Merge pull request #33 from olivroy/usethis

replace usethis by cli
FRBCesab · Jan 16, 2024 · 1032e1f · 1032e1f
2 parents 1cb6c13 + 990e7e1
commit 1032e1f
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Showing 4 changed files with 59 additions and 51 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -36,10 +36,10 @@ Imports:
     grDevices,
     R2jags,
     stats,
-    usethis
+    cli
 Suggests: 
     knitr,
     rmarkdown
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 VignetteBuilder: knitr
diff --git a/R/bugs-funs.R b/R/bugs-funs.R
@@ -701,14 +701,14 @@ diagnostic <- function(data, threshold = 1.1) {
   if (length(pos)) {
 
     no_converged <- names(bugs)[pos]
-
-    usethis::ui_oops(paste0("Some parameters have not converged for the ", 
-                            "following count series: ", 
-                            "{usethis::ui_value(no_converged)}."))
+    cli::cli_alert_danger(c(
+      "Some parameters have not converged for the following count series: ",
+      "{.val {no_converged}}."
+    ))
 
   } else {
 
-    usethis::ui_done("All models have converged.")
+    cli::cli_alert_success("All models have converged.")
   }
 
   invisible(NULL)

diff --git a/R/format-funs.R b/R/format-funs.R
@@ -1118,10 +1118,10 @@ format_data <- function(data, info = NULL, date = "date", count = "count",
     count_series <- count_series[-which(names(count_series) %in% series_to_del)]
 
     if (length(n_rows) < length(count_series)) {
-      usethis::ui_oops(paste0("Removing the following series without valid ", 
-                              "precision measures: ", 
-                              usethis::ui_value(paste0(series_to_del, 
-                                                       collapse = ", "))))
+      cli::cli_alert_danger(c(
+        "Removing the following series without valid precision measures: ",
+        "{.val {series_to_del}}"
+      ))
     }
   }
 
@@ -1135,10 +1135,11 @@ format_data <- function(data, info = NULL, date = "date", count = "count",
 
     if (!na_rm) {
 
-      stop("The following count series have not enough data (< 4):\n", 
-           usethis::ui_value(paste0(series_to_del, 
-                                    collapse = ", ")),
-           "\nRemove these count series or use 'na_rm = TRUE'.")
+      cli::cli_abort(c(
+        "The following count series have not enough data (< 4):", 
+        "{.val {series_to_del}}",
+        i = "Remove these count series or use 'na_rm = TRUE'."
+      ))
 
     } else {
 
@@ -1147,10 +1148,10 @@ format_data <- function(data, info = NULL, date = "date", count = "count",
     }
 
     if (length(n_rows) < length(count_series)) {
-      usethis::ui_oops(paste0("Removing the following series without enough ", 
-                              "data (< 4) ", 
-                              usethis::ui_value(paste0(series_to_del, 
-                                                       collapse = ", "))))
+      cli::cli_alert_danger(c(
+        "Removing the following series without enough data (< 4) ",
+        "{.val {series_to_del}}"
+      ))
     }
   }
 
@@ -1191,10 +1192,10 @@ format_data <- function(data, info = NULL, date = "date", count = "count",
     count_series <- count_series[-which(names(count_series) %in% series_to_del)]
 
     if (length(n_rows) < length(count_series)) {
-      usethis::ui_oops(paste0("Removing the following series without valid ", 
-                              "precision measures: ", 
-                              usethis::ui_value(paste0(series_to_del, 
-                                                       collapse = ", "))))
+      cli::cli_alert_danger(c(
+        "Removing the following series without valid precision measures: ",
+        "{.val {series_to_del}}"
+      ))
     }
   }
 
@@ -1209,9 +1210,10 @@ format_data <- function(data, info = NULL, date = "date", count = "count",
 
     if (any(count_series[[i]][ , "lower_ci_conv"] ==
             count_series[[i]][ , "upper_ci_conv"])) {
-      stop(paste0("Lower and upper CI bounds cannot be strictly equal for ", 
-                  "the series.", 
-                  usethis::ui_value(names(count_series)[i])))
+      cli::cli_abort(c(
+        "Lower and upper CI bounds cannot be strictly equal for the series.",
+        "{.val {names(count_series)[i]}}"
+      ))
     }
   }
 
