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New mo algorithm, prepare for 2.0

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Dr. Matthijs Berends
2022-10-05 09:12:22 +02:00
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commit cd2acc4a29
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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