P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 21:22:01 +02:00
Code Releases Activity

updated taxonomy

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-12-12 00:14:56 +01:00
parent eed1c14b96
commit 8da2467209
46 changed files with 132944 additions and 57370 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
R/aa_globals.R
View File

@ -72,12 +72,12 @@ EUCAST_VERSION_EXPERT_RULES <- list(
TAXONOMY_VERSION <- list(
GBIF = list(
accessed_date = as.Date("2022-09-12"),
citation = "GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy. Checklist dataset \\doi{10.15468/39omei}.",
accessed_date = as.Date("2022-12-11"),
citation = "GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset \\doi{10.15468/39omei}.",
url = "https://www.gbif.org"
),
LPSN = list(
accessed_date = as.Date("2022-09-12"),
accessed_date = as.Date("2022-12-11"),
citation = "Parte, AC *et al.* (2020). **List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.** International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \\doi{10.1099/ijsem.0.004332}.",
url = "https://lpsn.dsmz.de"
),

2
R/join_microorganisms.R
View File

@ -182,7 +182,7 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
}
if (type %like% "full|left|right|inner" && NROW(joined) > NROW(x)) {
warning_("in `", type, "_join()`: the newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of `x`.")
warning_("in `", type, "_microorganisms()`: the newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of `x`.")
}
as_original_data_class(joined, class(x.bak))

BIN
R/sysdata.rda
View File

Binary file not shown.

9
R/zzz.R
View File

@ -206,8 +206,13 @@ create_MO_lookup <- function() {
MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
# all the rest
MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
if (length(MO_FULLNAME_LOWER) != nrow(MO_lookup)) {
packageStartupMessage("fullname_lower not same size - applied tolower(), update sysdata.rda!")
MO_lookup$fullname_lower <- tolower(MO_lookup$fullname)
} else {
MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
}
MO_lookup$full_first <- substr(MO_lookup$fullname_lower, 1, 1)
MO_lookup$species_first <- substr(MO_lookup$species, 1, 1)