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(v2.1.1.9082) algorithm updates
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@ -455,7 +455,7 @@ sort(table(taxonomy_lpsn$status))
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# Read MycoBank data ------------------------------------------------------------------------------
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taxonomy_mycobank <- readxl::read_excel(file_mycobank, guess_max = 1e5)
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taxonomy_mycobank <- read_excel(file_mycobank, guess_max = 1e5)
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taxonomy_mycobank.bak <- taxonomy_mycobank
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taxonomy_mycobank <- taxonomy_mycobank %>%
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@ -1224,10 +1224,12 @@ nonbacterial_genera <- nonbacterial_genera[nonbacterial_genera %unlike% "unknown
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# see https://doi.org/10.1099/mic.0.001269
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taxonomy <- taxonomy %>%
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mutate(prevalence = case_when(
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# genera of the pathogens mentioned in the World Health Organization's (WHO) Priority Pathogen List
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genus %in% MO_WHO_PRIORITY_GENERA ~ 1.0,
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# 'established' means 'have infected at least three persons in three or more references'
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paste(genus, species) %in% established & rank %in% c("species", "subspecies") ~ 1.0,
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paste(genus, species) %in% established & rank %in% c("species", "subspecies") ~ 1.15,
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# other genera in the 'established' group
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genus %in% established_genera & rank == "genus" ~ 1.0,
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genus %in% established_genera & rank == "genus" ~ 1.15,
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# 'putative' means 'fewer than three known cases'
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paste(genus, species) %in% putative & rank %in% c("species", "subspecies") ~ 1.25,
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@ -2148,7 +2150,7 @@ microorganisms <- taxonomy
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# set class <mo>
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class(microorganisms$mo) <- c("mo", "character")
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microorganisms <- microorganisms %>% arrange(fullname)
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microorganisms <- microorganisms %>% arrange(fullname) %>% df_remove_nonASCII()
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usethis::use_data(microorganisms, overwrite = TRUE, version = 2, compress = "xz")
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rm(microorganisms)
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