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mirror of https://github.com/msberends/AMR.git synced 2025-07-12 08:21:51 +02:00

(v2.1.1.9082) algorithm updates

This commit is contained in:
2024-09-30 18:46:55 +02:00
parent ac1c40d8bb
commit 681fe011fe
25 changed files with 15593 additions and 15505 deletions

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@ -455,7 +455,7 @@ sort(table(taxonomy_lpsn$status))
# Read MycoBank data ------------------------------------------------------------------------------
taxonomy_mycobank <- readxl::read_excel(file_mycobank, guess_max = 1e5)
taxonomy_mycobank <- read_excel(file_mycobank, guess_max = 1e5)
taxonomy_mycobank.bak <- taxonomy_mycobank
taxonomy_mycobank <- taxonomy_mycobank %>%
@ -1224,10 +1224,12 @@ nonbacterial_genera <- nonbacterial_genera[nonbacterial_genera %unlike% "unknown
# see https://doi.org/10.1099/mic.0.001269
taxonomy <- taxonomy %>%
mutate(prevalence = case_when(
# genera of the pathogens mentioned in the World Health Organization's (WHO) Priority Pathogen List
genus %in% MO_WHO_PRIORITY_GENERA ~ 1.0,
# 'established' means 'have infected at least three persons in three or more references'
paste(genus, species) %in% established & rank %in% c("species", "subspecies") ~ 1.0,
paste(genus, species) %in% established & rank %in% c("species", "subspecies") ~ 1.15,
# other genera in the 'established' group
genus %in% established_genera & rank == "genus" ~ 1.0,
genus %in% established_genera & rank == "genus" ~ 1.15,
# 'putative' means 'fewer than three known cases'
paste(genus, species) %in% putative & rank %in% c("species", "subspecies") ~ 1.25,
@ -2148,7 +2150,7 @@ microorganisms <- taxonomy
# set class <mo>
class(microorganisms$mo) <- c("mo", "character")
microorganisms <- microorganisms %>% arrange(fullname)
microorganisms <- microorganisms %>% arrange(fullname) %>% df_remove_nonASCII()
usethis::use_data(microorganisms, overwrite = TRUE, version = 2, compress = "xz")
rm(microorganisms)