@@ -1270,9 +1272,10 @@ format_data <- function(data, info = NULL, date = "date", count = "count",
                                           paste0(id, "_data.RData")))
   }
 
-
-  usethis::ui_done(paste0("Detecting {usethis::ui_value(length(", 
-                          "data_series))} count series"))
+
+  cli::cli_alert_success(
+    "Detecting {.val {length(data_series)}} count series."
+  )
 
   data_series
 }
@@ -1302,8 +1305,10 @@ is_na_counts <- function(data, col, na_rm) {
     } else {
 
       pos <- which(is.na(data[ , col]))
-      usethis::ui_info(paste0("Removing {usethis::ui_value(length(pos))} ",
-                              "rows with NA values in '", col, "' field."))
+
+      cli::cli_alert_info(c(
+        "Removing {.val {length(pos)}} rows with NA values in {.field {col}} field."
+      ))
 
       data <- data[-pos, ]
     }

diff --git a/R/series-funs.R b/R/series-funs.R
@@ -34,11 +34,12 @@ get_series <- function(data, quiet = TRUE) {
   series_infos$"id" <- gsub("[[:punct:]]", "_", series_infos$"id")
 
   if (!quiet)
-    usethis::ui_done(paste0("Detecting {usethis::ui_value(nrow(series_infos))}",
-                            " series with {usethis::ui_value(length(unique(",
-                            "series_infos$location)))} location(s) and ",
-                            "{usethis::ui_value(length(unique(",
-                            "series_infos$species)))} species"))
+
+    cli::cli_alert_success(c(
+      "Detecting {.val {nrow(series_infos)}} series with ",
+      "{.val {length(unique(series_infos$location))}} location{?s}  and ",
+      "{.val {length(unique(series_infos$species))}} species."
+    ))
 
   series_infos
 }
@@ -117,8 +118,9 @@ filter_series <- function(data, species = NULL, location = NULL) {
 
   if (is.null(species) && is.null(location)) {
 
-    usethis::ui_oops(paste0("No species nor location provided to filter ", 
-                            "series."))
+    cli::cli_alert_danger(
+      "No species nor location provided to filter series"
+    )
 
     return(NULL)
   }
@@ -173,15 +175,16 @@ filter_series <- function(data, species = NULL, location = NULL) {
     series_match <- which(species_detected & location_detected)
 
     if (length(series_match)) {
-      usethis::ui_done(paste0("Found {usethis::ui_value(length(", 
-                              "series_match))} series with ", 
-                              "{usethis::ui_value(species)} and ", 
-                              "{usethis::ui_value(location)}."))
+
+      cli::cli_alert_success(c(
+        "Found {.val {length(series_match)}} series with ",
+        "{.val {species}} and {.val {location}}."
+      ))
     } else {
 
-      usethis::ui_oops(paste0("No series found with ", 
-                              "{usethis::ui_value(species)} and ", 
-                              "{usethis::ui_value(location)}."))
+      cli::cli_alert_danger(
+        "No series found with {.val {species}} and {.val {location}}."
+      )
 
       return(NULL)
     }
@@ -194,18 +197,18 @@ filter_series <- function(data, species = NULL, location = NULL) {
 
     series_match <- species_detected
 
-    usethis::ui_done(paste0("Found {usethis::ui_value(",
-                            "sum(species_detected))} ",
-                            "series with {usethis::ui_value(species)}."))
+    cli::cli_alert_success(
+      "Found {.val {sum(species_detected)}} series with {.val {species}}."
+    )
   }
 
   if (is.null(species) && !is.null(location)) {
 
     series_match <- location_detected
 
-    usethis::ui_done(paste0("Found {usethis::ui_value(",
-                            "sum(location_detected))} ",
-                            "series with {usethis::ui_value(location)}."))
+    cli::cli_alert_success(
+      "Found {.val {sum(location_detected)}} series with {.val {location}}."
+    )
   }
 
   data[series_match]