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prepare for documentation

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dr. M.S. (Matthijs) Berends
2026-05-03 11:50:05 +02:00
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@@ -109,7 +109,7 @@
#' - `status` \cr Status of the taxon, either `r vector_or(microorganisms$status, documentation = TRUE)`
#' - `kingdom`, `phylum`, `class`, `order`, `family`, `genus`, `species`, `subspecies`\cr Taxonomic rank of the microorganism. Note that for fungi, *phylum* is equal to their taxonomic *division*. Also, for fungi, *subkingdom* and *subdivision* were left out since they do not occur in the bacterial taxonomy.
#' - `rank`\cr Text of the taxonomic rank of the microorganism, such as `"species"` or `"genus"`
#' - `ref`\cr Abbreviated authority citation for the nomenclatural act that established the current name combination, following ICNP conventions. For species described in their current genus (sp. nov.), this is the original description author(s) and year. For species transferred to a different genus (comb. nov.), this is the reclassification author(s) and year. Emendations are excluded. For synonyms, this is the authority under which the synonym was originally published. Data sourced primarily from LPSN, supplemented by GBIF where LPSN coverage is absent.
#' - `ref`\cr Abbreviated authority citation for the nomenclatural act that established the current name combination, following ICNP conventions. For species described in their current genus (*sp. nov.*), this is the original description author(s) and year. For species transferred to a different genus (*comb. nov.*), this is the reclassification author(s) and year. Emendations are excluded. For synonyms, this is the authority under which the synonym was originally published. This field is directly retrieved from the source specified in the column `source`. Diacritics were removed to comply with CRAN, that only allows ASCII characters.
#' - `oxygen_tolerance` \cr Oxygen tolerance, either `r vector_or(microorganisms$oxygen_tolerance, documentation = TRUE)`. These data were retrieved from BacDive (see *Source*). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently `r round(length(microorganisms$oxygen_tolerance[which(!is.na(microorganisms$oxygen_tolerance))]) / nrow(microorganisms[which(microorganisms$kingdom == "Bacteria"), ]) * 100, 1)`% of all `r format_included_data_number(nrow(microorganisms[which(microorganisms$kingdom == "Bacteria"), ]))` bacteria in the data set contain an oxygen tolerance.
#' - `source`\cr Either `r vector_or(microorganisms$source, documentation = TRUE)` (see *Source*)
#' - `lpsn`\cr Identifier ('Record number') of `r TAXONOMY_VERSION$LPSN$name`. This will be the first/highest LPSN identifier to keep one identifier per row. For example, *Acetobacter ascendens* has LPSN Record number 7864 and 11011. Only the first is available in the `microorganisms` data set. ***This is a unique identifier***, though available for only `r format_included_data_number(sum(!is.na(microorganisms$lpsn)))` records.