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update mo algorithm

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dr. M.S. (Matthijs) Berends
2022-12-20 16:14:04 +01:00
parent b1b7534c78
commit f0a2cdbf5e
21 changed files with 48772 additions and 48747 deletions
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39
data-raw/reproduction_of_microorganisms.R
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@ -831,35 +831,50 @@ putative <- pathogens %>%
established <- established[established %unlike% "unknown"]
putative <- putative[putative %unlike% "unknown"]
other_bacterial_genera <- c(established, putative) %>%
established_genera <- established %>%
strsplit(" ", fixed = TRUE) %>%
sapply(function(x) x[1]) %>%
sort() %>%
unique()
other_genera <- AMR:::MO_PREVALENT_GENERA %>%
putative_genera <- putative %>%
strsplit(" ", fixed = TRUE) %>%
sapply(function(x) x[1]) %>%
sort() %>%
unique()
nonbacterial_genera <- AMR:::MO_PREVALENT_GENERA %>%
c(unlist(mo_current(.)),
unlist(mo_synonyms(., keep_synonyms = FALSE))) %>%
strsplit(" ", fixed = TRUE) %>%
sapply(function(x) x[1]) %>%
sort() %>%
unique()
other_genera <- other_genera[other_genera %unlike% "unknown"]
nonbacterial_genera <- nonbacterial_genera[nonbacterial_genera %unlike% "unknown"]
# update prevalence based on taxonomy (following the recent and thorough work of Bartlett et al., 2022)
# see https://doi.org/10.1099/mic.0.001269
taxonomy <- taxonomy %>%
mutate(prevalence = case_when(
# 'established' gets a 1 and means 'have infected at least three persons in three or more references'
paste(genus, species) %in% established & rank %in% c("genus", "species", "subspecies") ~ 1.0,
# 'putative' gets a 2 and means 'fewer than three known cases'
paste(genus, species) %in% putative & rank %in% c("genus", "species", "subspecies") ~ 2.0,
# other species from a genus in either group get a 2.5
genus %in% other_bacterial_genera & rank %in% c("genus", "species", "subspecies") ~ 2.5,
# 'established' means 'have infected at least three persons in three or more references'
paste(genus, species) %in% established & rank %in% c("species", "subspecies") ~ 1.0,
# other genera in the 'established' group
genus %in% established_genera & rank == "genus" ~ 1.0,
# 'putative' means 'fewer than three known cases'
paste(genus, species) %in% putative & rank %in% c("species", "subspecies") ~ 1.25,
# other genera in the 'putative' group
genus %in% putative_genera & rank == "genus" ~ 1.25,
# species and subspecies in 'established' and 'putative' groups
genus %in% c(established_genera, putative_genera) & rank %in% c("species", "subspecies") ~ 1.5,
# 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") ~ 2.5,
# all others get a 3
TRUE ~ 3.0))
genus %in% AMR:::MO_PREVALENT_GENERA & kingdom != "Bacteria" & rank %in% c("genus", "species", "subspecies") ~ 1.5,
# all others
TRUE ~ 2.0))
table(taxonomy$prevalence, useNA = "always")
# (a lot will be removed further below)