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(v1.5.0.9041) SNOMED update
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@ -31,12 +31,12 @@ structure_txt <- function(dataset) {
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paste0("A data set with ",
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format(nrow(dataset), big.mark = ","), " rows and ",
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ncol(dataset), " columns, containing the following column names: \n",
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AMR:::vector_or(colnames(dataset), quotes = "*", last_sep = " and "), ".")
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AMR:::vector_or(colnames(dataset), quotes = "*", last_sep = " and ", sort = FALSE), ".")
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}
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download_txt <- function(filename) {
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msg <- paste0("It was last updated on ",
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trimws(format(file.mtime(paste0("../data/", filename, ".rda")), "%e %B %Y %H:%M:%S %Z")),
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trimws(format(file.mtime(paste0("../data/", filename, ".rda")), "%e %B %Y %H:%M:%S %Z", tz = "UTC")),
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". Find more info about the structure of this data set [here](https://msberends.github.io/AMR/reference/", ifelse(filename == "antivirals", "antibiotics", filename), ".html).\n")
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github_base <- "https://github.com/msberends/AMR/raw/master/data-raw/"
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filename <- paste0("../data-raw/", filename)
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@ -104,12 +104,15 @@ This data set is in R available as `microorganisms`, after you load the `AMR` pa
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`r download_txt("microorganisms")`
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**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.
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### Source
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Our full taxonomy of microorganisms is based on the authoritative and comprehensive:
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* [Catalogue of Life](http://www.catalogueoflife.org) (included version: `r AMR:::catalogue_of_life$year`)
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* [List of Prokaryotic names with Standing in Nomenclature](https://lpsn.dsmz.de) (LPSN, last updated: `r AMR:::catalogue_of_life$yearmonth_LPSN`)
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* [Catalogue of Life](http://www.catalogueoflife.org) (included version: `r AMR:::CATALOGUE_OF_LIFE$year`)
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* [List of Prokaryotic names with Standing in Nomenclature](https://lpsn.dsmz.de) (LPSN, last updated: `r AMR:::CATALOGUE_OF_LIFE$yearmonth_LPSN`)
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* `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$current_version`
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### Example content
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@ -147,8 +150,8 @@ This data set is in R available as `microorganisms.old`, after you load the `AMR
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This data set contains old, previously accepted taxonomic names. The data sources are the same as the `microorganisms` data set:
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* [Catalogue of Life](http://www.catalogueoflife.org) (included version: `r AMR:::catalogue_of_life$year`)
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* [List of Prokaryotic names with Standing in Nomenclature](https://lpsn.dsmz.de) (LPSN, last updated: `r AMR:::catalogue_of_life$yearmonth_LPSN`)
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* [Catalogue of Life](http://www.catalogueoflife.org) (included version: `r AMR:::CATALOGUE_OF_LIFE$year`)
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* [List of Prokaryotic names with Standing in Nomenclature](https://lpsn.dsmz.de) (LPSN, last updated: `r AMR:::CATALOGUE_OF_LIFE$yearmonth_LPSN`)
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### Example content
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