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new species groups, updated clinical breakpoints

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dr. M.S. (Matthijs) Berends
2023-07-08 17:30:05 +02:00
parent 2d97cca6d9
commit acb534102b
172 changed files with 44445 additions and 52835 deletions
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11
data-raw/reproduction_of_microorganisms.R
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@ -869,7 +869,7 @@ taxonomy <- taxonomy %>%
# other species from a genus in either group
genus %in% nonbacterial_genera & rank %in% c("genus", "species", "subspecies") ~ 1.5,
# we keep track of prevalent genera too of non-bacterial species
genus %in% AMR:::MO_PREVALENT_GENERA & kingdom != "Bacteria" & rank %in% c("genus", "species", "subspecies") ~ 1.5,
genus %in% AMR:::MO_PREVALENT_GENERA & kingdom != "Bacteria" & rank %in% c("genus", "species", "subspecies") ~ 1.25,
# all others
TRUE ~ 2.0
@ -1298,6 +1298,15 @@ AMR::microorganisms %>%
View()
# Some manual fixes -------------------------------------------------------
# Candida haemulonis and C. duobushaemulonis should be Candida haemulonii and C. duobushaemulonii
# not sure how this can be, but GBIF contained spelling errors?
# see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3486233/
taxonomy$species[which(taxonomy$fullname %like% "^Candida .*haemulonis")] <- gsub("nis$", "nii", taxonomy$species[which(taxonomy$fullname %like% "^Candida .*haemulonis")])
taxonomy$fullname[which(taxonomy$fullname %like% "^Candida .*haemulonis")] <- gsub("nis$", "nii", taxonomy$fullname[which(taxonomy$fullname %like% "^Candida .*haemulonis")])
# Add SNOMED CT -----------------------------------------------------------
# we will use Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)