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tesselle · Dec 16, 2024 · 69c0268 · 69c0268
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commit 69c0268
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diff --git a/R/diversity_alpha.R b/R/diversity_alpha.R
@@ -59,8 +59,8 @@ setMethod(
 
     F1 <- sum(x == 1) # Number of singleton species
     if (F1 == N_rare)
-      stop("ACE is undefined when all rare species are singletons, ",
-           "consider using the bias-corrected Chao1 index instead.",
+      stop(tr_("ACE is undefined when all rare species are singletons."),
+           tr_("Consider using the bias-corrected Chao1 estimator instead."),
            call. = FALSE)
 
     ## Sample coverage estimate for rare species
@@ -186,11 +186,13 @@ setMethod(
       }
     }
     if (improved) {
-      f3 <- sum(x == 3) # Number of tripleton species
-      f4 <- sum(x == 4) # Number of quadrupleton species
+      f3 <- sum(x == 3) # Number of triple species
+      f4 <- sum(x == 4) # Number of quadruple species
       if (f4 == 0)
-        stop("Improved Chao1 estimator is undefined ",
-             "when there is no quadrupleton species.", call. = FALSE)
+        stop(
+          tr_("Improved Chao1 estimator is undefined when there is no quadruple species."),
+          call. = FALSE
+        )
 
       k <- f1 - ((N - 3) / (N - 1)) * ((f2 * f3) / (2 * f4))
       D <- D + ((N - 3) / N) * (f3 / (4 * f4)) * max(k, 0)
@@ -230,8 +232,10 @@ setMethod(
       q3 <- sum(q == 3) # Number of triple species
       q4 <- sum(q == 4) # Number of quadruple species
       if (q4 == 0)
-        stop("Improved Chao2 estimator is undefined ",
-             "when there is no quadruple species.", call. = FALSE)
+        stop(
+          tr_("Improved Chao2 estimator is undefined when there is no quadruple species."),
+          call. = FALSE
+        )
 
       k <- q1 - ((t - 3) / (t - 1)) * ((q2 * q3) / (2 * q4))
       D <- D + ((t - 3) / (4 * t)) * (q3 / q4) * max(k, 0)
@@ -262,8 +266,8 @@ setMethod(
 
     q1 <- sum(q == 1) # Number of unique species in the assemblage
     if (q1 == N_infr)
-      stop("ICE is undefined when all infrequent species are unique, ",
-           "consider using the bias-corrected Chao2 estimator instead.",
+      stop(tr_("ICE is undefined when all rare species are singletons."),
+           tr_("Consider using the bias-corrected Chao2 estimator instead."),
            call. = FALSE)
 
     ## Sample coverage estimate

diff --git a/R/plot_diceleraas.R b/R/plot_diceleraas.R
@@ -110,7 +110,8 @@ setMethod(
 
     ## Add annotation
     if (ann) {
-      graphics::title(main = main, sub = sub, xlab = "Count", ylab = NULL, ...)
+      graphics::title(main = main, sub = sub,
+                      xlab = tr_("Absolute frequency"), ylab = NULL, ...)
     }
 
     invisible(object)

diff --git a/R/plot_diversity.R b/R/plot_diversity.R
@@ -65,12 +65,12 @@ plot.DiversityIndex <- function(x, log = "x",
   if (ann) {
     y_lab <- switch (
       class(x),
-      HeterogeneityIndex = "Heterogeneity",
-      EvennessIndex = "Evenness",
-      RichnessIndex = "Richness",
-      "Diversity"
+      HeterogeneityIndex = tr_("Heterogeneity"),
+      EvennessIndex = tr_("Evenness"),
+      RichnessIndex = tr_("Richness"),
+      tr_("Diversity")
     )
-    graphics::title(main = main, sub = sub, xlab = "Sample size",
+    graphics::title(main = main, sub = sub, xlab = tr_("Sample size"),
                     ylab = sprintf("%s (%s)", y_lab, x@method))
   }
 
@@ -134,8 +134,8 @@ setMethod(
 
     ## Add annotation
     if (ann) {
-      graphics::title(main = main, sub = sub, xlab = "Sample size",
-                      ylab = "Diversity", ...)
+      graphics::title(main = main, sub = sub, xlab = tr_("Sample size"),
+                      ylab = tr_("Diversity"), ...)
     }
 
     ## Legend
@@ -270,7 +270,7 @@ setMethod(
     ## Add annotation
     if (ann) {
       graphics::title(main = main, sub = sub, xlab = "alpha",
-                      ylab = "Diversity", ...)
+                      ylab = tr_("Diversity"), ...)
     }
 
