mirror of
https://github.com/msberends/AMR.git
synced 2025-07-09 01:22:25 +02:00
sort sir history
This commit is contained in:
@ -101,46 +101,48 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
|
||||
MO_staph <- AMR::microorganisms
|
||||
MO_staph <- MO_staph[which(MO_staph$genus == "Staphylococcus"), , drop = FALSE]
|
||||
if (type == "CoNS") {
|
||||
MO_staph[which(MO_staph$species %in% c(
|
||||
"coagulase-negative", "argensis", "arlettae",
|
||||
"auricularis", "borealis", "caeli", "capitis", "caprae",
|
||||
"carnosus", "casei", "caseolyticus", "chromogenes", "cohnii", "condimenti",
|
||||
"croceilyticus",
|
||||
"debuckii", "devriesei", "edaphicus", "epidermidis",
|
||||
"equorum", "felis", "fleurettii", "gallinarum",
|
||||
"haemolyticus", "hominis", "jettensis", "kloosii",
|
||||
"lentus", "lugdunensis", "massiliensis", "microti",
|
||||
"muscae", "nepalensis", "pasteuri", "petrasii",
|
||||
"pettenkoferi", "piscifermentans", "pragensis", "pseudoxylosus",
|
||||
"pulvereri", "rostri", "saccharolyticus", "saprophyticus",
|
||||
"sciuri", "simulans", "stepanovicii", "succinus",
|
||||
"ureilyticus",
|
||||
"vitulinus", "vitulus", "warneri", "xylosus",
|
||||
"caledonicus", "canis",
|
||||
"durrellii", "lloydii",
|
||||
"ratti", "taiwanensis", "veratri", "urealyticus"
|
||||
) |
|
||||
# old, now renamed to S. schleiferi (but still as synonym in our data of course):
|
||||
(MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
|
||||
"mo",
|
||||
drop = TRUE
|
||||
MO_staph[
|
||||
which(MO_staph$species %in% c(
|
||||
"coagulase-negative", "argensis", "arlettae",
|
||||
"auricularis", "borealis", "caeli", "capitis", "caprae",
|
||||
"carnosus", "casei", "caseolyticus", "chromogenes", "cohnii", "condimenti",
|
||||
"croceilyticus",
|
||||
"debuckii", "devriesei", "edaphicus", "epidermidis",
|
||||
"equorum", "felis", "fleurettii", "gallinarum",
|
||||
"haemolyticus", "hominis", "jettensis", "kloosii",
|
||||
"lentus", "lugdunensis", "massiliensis", "microti",
|
||||
"muscae", "nepalensis", "pasteuri", "petrasii",
|
||||
"pettenkoferi", "piscifermentans", "pragensis", "pseudoxylosus",
|
||||
"pulvereri", "rostri", "saccharolyticus", "saprophyticus",
|
||||
"sciuri", "simulans", "stepanovicii", "succinus",
|
||||
"ureilyticus",
|
||||
"vitulinus", "vitulus", "warneri", "xylosus",
|
||||
"caledonicus", "canis",
|
||||
"durrellii", "lloydii",
|
||||
"ratti", "taiwanensis", "veratri", "urealyticus"
|
||||
) |
|
||||
# old, now renamed to S. schleiferi (but still as synonym in our data of course):
|
||||
(MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
|
||||
"mo",
|
||||
drop = TRUE
|
||||
]
|
||||
} else if (type == "CoPS") {
|
||||
MO_staph[which(MO_staph$species %in% c(
|
||||
"coagulase-positive", "coagulans",
|
||||
"agnetis", "argenteus",
|
||||
"cornubiensis",
|
||||
"delphini", "lutrae",
|
||||
"hyicus", "intermedius",
|
||||
"pseudintermedius", "pseudointermedius",
|
||||
"schweitzeri", "simiae",
|
||||
"roterodami",
|
||||
"singaporensis"
|
||||
) |
|
||||
# old, now renamed to S. coagulans (but still as synonym in our data of course):
|
||||
(MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
|
||||
"mo",
|
||||
drop = TRUE
|
||||
MO_staph[
|
||||
which(MO_staph$species %in% c(
|
||||
"coagulase-positive", "coagulans",
|
||||
"agnetis", "argenteus",
|
||||
"cornubiensis",
|
||||
"delphini", "lutrae",
