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(v2.1.1.9251) fix colour on GitHub docs
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Package: AMR
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Version: 2.1.1.9250
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Version: 2.1.1.9251
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Date: 2025-04-21
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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2
NEWS.md
2
NEWS.md
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# AMR 2.1.1.9250
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# AMR 2.1.1.9251
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*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://amr-for-r.org/#get-this-package).)*
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@ -1200,7 +1200,8 @@ has_colour <- function() {
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AMR_env$supports_colour <- !is.null(has_color) && isTRUE(has_color())
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}
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}
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isTRUE(AMR_env$supports_colour)
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# always FALSE for GitHub documents (`index.Rmd` and `README.Rmd`)
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isTRUE(AMR_env$supports_colour) && !identical(getOption("rmarkdown.output.format"), "github_document")
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}
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# set colours if console has_colour()
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@ -1,5 +1,5 @@
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<!-- README.md is generated from README.Rmd. Please edit that file -->
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<!-- README.md is generated from README.Rmd; please edit that file. -->
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# The `AMR` Package for R
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@ -658,9 +658,11 @@ if (files_changed()) {
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# Update index.md and README.md -------------------------------------------
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if (files_changed("man/microorganisms.Rd") | files_changed("man/antimicrobials.Rd") | files_changed("man/clinical_breakpoints.Rd") | files_changed("man/antibiogram.Rd")) {
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usethis::ui_info("Update index.md")
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usethis::ui_info("Rendering {usethis::ui_field('index.md')} and {usethis::ui_field('README.md')}")
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suppressWarnings(rmarkdown::render("index.Rmd", quiet = TRUE))
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suppressWarnings(rmarkdown::render("README.Rmd", quiet = TRUE))
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unlink("index.html") # remove previews from folder
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unlink("README.html")
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}
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# Finished ----------------------------------------------------------------
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47
index.md
47
index.md
@ -152,24 +152,25 @@ example_isolates %>%
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select(bacteria,
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aminoglycosides(),
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carbapenems())
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#> [34mℹ Using column '[1mmo[22m' as input for [48;5;255mmo_fullname()[49m[39m
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#> [34mℹ Using column '[1mmo[22m' as input for [48;5;255mmo_is_gram_negative()[49m[39m
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#> [34mℹ Using column '[1mmo[22m' as input for [48;5;255mmo_is_intrinsic_resistant()[49m[39m
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#> [34mℹ For [48;5;255maminoglycosides()[49m using columns '[1mGEN[22m' (gentamicin), '[1mTOB[22m' (tobramycin), '[1mAMK[22m' (amikacin), and '[1mKAN[22m' (kanamycin)[39m
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#> [34mℹ For [48;5;255mcarbapenems()[49m using columns '[1mIPM[22m' (imipenem) and '[1mMEM[22m' (meropenem)[39m
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#> ℹ Using column 'mo' as input for mo_fullname()
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#> ℹ Using column 'mo' as input for mo_is_gram_negative()
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#> ℹ Using column 'mo' as input for mo_is_intrinsic_resistant()
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#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023). This note will be shown once per session.
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#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
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#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
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#> # A tibble: 35 × 7
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#> bacteria GEN TOB AMK KAN IPM MEM
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#> <chr> <sir> <sir> <sir> <sir> <sir> <sir>
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#> 1 Pseudomonas aeruginosa [48;5;222m[38;5;232m I [39m[49m [48;5;79m[38;5;232m S [39m[49m [38;5;249m NA[39m [48;5;217m[38;5;232m R [39m[49m [48;5;79m[38;5;232m S [39m[49m [38;5;249m NA[39m
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#> 2 Pseudomonas aeruginosa [48;5;222m[38;5;232m I [39m[49m [48;5;79m[38;5;232m S [39m[49m [38;5;249m NA[39m [48;5;217m[38;5;232m R [39m[49m [48;5;79m[38;5;232m S [39m[49m [38;5;249m NA[39m
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#> 3 Pseudomonas aeruginosa [48;5;222m[38;5;232m I [39m[49m [48;5;79m[38;5;232m S [39m[49m [38;5;249m NA[39m [48;5;217m[38;5;232m R [39m[49m [48;5;79m[38;5;232m S [39m[49m [38;5;249m NA[39m
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#> 4 Pseudomonas aeruginosa [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;217m[38;5;232m R [39m[49m [38;5;249m NA[39m [48;5;79m[38;5;232m S [39m[49m
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#> 5 Pseudomonas aeruginosa [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;217m[38;5;232m R [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m
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#> 6 Pseudomonas aeruginosa [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;217m[38;5;232m R [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m