     ## Legend

diff --git a/R/plot_rank.R b/R/plot_rank.R
@@ -76,8 +76,8 @@ setMethod(
 
     ## Add annotation
     if (ann) {
-      graphics::title(main = main, sub = sub, xlab = "Rank",
-                      ylab = "Frequency", ...)
+      graphics::title(main = main, sub = sub, xlab = tr_("Rank"),
+                      ylab = tr_("Frequency"), ...)
     }
 
     ## Legend

diff --git a/R/rarefaction.R b/R/rarefaction.R
@@ -121,8 +121,8 @@ plot.RarefactionIndex <- function(x, color = NULL, symbol = FALSE,
 
   ## Add annotation
   if (ann) {
-    graphics::title(main = main, sub = sub, xlab = "Sample size",
-                    ylab = "Expected species index")
+    graphics::title(main = main, sub = sub, xlab = tr_("Sample size"),
+                    ylab = tr_("Expected species index"))
   }
 
   ## Legend

diff --git a/R/statistics.R b/R/statistics.R
@@ -45,13 +45,11 @@ setMethod(
 #' @noRd
 combination <- function(n, k) {
   # Validation
-  if (!is.numeric(n))
-    stop("`n` must be a numeric vector.")
-  if (!is.numeric(k))
-    stop("`k` must be a numeric vector.")
+  arkhe::assert_scalar(n, "numeric")
+  arkhe::assert_scalar(k, "numeric")
 
   if (n > 170 | k > 170) {
-    if (getOption("tabula.verbose")) message("Ramanujan approximation of x!")
+    if (getOption("tabula.verbose")) message(tr_("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-internal.R b/R/tabula-internal.R
@@ -1,5 +1,10 @@
 # HELPERS
 
+## https://michaelchirico.github.io/potools/articles/developers.html
+tr_ <- function(...) {
+  enc2utf8(gettext(paste0(...), domain = "R-tabula"))
+}
+
 is_incidence <- function(x) {
   if (is.logical(x)) return(TRUE)
   x <- as.numeric(x)

diff --git a/README.Rmd b/README.Rmd
@@ -20,7 +20,7 @@ Sys.setlocale("LC_MESSAGES", 'en_GB.UTF-8') # Force locale
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/tesselle/tabula/workflows/R-CMD-check/badge.svg)](https://github.com/tesselle/tabula/actions)
-[![codecov](https://codecov.io/gh/tesselle/tabula/branch/master/graph/badge.svg)](https://app.codecov.io/gh/tesselle/tabula)
+[![codecov](https://codecov.io/gh/tesselle/tabula/branch/main/graph/badge.svg)](https://app.codecov.io/gh/tesselle/tabula)
 [![CodeFactor](https://www.codefactor.io/repository/github/tesselle/tabula/badge)](https://www.codefactor.io/repository/github/tesselle/tabula)
 [![Dependencies](https://tinyverse.netlify.app/badge/tabula)](https://cran.r-project.org/package=tabula)
 

diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/tesselle/tabula/workflows/R-CMD-check/badge.svg)](https://github.com/tesselle/tabula/actions)
-[![codecov](https://codecov.io/gh/tesselle/tabula/branch/master/graph/badge.svg)](https://app.codecov.io/gh/tesselle/tabula)
+[![codecov](https://codecov.io/gh/tesselle/tabula/branch/main/graph/badge.svg)](https://app.codecov.io/gh/tesselle/tabula)
 [![CodeFactor](https://www.codefactor.io/repository/github/tesselle/tabula/badge)](https://www.codefactor.io/repository/github/tesselle/tabula)
 [![Dependencies](https://tinyverse.netlify.app/badge/tabula)](https://cran.r-project.org/package=tabula)
 

diff --git a/inst/po/fr/LC_MESSAGES/R-tabula.mo b/inst/po/fr/LC_MESSAGES/R-tabula.mo
diff --git a/inst/tinytest/_tinysnapshot/plot_dice_leraas.svg b/inst/tinytest/_tinysnapshot/plot_dice_leraas.svg
diff --git a/inst/tinytest/test_diversity.R b/inst/tinytest/test_diversity.R
@@ -1,3 +1,5 @@
+Sys.setlocale("LC_MESSAGES", 'en_GB.UTF-8') # Force locale
+
 source("helpers.R")
 data("cantabria")
 

diff --git a/inst/tinytest/test_plots.R b/inst/tinytest/test_plots.R
@@ -1,4 +1,6 @@
 if (at_home()) {
+  Sys.setlocale("LC_MESSAGES", 'en_GB.UTF-8') # Force locale
+
   source("helpers.R")
   using("tinysnapshot")
   options(tinysnapshot_device = "svglite")