|
||||
"hyicus", "intermedius",
|
||||
"pseudintermedius", "pseudointermedius",
|
||||
"schweitzeri", "simiae",
|
||||
"roterodami",
|
||||
"singaporensis"
|
||||
) |
|
||||
# old, now renamed to S. coagulans (but still as synonym in our data of course):
|
||||
(MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
|
||||
"mo",
|
||||
drop = TRUE
|
||||
]
|
||||
}
|
||||
}
|
||||
@ -254,14 +256,15 @@ create_AB_AV_lookup <- function(df) {
|
||||
}
|
||||
new_df$generalised_loinc <- lapply(new_df$loinc, generalise_antibiotic_name)
|
||||
new_df$generalised_all <- unname(lapply(
|
||||
as.list(as.data.frame(t(new_df[,
|
||||
c(
|
||||
colnames(new_df)[colnames(new_df) %in% c("ab", "av", "atc", "cid", "name")],
|
||||
colnames(new_df)[colnames(new_df) %like% "generalised"]
|
||||
),
|
||||
drop = FALSE
|
||||
]),
|
||||
stringsAsFactors = FALSE
|
||||
as.list(as.data.frame(
|
||||
t(new_df[,
|
||||
c(
|
||||
colnames(new_df)[colnames(new_df) %in% c("ab", "av", "atc", "cid", "name")],
|
||||
colnames(new_df)[colnames(new_df) %like% "generalised"]
|
||||
),
|
||||
drop = FALSE
|
||||
]),
|
||||
stringsAsFactors = FALSE
|
||||
)),
|
||||
function(x) {
|
||||
x <- generalise_antibiotic_name(unname(unlist(x)))
|
||||
@ -472,7 +475,7 @@ suppressMessages(devtools::document(quiet = TRUE))
|
||||
if (!"styler" %in% rownames(utils::installed.packages())) {
|
||||
message("Package 'styler' not installed!")
|
||||
} else if (interactive()) {
|
||||
# # only when sourcing this file ourselves
|
||||
# only when sourcing this file ourselves
|
||||
# usethis::ui_info("Styling package")
|
||||
# styler::style_pkg(
|
||||
# style = styler::tidyverse_style,
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
|
||||
license_text <- readLines("docs/LICENSE-text.html")
|
||||
license_text <- paste(license_text, collapse = "|||")
|
||||
license_text <- gsub("licen(s|c)e", "Survey", license_text, ignore.case = TRUE)
|
||||
|
||||
@ -66,33 +66,36 @@ read_EUCAST <- function(sheet, file, guideline_name) {
|
||||
|
||||
# in the info header in the Excel file, EUCAST mentions which genera are targeted
|
||||
if (sheet %like% "anaerob.*Gram.*posi") {
|
||||
sheet <- paste0(c(
|
||||
"Actinomyces", "Bifidobacterium", "Clostridioides",
|
||||
"Clostridium", "Cutibacterium", "Eggerthella",
|
||||
"Eubacterium", "Lactobacillus", "Propionibacterium",
|
||||
"Staphylococcus saccharolyticus"
|
||||
),
|
||||
collapse = "_"
|
||||
sheet <- paste0(
|
||||
c(
|
||||
"Actinomyces", "Bifidobacterium", "Clostridioides",
|
||||
"Clostridium", "Cutibacterium", "Eggerthella",
|
||||
"Eubacterium", "Lactobacillus", "Propionibacterium",
|
||||
"Staphylococcus saccharolyticus"
|
||||
),
|
||||
collapse = "_"
|
||||
)
|
||||
} else if (sheet %like% "anaerob.*Gram.*nega") {
|
||||
sheet <- paste0(c(
|
||||
"Bacteroides",
|
||||
"Bilophila",
|
||||
"Fusobacterium",
|
||||
"Mobiluncus",
|
||||
"Parabacteroides",
|
||||
"Porphyromonas",
|
||||
"Prevotella"
|
||||
),
|
||||
collapse = "_"
|
||||
sheet <- paste0(
|
||||
c(
|
||||
"Bacteroides",
|
||||
"Bilophila",
|
||||
"Fusobacterium",
|
||||
"Mobiluncus",
|
||||
"Parabacteroides",
|
||||
"Porphyromonas",
|
||||
"Prevotella"
|
||||
),
|
||||
collapse = "_"
|
||||
)
|
||||
} else if (sheet == "Streptococcus A,B,C,G") {
|
||||
sheet <- paste0(microorganisms %>%
|
||||
filter(genus == "Streptococcus") %>%
|
||||
