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set up Git LFS for large files

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dr. M.S. (Matthijs) Berends
2022-08-26 14:02:08 +02:00
parent e05d0365a9
commit 4da32e3d40
31 changed files with 97 additions and 9 deletions
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vignettes/datasets.Rmd
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@ -25,7 +25,7 @@ knitr::opts_chunk$set(
library(AMR)
library(dplyr)
options(knitr.kable.NA = '')
options(knitr.kable.NA = "")
structure_txt <- function(dataset) {
paste0("A data set with ",
@ -94,8 +94,6 @@ All reference data (about microorganisms, antibiotics, R/SI interpretation, EUCA
On this page, we explain how to download them and how the structure of the data sets look like.
<p class="dataset-within-r">If you are reading this page from within R, please <a href="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a>, which is automatically updated with every code change.</p>
## Microorganisms (currently accepted names)
`r structure_txt(microorganisms)`
@ -104,8 +102,6 @@ This data set is in R available as `microorganisms`, after you load the `AMR` pa
`r download_txt("microorganisms")`
**NOTE: The exported files for SAS, SPSS and Stata do not contain SNOMED codes, as their file size would exceed 100 MB; the file size limit of GitHub.** Advice? Use R instead.
### Source
Our full taxonomy of microorganisms is based on the authoritative and comprehensive: