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update prevalence with new phyla

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dr. M.S. (Matthijs) Berends
2022-12-09 13:37:08 +01:00
parent ac55aa84de
commit 56dad34e68
19 changed files with 15708 additions and 15695 deletions
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13
data-raw/reproduction_of_microorganisms.R
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@ -733,11 +733,14 @@ taxonomy <- taxonomy %>%
~ 1,
kingdom %in% c("Archaea", "Bacteria", "Chromista", "Fungi") &
(phylum %in% c(
"Proteobacteria",
"Firmicutes",
"Bacillota", # this one is new - this was renamed from Firmicutes by Gibbons et al., 2021
"Actinobacteria",
"Sarcomastigophora"
"Sarcomastigophora",
"Firmicutes", # old, now Bacillota
"Bacillota",
"Proteobacteria", # old, now Pseudomonadota
"Pseudomonadota",
"Actinobacteria", # old, now Actinomycetota
"Actinomycetota"
) |
genus %in% MO_PREVALENT_GENERA)
~ 2,