- Switch computable from TRUE to FALSE.

R/fit.R

@@ -168,7 +168,7 @@ ssd_fit_dists <- function(
     nrow = 6L,
     rescale = FALSE,
     reweight = FALSE,
-    computable = TRUE,
+    computable = FALSE,
     at_boundary_ok = TRUE,
     all_dists = FALSE,
     min_pmix = ssd_min_pmix(nrow(data)),

tests/testthat/test-fit.R

@@ -66,8 +66,8 @@ test_that("ssd_fit_dists not happy with left as left by default", {
 
 test_that("ssd_fit_dists returns object class fitdists", {
   fit <- ssd_fit_dists(ssddata::ccme_boron,
-    dists = c("lnorm", "llogis"),
-    rescale = FALSE
+                       dists = c("lnorm", "llogis"),
+                       rescale = FALSE
   )
   expect_s3_class(fit, "fitdists")
 })
@@ -217,33 +217,33 @@ test_that("ssd_fit_dists warns to rescale data", {
 test_that("ssd_fit_dists doesn't warns to rescale data if already rescaled", {
   data <- data.frame(Conc = rep(2, 6))
   expect_error(expect_warning(ssd_fit_dists(data, rescale = TRUE, dist = "lnorm"),
-    regexp = "^Distribution 'lnorm' failed to fit:"
+                              regexp = "^Distribution 'lnorm' failed to fit:"
   ))
 })
 
 test_that("ssd_fit_dists warns of optimizer convergence code error", {
   data <- ssddata::ccme_boron
   expect_error(
     expect_warning(ssd_fit_dists(data, control = list(maxit = 1), dist = "lnorm"),
-      regexp = "^Distribution 'lnorm' failed to converge \\(try rescaling data\\): Iteration limit maxit reach \\(try increasing the maximum number of iterations in control\\)\\.$"
+                   regexp = "^Distribution 'lnorm' failed to converge \\(try rescaling data\\): Iteration limit maxit reach \\(try increasing the maximum number of iterations in control\\)\\.$"
     )
   )
 })
 
 test_that("ssd_fit_dists estimates for ssddata::ccme_boron on bcanz dists", {
   fits <- ssd_fit_dists(ssddata::ccme_boron, rescale = TRUE)
-
+  
   tidy <- tidy(fits)
   expect_s3_class(tidy, "tbl")
   expect_snapshot_data(tidy, "tidy_stable_rescale")
 })
 
 test_that("ssd_fit_dists not reorder", {
   fit <- ssd_fit_dists(ssddata::ccme_boron,
-    dists = c("lnorm", "llogis"),
-    rescale = FALSE
+                       dists = c("lnorm", "llogis"),
+                       rescale = FALSE
   )
-
+  
   expect_identical(npars(fit), c(lnorm = 2L, llogis = 2L))
   expect_equal(logLik(fit), c(lnorm = -117.514216489547, llogis = -118.507435324581))
 })
@@ -253,85 +253,82 @@ test_that("ssd_fit_dists equal weights no effect", {
   data <- ssddata::ccme_boron
   data$weight <- rep(2, nrow(data))
   fits_weight <- ssd_fit_dists(data)
-
+  
   expect_equal(estimates(fits_weight), estimates(fits))
 })
 
 test_that("ssd_fit_dists computable = TRUE allows for fits without standard errors", {
   data <- ssddata::ccme_boron
   data$Other <- data$Conc
   data$Conc <- data$Conc / max(data$Conc)
-
+  
   expect_warning(
-    expect_warning(
-      ssd_fit_dists(data, right = "Other", rescale = FALSE, at_boundary_ok = FALSE),
-      "^Distribution 'lnorm_lnorm' failed to fit \\(try rescaling data\\)"
-    ),
-    "^Distribution 'lgumbel' failed to compute standard errors \\(try rescaling data\\)\\.$"
+    ssd_fit_dists(data, right = "Other", rescale = FALSE, at_boundary_ok = FALSE),
+    "^Distribution 'lnorm_lnorm' failed to fit \\(try rescaling data\\)"
   )
-
+  
   set.seed(102)
-  fits <- ssd_fit_dists(data, right = "Other", dists = c("lgumbel", "llogis", "lnorm", "lnorm_lnorm"), rescale = FALSE, computable = FALSE, at_boundary_ok = TRUE)
-
+  fits <- ssd_fit_dists(data, right = "Other", dists = c("lgumbel", "llogis", "lnorm", "lnorm_lnorm"), rescale = FALSE, at_boundary_ok = TRUE)
+  
   tidy <- tidy(fits)
   expect_s3_class(tidy, "tbl")
   expect_snapshot_data(tidy, "tidy_stable_computable", digits = 3)
 })
 
