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(v1.2.0.9003) better terminal colour support
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.2.0.9002
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Date: 2020-06-03
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Version: 1.2.0.9003
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Date: 2020-06-05
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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4
NEWS.md
4
NEWS.md
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# AMR 1.2.0.9002
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## <small>Last updated: 03-Jun-2020</small>
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# AMR 1.2.0.9003
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## <small>Last updated: 05-Jun-2020</small>
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### Changed
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* Fixed a bug where `eucast_rules()` would not work on a tibble when the `tibble` or `dplyr` package was loaded
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@ -250,26 +250,63 @@ dataset_UTF8_to_ASCII <- function(df) {
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df
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}
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# replace crayon::has_color, but now also FALSE on non-interactive mode
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has_colour <- function () {
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if (Sys.getenv("TERM") == "dumb" | !interactive()) {
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# this is a base R version of crayon::has_color
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enabled <- getOption("crayon.enabled")
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if (!is.null(enabled)) {
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return(isTRUE(enabled))
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}
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rstudio_with_ansi_support <- function(x) {
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if (Sys.getenv("RSTUDIO", "") == "") {
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return(FALSE)
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}
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if ((cols <- Sys.getenv("RSTUDIO_CONSOLE_COLOR", "")) != "" && !is.na(as.numeric(cols))) {
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return(TRUE)
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}
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tryCatch(get("isAvailable", envir = asNamespace("rstudioapi"))(), error = function(e) return(FALSE)) &&
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tryCatch(get("hasFun", envir = asNamespace("rstudioapi"))("getConsoleHasColor"), error = function(e) return(FALSE))
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}
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if (rstudio_with_ansi_support() && sink.number() == 0) {
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return(TRUE)
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}
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if (!isatty(stdout())) {
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return(FALSE)
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}
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if (tolower(Sys.info()["sysname"]) == "windows") {
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if (Sys.getenv("ConEmuANSI") == "ON" | Sys.getenv("CMDER_ROOT") != "") {
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if (Sys.getenv("ConEmuANSI") == "ON") {
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return(TRUE)
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} else {
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}
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if (Sys.getenv("CMDER_ROOT") != "") {
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return(TRUE)
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}
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return(FALSE)
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}
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emacs_version <- function () {
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ver <- Sys.getenv("INSIDE_EMACS")
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if (ver == "") {
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return(NA_integer_)
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}
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"COLORTERM" %in% names(Sys.getenv()) | grepl("^screen|^xterm|^vt100|color|ansi|cygwin|linux",
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Sys.getenv("TERM"),
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ver <- gsub("'", "", ver)
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ver <- strsplit(ver, ",", fixed = TRUE)[[1]]
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ver <- strsplit(ver, ".", fixed = TRUE)[[1]]
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as.numeric(ver)
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}
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if ((Sys.getenv("EMACS") != "" || Sys.getenv("INSIDE_EMACS") != "") &&
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!is.na(emacs_version()[1]) && emacs_version()[1] >= 23) {
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return(TRUE)
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}
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if ("COLORTERM" %in% names(Sys.getenv())) {
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return(TRUE)
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}
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if (Sys.getenv("TERM") == "dumb") {
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return(FALSE)
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}
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grepl(pattern = "^screen|^xterm|^vt100|color|ansi|cygwin|linux",
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x = Sys.getenv("TERM"),
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ignore.case = TRUE,
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perl = TRUE)
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}
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# the crayon colours
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try_colour <- function(..., before, after, collapse = " ") {
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txt <- paste0(unlist(list(...)), collapse = collapse)
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@ -614,7 +614,7 @@ eucast_rules <- function(x,
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if (info == TRUE) {
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cat(font_bold(paste0("\nRules by this AMR package (",
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font_red(paste0("v", utils::packageVersion("AMR"), ", ",
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format(utils::packageDate("AMR"), "%Y"))), ")\n")))
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format(utils::packageDate("AMR"), "%Y"))), "), see ?eucast_rules\n")))
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}
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ab_enzyme <- subset(antibiotics, name %like% "/")[, c("ab", "name")]
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@ -101,6 +101,7 @@ filter_ab_class <- function(x,
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return(x.bak)
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}
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# get reference data
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ab_class.bak <- ab_class
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ab_class <- gsub("[^a-zA-Z0-9]+", ".*", ab_class)
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ab_class <- gsub("(ph|f)", "(ph|f)", ab_class)
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ab_class <- gsub("(t|th)", "(t|th)", ab_class)
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@ -109,6 +110,10 @@ filter_ab_class <- function(x,
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atc_group1 %like% ab_class |
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atc_group2 %like% ab_class)
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ab_group <- find_ab_group(ab_class)
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if (ab_group == "") {
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message(font_blue(paste0("NOTE: unknown antimicrobial class '", ab_class.bak, "', data left unchanged.")))
