(v1.2.0.9003) better terminal colour support

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.2.0.9002
+Version: 1.2.0.9003
-Date: 2020-06-03
+Date: 2020-06-05
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 1.2.0.9002
+# AMR 1.2.0.9003
-## <small>Last updated: 03-Jun-2020</small>
+## <small>Last updated: 05-Jun-2020</small>
 
 ### Changed
 * Fixed a bug where `eucast_rules()` would not work on a tibble when the `tibble` or `dplyr` package was loaded

R/aa_helper_functions.R

@@ -250,26 +250,63 @@ dataset_UTF8_to_ASCII <- function(df) {
   df
 }
 
-
+has_colour <- function () {
-# replace crayon::has_color, but now also FALSE on non-interactive mode
+  # this is a base R version of crayon::has_color
-has_colour <- function() {
+  enabled <- getOption("crayon.enabled")
-  if (Sys.getenv("TERM") == "dumb" | !interactive()) {
+  if (!is.null(enabled)) {
+    return(isTRUE(enabled))
+  }
+  rstudio_with_ansi_support <- function(x) {
+    if (Sys.getenv("RSTUDIO", "") == "") {
+      return(FALSE)
+    }
+    if ((cols <- Sys.getenv("RSTUDIO_CONSOLE_COLOR", "")) != "" && !is.na(as.numeric(cols))) {
+      return(TRUE)
+    }
+    tryCatch(get("isAvailable", envir = asNamespace("rstudioapi"))(), error = function(e) return(FALSE)) &&
+      tryCatch(get("hasFun", envir = asNamespace("rstudioapi"))("getConsoleHasColor"), error = function(e) return(FALSE))
+  }
+  if (rstudio_with_ansi_support() && sink.number() == 0) {
+    return(TRUE)
+  }
+  if (!isatty(stdout())) {
     return(FALSE)
   }
   if (tolower(Sys.info()["sysname"]) == "windows") {
-    if (Sys.getenv("ConEmuANSI") == "ON" | Sys.getenv("CMDER_ROOT") != "") {
+    if (Sys.getenv("ConEmuANSI") == "ON") {
       return(TRUE)
-    } else {
-      return(FALSE)
     }
+    if (Sys.getenv("CMDER_ROOT") != "") {
+      return(TRUE)
+    }
+    return(FALSE)
   }
-  "COLORTERM" %in% names(Sys.getenv()) | grepl("^screen|^xterm|^vt100|color|ansi|cygwin|linux",
+  emacs_version <- function () {
-                                               Sys.getenv("TERM"), 
+    ver <- Sys.getenv("INSIDE_EMACS")
-                                               ignore.case = TRUE,
+    if (ver == "") {
-                                               perl = TRUE)
+      return(NA_integer_)
+    }
+    ver <- gsub("'", "", ver)
+    ver <- strsplit(ver, ",", fixed = TRUE)[[1]]
+    ver <- strsplit(ver, ".", fixed = TRUE)[[1]]
+    as.numeric(ver)
+  }
+  if ((Sys.getenv("EMACS") != "" || Sys.getenv("INSIDE_EMACS") != "") &&
+      !is.na(emacs_version()[1]) && emacs_version()[1] >= 23) {
+    return(TRUE)
+  }
+  if ("COLORTERM" %in% names(Sys.getenv())) {
+    return(TRUE)
+  }
+  if (Sys.getenv("TERM") == "dumb") {
+    return(FALSE)
+  }
+  grepl(pattern = "^screen|^xterm|^vt100|color|ansi|cygwin|linux", 
+        x = Sys.getenv("TERM"),
+        ignore.case = TRUE,
+        perl = TRUE)
 }
 
-
 # the crayon colours
 try_colour <- function(..., before, after, collapse = " ") {
   txt <- paste0(unlist(list(...)), collapse = collapse)

R/eucast_rules.R

@@ -614,7 +614,7 @@ eucast_rules <- function(x,
     if (info == TRUE) {
       cat(font_bold(paste0("\nRules by this AMR package (",
                            font_red(paste0("v", utils::packageVersion("AMR"), ", ", 
-                                           format(utils::packageDate("AMR"), "%Y"))), ")\n")))
+                                           format(utils::packageDate("AMR"), "%Y"))), "), see ?eucast_rules\n")))
     }
     
     ab_enzyme <- subset(antibiotics, name %like% "/")[, c("ab", "name")]

