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dr. M.S. (Matthijs) Berends
2025-04-08 15:54:30 +01:00
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4
vignettes/WHONET.Rmd
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@ -32,7 +32,7 @@ library(readxl)
data <- read_excel(path = "path/to/your/file.xlsx")
```
This package comes with an [example data set `WHONET`](https://msberends.github.io/AMR/reference/WHONET.html). We will use it for this analysis.
This package comes with an [example data set `WHONET`](https://amr-for-r.org/reference/WHONET.html). We will use it for this analysis.
### Preparation
@ -47,7 +47,7 @@ library(cleaner) # to create frequency tables
We will have to transform some variables to simplify and automate the analysis:
* Microorganisms should be transformed to our own microorganism codes (called an `mo`) using [our Catalogue of Life reference data set](https://msberends.github.io/AMR/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms.
* Microorganisms should be transformed to our own microorganism codes (called an `mo`) using [our Catalogue of Life reference data set](https://amr-for-r.org/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms.
* Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values `"S"`, `"I"` or `"R"`. That is exactly where the `as.sir()` function is for.
```{r}

4
vignettes/datasets.Rmd
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@ -40,7 +40,7 @@ download_txt <- function(filename) {
msg <- paste0(
"It was last updated on ",
trimws(format(file.mtime(paste0("../data/", filename, ".rda")), "%e %B %Y %H:%M:%S %Z", tz = "UTC")),
". Find more info about the contents, (scientific) source, and structure of this [data set here](https://msberends.github.io/AMR/reference/", ifelse(filename == "antivirals", "antimicrobials", filename), ".html).\n"
". Find more info about the contents, (scientific) source, and structure of this [data set here](https://amr-for-r.org/reference/", ifelse(filename == "antivirals", "antimicrobials", filename), ".html).\n"
)
github_base <- "https://github.com/msberends/AMR/raw/main/data-raw/datasets/"
local_filename <- paste0("../data-raw/datasets/", filename)
@ -110,7 +110,7 @@ print_df <- function(x, rows = 6) {
All reference data (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) in this `AMR` package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated text files that are machine-readable and suitable for input in any software program, such as laboratory information systems.
> If you are working in Python, be sure to use our [AMR for Python](https://msberends.github.io/AMR/articles/AMR_for_Python.html) package. It allows all relevant AMR data sets to be natively available in Python.
> If you are working in Python, be sure to use our [AMR for Python](https://amr-for-r.org/articles/AMR_for_Python.html) package. It allows all relevant AMR data sets to be natively available in Python.
## `microorganisms`: Full Microbial Taxonomy

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vignettes/welcome_to_AMR.Rmd
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@ -22,11 +22,11 @@ knitr::opts_chunk$set(
)
```
Note: to keep the package size as small as possible, we only include this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDROs, find explanation of EUCAST and CLSI breakpoints, and much more: <https://msberends.github.io/AMR/articles/>.
Note: to keep the package size as small as possible, we only include this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDROs, find explanation of EUCAST and CLSI breakpoints, and much more: <https://www.amr-for-r.org/articles/>.
----
The `AMR` package is a [free and open-source](https://msberends.github.io/AMR/#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. [Many different researchers](https://msberends.github.io/AMR/authors.html) from around the globe are continually helping us to make this a successful and durable project!
The `AMR` package is a [free and open-source](https://www.amr-for-r.org/) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. [Many different researchers](https://www.amr-for-r.org/authors.html) from around the globe are continually helping us to make this a successful and durable project!
This work was published in the Journal of Statistical Software (Volume 104(3); [DOI 10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)).
@ -55,12 +55,12 @@ This package can be used for:
* Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to SIR
* Principal component analysis for AMR
All reference data sets (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) in this `AMR` package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find [all download links on our website](https://msberends.github.io/AMR/articles/datasets.html), which is automatically updated with every code change.
All reference data sets (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) in this `AMR` package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find [all download links on our website](https://www.amr-for-r.org/articles/datasets.html), which is automatically updated with every code change.
This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl), and is being [actively and durably maintained](https://msberends.github.io/AMR/news/) by two public healthcare organisations in the Netherlands.
This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl), and is being [actively and durably maintained](https://www.amr-for-r.org/news/) by two public healthcare organisations in the Netherlands.
----
<small>
This AMR package for R is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](https://msberends.github.io/AMR/LICENSE-text.html). These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package.
This AMR package for R is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](https://www.amr-for-r.org/LICENSE-text.html). These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package.
</small>