mutate(lancefield = mo_name(mo, Lancefield = TRUE)) %>%
|
||||
filter(lancefield %like% "^Streptococcus group") %>%
|
||||
pull(fullname),
|
||||
collapse = "_"
|
||||
sheet <- paste0(
|
||||
microorganisms %>%
|
||||
filter(genus == "Streptococcus") %>%
|
||||
mutate(lancefield = mo_name(mo, Lancefield = TRUE)) %>%
|
||||
filter(lancefield %like% "^Streptococcus group") %>%
|
||||
pull(fullname),
|
||||
collapse = "_"
|
||||
)
|
||||
} else if (sheet %like% "PK.*PD") {
|
||||
sheet <- "UNKNOWN"
|
||||
|
||||
@ -142,14 +142,15 @@ abx2 <- bind_rows(abx_atc1, abx_atc2)
|
||||
rm(abx_atc1)
|
||||
rm(abx_atc2)
|
||||
|
||||
abx2$ab[is.na(abx2$ab)] <- toupper(abbreviate(gsub(
|
||||
"[/0-9-]",
|
||||
" ",
|
||||
abx2$name[is.na(abx2$ab)]
|
||||
),
|
||||
minlength = 3,
|
||||
method = "left.kept",
|
||||
strict = TRUE
|
||||
abx2$ab[is.na(abx2$ab)] <- toupper(abbreviate(
|
||||
gsub(
|
||||
"[/0-9-]",
|
||||
" ",
|
||||
abx2$name[is.na(abx2$ab)]
|
||||
),
|
||||
minlength = 3,
|
||||
method = "left.kept",
|
||||
strict = TRUE
|
||||
))
|
||||
|
||||
n_distinct(abx2$ab)
|
||||
@ -197,24 +198,26 @@ get_CID <- function(ab) {
|
||||
p$tick()
|
||||
|
||||
CID[i] <- tryCatch(
|
||||
data.table::fread(paste0(
|
||||
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
|
||||
URLencode(ab[i], reserved = TRUE),
|
||||
"/cids/TXT?name_type=complete"
|
||||
),
|
||||
showProgress = FALSE
|
||||
data.table::fread(
|
||||
paste0(
|
||||
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
|
||||
URLencode(ab[i], reserved = TRUE),
|
||||
"/cids/TXT?name_type=complete"
|
||||
),
|
||||
showProgress = FALSE
|
||||
)[[1]][1],
|
||||
error = function(e) NA_integer_
|
||||
)
|
||||
if (is.na(CID[i])) {
|
||||
# try with removing the text in brackets
|
||||
CID[i] <- tryCatch(
|
||||
data.table::fread(paste0(
|
||||
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
|
||||
URLencode(trimws(gsub("[(].*[)]", "", ab[i])), reserved = TRUE),
|
||||
"/cids/TXT?name_type=complete"
|
||||
),
|
||||
showProgress = FALSE
|
||||
data.table::fread(
|
||||
paste0(
|
||||
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
|
||||
URLencode(trimws(gsub("[(].*[)]", "", ab[i])), reserved = TRUE),
|
||||
"/cids/TXT?name_type=complete"
|
||||
),
|
||||
showProgress = FALSE
|
||||
)[[1]][1],
|
||||
error = function(e) NA_integer_
|
||||
)
|
||||
@ -223,12 +226,13 @@ get_CID <- function(ab) {
|
||||
# try match on word and take the lowest CID value (sorted)
|
||||
ab[i] <- gsub("[^a-z0-9]+", " ", ab[i], ignore.case = TRUE)
|
||||
CID[i] <- tryCatch(
|
||||
data.table::fread(paste0(
|
||||
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
|
||||
URLencode(ab[i], reserved = TRUE),
|
||||
"/cids/TXT?name_type=word"
|
||||
),
|
||||
showProgress = FALSE
|
||||
data.table::fread(
|
||||
paste0(
|
||||
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
|
||||
URLencode(ab[i], reserved = TRUE),
|
||||
"/cids/TXT?name_type=word"
|
||||
),
|
||||
showProgress = FALSE
|
||||
)[[1]][1],
|
||||
error = function(e) NA_integer_
|
||||
)
|
||||
@ -260,13 +264,14 @@ get_synonyms <- function(CID, clean = TRUE) {
|
||||
}
|
||||
|
||||
synonyms_txt <- tryCatch(
|
||||
data.table::fread(paste0(
|
||||
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastidentity/cid/",
|
||||
CID[i],
|
||||
"/synonyms/TXT"
|
||||
),
|
||||
sep = "\n",
|
||||
showProgress = FALSE
|
||||
data.table::fread(
|
||||
