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website update
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.github/workflows/check.yaml
vendored
41
.github/workflows/check.yaml
vendored
@ -25,12 +25,8 @@
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on:
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push:
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branches:
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- development
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- main
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pull_request:
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branches:
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- main
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# run after a git push on any branch in this repo
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branches: '**'
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schedule:
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# run a schedule everyday at 1 AM.
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# this is to check that all dependencies are still available (see R/zzz.R)
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@ -55,32 +51,21 @@ jobs:
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- {os: macOS-latest, r: '4.1', allowfail: false}
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- {os: macOS-latest, r: '4.0', allowfail: false}
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- {os: macOS-latest, r: '3.6', allowfail: false}
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- {os: macOS-latest, r: '3.5', allowfail: false}
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- {os: macOS-latest, r: '3.4', allowfail: false}
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# - {os: macOS-latest, r: '3.3', allowfail: false}
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# - {os: macOS-latest, r: '3.2', allowfail: false}
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# - {os: macOS-latest, r: '3.1', allowfail: true}
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# - {os: macOS-latest, r: '3.0', allowfail: true}
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- {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-22.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '4.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: windows-latest, r: 'devel', allowfail: true}
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- {os: windows-latest, r: '4.1', allowfail: false}
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- {os: windows-latest, r: '4.0', allowfail: false}
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- {os: windows-latest, r: '3.6', allowfail: false}
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- {os: windows-latest, r: '3.5', allowfail: false}
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- {os: windows-latest, r: '3.4', allowfail: false}
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# - {os: windows-latest, r: '3.3', allowfail: false}
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# - {os: windows-latest, r: '3.2', allowfail: true}
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# - {os: windows-latest, r: '3.1', allowfail: true}
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# - {os: windows-latest, r: '3.0', allowfail: true}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.8.1.9020
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Version: 1.8.1.9021
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Date: 2022-08-21
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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
@ -1,4 +1,4 @@
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# AMR 1.8.1.9020
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# AMR 1.8.1.9021
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### New
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* EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.
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1
R/plot.R
1
R/plot.R
@ -60,6 +60,7 @@
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#' # when providing the microorganism and antibiotic, colours will show interpretations:
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#' plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
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#' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
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#' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "uk")
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#'
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#' \donttest{
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#' if (require("ggplot2")) {
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@ -33,6 +33,7 @@ template:
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bslib:
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code_font: {google: "Fira Code"}
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body-text-align: "justify"
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line-height-base: 1.75
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# the green "success" colour of this bootstrap theme should be the same as the green in our logo
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success: "#128f76"
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link-color: "#128f76"
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@ -142,6 +142,7 @@ plot(some_rsi_values)
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# when providing the microorganism and antibiotic, colours will show interpretations:
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plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
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plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
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plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "uk")
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\donttest{
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if (require("ggplot2")) {
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@ -28,15 +28,16 @@
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$(document).ready(function() {
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// replace \donttest and \dontrun texts in Examples
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if ($(".ref-examples pre").length > 0) {
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$(".ref-examples pre").html($(".ref-examples pre").html().replaceAll("# \\donttest{", ""));
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$(".ref-examples pre").html($(".ref-examples pre").html().replaceAll("# \\dontrun{", ""));
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$(".ref-examples pre").html($(".ref-examples pre").html().replaceAll("# }", ""));
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if ($("#ref-examples ~ div pre").length > 0) {
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$("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\donttest{", ""));
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$("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\dontrun{", ""));
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$("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# }", ""));
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}
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// remove leading newline in code examples on changelog
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if ($("body .template-news").length > 0) {
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$("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n<span', 'sourceCode R"><span'));
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$("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R"><span></span>\n<span', 'sourceCode R"><span'));
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}
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// add doctoral titles to authors
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@ -21,7 +21,7 @@ knitr::opts_chunk$set(
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```
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## Needed R packages
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As with many uses in R, we need some additional packages for AMR data analysis. Our package works closely together with the [tidyverse packages](https://www.tidyverse.org) [`dplyr`](https://dplyr.tidyverse.org/) and [`ggplot2`](https://ggplot2.tidyverse.org) by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.
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As with many uses in R, we need some additional packages for AMR data analysis. Our package works closely together with the [tidyverse packages](https://www.tidyverse.org) [`dplyr`](https://dplyr.tidyverse.org/) and [`ggplot2`](https://ggplot2.tidyverse.org). The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.
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Our `AMR` package depends on these packages and even extends their use and functions.
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@ -57,7 +57,7 @@ The function will look for a date column itself if `col_date` is not set.
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When running any of these commands, a summary of the regression model will be printed unless using `resistance_predict(..., info = FALSE)`.
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```{r, echo = FALSE}
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```{r, echo = FALSE, message = FALSE}
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predict_TZP <- example_isolates %>%
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resistance_predict(col_ab = "TZP", model = "binomial")
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```
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