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(v1.1.0.9020) updated taxonomy

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dr. M.S. (Matthijs) Berends
2020-05-27 16:37:49 +02:00
parent ae1969b941
commit 86d44054f0
55 changed files with 68063 additions and 70233 deletions
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3
R/aa_helper_functions.R
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@ -78,8 +78,7 @@ check_dataset_integrity <- function() {
check_microorganisms <- all(c("mo", "fullname", "kingdom", "phylum",
"class", "order", "family", "genus",
"species", "subspecies", "rank",
"col_id", "species_id", "source",
"ref", "prevalence", "snomed") %in% colnames(microorganisms),
"species_id", "source", "ref", "prevalence") %in% colnames(microorganisms),
na.rm = TRUE) & NROW(microorganisms) == NROW(MO_lookup)
check_antibiotics <- all(c("ab", "atc", "cid", "name", "group",
"atc_group1", "atc_group2", "abbreviations",