paste0(
|
||||
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastidentity/cid/",
|
||||
CID[i],
|
||||
"/synonyms/TXT"
|
||||
),
|
||||
sep = "\n",
|
||||
showProgress = FALSE
|
||||
)[[1]],
|
||||
error = function(e) NA_character_
|
||||
)
|
||||
|
||||
@ -106,31 +106,32 @@ antivirals <- antivirals %>%
|
||||
oral_units,
|
||||
iv_ddd,
|
||||
iv_units
|
||||
) %>%
|
||||
) %>%
|
||||
AMR:::dataset_UTF8_to_ASCII()
|
||||
|
||||
av_codes <- tibble(name = antivirals$name %>%
|
||||
strsplit("(, | and )") %>%
|
||||
unlist() %>%
|
||||
unique() %>%
|
||||
sort()) %>%
|
||||
mutate(av_1st = toupper(abbreviate(name, minlength = 3, use.classes = FALSE))) %>%
|
||||
strsplit("(, | and )") %>%
|
||||
unlist() %>%
|
||||
unique() %>%
|
||||
sort()) %>%
|
||||
mutate(av_1st = toupper(abbreviate(name, minlength = 3, use.classes = FALSE))) %>%
|
||||
filter(!name %in% c("acid", "dipivoxil", "disoproxil", "marboxil", "alafenamide"))
|
||||
|
||||
replace_with_av_code <- function(name) {
|
||||
unname(av_codes$av_1st[match(name, av_codes$name)])
|
||||
}
|
||||
|
||||
names_codes <- antivirals %>%
|
||||
names_codes <- antivirals %>%
|
||||
separate(name,
|
||||
into = paste0("name", c(1:7)),
|
||||
sep = "(, | and )",
|
||||
remove = FALSE,
|
||||
fill = "right") %>%
|
||||
into = paste0("name", c(1:7)),
|
||||
sep = "(, | and )",
|
||||
remove = FALSE,
|
||||
fill = "right"
|
||||
) %>%
|
||||
# remove empty columns
|
||||
select(!where(function(x) all(is.na(x)))) %>%
|
||||
mutate_at(vars(matches("name[1-9]")), replace_with_av_code) %>%
|
||||
unite(av, matches("name[1-9]"), sep = "+", na.rm = TRUE) %>%
|
||||
select(!where(function(x) all(is.na(x)))) %>%
|
||||
mutate_at(vars(matches("name[1-9]")), replace_with_av_code) %>%
|
||||
unite(av, matches("name[1-9]"), sep = "+", na.rm = TRUE) %>%
|
||||
mutate(name = gsub("(, | and )", "/", name))
|
||||
substr(names_codes$name, 1, 1) <- toupper(substr(names_codes$name, 1, 1))
|
||||
|
||||
@ -143,8 +144,9 @@ antivirals <- antivirals %>% AMR:::dataset_UTF8_to_ASCII()
|
||||
|
||||
# add loinc, see 'data-raw/loinc.R'
|
||||
loinc_df <- read.csv("data-raw/Loinc.csv",
|
||||
row.names = NULL,
|
||||
stringsAsFactors = FALSE)
|
||||
row.names = NULL,
|
||||
stringsAsFactors = FALSE
|
||||
)
|
||||
|
||||
loinc_df <- loinc_df %>% filter(CLASS == "DRUG/TOX")
|
||||
av_names <- antivirals %>%
|
||||
|
||||
@ -173,7 +173,7 @@ dosage_new <- bind_rows(
|
||||
as.data.frame(stringsAsFactors = FALSE)
|
||||
rownames(dosage_new) <- NULL
|
||||
|
||||
dosage <- bind_rows(dosage_new, AMR::dosage) %>%
|
||||
dosage <- bind_rows(dosage_new, AMR::dosage) %>%
|
||||
dataset_UTF8_to_ASCII()
|
||||
|
||||
usethis::use_data(dosage, internal = FALSE, overwrite = TRUE, version = 2)
|
||||
|
||||
@ -37,10 +37,10 @@
|
||||
# CSV file (~12,5 MB) as "taxonomy.csv". Their API unfortunately does
|
||||
# not include the full taxonomy and is currently (2022) pretty worthless.
|
||||
# 3. For data about human pathogens, we use Bartlett et al. (2022),
|
||||
# https://doi.org/10.1099/mic.0.001269. Their latest supplementary material
|
||||
# https://doi.org/10.1099/mic.0.001269. Their latest supplementary material
|
||||
# can be found here: https://github.com/padpadpadpad/bartlett_et_al_2022_human_pathogens.
|
||||
#. Download their latest xlsx file in the `data` folder and save it to our
|
||||
#. `data-raw` folder.
