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disk documentation fix

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dr. M.S. (Matthijs) Berends 2022-08-21 16:52:09 +02:00
parent 952d16de33
commit d6676e9443
7 changed files with 15 additions and 14 deletions
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19
.Rbuildignore
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@ -23,14 +23,15 @@
^data-raw$ ^data-raw$
^\.lintr$ ^\.lintr$
^tests/testthat/_snaps$ ^tests/testthat/_snaps$
^vignettes/AMR.Rmd$ ^vignettes/AMR\.Rmd$
^vignettes/benchmarks.Rmd$ ^vignettes/benchmarks\.Rmd$
^vignettes/datasets.Rmd$ ^vignettes/*\.not$
^vignettes/EUCAST.Rmd$ ^vignettes/datasets\.Rmd$
^vignettes/MDR.Rmd$ ^vignettes/EUCAST\.Rmd$
^vignettes/PCA.Rmd$ ^vignettes/MDR\.Rmd$
^vignettes/resistance_predict.Rmd$ ^vignettes/PCA\.Rmd$
^vignettes/SPSS.Rmd$ ^vignettes/resistance_predict\.Rmd$
^vignettes/WHONET.Rmd$ ^vignettes/SPSS\.Rmd$
^vignettes/WHONET\.Rmd$
^logo.svg$ ^logo.svg$
^CRAN-SUBMISSION$ ^CRAN-SUBMISSION$

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.8.1.9019 Version: 1.8.1.9020
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 1.8.1.9019 # AMR 1.8.1.9020
### 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.

2
R/disk.R
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@ -44,7 +44,7 @@
#' df[, 2:5] <- lapply(df[, 2:5], as.disk) #' df[, 2:5] <- lapply(df[, 2:5], as.disk)
#' str(df) #' str(df)
#' #'
#' #' \donttest{ #' \donttest{
#' # transforming is easier with dplyr: #' # transforming is easier with dplyr:
#' if (require("dplyr")) { #' if (require("dplyr")) {
#' df %>% mutate(across(AMP:TOB, as.disk)) #' df %>% mutate(across(AMP:TOB, as.disk))

2
man/as.disk.Rd
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@ -43,7 +43,7 @@ df <- data.frame(microorganism = "Escherichia coli",
df[, 2:5] <- lapply(df[, 2:5], as.disk) df[, 2:5] <- lapply(df[, 2:5], as.disk)
str(df) str(df)
#' \donttest{ \donttest{
# transforming is easier with dplyr: # transforming is easier with dplyr:
if (require("dplyr")) { if (require("dplyr")) {
df \%>\% mutate(across(AMP:TOB, as.disk)) df \%>\% mutate(across(AMP:TOB, as.disk))

2
vignettes/AMR.Rmd
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@ -1,6 +1,6 @@
--- ---
title: "How to conduct AMR data analysis" title: "How to conduct AMR data analysis"
author: "Dr Matthijs Berends" author: "Dr. Matthijs Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`' date: '`r format(Sys.Date(), "%d %B %Y")`'
output: output:
rmarkdown::html_vignette: rmarkdown::html_vignette:

0
vignettes/benchmarks.Rmd → vignettes/benchmarks.Rmd.not
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