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(v2.1.1.9082) algorithm updates

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dr. M.S. (Matthijs) Berends
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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R/aa_helper_functions.R
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@ -1547,6 +1547,7 @@ add_MO_lookup_to_AMR_env <- function() {
MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 1.25
MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 1.5
MO_lookup[which(MO_lookup$kingdom == "Chromista"), "kingdom_index"] <- 1.75
MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 2
# all the rest
MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 3