|
||||
# . Download their latest xlsx file in the `data` folder and save it to our
|
||||
# . `data-raw` folder.
|
||||
# 4. Set this folder_location to the path where these two files are:
|
||||
folder_location <- "~/Downloads/backbone/"
|
||||
file_gbif <- paste0(folder_location, "Taxon.tsv")
|
||||
@ -65,7 +65,7 @@ devtools::load_all(".") # load AMR package
|
||||
|
||||
get_author_year <- function(ref) {
|
||||
# Only keep first author, e.g. transform 'Smith, Jones, 2011' to 'Smith et al., 2011'
|
||||
|
||||
|
||||
authors2 <- iconv(ref, from = "UTF-8", to = "ASCII//TRANSLIT")
|
||||
authors2 <- gsub(" ?\\(Approved Lists [0-9]+\\) ?", " () ", authors2)
|
||||
authors2 <- gsub(" [)(]+ $", "", authors2)
|
||||
@ -73,21 +73,21 @@ get_author_year <- function(ref) {
|
||||
authors2 <- trimws(gsub("^[(](.*)[)]$", "\\1", authors2))
|
||||
# only take part after brackets if there's a name
|
||||
authors2 <- ifelse(grepl(".*[)] [a-zA-Z]+.*", authors2),
|
||||
gsub(".*[)] (.*)", "\\1", authors2),
|
||||
authors2
|
||||
gsub(".*[)] (.*)", "\\1", authors2),
|
||||
authors2
|
||||
)
|
||||
# replace parentheses with emend. to get the latest authors
|
||||
authors2 <- gsub("(", " emend. ", authors2, fixed = TRUE)
|
||||
authors2 <- gsub(")", "", authors2, fixed = TRUE)
|
||||
authors2 <- gsub(" +", " ", authors2)
|
||||
authors2 <- trimws(authors2)
|
||||
|
||||
|
||||
# get year from last 4 digits
|
||||
lastyear <- as.integer(gsub(".*([0-9]{4})$", "\\1", authors2))
|
||||
# can never be later than now
|
||||
lastyear <- ifelse(lastyear > as.integer(format(Sys.Date(), "%Y")),
|
||||
NA,
|
||||
lastyear
|
||||
NA,
|
||||
lastyear
|
||||
)
|
||||
# get authors without last year
|
||||
authors <- gsub("(.*)[0-9]{4}$", "\\1", authors2)
|
||||
@ -119,8 +119,8 @@ get_author_year <- function(ref) {
|
||||
authors[nchar(authors) <= 3] <- ""
|
||||
# combine author and year if year is available
|
||||
ref <- ifelse(!is.na(lastyear),
|
||||
paste0(authors, ", ", lastyear),
|
||||
authors
|
||||
paste0(authors, ", ", lastyear),
|
||||
authors
|
||||
)
|
||||
# fix beginning and ending
|
||||
ref <- gsub(", $", "", ref)
|
||||
@ -128,7 +128,7 @@ get_author_year <- function(ref) {
|
||||
ref <- gsub("^(emend|et al.,?)", "", ref)
|
||||
ref <- trimws(ref)
|
||||
ref <- gsub("'", "", ref)
|
||||
|
||||
|
||||
# a lot start with a lowercase character - fix that
|
||||
ref[!grepl("^d[A-Z]", ref)] <- gsub("^([a-z])", "\\U\\1", ref[!grepl("^d[A-Z]", ref)], perl = TRUE)
|
||||
# specific one for the French that are named dOrbigny
|
||||
@ -222,9 +222,9 @@ include_fungal_orders <- c(
|
||||
# get latest taxonomic names of these fungal orders
|
||||
include_fungal_orders_ids <- taxonomy_gbif.bak %>%
|
||||
filter(order %in% include_fungal_orders)
|
||||
include_fungal_orders <- taxonomy_gbif.bak %>%
|
||||
filter(taxonID %in% c(include_fungal_orders_ids$taxonID, include_fungal_orders_ids$acceptedNameUsageID)) %>%
|
||||
distinct(order) %>%
|
||||
include_fungal_orders <- taxonomy_gbif.bak %>%
|
||||
filter(taxonID %in% c(include_fungal_orders_ids$taxonID, include_fungal_orders_ids$acceptedNameUsageID)) %>%
