Change default options

tesselle · Jan 2, 2025 · d9f3fb4 · d9f3fb4
1 parent 43ebf19
commit d9f3fb4
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Showing 9 changed files with 58 additions and 44 deletions.
diff --git a/R/diversity_alpha.R b/R/diversity_alpha.R
@@ -59,9 +59,12 @@ setMethod(
 
     F1 <- sum(x == 1) # Number of singleton species
     if (F1 == N_rare) {
-      warning(tr_("ACE is undefined when all rare species are singletons."), "\n",
-              tr_("Consider using the bias-corrected Chao1 estimator instead."),
-              call. = FALSE)
+      if (getOption("tabula.verbose")) {
+        message(
+          tr_("ACE is undefined when all rare species are singletons."), "\n",
+          tr_("Consider using the bias-corrected Chao1 estimator instead.")
+        )
+      }
       return(NA_real_)
     }
 
@@ -191,10 +194,11 @@ setMethod(
       f3 <- sum(x == 3) # Number of triple species
       f4 <- sum(x == 4) # Number of quadruple species
       if (f4 == 0) {
-        warning(
-          tr_("Improved Chao1 estimator is undefined when there is no quadruple species."),
-          call. = FALSE
-        )
+        if (getOption("tabula.verbose")) {
+          message(
+            tr_("Improved Chao1 estimator is undefined when there is no quadruple species.")
+          )
+        }
         return(NA_real_)
       }
 
@@ -236,10 +240,11 @@ setMethod(
       q3 <- sum(q == 3) # Number of triple species
       q4 <- sum(q == 4) # Number of quadruple species
       if (q4 == 0) {
-        warning(
-          tr_("Improved Chao2 estimator is undefined when there is no quadruple species."),
-          call. = FALSE
-        )
+        if (getOption("tabula.verbose")) {
+          message(
+            tr_("Improved Chao2 estimator is undefined when there is no quadruple species.")
+          )
+        }
         return(NA_real_)
       }
 
@@ -272,9 +277,12 @@ setMethod(
 
     q1 <- sum(q == 1) # Number of unique species in the assemblage
     if (q1 == N_infr) {
-      warning(tr_("ICE is undefined when all rare species are singletons."), "\n",
-              tr_("Consider using the bias-corrected Chao2 estimator instead."),
-              call. = FALSE)
+      if (getOption("tabula.verbose")) {
+        message(
+          tr_("ICE is undefined when all rare species are singletons."), "\n",
+          tr_("Consider using the bias-corrected Chao2 estimator instead.")
+        )
+      }
       return(NA_real_)
     }
 

diff --git a/R/statistics.R b/R/statistics.R
@@ -49,7 +49,7 @@ combination <- function(n, k) {
   arkhe::assert_scalar(k, "numeric")
 
   if (n > 170 | k > 170) {
-    if (getOption("tabula.verbose")) message(tr_("Ramanujan approximation of x!"))
+    ## Ramanujan approximation of x!
     c <- exp(ramanujan(n) - ramanujan(k) - ramanujan(n - k))
   } else {
     c <- factorial(n) / (factorial(k) * factorial(n - k))

diff --git a/R/tabula-package.R b/R/tabula-package.R
@@ -8,6 +8,13 @@
 #'  **JOSS:** \tab \doi{10.21105/joss.01821} \cr
 #' }
 #'
+#' @section Package options:
+#'  \pkg{tabula} uses the following [options()] to configure behavior:
+#'  * `tabula.progress`: a [`logical`] scalar. Should progress bars be
+#'    displayed? Defaults to [interactive()].
+#'  * `tabula.verbose`: a [`logical`] scalar. Should \R report extra information
+#'    on progress? Defaults to [interactive()].
+#'
 #' @author
 #' **Full list of authors and contributors** (alphabetic order)
 #'

diff --git a/R/zzz.R b/R/zzz.R
@@ -1,8 +1,8 @@
 .onLoad <- function(libname, pkgname){
   op <- options()
   op.tabula <- list(
-    tabula.progress = TRUE,
-    tabula.verbose = FALSE
+    tabula.progress = interactive(),
+    tabula.verbose = interactive()
   )
   toset <- !(names(op.tabula) %in% names(op))
   if(any(toset)) options(op.tabula[toset])

diff --git a/inst/tinytest/test_index.R b/inst/tinytest/test_index.R
@@ -7,8 +7,7 @@ expect_equal(round(index_menhinick(n), 3), 1.534) # 1.534
 expect_equal(round(index_margalef(n), 3), 3.7) # 3.7
 expect_equal(round(index_berger(n), 3), 0.206) # 0.2059
 expect_equal(round(index_chao1(n, unbiased = TRUE), 3), 21.491) # 21.49
-expect_warning(index_chao1(n, unbiased = TRUE, improved = TRUE)) # 22.65 (?)
-expect_equal(suppressWarnings(index_chao1(n, unbiased = TRUE, improved = TRUE)), NA_real_) # 22.65 (?)
+expect_equal(index_chao1(n, unbiased = TRUE, improved = TRUE), NA_real_) # 22.65 (?)
 expect_equal(round(index_ace(n), 3), 22.087) # 22.09
 expect_equal(round(index_squares(n), 3), 21.924) # 21.92
 

