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(v1.5.0.9041) SNOMED update

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dr. M.S. (Matthijs) Berends
2021-03-11 21:42:30 +01:00
parent 8d6ceb6a15
commit 4e0a9533ad
65 changed files with 86943 additions and 67626 deletions
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15
vignettes/datasets.Rmd
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@ -31,12 +31,12 @@ structure_txt <- function(dataset) {
paste0("A data set with ",
format(nrow(dataset), big.mark = ","), " rows and ",
ncol(dataset), " columns, containing the following column names: \n",
AMR:::vector_or(colnames(dataset), quotes = "*", last_sep = " and "), ".")
AMR:::vector_or(colnames(dataset), quotes = "*", last_sep = " and ", sort = FALSE), ".")
}
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")),
trimws(format(file.mtime(paste0("../data/", filename, ".rda")), "%e %B %Y %H:%M:%S %Z", tz = "UTC")),
". Find more info about the structure of this data set [here](https://msberends.github.io/AMR/reference/", ifelse(filename == "antivirals", "antibiotics", filename), ".html).\n")
github_base <- "https://github.com/msberends/AMR/raw/master/data-raw/"
filename <- paste0("../data-raw/", filename)
@ -104,12 +104,15 @@ 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:
* [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`)
* [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$current_version`
### Example content
@ -147,8 +150,8 @@ This data set is in R available as `microorganisms.old`, after you load the `AMR
This data set contains old, previously accepted taxonomic names. The data sources are the same as the `microorganisms` data set:
* [Catalogue of Life](http://www.catalogueoflife.org) (included version: `r AMR:::catalogue_of_life$year`)
* [List of Prokaryotic names with Standing in Nomenclature](https://lpsn.dsmz.de) (LPSN, last updated: `r AMR:::catalogue_of_life$yearmonth_LPSN`)
* [Catalogue of Life](http://www.catalogueoflife.org) (included version: `r AMR:::CATALOGUE_OF_LIFE$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