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#> 7 Stenotrophomonas maltophilia [48;5;217m[38;5;232m R [39m[49m [48;5;217m[38;5;232m R [39m[49m [48;5;217m[38;5;232m R [39m[49m [48;5;217m[38;5;232m R [39m[49m [48;5;217m[38;5;232m R [39m[49m [48;5;217m[38;5;232m R [39m[49m
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#> 8 Pseudomonas aeruginosa [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;217m[38;5;232m R [39m[49m [38;5;249m NA[39m [48;5;79m[38;5;232m S [39m[49m
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#> 9 Pseudomonas aeruginosa [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;217m[38;5;232m R [39m[49m [38;5;249m NA[39m [48;5;79m[38;5;232m S [39m[49m
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#> 10 Pseudomonas aeruginosa [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;217m[38;5;232m R [39m[49m [48;5;79m[38;5;232m S [39m[49m [48;5;79m[38;5;232m S [39m[49m
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#> 1 Pseudomonas aeruginosa I S NA R S NA
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#> 2 Pseudomonas aeruginosa I S NA R S NA
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#> 3 Pseudomonas aeruginosa I S NA R S NA
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#> 4 Pseudomonas aeruginosa S S S R NA S
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#> 5 Pseudomonas aeruginosa S S S R S S
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#> 6 Pseudomonas aeruginosa S S S R S S
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#> 7 Stenotrophomonas maltophilia R R R R R R
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#> 8 Pseudomonas aeruginosa S S S R NA S
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#> 9 Pseudomonas aeruginosa S S S R NA S
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#> 10 Pseudomonas aeruginosa S S S R S S
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#> # ℹ 25 more rows
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```
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@ -193,9 +194,9 @@ output format automatically (such as markdown, LaTeX, HTML, etc.).
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``` r
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antibiogram(example_isolates,
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antimicrobials = c(aminoglycosides(), carbapenems()))
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#> [34mℹ For [48;5;255maminoglycosides()[49m using columns '[1mGEN[22m' (gentamicin), '[1mTOB[22m' (tobramycin), '[1mAMK[22m' (amikacin), and '[1mKAN[22m' (kanamycin)[39m
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#> [34mℹ For [48;5;255mcarbapenems()[49m using columns '[1mIPM[22m' (imipenem) and '[1mMEM[22m' (meropenem)[39m
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#> [31mℹ 502 combinations had less than [48;5;255mminimum = 30[49m results and were ignored[39m
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#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
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#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
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#> ℹ 502 combinations had less than minimum = 30 results and were ignored
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```
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| Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
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antibiogram(example_isolates,
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antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
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mo_transform = "gramstain")
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#> [31mℹ 3 combinations had less than [48;5;255mminimum = 30[49m results and were ignored[39m
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#> ℹ 3 combinations had less than minimum = 30 results and were ignored
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```
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| Pathogen | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
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mo_transform = "gramstain",
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ab_transform = "name",
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language = "uk") # Ukrainian
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#> [31mℹ 3 combinations had less than [48;5;255mminimum = 30[49m results and were ignored[39m
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#> ℹ 3 combinations had less than minimum = 30 results and were ignored
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```
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| Збудник | Гентаміцин | Тобраміцин | Ципрофлоксацин |
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@ -320,13 +321,13 @@ out <- example_isolates %>%
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# calculate AMR using resistance(), over all aminoglycosides and polymyxins:
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summarise(across(c(aminoglycosides(), polymyxins()),
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resistance))
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#> [34mℹ For [48;5;255maminoglycosides()[49m using columns '[1mGEN[22m' (gentamicin), '[1mTOB[22m' (tobramycin), '[1mAMK[22m' (amikacin), and '[1mKAN[22m' (kanamycin)[39m
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#> [34mℹ For [48;5;255mpolymyxins()[49m using column '[1mCOL[22m' (colistin)[39m
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#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
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#> ℹ For polymyxins() using column 'COL' (colistin)
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#> Warning: There was 1 warning in `summarise()`.
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#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
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#> ℹ In group 3: `ward = "Outpatient"`.
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#> Caused by warning:
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#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" ([48;5;255mminimum[49m = 30).
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#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (minimum = 30).
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out
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#> # A tibble: 3 × 6
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#> ward GEN TOB AMK KAN COL
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