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(v2.1.1.9081) HUGE microorganisms update for fungi!

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dr. M.S. (Matthijs) Berends
2024-09-29 22:17:56 +02:00
parent a558f4c121
commit ac1c40d8bb
119 changed files with 36445 additions and 67400 deletions
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10
vignettes/datasets.Rmd
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@ -80,7 +80,7 @@ download_txt <- function(filename) {
create_txt(excel, "xlsx", "Microsoft Excel workbook", file.exists(excel)),
create_txt(feather, "feather", "Apache Feather file", file.exists(feather)),
create_txt(parquet, "parquet", "Apache Parquet file", file.exists(parquet)),
create_txt(xpt, "xpt", "SAS transport (XPT) file", file.exists(xpt)),
# create_txt(xpt, "xpt", "SAS transport (XPT) file", file.exists(xpt)),
create_txt(spss, "sav", "IBM SPSS Statistics data file", file.exists(spss)),
create_txt(stata, "dta", "Stata DTA file", file.exists(stata))
)
@ -111,7 +111,7 @@ print_df <- function(x, rows = 6) {
}
```
All reference data (about microorganisms, antibiotics, 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, SAS, 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.
All reference data (about microorganisms, antibiotics, 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.
On this page, we explain how to download them and how the structure of the data sets look like.
@ -123,7 +123,7 @@ 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 contain only the first 50 SNOMED codes per record, as their file size would otherwise exceed 100 MB; the file size limit of GitHub.** Their file structures and compression techniques are very inefficient. Advice? Use R instead. It's free and much better in many ways.
**NOTE: The exported files for SPSS and Stata contain only the first 50 SNOMED codes per record, as their file size would otherwise exceed 100 MB; the file size limit of GitHub.** Their file structures and compression techniques are very inefficient. Advice? Use R instead. It's free and much better in many ways.
The tab-separated text file and Microsoft Excel workbook both contain all SNOMED codes as comma separated values.
@ -166,7 +166,7 @@ This data set is in R available as `antibiotics`, after you load the `AMR` packa
`r download_txt("antibiotics")`
The tab-separated text file and Microsoft Excel workbook, and SAS, SPSS and Stata files all contain the ATC codes, common abbreviations, trade names and LOINC codes as comma separated values.
The tab-separated text, Microsoft Excel, SPSS, and Stata files all contain the ATC codes, common abbreviations, trade names and LOINC codes as comma separated values.
### Source
@ -194,7 +194,7 @@ This data set is in R available as `antivirals`, after you load the `AMR` packag
`r download_txt("antivirals")`
The tab-separated text file and Microsoft Excel workbook, and SAS, SPSS and Stata files all contain the trade names and LOINC codes as comma separated values.
The tab-separated text, Microsoft Excel, SPSS, and Stata files all contain the trade names and LOINC codes as comma separated values.
### Source

2
vignettes/welcome_to_AMR.Rmd
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@ -55,7 +55,7 @@ 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, antibiotics, 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, SAS, 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, antibiotics, 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.
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.