rename multi to multi_ci

bcgov · Jan 8, 2024 · bbe1b1a · bbe1b1a
1 parent f74ca10
commit bbe1b1a
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Showing 23 changed files with 113 additions and 110 deletions.
diff --git a/R/hc.R b/R/hc.R
@@ -81,7 +81,7 @@ ssd_hc.fitdists <- function(
     delta = 7, 
     min_pboot = 0.99,
     parametric = TRUE, 
-    multi = TRUE,
+    multi_ci = TRUE,
     weighted = TRUE,
     control = NULL,
     samples = FALSE,
@@ -106,7 +106,7 @@ ssd_hc.fitdists <- function(
     delta = delta,
     min_pboot = min_pboot,
     parametric = parametric,
-    multi = multi,
+    multi = multi_ci,
     fix_weights = weighted,
     control = control,
     samples = samples,

diff --git a/R/hp.R b/R/hp.R
@@ -37,7 +37,7 @@ ssd_hp.fitdists <- function(
     average = TRUE, 
     multi_est = TRUE,
     delta = 7, min_pboot = 0.99,
-    parametric = TRUE, multi = TRUE, control = NULL, 
+    parametric = TRUE, multi_ci = TRUE, control = NULL, 
     samples = FALSE,
     save_to = NULL, weighted = TRUE, ...
 ) {
@@ -49,7 +49,7 @@ ssd_hp.fitdists <- function(
   hcp <- ssd_hcp_fitdists(
     x = x, value = conc, ci = ci, level = level, nboot = nboot,
     average = average, multi_est = multi_est, delta = delta, min_pboot = min_pboot,
-    parametric = parametric, multi = multi, control = control, 
+    parametric = parametric, multi = multi_ci, control = control, 
     save_to = save_to, samples = samples, hc = FALSE,  fix_weights = weighted,
   )
   hcp <- dplyr::rename(hcp, conc = "value")

diff --git a/R/params.R b/R/params.R
@@ -56,7 +56,9 @@
 #' @param min_pboot A number of the minimum proportion of bootstrap samples that must successfully 
 #' fit in the sense of returning a likelihood.
 #' @param min_pmix A number between 0 and 0.5 specifying the minimum proportion in mixture models.
-#' @param multi_est A flag specifying whether to calculate model averaged estimates using the multi as opposed to the mean method.
+#' @param multi A flag specifying whether to calculate estimates for all implemented distributions.
+#' @param multi_ci A flag specifying whether to treat the distributions as constituting a single distribution for generating model averaged confidence intervals.
+#' @param multi_est A flag specifying whether to treat the distributions as constituting a single distribution for calculating the model averaged estimates.
 #' @param na.rm A flag specifying whether to silently remove missing values or 
 #' remove them with a warning.
 #' @param n positive number of observations.
@@ -78,7 +80,6 @@
 #' @param rescale A flag specifying whether to rescale concentration values by dividing by the geometric mean of the minimum and maximum positive finite values.
 #' @param ribbon A flag indicating whether to plot the confidence interval as a grey ribbon as opposed to green solid lines.
 #' @param right A string of the column in data with the right concentration values.
-#' @param multi A flag specifying whether to treat the distributions as constituting a single distribution.
 #' @param save_to A string specifying a directory to save the bootstrap datasets and parameter estimates to or NULL.
 #' @param samples A flag specfying whether to include the bootstrap samples in the output. 
 #' @param scale scale parameter.

diff --git a/R/plot-cdf.R b/R/plot-cdf.R
@@ -30,8 +30,8 @@ ssd_plot_cdf <- function(x, ...) {
 #' @examples
 #' fits <- ssd_fit_dists(ssddata::ccme_boron)
 #' ssd_plot_cdf(fits)
-ssd_plot_cdf.fitdists <- function(x, average = FALSE, delta = 7, multi = TRUE, ...) {
-  pred <- ssd_hc(x, percent = 1:99, average = average, delta = delta, multi = multi)
+ssd_plot_cdf.fitdists <- function(x, average = FALSE, delta = 7, multi_ci = TRUE, ...) {
+  pred <- ssd_hc(x, percent = 1:99, average = average, delta = delta, multi_ci = multi_ci)
   data <- ssd_data(x)
   cols <- .cols_fitdists(x)
 

