 #' @examples
 #' fits <- ssd_fit_bcanz(ssddata::ccme_boron)
 #' ssd_hc_bcanz(fits, nboot = 100)
-ssd_hc_bcanz <- function(x, nboot = 10000, delta = 10, min_pboot = 0.9) {
+ssd_hc_bcanz <- function(x, nboot = 10000, delta = 10, min_pboot = 0.95) {
   ssd_hc(x,
     proportion = c(0.01, 0.05, 0.1, 0.2),
     ci = TRUE,

diff --git a/R/hc-burrlioz.R b/R/hc-burrlioz.R
@@ -26,7 +26,7 @@
 #'
 #' @export
 ssd_hc_burrlioz <- function(x, percent, proportion = 0.05, ci = FALSE, level = 0.95, nboot = 1000,
-                            min_pboot = 0.99, parametric = FALSE) {
+                            min_pboot = 0.95, parametric = FALSE) {
   lifecycle::deprecate_warn("0.3.5", "ssd_hc_burrlioz()", "ssd_hc()")
   chk_s3_class(x, "fitburrlioz")
 

diff --git a/R/hc.R b/R/hc.R
@@ -121,7 +121,7 @@ ssd_hc.fitdists <- function(
     ci = FALSE, 
     level = 0.95, 
     nboot = 1000,
-    min_pboot = 0.99,
+    min_pboot = 0.95,
     multi_est = TRUE,
     multi_ci = TRUE,
     weighted = TRUE,
@@ -182,7 +182,7 @@ ssd_hc.fitburrlioz <- function(
     ci = FALSE, 
     level = 0.95, 
     nboot = 1000,
-    min_pboot = 0.99, 
+    min_pboot = 0.95, 
     parametric = FALSE, 
     samples = FALSE, 
     save_to = NULL, 

diff --git a/R/hp.R b/R/hp.R
@@ -40,7 +40,7 @@ ssd_hp.fitdists <- function(
     ci = FALSE, 
     level = 0.95, 
     nboot = 1000,
-    min_pboot = 0.99,
+    min_pboot = 0.95,
     multi_est = TRUE,
     multi_ci = TRUE,
     weighted = TRUE,
@@ -91,7 +91,7 @@ ssd_hp.fitburrlioz <- function(
     ci = FALSE, 
     level = 0.95, 
     nboot = 1000,
-    min_pboot = 0.99, 
+    min_pboot = 0.95, 
     parametric = FALSE, 
     samples = FALSE,
     save_to = NULL, 

diff --git a/R/predict.R b/R/predict.R
@@ -36,7 +36,7 @@ predict.fitdists <- function(
     ci = FALSE, 
     level = 0.95, 
     nboot = 1000,
-    min_pboot = 0.99,
+    min_pboot = 0.95,
     multi_est = TRUE,
     multi_ci = TRUE,
     weighted = TRUE,
@@ -96,7 +96,7 @@ predict.fitburrlioz <- function(
     ci = FALSE,
     level = 0.95, 
     nboot = 1000,
-    min_pboot = 0.99,
+    min_pboot = 0.95,
     parametric = TRUE,
     ...) {
   chk_unused(...)

diff --git a/man/predict.fitburrlioz.Rd b/man/predict.fitburrlioz.Rd
diff --git a/man/predict.fitdists.Rd b/man/predict.fitdists.Rd
diff --git a/man/ssd_hc.Rd b/man/ssd_hc.Rd
diff --git a/man/ssd_hc_bcanz.Rd b/man/ssd_hc_bcanz.Rd
diff --git a/man/ssd_hc_burrlioz.Rd b/man/ssd_hc_burrlioz.Rd
diff --git a/man/ssd_hp.Rd b/man/ssd_hp.Rd
diff --git a/tests/testthat/test-zzz-unstable.R b/tests/testthat/test-zzz-unstable.R
@@ -199,7 +199,7 @@ test_that("ssd_hc cis with error", {
   data <- data.frame(Conc = conc)
   fit <- ssd_fit_dists(data, dists = "lnorm_lnorm", min_pmix = 0.1)
   expect_identical(attr(fit, "min_pmix"), 0.1)
-  expect_warning(hc_err <- ssd_hc(fit, ci = TRUE, nboot = 100))
+  expect_warning(hc_err <- ssd_hc(fit, ci = TRUE, min_pboot = 0.99, nboot = 100))
   expect_s3_class(hc_err, "tbl")
   expect_snapshot_data(hc_err, "hc_err_na")
   hc_err <- ssd_hc(fit, ci = TRUE, nboot = 100, min_pboot = 0.92, multi_ci = FALSE)
@@ -231,7 +231,7 @@ test_that("ssd_hp cis with error", {
   data <- data.frame(Conc = conc)
   fit <- ssd_fit_dists(data, dists = "lnorm_lnorm", min_pmix = 0.1)
   expect_identical(attr(fit, "min_pmix"), 0.1)
-  expect_warning(hp_err <- ssd_hp(fit, conc = 1, ci = TRUE, nboot = 100))
+  expect_warning(hp_err <- ssd_hp(fit, conc = 1, ci = TRUE, nboot = 100, min_pboot = 0.99))
   expect_s3_class(hp_err, "tbl")
   expect_snapshot_data(hp_err, "hp_err_na")
   hp_err <- ssd_hp(fit, conc = 1, ci = TRUE, nboot = 100, min_pboot = 0.92, multi_ci = FALSE, weighted = FALSE)