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return(x.bak)
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}
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# get the columns with a group names in the chosen ab class
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agents <- ab_in_data[names(ab_in_data) %in% ab_reference$ab]
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if (length(agents) == 0) {
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@ -127,12 +127,12 @@ countries_plot <- ggplot(countries_geometry) +
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countries_plot_mini <- countries_plot
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countries_plot_mini$data <- countries_plot_mini$data %>% filter(ID != "Antarctica")
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countries_plot_mini <- countries_plot_mini + scale_colour_gradient(low = "#81899B", high = "#81899B")
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# countries_plot_mini <- countries_plot_mini + scale_colour_gradient(low = "#81899B", high = "#81899B")
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countries_plot_big <- countries_plot +
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labs(title = tools::toTitleCase("Countries where the AMR package for R was downloaded from"),
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subtitle = paste0("Between March 2018 (first release) and ", format(Sys.Date(), "%B %Y"), "." #,
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#"The dots denote visitors on our website https://gitlab.io/msberends/AMR."
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)) +
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labs(title = tools::toTitleCase("Countries the AMR package for R was downloaded from"),
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subtitle = paste0("Between March 2018 (first release) and ",
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format(Sys.Date(), "%B %Y")),
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caption = "Source: https://cran-logs.rstudio.com") +
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theme(plot.title = element_text(size = 16, hjust = 0.5),
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plot.subtitle = element_text(size = 12, hjust = 0.5)) +
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geom_text(aes(x = -170,
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@ -142,12 +142,7 @@ countries_plot_big <- countries_plot +
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paste(sort(countries_name[!is.na(countries_name)]), collapse = ", ")),
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200)),
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hjust = 0,
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size = 4) # +
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# # points of visitors
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# geom_point(data = ip_tbl,
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# aes(x = x, y = y),
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# size = 1,
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# colour = "#81899B")
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size = 4)
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# main website page
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ggsave("pkgdown/logos/countries.png",
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
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</span>
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</div>
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@ -229,13 +229,13 @@
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<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1209002" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9002">
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<a href="#amr-1209002" class="anchor"></a>AMR 1.2.0.9002<small> Unreleased </small>
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<div id="amr-1209003" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9003">
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<a href="#amr-1209003" class="anchor"></a>AMR 1.2.0.9003<small> Unreleased </small>
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</h1>
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<div id="last-updated-03-jun-2020" class="section level2">
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<div id="last-updated-05-jun-2020" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-03-jun-2020" class="anchor"></a><small>Last updated: 03-Jun-2020</small>
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<a href="#last-updated-05-jun-2020" class="anchor"></a><small>Last updated: 05-Jun-2020</small>
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</h2>
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<div id="changed" class="section level3">
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<h3 class="hasAnchor">
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@ -10,7 +10,7 @@ articles:
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WHONET: WHONET.html
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benchmarks: benchmarks.html
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resistance_predict: resistance_predict.html
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last_built: 2020-06-03T12:33Z
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last_built: 2020-06-05T11:55Z
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urls:
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reference: https://msberends.gitlab.io/AMR/reference
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article: https://msberends.gitlab.io/AMR/articles
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@ -82,7 +82,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
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</span>
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</div>
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