diff --git a/R/predict.R b/R/predict.R
@@ -33,7 +33,7 @@ predict.fitdists <- function(object, percent = 1:99, ci = FALSE,
                              average = TRUE, delta = 7,
                              min_pboot = 0.99,
                              parametric = TRUE,
-                             multi = TRUE,
+                             multi_ci = TRUE,
                              weighted = TRUE,
                              control = NULL,
                              ...) {
@@ -42,7 +42,7 @@ predict.fitdists <- function(object, percent = 1:99, ci = FALSE,
     percent = percent, ci = ci, level = level,
     nboot = nboot, min_pboot = min_pboot,
     average = average, delta = delta, parametric = parametric,
-    multi = multi, weighted = weighted, control = control
+    multi_ci = multi_ci, weighted = weighted, control = control
   )
 }
 

diff --git a/man/estimates.fitdists.Rd b/man/estimates.fitdists.Rd
diff --git a/man/params.Rd b/man/params.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_hp.Rd b/man/ssd_hp.Rd
diff --git a/man/ssd_plot_cdf.Rd b/man/ssd_plot_cdf.Rd
diff --git a/tests/testthat/test-burrIII3.R b/tests/testthat/test-burrIII3.R
@@ -24,15 +24,15 @@ test_that("burrIII3 gives cis with ccme_chloride", {
   fit <- ssd_fit_dists(ssddata::ccme_chloride, dists = "burrIII3")
   expect_s3_class(fit, "fitdists")
   set.seed(99)
-  hc <- ssd_hc(fit, nboot = 10, ci = TRUE, multi = FALSE, samples = TRUE, weighted = FALSE)
+  hc <- ssd_hc(fit, nboot = 10, ci = TRUE, multi_ci = FALSE, samples = TRUE, weighted = FALSE)
   expect_snapshot_data(hc, "hc_chloride")
 })
 
 test_that("burrIII3 gives cis with ccme_uranium", {
   fit <- ssd_fit_dists(ssddata::ccme_uranium, dists = "burrIII3")
   expect_s3_class(fit, "fitdists")
   set.seed(99)
-  hc <- ssd_hc(fit, nboot = 10, ci = TRUE, multi = FALSE, samples = TRUE, weighted = FALSE)
+  hc <- ssd_hc(fit, nboot = 10, ci = TRUE, multi_ci = FALSE, samples = TRUE, weighted = FALSE)
   expect_snapshot_data(hc, "hc_uranium")
 })
 

diff --git a/tests/testthat/test-gompertz.R b/tests/testthat/test-gompertz.R
@@ -25,7 +25,7 @@ test_that("bootstrap gompertz with problem data", {
   data <- data.frame(Conc = ssd_rgompertz(6, location = 0.6, shape = 0.07))
   fit <- ssdtools::ssd_fit_dists(data, dists = "gompertz")
   set.seed(99)
-  hc <- ssd_hc(fit, ci = TRUE, nboot = 100, min_pboot = 0.8, multi = FALSE,
+  hc <- ssd_hc(fit, ci = TRUE, nboot = 100, min_pboot = 0.8, multi_ci = FALSE,
                samples = TRUE, weighted = FALSE)
   expect_snapshot_data(hc, "hc_prob")
 })
diff --git a/tests/testthat/test-hc-root.R b/tests/testthat/test-hc-root.R
@@ -16,9 +16,9 @@
 test_that("hc multi lnorm", {
   fits <- ssd_fit_dists(ssddata::ccme_boron, dists = "lnorm")
   set.seed(102)
-  hc_dist <- ssd_hc(fits, average = FALSE, multi = FALSE, weighted = FALSE)
-  hc_average <- ssd_hc(fits, average = TRUE, multi = FALSE, weighted = FALSE)
-  hc_multi <- ssd_hc(fits, average = TRUE, multi = TRUE)
+  hc_dist <- ssd_hc(fits, average = FALSE, multi_ci = FALSE, weighted = FALSE)
+  hc_average <- ssd_hc(fits, average = TRUE, multi_ci = FALSE, weighted = FALSE)
+  hc_multi <- ssd_hc(fits, average = TRUE, multi_ci = TRUE)
   expect_identical(hc_dist$est, hc_average$est)
   expect_equal(hc_multi, hc_average)
 
