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(v2.1.1.9225) fix geom_hline()/_vline() in MIC plotting, add EUCAT 1.2 in full, add London contribs, fix mo codes, add Kleb pneu complex

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dr. M.S. (Matthijs) Berends
2025-03-26 17:19:17 +01:00
parent 8deaf2c8eb
commit e6f88241b2
53 changed files with 552 additions and 334 deletions
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20
data-raw/reproduction_of_microorganisms.groups.R
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@@ -27,8 +27,9 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# this data set is being used in the clinical_breakpoints data set, and thus by as.sir().
# it prevents the breakpoints table from being extremely long for species that are part of a species group.
# This data set is being used in the clinical_breakpoints data set, and thus by as.sir().
# It prevents the breakpoints table from being extremely long for species that are part of a species group.
# Also used by eucast_rules() to expand group names.
library(dplyr)
library(readr)
@@ -143,6 +144,10 @@ microorganisms.groups <- whonet_organisms %>%
filter(mo_group != "B_CTRBC_FRND-C") %>%
bind_rows(tibble(mo_group = as.mo("B_CTRBC_FRND-C"),
mo = paste("Citrobacter", c("freundii", "braakii", "gillenii", "murliniae", "portucalensis", "sedlakii", "werkmanii", "youngae")) %>% as.mo(keep_synonyms = TRUE))) %>%
# Klebsiella pneumoniae complex
filter(mo_group != "B_KLBSL_PNMN-C") %>%
bind_rows(tibble(mo_group = as.mo("B_KLBSL_PNMN-C"),
mo = paste("Klebsiella", c("africana", "pneumoniae", "quasipneumoniae", "quasivariicola", "variicola")) %>% as.mo(keep_synonyms = TRUE))) %>%
# Yersinia pseudotuberculosis complex in the NCBI Taxonomy Browser:
# https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1649845
filter(mo_group != "B_YERSN_PSDT-C") %>%
@@ -164,22 +169,19 @@ for (group in unique(microorganisms.groups$mo_group)) {
filter(mo %like% spp & rank == "subspecies") %>%
pull(mo)
# add them
microorganisms.groups <- microorganisms.groups %>% bind_rows(tibble(mo_group = group, mo = mos))
microorganisms.groups <- microorganisms.groups %>% bind_rows(tibble(mo_group = as.mo(group), mo = mos))
}
# add full names, arrange and clean
microorganisms.groups <- microorganisms.groups %>%
mutate(mo_group_name = mo_name(mo_group, keep_synonyms = TRUE, language = NULL),
mo_name = mo_name(mo, keep_synonyms = TRUE, language = NULL)) %>%
mo_name = mo_name(mo, keep_synonyms = TRUE, language = NULL)) %>%
arrange(mo_group_name, mo_name) %>%
filter(mo_group != mo) %>%
distinct() %>%
filter(mo_group != mo) %>%
distinct() %>%
dataset_UTF8_to_ASCII()
mo_uncertainties()
# add subspecies to all species
class(microorganisms.groups$mo_group) <- c("mo", "character")
class(microorganisms.groups$mo) <- c("mo", "character")
usethis::use_data(microorganisms.groups, internal = FALSE, overwrite = TRUE, compress = "xz", version = 2)