diff --git a/inst/tinytest/test_statistics.R b/inst/tinytest/test_statistics.R
@@ -9,6 +9,3 @@ expect_equal(tabula:::combination(4, 3), 4)
 # Ramanujan factorial approx.
 expect_equal(tabula:::combination(171, 3), 818816.247275706)
 expect_error(tabula:::combination(3, "a"))
-
-options("tabula.verbose" = TRUE)
-expect_message(tabula:::combination(171, 3), "Ramanujan approximation of x!")
diff --git a/man/tabula-package.Rd b/man/tabula-package.Rd
diff --git a/po/R-fr.po b/po/R-fr.po
@@ -1,7 +1,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: tabula 3.1.1.9000\n"
-"POT-Creation-Date: 2025-01-02 17:05+0100\n"
+"POT-Creation-Date: 2025-01-02 18:37+0100\n"
 "PO-Revision-Date: 2024-12-16 19:01+0100\n"
 "Last-Translator: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne."
 "fr>\n"
@@ -12,37 +12,37 @@ msgstr ""
 "Content-Transfer-Encoding: 8bit\n"
 "Plural-Forms: nplurals=2; plural=(n > 1);\n"
 
-#: diversity_alpha.R:62
+#: diversity_alpha.R:64
 msgid "ACE is undefined when all rare species are singletons."
 msgstr ""
 "L'estimateur ACE est indéfini lorsque toutes les espèces rares sont des "
 "singletons."
 
-#: diversity_alpha.R:63
+#: diversity_alpha.R:65
 msgid "Consider using the bias-corrected Chao1 estimator instead."
 msgstr "Envisagez plutôt d'utiliser l'estimateur Chao1 non biaisé."
 
-#: diversity_alpha.R:195
+#: diversity_alpha.R:199
 msgid ""
 "Improved Chao1 estimator is undefined when there is no quadruple species."
 msgstr ""
 "L'estimateur Chao1 amélioré est indéfini lorsqu'il n'y a pas d'espèce "
 "quadruple."
 
-#: diversity_alpha.R:240
+#: diversity_alpha.R:245
 msgid ""
 "Improved Chao2 estimator is undefined when there is no quadruple species."
 msgstr ""
 "L'estimateur Chao2 amélioré est indéfini lorsqu'il n'y a pas d'espèce "
 "quadruple."
 
-#: diversity_alpha.R:275
+#: diversity_alpha.R:282
 msgid "ICE is undefined when all rare species are singletons."
 msgstr ""
 "L'estimateur ICE est indéfini lorsque toutes les espèces rares sont des "
 "singletons."
 
-#: diversity_alpha.R:276
+#: diversity_alpha.R:283
 msgid "Consider using the bias-corrected Chao2 estimator instead."
 msgstr "Envisagez plutôt d'utiliser l'estimateur Chao2 non biaisé."
 
@@ -81,7 +81,3 @@ msgstr "Fréquence"
 #: rarefaction.R:126
 msgid "Expected species index"
 msgstr "Indice de diversité attendu"
-
-#: statistics.R:52
-msgid "Ramanujan approximation of x!"
-msgstr ""
diff --git a/po/R-tabula.pot b/po/R-tabula.pot
@@ -1,7 +1,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: tabula 3.1.1.9000\n"
-"POT-Creation-Date: 2025-01-02 17:05+0100\n"
+"POT-Creation-Date: 2025-01-02 18:37+0100\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -10,29 +10,29 @@ msgstr ""
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
 
-#: diversity_alpha.R:62
+#: diversity_alpha.R:64
 msgid "ACE is undefined when all rare species are singletons."
 msgstr ""
 
-#: diversity_alpha.R:63
+#: diversity_alpha.R:65
 msgid "Consider using the bias-corrected Chao1 estimator instead."
 msgstr ""
 
-#: diversity_alpha.R:195
+#: diversity_alpha.R:199
 msgid ""
 "Improved Chao1 estimator is undefined when there is no quadruple species."
 msgstr ""
 
-#: diversity_alpha.R:240
+#: diversity_alpha.R:245
 msgid ""
 "Improved Chao2 estimator is undefined when there is no quadruple species."
 msgstr ""
 
-#: diversity_alpha.R:275
+#: diversity_alpha.R:282
 msgid "ICE is undefined when all rare species are singletons."
 msgstr ""
 
-#: diversity_alpha.R:276
+#: diversity_alpha.R:283
 msgid "Consider using the bias-corrected Chao2 estimator instead."
 msgstr ""
 
@@ -71,7 +71,3 @@ msgstr ""
 #: rarefaction.R:126
 msgid "Expected species index"
 msgstr ""
-
-#: statistics.R:52
-msgid "Ramanujan approximation of x!"
-msgstr ""