P281424
/
AMR
mirror of https://github.com/msberends/AMR.git
1
0
Fork 0
Code Releases Activity

website update

This commit is contained in:
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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

41
.github/workflows/check.yaml vendored
View File

@ -25,12 +25,8 @@
on:
push:
branches:
- development
- main
pull_request:
branches:
- main
# run after a git push on any branch in this repo
branches: '**'
schedule:
# run a schedule everyday at 1 AM.
# 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: '4.0', allowfail: false}
- {os: macOS-latest, r: '3.6', allowfail: false}
- {os: macOS-latest, r: '3.5', allowfail: false}
- {os: macOS-latest, r: '3.4', allowfail: false}
# - {os: macOS-latest, r: '3.3', allowfail: false}
# - {os: macOS-latest, r: '3.2', allowfail: false}
# - {os: macOS-latest, r: '3.1', allowfail: true}
# - {os: macOS-latest, r: '3.0', allowfail: true}
- {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/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: ubuntu-22.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '4.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: windows-latest, r: 'devel', allowfail: true}
- {os: windows-latest, r: '4.1', allowfail: false}
- {os: windows-latest, r: '4.0', 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:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}

2
DESCRIPTION
View File

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

2
NEWS.md
View File

@ -1,4 +1,4 @@
# AMR 1.8.1.9020
# AMR 1.8.1.9021
### 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.

1
R/plot.R
View File

@ -60,6 +60,7 @@
#' # when providing the microorganism and antibiotic, colours will show interpretations:
#' 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", language = "uk")
#'
#' \donttest{
#' if (require("ggplot2")) {

1
_pkgdown.yml
View File

@ -33,6 +33,7 @@ template:
bslib:
code_font: {google: "Fira Code"}
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
success: "#128f76"
link-color: "#128f76"

1
man/plot.Rd
View File

@ -142,6 +142,7 @@ plot(some_rsi_values)
# when providing the microorganism and antibiotic, colours will show interpretations:
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", language = "uk")
\donttest{
if (require("ggplot2")) {

9
pkgdown/extra.js
View File

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

4
vignettes/resistance_predict.Rmd
View File

@ -21,7 +21,7 @@ knitr::opts_chunk$set(
```
## 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.
@ -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)`.
```{r, echo = FALSE}
```{r, echo = FALSE, message = FALSE}
predict_TZP <- example_isolates %>%
resistance_predict(col_ab = "TZP", model = "binomial")
```