diff --git a/inst/tinytest/test_rarefaction.R b/inst/tinytest/test_rarefaction.R
@@ -1,3 +1,5 @@
+Sys.setlocale("LC_MESSAGES", 'en_GB.UTF-8') # Force locale
+
 # Data from Magurran 1988, p. 128-129
 trap <- matrix(data = c(9, 3, 0, 4, 2, 1, 1, 0, 1, 0, 1, 1,
                         1, 0, 1, 0, 0, 0, 1, 2, 0, 5, 3, 0),

diff --git a/inst/tinytest/test_richness.R b/inst/tinytest/test_richness.R
@@ -1,3 +1,5 @@
+Sys.setlocale("LC_MESSAGES", 'en_GB.UTF-8') # Force locale
+
 source("helpers.R")
 data("cantabria")
 

diff --git a/po/R-fr.po b/po/R-fr.po
@@ -0,0 +1,80 @@
+msgid ""
+msgstr ""
+"Project-Id-Version: tabula 3.1.1.9000\n"
+"POT-Creation-Date: 2024-12-16 19:01+0100\n"
+"PO-Revision-Date: 2024-12-16 19:01+0100\n"
+"Last-Translator: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>\n"
+"Language-Team: fr\n"
+"Language: fr\n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+"Plural-Forms: nplurals=2; plural=(n > 1);\n"
+
+#: diversity_alpha.R:62
+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
+msgid "Consider using the bias-corrected Chao1 estimator instead."
+msgstr "Envisagez plutôt d'utiliser l'estimateur Chao1 non biaisé."
+
+#: diversity_alpha.R:193
+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:236
+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:269
+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:270
+msgid "Consider using the bias-corrected Chao2 estimator instead."
+msgstr "Envisagez plutôt d'utiliser l'estimateur Chao2 non biaisé."
+
+#: plot_diceleraas.R:114
+msgid "Absolute frequency"
+msgstr "Fréquence absolue"
+
+#: plot_diversity.R:68
+msgid "Heterogeneity"
+msgstr "Hétérogénéité"
+
+#: plot_diversity.R:69
+msgid "Evenness"
+msgstr "Équitabilité"
+
+#: plot_diversity.R:70
+msgid "Richness"
+msgstr "Richesse"
+
+#: plot_diversity.R:71 plot_diversity.R:138 plot_diversity.R:273
+msgid "Diversity"
+msgstr "Diversité"
+
+#: plot_diversity.R:73 plot_diversity.R:137 rarefaction.R:124
+msgid "Sample size"
+msgstr "Effectif"
+
+#: plot_rank.R:79
+msgid "Rank"
+msgstr "Rang"
+
+#: plot_rank.R:80
+msgid "Frequency"
+msgstr "Fréquence"
+
+#: rarefaction.R:125
+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
@@ -0,0 +1,77 @@
+msgid ""
+msgstr ""
+"Project-Id-Version: tabula 3.1.1.9000\n"
+"POT-Creation-Date: 2024-12-16 19:01+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"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#: diversity_alpha.R:62
+msgid "ACE is undefined when all rare species are singletons."
+msgstr ""
+
+#: diversity_alpha.R:63
+msgid "Consider using the bias-corrected Chao1 estimator instead."
+msgstr ""
+
+#: diversity_alpha.R:193
+msgid ""
+"Improved Chao1 estimator is undefined when there is no quadruple species."
+msgstr ""
+
+#: diversity_alpha.R:236
+msgid ""
+"Improved Chao2 estimator is undefined when there is no quadruple species."
+msgstr ""
+
+#: diversity_alpha.R:269
+msgid "ICE is undefined when all rare species are singletons."
+msgstr ""
+
+#: diversity_alpha.R:270
+msgid "Consider using the bias-corrected Chao2 estimator instead."
+msgstr ""
+
+#: plot_diceleraas.R:114
+msgid "Absolute frequency"
+msgstr ""
+
+#: plot_diversity.R:68
+msgid "Heterogeneity"
+msgstr ""
+
+#: plot_diversity.R:69
+msgid "Evenness"
+msgstr ""
+
+#: plot_diversity.R:70
+msgid "Richness"
+msgstr ""
+
+#: plot_diversity.R:71 plot_diversity.R:138 plot_diversity.R:273
+msgid "Diversity"
+msgstr ""
+
+#: plot_diversity.R:73 plot_diversity.R:137 rarefaction.R:124
+msgid "Sample size"
+msgstr ""
+
+#: plot_rank.R:79
+msgid "Rank"
+msgstr ""
+
+#: plot_rank.R:80
+msgid "Frequency"
+msgstr ""
+
+#: rarefaction.R:125
+msgid "Expected species index"
+msgstr ""
+
+#: statistics.R:52
+msgid "Ramanujan approximation of x!"
+msgstr ""