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no overwriting taxonomy when adding microorganisms

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dr. M.S. (Matthijs) Berends 2023-01-12 11:33:28 +01:00
parent 1029aa2fdc
commit 51906d6f97
4 changed files with 21 additions and 18 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.8.2.9089 Version: 1.8.2.9090
Date: 2023-01-07 Date: 2023-01-12
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.8.2.9089 # AMR 1.8.2.9090
*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)* *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*

31
R/add_custom_microorganisms.R
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@ -136,12 +136,13 @@ add_custom_microorganisms <- function(x) {
stop_ifnot(all(x$rank %in% AMR_env$MO_lookup$rank), stop_ifnot(all(x$rank %in% AMR_env$MO_lookup$rank),
"the 'rank' column can only contain these values: ", vector_or(AMR_env$MO_lookup$rank)) "the 'rank' column can only contain these values: ", vector_or(AMR_env$MO_lookup$rank))
} else { } else {
x$rank <- ifelse(!is.na(x$subspecies), "subspecies", x$rank <- ifelse(x$subspecies != "", "subspecies",
ifelse(!is.na(x$species), "species", ifelse(x$species != "", "species",
ifelse(!is.na(x$genus), "genus", ifelse(x$genus != "", "genus",
stop("in add_custom_microorganisms(): the 'genus' column cannot be empty", stop("in add_custom_microorganisms(): the 'genus' column cannot be empty",
call. = FALSE)))) call. = FALSE))))
} }
x$source <- "Added by user"
if (!"fullname" %in% colnames(x)) { if (!"fullname" %in% colnames(x)) {
x$fullname <- trimws2(paste(x$genus, x$species, x$subspecies)) x$fullname <- trimws2(paste(x$genus, x$species, x$subspecies))
} }
@ -150,6 +151,11 @@ add_custom_microorganisms <- function(x) {
if (!"class" %in% colnames(x)) x$class <- "" if (!"class" %in% colnames(x)) x$class <- ""
if (!"order" %in% colnames(x)) x$order <- "" if (!"order" %in% colnames(x)) x$order <- ""
if (!"family" %in% colnames(x)) x$family <- "" if (!"family" %in% colnames(x)) x$family <- ""
x$kingdom[is.na(x$kingdom)] <- ""
x$phylum[is.na(x$phylum)] <- ""
x$class[is.na(x$class)] <- ""
x$order[is.na(x$order)] <- ""
x$family[is.na(x$family)] <- ""
for (col in colnames(x)) { for (col in colnames(x)) {
if (is.list(AMR_env$MO_lookup[, col, drop = TRUE])) { if (is.list(AMR_env$MO_lookup[, col, drop = TRUE])) {
@ -160,17 +166,12 @@ add_custom_microorganisms <- function(x) {
# fill in other columns # fill in other columns
x$status <- "accepted" x$status <- "accepted"
x$prevalence <- 1 x$prevalence <- 1
x$kingdom <- AMR_env$MO_lookup$kingdom[match(x$genus, AMR_env$MO_lookup$genus)]
x$phylum <- AMR_env$MO_lookup$phylum[match(x$genus, AMR_env$MO_lookup$genus)]
x$class <- AMR_env$MO_lookup$class[match(x$genus, AMR_env$MO_lookup$genus)]
x$order <- AMR_env$MO_lookup$order[match(x$genus, AMR_env$MO_lookup$genus)]
x$family <- AMR_env$MO_lookup$family[match(x$genus, AMR_env$MO_lookup$genus)]
x$kingdom[is.na(x$kingdom)] <- "" x$kingdom[which(x$kingdom == "" & x$genus != "")] <- AMR_env$MO_lookup$kingdom[match(x$genus[which(x$kingdom == "" & x$genus != "")], AMR_env$MO_lookup$genus)]
x$phylum[is.na(x$phylum)] <- "" x$phylum[which(x$phylum == "" & x$genus != "")] <- AMR_env$MO_lookup$phylum[match(x$genus[which(x$phylum == "" & x$genus != "")], AMR_env$MO_lookup$genus)]
x$class[is.na(x$class)] <- "" x$class[which(x$class == "" & x$genus != "")] <- AMR_env$MO_lookup$class[match(x$genus[which(x$class == "" & x$genus != "")], AMR_env$MO_lookup$genus)]
x$order[is.na(x$order)] <- "" x$order[which(x$order == "" & x$genus != "")] <- AMR_env$MO_lookup$order[match(x$genus[which(x$order == "" & x$genus != "")], AMR_env$MO_lookup$genus)]
x$family[is.na(x$family)] <- "" x$family[which(x$family == "" & x$genus != "")] <- AMR_env$MO_lookup$family[match(x$genus[which(x$family == "" & x$genus != "")], AMR_env$MO_lookup$genus)]
x$kingdom_index <- AMR_env$MO_lookup$kingdom_index[match(x$genus, AMR_env$MO_lookup$genus)] x$kingdom_index <- AMR_env$MO_lookup$kingdom_index[match(x$genus, AMR_env$MO_lookup$genus)]
x$fullname_lower <- tolower(x$fullname) x$fullname_lower <- tolower(x$fullname)
@ -184,7 +185,9 @@ add_custom_microorganisms <- function(x) {
} }
x$mo <- trimws2(x$mo) x$mo <- trimws2(x$mo)
x$mo[x$mo == ""] <- NA_character_ x$mo[x$mo == ""] <- NA_character_
x$mo[is.na(x$mo)] <- paste0("CUSTOM_", x$mo[is.na(x$mo)] <- paste0("CUSTOM",
seq(from = sum(AMR_env$MO_lookup$source == "Added by user", na.rm = TRUE) + 1, to = nrow(x), by = 1),
"_",
toupper(unname(abbreviate(gsub(" +", " _ ", toupper(unname(abbreviate(gsub(" +", " _ ",
gsub("[^A-Za-z0-9-]", " ", gsub("[^A-Za-z0-9-]", " ",
trimws2(paste(x$genus, x$species, x$subspecies)))), trimws2(paste(x$genus, x$species, x$subspecies)))),

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