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AMR
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(v1.2.0.9003) better terminal colour support

This commit is contained in:
dr. M.S. (Matthijs) Berends 2020-06-05 13:56:05 +02:00
parent 2c8d600914
commit 40221e5244
19 changed files with 79 additions and 42 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.2.0.9002
Date: 2020-06-03
Version: 1.2.0.9003
Date: 2020-06-05
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

4
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.2.0.9002
## <small>Last updated: 03-Jun-2020</small>
# AMR 1.2.0.9003
## <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

61
R/aa_helper_functions.R
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@ -250,26 +250,63 @@ dataset_UTF8_to_ASCII <- function(df) {
df
}
# replace crayon::has_color, but now also FALSE on non-interactive mode
has_colour <- function() {
if (Sys.getenv("TERM") == "dumb" | !interactive()) {
has_colour <- function () {
# this is a base R version of crayon::has_color
enabled <- getOption("crayon.enabled")
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",
Sys.getenv("TERM"),
ignore.case = TRUE,
perl = TRUE)
emacs_version <- function () {
ver <- Sys.getenv("INSIDE_EMACS")
if (ver == "") {
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)

2
R/eucast_rules.R
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@ -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")]

5
R/filter_ab_class.R
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@ -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) {

17
data-raw/country_analysis.R
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@ -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"),
subtitle = paste0("Between March 2018 (first release) and ", format(Sys.Date(), "%B %Y"), "." #,
#"The dots denote visitors on our website https://gitlab.io/msberends/AMR."
)) +
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")),
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) # +
# # points of visitors
# geom_point(data = ip_tbl,
# aes(x = x, y = y),
# size = 1,
# colour = "#81899B")
size = 4)
# main website page
ggsave("pkgdown/logos/countries.png",

2
docs/404.html
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@ -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>

2
docs/LICENSE-text.html
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@ -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>

2
docs/articles/index.html
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@ -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>

2
docs/authors.html
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@ -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>

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docs/index.html
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@ -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>

12
docs/news/index.html
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@ -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">
<h1 class="page-header" data-toc-text="1.2.0.9002">
<a href="#amr-1209002" class="anchor"></a>AMR 1.2.0.9002<small> Unreleased </small>
<div id="amr-1209003" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9003">
<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">

2
docs/pkgdown.yml
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@ -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

2
docs/reference/filter_ab_class.html
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@ -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>

2
docs/reference/index.html
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@ -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>

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