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super big huge update

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dr. M.S. (Matthijs) Berends
2022-09-16 23:15:23 +02:00
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37
vignettes/datasets.Rmd
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@ -115,7 +115,7 @@ 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.
## `microorganisms`: Microbial Taxonomy (currently accepted names)
## `microorganisms`: Full Microbial Taxonomy
`r structure_txt(microorganisms)`
@ -127,11 +127,11 @@ This data set is in R available as `microorganisms`, after you load the `AMR` pa
### Source
Our full taxonomy of microorganisms is based on the authoritative and comprehensive:
This data set contains the full microbial taxonomy of `r nr2char(length(unique(AMR::microorganisms$kingdom[!AMR::microorganisms$kingdom %like% "unknown"])))` kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF):
* [Catalogue of Life](http://www.catalogueoflife.org) (included version: `r AMR:::CATALOGUE_OF_LIFE$year`)
* [List of Prokaryotic names with Standing in Nomenclature](https://lpsn.dsmz.de) (LPSN, last updated: `r AMR:::CATALOGUE_OF_LIFE$yearmonth_LPSN`)
* `r AMR:::SNOMED_VERSION$current_source`, retrieved from the [`r AMR:::SNOMED_VERSION$title`](`r AMR:::SNOMED_VERSION$url`), OID `r AMR:::SNOMED_VERSION$current_oid`, version `r AMR:::SNOMED_VERSION$current_version`
* `r AMR:::TAXONOMY_VERSION$LPSN$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$LPSN$url`> on `r documentation_date(AMR:::TAXONOMY_VERSION$LPSN$accessed_date)`.
* `r AMR:::TAXONOMY_VERSION$GBIF$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$GBIF$url`> on `r documentation_date(AMR:::TAXONOMY_VERSION$GBIF$accessed_date)`.
* `r AMR:::TAXONOMY_VERSION$SNOMED$citation` URL: <`r AMR:::TAXONOMY_VERSION$SNOMED$url`>
### Example content
@ -153,33 +153,6 @@ microorganisms %>%
print_df()
```
## `microorganisms.old`: Microbial Taxonomy (previously accepted names)
`r structure_txt(microorganisms.old)`
**Note:** remember that the 'ref' columns contains the scientific reference to the old taxonomic entries, i.e. of column *'fullname'*. For the scientific reference of the new names, i.e. of column *'fullname_new'*, see the `microorganisms` data set.
This data set is in R available as `microorganisms.old`, after you load the `AMR` package.
`r download_txt("microorganisms.old")`
### Source
This data set contains old, previously accepted taxonomic names. The data sources are the same as the `microorganisms` data set:
* [Catalogue of Life](http://www.catalogueoflife.org) (included version: `r AMR:::CATALOGUE_OF_LIFE$year`)
* [List of Prokaryotic names with Standing in Nomenclature](https://lpsn.dsmz.de) (LPSN, last updated: `r AMR:::CATALOGUE_OF_LIFE$yearmonth_LPSN`)
### Example content
Example rows when filtering on *Escherichia*:
```{r, echo = FALSE}
microorganisms.old %>%
filter(fullname %like% "^Escherichia") %>%
print_df()
```
## `antibiotics`: Antibiotic Agents

4
vignettes/welcome_to_AMR.Rmd
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@ -36,7 +36,7 @@ This package is fully independent of any other R package and works on Windows, m
This package can be used for:
* Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature
* Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF)
* Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines
* Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records
* Determining first isolates to be used for AMR data analysis
@ -55,7 +55,7 @@ This package can be used for:
All reference data sets (about microorganisms, antibiotics, R/SI 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.
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). This R package 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)) but is actively and durably maintained (see [changelog)](https://msberends.github.io/AMR/news/index.html)) 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). This R package formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://research.rug.nl/en/publications/a-new-instrument-for-microbial-epidemiology-empowering-antimicrob) and [DOI 10.33612/diss.192486375](https://research.rug.nl/en/publications/data-science-for-infection-management-amp-antimicrobial-stewardsh)) but is actively and durably maintained (see [changelog)](https://msberends.github.io/AMR/news/index.html)) by two public healthcare organisations in the Netherlands.
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