 test_that("ssd_fit_dists works with slightly censored data", {
   data <- ssddata::ccme_boron
-
+  
   data$right <- data$Conc * 2
   data$Conc <- data$Conc * 0.5
-
+  
   fits <- ssd_fit_dists(data, dists = "lnorm", right = "right", rescale = FALSE)
-
+  
   tidy <- tidy(fits)
-
+  
   expect_equal(tidy$est, c(2.56052524750529, 1.17234562953404), tolerance = 1e-06)
   expect_equal(tidy$se, c(0.234063281091344, 0.175423555900586), tolerance = 1e-05)
 })
 
 test_that("ssd_fit_dists accepts 0 for left censored data", {
   data <- ssddata::ccme_boron
-
+  
   data$right <- data$Conc
   data$Conc[1] <- 0
-
+  
   fits <- ssd_fit_dists(data, dists = "lnorm", right = "right", rescale = FALSE)
-
+  
   tidy <- tidy(fits)
-
+  
   expect_equal(tidy$est, c(2.54093502870563, 1.27968456496323), tolerance = 1e-06)
   expect_equal(tidy$se, c(0.242558677928804, 0.175719927258761), tolerance = 1e-06)
 })
 
 test_that("ssd_fit_dists gives same values with zero and missing left values", {
   data <- ssddata::ccme_boron
-
+  
   data$right <- data$Conc
   data$Conc[1] <- 0
-
+  
   fits0 <- ssd_fit_dists(data, dists = "lnorm", right = "right")
-
+  
   data$Conc[1] <- NA
-
+  
   fitsna <- ssd_fit_dists(data, dists = "lnorm", right = "right")
-
+  
   expect_equal(tidy(fits0), tidy(fitsna))
 })
 
 test_that("ssd_fit_dists works with right censored data", {
   data <- ssddata::ccme_boron
-
+  
   data$right <- data$Conc
   data$right[1] <- Inf
-
+  
   expect_error(
     fits <- ssd_fit_dists(data, dists = "lnorm", right = "right"),
     "^Distributions cannot currently be fitted to right censored data\\.$"
   )
-
+  
   #
   # tidy <- tidy(fits)
   #
@@ -341,22 +338,22 @@ test_that("ssd_fit_dists works with right censored data", {
 
 test_that("ssd_fit_dists gives same answer for missing versus Inf right", {
   data <- ssddata::ccme_boron
-
+  
   data$right <- data$Conc
   data$right[1] <- Inf
-
+  
   expect_error(
     fits <- ssd_fit_dists(data, dists = "lnorm", right = "right"),
     "^Distributions cannot currently be fitted to right censored data\\.$"
   )
-
+  
   data$right[1] <- NA
-
+  
   expect_error(
     fits <- ssd_fit_dists(data, dists = "lnorm", right = "right"),
     "^Distributions cannot currently be fitted to right censored data\\.$"
   )
-
+  
   # fits0 <- ssd_fit_dists(data, dists = "lnorm", right = "right")
   #
   # data$right[1] <- NA
@@ -396,8 +393,9 @@ test_that("ssd_fit_dists at_boundary_ok message", {
   )
   expect_warning(
     ssd_fit_dists(ssddata::ccme_boron,
-      dists = c("lnorm", "burrIII3"),
-      at_boundary_ok = TRUE
+                  dists = c("lnorm", "burrIII3"),
+                  at_boundary_ok = TRUE,
+                  computable = TRUE
     ),
     "failed to compute standard errors \\(try rescaling data\\)\\.$"
   )
@@ -418,8 +416,8 @@ test_that("ssd_fit_dists unstable with anon_e", {
 
 test_that("ssd_fit_dists works min_pmix = 0.5 and at_boundary_ok = TRUE and computable = FALSE", {
   fit <- ssd_fit_dists(ssddata::ccme_boron,
-    dists = c("lnorm", "lnorm_lnorm"), min_pmix = 0.5,
-    at_boundary_ok = TRUE, computable = FALSE
+                       dists = c("lnorm", "lnorm_lnorm"), min_pmix = 0.5,
+                       at_boundary_ok = TRUE, computable = FALSE
   )
   tidy <- tidy(fit)
   expect_snapshot_data(tidy, "min_pmix_05")