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AMR
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website update

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dr. M.S. (Matthijs) Berends 2022-08-21 17:22:34 +02:00
parent d6676e9443
commit bdbc112f99
8 changed files with 25 additions and 36 deletions
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41
.github/workflows/check.yaml vendored
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@ -25,12 +25,8 @@
on: on:
push: push:
branches: # run after a git push on any branch in this repo
- development branches: '**'
- main
pull_request:
branches:
- main
schedule: schedule:
# run a schedule everyday at 1 AM. # run a schedule everyday at 1 AM.
# this is to check that all dependencies are still available (see R/zzz.R) # this is to check that all dependencies are still available (see R/zzz.R)
@ -55,32 +51,21 @@ jobs:
- {os: macOS-latest, r: '4.1', allowfail: false} - {os: macOS-latest, r: '4.1', allowfail: false}
- {os: macOS-latest, r: '4.0', allowfail: false} - {os: macOS-latest, r: '4.0', allowfail: false}
- {os: macOS-latest, r: '3.6', allowfail: false} - {os: macOS-latest, r: '3.6', allowfail: false}
- {os: macOS-latest, r: '3.5', allowfail: false} - {os: ubuntu-22.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: macOS-latest, r: '3.4', allowfail: false} - {os: ubuntu-22.04, r: '4.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
# - {os: macOS-latest, r: '3.3', allowfail: false} - {os: ubuntu-22.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
# - {os: macOS-latest, r: '3.2', allowfail: false} - {os: ubuntu-22.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
# - {os: macOS-latest, r: '3.1', allowfail: true} - {os: ubuntu-22.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
# - {os: macOS-latest, r: '3.0', allowfail: true} - {os: ubuntu-22.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-22.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-20.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-22.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-22.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-22.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-22.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: windows-latest, r: 'devel', allowfail: true} - {os: windows-latest, r: 'devel', allowfail: true}
- {os: windows-latest, r: '4.1', allowfail: false} - {os: windows-latest, r: '4.1', allowfail: false}
- {os: windows-latest, r: '4.0', allowfail: false} - {os: windows-latest, r: '4.0', allowfail: false}
- {os: windows-latest, r: '3.6', allowfail: false} - {os: windows-latest, r: '3.6', allowfail: false}
- {os: windows-latest, r: '3.5', allowfail: false}
- {os: windows-latest, r: '3.4', allowfail: false}
# - {os: windows-latest, r: '3.3', allowfail: false}
# - {os: windows-latest, r: '3.2', allowfail: true}
# - {os: windows-latest, r: '3.1', allowfail: true}
# - {os: windows-latest, r: '3.0', allowfail: true}
env: env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }} RSPM: ${{ matrix.config.rspm }}

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.8.1.9020 Version: 1.8.1.9021
Date: 2022-08-21 Date: 2022-08-21
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.8.1.9020 # AMR 1.8.1.9021
### New ### New
* 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. * 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.

1
R/plot.R
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@ -60,6 +60,7 @@
#' # when providing the microorganism and antibiotic, colours will show interpretations: #' # when providing the microorganism and antibiotic, colours will show interpretations:
#' plot(some_mic_values, mo = "S. aureus", ab = "ampicillin") #' plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
#' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro") #' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
#' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "uk")
#' #'
#' \donttest{ #' \donttest{
#' if (require("ggplot2")) { #' if (require("ggplot2")) {

1
_pkgdown.yml
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@ -33,6 +33,7 @@ template:
bslib: bslib:
code_font: {google: "Fira Code"} code_font: {google: "Fira Code"}
body-text-align: "justify" body-text-align: "justify"
line-height-base: 1.75
# the green "success" colour of this bootstrap theme should be the same as the green in our logo # the green "success" colour of this bootstrap theme should be the same as the green in our logo
success: "#128f76" success: "#128f76"
link-color: "#128f76" link-color: "#128f76"

1
man/plot.Rd
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@ -142,6 +142,7 @@ plot(some_rsi_values)
# when providing the microorganism and antibiotic, colours will show interpretations: # when providing the microorganism and antibiotic, colours will show interpretations:
plot(some_mic_values, mo = "S. aureus", ab = "ampicillin") plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
plot(some_disk_values, mo = "Escherichia coli", ab = "cipro") plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "uk")
\donttest{ \donttest{
if (require("ggplot2")) { if (require("ggplot2")) {

9
pkgdown/extra.js
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@ -28,15 +28,16 @@
$(document).ready(function() { $(document).ready(function() {
// replace \donttest and \dontrun texts in Examples // replace \donttest and \dontrun texts in Examples
if ($(".ref-examples pre").length > 0) { if ($("#ref-examples ~ div pre").length > 0) {
$(".ref-examples pre").html($(".ref-examples pre").html().replaceAll("# \\donttest{", "")); $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\donttest{", ""));
$(".ref-examples pre").html($(".ref-examples pre").html().replaceAll("# \\dontrun{", "")); $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\dontrun{", ""));
$(".ref-examples pre").html($(".ref-examples pre").html().replaceAll("# }", "")); $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# }", ""));
} }
// remove leading newline in code examples on changelog // remove leading newline in code examples on changelog
if ($("body .template-news").length > 0) { if ($("body .template-news").length > 0) {
$("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n<span', 'sourceCode R"><span')); $("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n<span', 'sourceCode R"><span'));
$("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R"><span></span>\n<span', 'sourceCode R"><span'));
} }
// add doctoral titles to authors // add doctoral titles to authors

4
vignettes/resistance_predict.Rmd
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@ -21,7 +21,7 @@ knitr::opts_chunk$set(
``` ```
## Needed R packages ## Needed R packages
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. 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.
Our `AMR` package depends on these packages and even extends their use and functions. Our `AMR` package depends on these packages and even extends their use and functions.
@ -57,7 +57,7 @@ The function will look for a date column itself if `col_date` is not set.
When running any of these commands, a summary of the regression model will be printed unless using `resistance_predict(..., info = FALSE)`. When running any of these commands, a summary of the regression model will be printed unless using `resistance_predict(..., info = FALSE)`.
```{r, echo = FALSE} ```{r, echo = FALSE, message = FALSE}
predict_TZP <- example_isolates %>% predict_TZP <- example_isolates %>%
resistance_predict(col_ab = "TZP", model = "binomial") resistance_predict(col_ab = "TZP", model = "binomial")
``` ```