update prevalence with new phyla

2025-07-08 20:41:58 +02:00 · 2022-12-09 13:37:08 +01:00
parent ac55aa84de
commit 56dad34e68
19 changed files with 15708 additions and 15695 deletions
--- a/data-raw/microorganisms.dta
+++ b/data-raw/microorganisms.dta
--- a/data-raw/microorganisms.feather
+++ b/data-raw/microorganisms.feather
--- a/data-raw/microorganisms.md5
+++ b/data-raw/microorganisms.md5
@ -1 +1 @@
-4cb5e83062897061b17ddac6d5cd31d7
+0a4241916334341aa70923aac880997d
--- a/data-raw/microorganisms.parquet
+++ b/data-raw/microorganisms.parquet
--- a/data-raw/microorganisms.rds
+++ b/data-raw/microorganisms.rds
--- a/data-raw/microorganisms.sas
+++ b/data-raw/microorganisms.sas
--- a/data-raw/microorganisms.sav
+++ b/data-raw/microorganisms.sav
--- a/data-raw/microorganisms.txt
+++ b/data-raw/microorganisms.txt
--- a/data-raw/microorganisms.xlsx
+++ b/data-raw/microorganisms.xlsx
--- a/data-raw/reproduction_of_microorganisms.R
+++ b/data-raw/reproduction_of_microorganisms.R
@ -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,