@@ -30,8 +30,8 @@ test_that("hc multi lnorm", {
 test_that("hc multi all", {
   fits <- ssd_fit_dists(ssddata::ccme_boron)
   set.seed(102)
-  hc_average <- ssd_hc(fits, average = TRUE, multi = FALSE)
-  hc_multi <- ssd_hc(fits, average = TRUE, multi = TRUE)
+  hc_average <- ssd_hc(fits, average = TRUE, multi_ci = FALSE)
+  hc_multi <- ssd_hc(fits, average = TRUE, multi_ci = TRUE)
   expect_equal(hc_average$est, 1.24151700389853)
   expect_equal(hc_multi$est, 1.25677449265554)
   testthat::expect_snapshot({
@@ -42,8 +42,8 @@ test_that("hc multi all", {
 test_that("hc multi all multiple hcs", {
   fits <- ssd_fit_dists(ssddata::ccme_boron)
   set.seed(102)
-  hc_average <- ssd_hc(fits, percent = c(5,10), average = TRUE, multi = FALSE, weighted = FALSE)
-  hc_multi <- ssd_hc(fits, percent = c(5,10), average = TRUE, multi = TRUE)
+  hc_average <- ssd_hc(fits, percent = c(5,10), average = TRUE, multi_ci = FALSE, weighted = FALSE)
+  hc_multi <- ssd_hc(fits, percent = c(5,10), average = TRUE, multi_ci = TRUE)
   expect_equal(hc_average$est, c(1.24151700389853, 2.37337471483992))
   expect_equal(hc_multi$est, c(1.25677449265554, 2.38164905743083))
   testthat::expect_snapshot({
@@ -54,9 +54,9 @@ test_that("hc multi all multiple hcs", {
 test_that("hc multi all multiple hcs cis", {
   fits <- ssd_fit_dists(ssddata::ccme_boron)
   set.seed(102)
-  hc_average <- ssd_hc(fits, percent = c(5,10), average = TRUE, multi = FALSE, nboot = 10, ci = TRUE, weighted = FALSE)
+  hc_average <- ssd_hc(fits, percent = c(5,10), average = TRUE, multi_ci = FALSE, nboot = 10, ci = TRUE, weighted = FALSE)
   set.seed(105)
-  hc_multi <- ssd_hc(fits, percent = c(5,10), average = TRUE, multi = TRUE, nboot = 10, ci = TRUE)
+  hc_multi <- ssd_hc(fits, percent = c(5,10), average = TRUE, multi_ci = TRUE, nboot = 10, ci = TRUE)
   expect_equal(hc_average$est, c(1.24151700389853, 2.37337471483992))
   expect_equal(hc_multi$est, c(1.25677449265554, 2.38164905743083))
   testthat::expect_snapshot({
@@ -67,11 +67,11 @@ test_that("hc multi all multiple hcs cis", {
 test_that("hc multi lnorm ci", {
   fits <- ssd_fit_dists(ssddata::ccme_boron, dists = "lnorm")
   set.seed(102)
-  hc_dist <- ssd_hc(fits, average = FALSE, ci = TRUE, nboot = 100, multi = FALSE, weighted = FALSE)
+  hc_dist <- ssd_hc(fits, average = FALSE, ci = TRUE, nboot = 100, multi_ci = FALSE, weighted = FALSE)
   set.seed(102)
-  hc_average <- ssd_hc(fits, average = TRUE, ci = TRUE, nboot = 100, multi = FALSE, weighted = FALSE)
+  hc_average <- ssd_hc(fits, average = TRUE, ci = TRUE, nboot = 100, multi_ci = FALSE, weighted = FALSE)
   set.seed(102)
-  hc_multi <- ssd_hc(fits, average = TRUE, multi = TRUE, ci = TRUE, nboot = 100)
+  hc_multi <- ssd_hc(fits, average = TRUE, multi_ci = TRUE, ci = TRUE, nboot = 100)
 
   testthat::expect_snapshot({
     hc_average