R/filter_ab_class.R

@@ -101,6 +101,7 @@ filter_ab_class <- function(x,
     return(x.bak)
   }
   # get reference data
+  ab_class.bak <- ab_class
   ab_class <- gsub("[^a-zA-Z0-9]+", ".*", ab_class)
   ab_class <- gsub("(ph|f)", "(ph|f)", ab_class)
   ab_class <- gsub("(t|th)", "(t|th)", ab_class)
@@ -109,6 +110,10 @@ filter_ab_class <- function(x,
                            atc_group1 %like% ab_class | 
                            atc_group2 %like% ab_class)
   ab_group <- find_ab_group(ab_class)
+  if (ab_group == "") {
+    message(font_blue(paste0("NOTE: unknown antimicrobial class '", ab_class.bak, "', data left unchanged.")))
+    return(x.bak)
+  }
   # get the columns with a group names in the chosen ab class
   agents <- ab_in_data[names(ab_in_data) %in% ab_reference$ab]
   if (length(agents) == 0) {

data-raw/country_analysis.R

@@ -127,12 +127,12 @@ countries_plot <- ggplot(countries_geometry) +
 
 countries_plot_mini <- countries_plot
 countries_plot_mini$data <- countries_plot_mini$data %>% filter(ID != "Antarctica")
-countries_plot_mini <- countries_plot_mini + scale_colour_gradient(low = "#81899B", high = "#81899B")
+# countries_plot_mini <- countries_plot_mini + scale_colour_gradient(low = "#81899B", high = "#81899B")
 countries_plot_big <- countries_plot +
-  labs(title = tools::toTitleCase("Countries where the AMR package for R was downloaded from"),
+  labs(title = tools::toTitleCase("Countries the AMR package for R was downloaded from"),
-       subtitle = paste0("Between March 2018 (first release) and ", format(Sys.Date(), "%B %Y"), "." #,
+       subtitle = paste0("Between March 2018 (first release) and ",
-                         #"The dots denote visitors on our website https://gitlab.io/msberends/AMR."
+                         format(Sys.Date(), "%B %Y")),
-                         )) +
+       caption = "Source: https://cran-logs.rstudio.com") +
   theme(plot.title = element_text(size = 16, hjust = 0.5),
         plot.subtitle = element_text(size = 12, hjust = 0.5)) +
   geom_text(aes(x = -170,
@@ -142,12 +142,7 @@ countries_plot_big <- countries_plot +
                                                  paste(sort(countries_name[!is.na(countries_name)]), collapse = ", ")),
                                           200)),
             hjust = 0,
-             size = 4) # +
+             size = 4) 
-  # # points of visitors
-  # geom_point(data = ip_tbl,
-  #            aes(x = x, y = y), 
-  #            size = 1,
-  #            colour = "#81899B")
 
 # main website page
 ggsave("pkgdown/logos/countries.png",

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
       </span>
     </div>
 

docs/index.html

@@ -43,7 +43,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
       </span>
     </div>
 

docs/news/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
       </span>
     </div>
 
@@ -229,13 +229,13 @@
       <small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1209002" class="section level1">
+    <div id="amr-1209003" class="section level1">
-<h1 class="page-header" data-toc-text="1.2.0.9002">
+<h1 class="page-header" data-toc-text="1.2.0.9003">
-<a href="#amr-1209002" class="anchor"></a>AMR 1.2.0.9002<small> Unreleased </small>
+<a href="#amr-1209003" class="anchor"></a>AMR 1.2.0.9003<small> Unreleased </small>
 </h1>
-<div id="last-updated-03-jun-2020" class="section level2">
+<div id="last-updated-05-jun-2020" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-03-jun-2020" class="anchor"></a><small>Last updated: 03-Jun-2020</small>
+<a href="#last-updated-05-jun-2020" class="anchor"></a><small>Last updated: 05-Jun-2020</small>
 </h2>
 <div id="changed" class="section level3">
 <h3 class="hasAnchor">

docs/pkgdown.yml

@@ -10,7 +10,7 @@ articles:
   WHONET: WHONET.html
   benchmarks: benchmarks.html
   resistance_predict: resistance_predict.html
-last_built: 2020-06-03T12:33Z
+last_built: 2020-06-05T11:55Z
 urls:
   reference: https://msberends.gitlab.io/AMR/reference
   article: https://msberends.gitlab.io/AMR/articles

docs/reference/filter_ab_class.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
       </span>
     </div>
 

docs/reference/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
       </span>
     </div>