|
||||
distinct(order) %>%
|
||||
pull(order)
|
||||
|
||||
# check some columns to validate below filters
|
||||
@ -361,7 +361,7 @@ for (page in LETTERS) {
|
||||
names <- names[ranks != "species"]
|
||||
ranks <- ranks[ranks != "species"]
|
||||
ranks[ranks == "domain"] <- "kingdom"
|
||||
|
||||
|
||||
df <- names %>%
|
||||
tibble() %>%
|
||||
t() %>%
|
||||
@ -369,7 +369,7 @@ for (page in LETTERS) {
|
||||
setNames(ranks) %>%
|
||||
# no candidates please
|
||||
filter(genus %unlike% "^(Candidatus|\\[)")
|
||||
|
||||
|
||||
taxonomy_lpsn_missing <- taxonomy_lpsn_missing %>%
|
||||
bind_rows(df)
|
||||
}
|
||||
@ -491,14 +491,14 @@ saveRDS(taxonomy_lpsn, "data-raw/taxonomy_lpsn.rds", version = 2)
|
||||
taxonomy_gbif <- taxonomy_gbif %>%
|
||||
# clean NAs and add fullname
|
||||
mutate(across(kingdom:subspecies, function(x) ifelse(is.na(x), "", x)),
|
||||
fullname = trimws(case_when(
|
||||
rank == "family" ~ family,
|
||||
rank == "order" ~ order,
|
||||
rank == "class" ~ class,
|
||||
rank == "phylum" ~ phylum,
|
||||
rank == "kingdom" ~ kingdom,
|
||||
TRUE ~ paste(genus, species, subspecies)
|
||||
)), .before = 1
|
||||
fullname = trimws(case_when(
|
||||
rank == "family" ~ family,
|
||||
rank == "order" ~ order,
|
||||
rank == "class" ~ class,
|
||||
rank == "phylum" ~ phylum,
|
||||
rank == "kingdom" ~ kingdom,
|
||||
TRUE ~ paste(genus, species, subspecies)
|
||||
)), .before = 1
|
||||
) %>%
|
||||
# keep only one GBIF taxon ID per full name
|
||||
arrange(fullname, gbif) %>%
|
||||
@ -507,14 +507,14 @@ taxonomy_gbif <- taxonomy_gbif %>%
|
||||
taxonomy_lpsn <- taxonomy_lpsn %>%
|
||||
# clean NAs and add fullname
|
||||
mutate(across(kingdom:subspecies, function(x) ifelse(is.na(x), "", x)),
|
||||
fullname = trimws(case_when(
|
||||
rank == "family" ~ family,
|
||||
rank == "order" ~ order,
|
||||
rank == "class" ~ class,
|
||||
rank == "phylum" ~ phylum,
|
||||
rank == "kingdom" ~ kingdom,
|
||||
TRUE ~ paste(genus, species, subspecies)
|
||||
)), .before = 1
|
||||
fullname = trimws(case_when(
|
||||
rank == "family" ~ family,
|
||||
rank == "order" ~ order,
|
||||
rank == "class" ~ class,
|
||||
rank == "phylum" ~ phylum,
|
||||
rank == "kingdom" ~ kingdom,
|
||||
TRUE ~ paste(genus, species, subspecies)
|
||||
)), .before = 1
|
||||
) %>%
|
||||
# keep only one LPSN record ID per full name
|
||||
arrange(fullname, lpsn) %>%
|
||||
@ -536,23 +536,25 @@ taxonomy_lpsn$lpsn_parent[taxonomy_lpsn$rank == "subspecies"] <- taxonomy_lpsn$l
|
||||
taxonomy <- taxonomy_lpsn %>%
|
||||
# join GBIF identifiers to them
|
||||
left_join(taxonomy_gbif %>% select(kingdom, fullname, starts_with("gbif")),
|
||||
by = c("kingdom", "fullname")
|
||||
by = c("kingdom", "fullname")
|
||||
)
|
||||
|
||||
# for everything else, add the GBIF data
|
||||
taxonomy <- taxonomy %>%
|
||||
bind_rows(taxonomy_gbif %>%
|
||||
filter(!paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname))) %>%
|
||||
filter(!paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname))) %>%
|
||||
arrange(fullname) %>%
|
||||
filter(fullname != "")
|
||||
|
||||
# get missing entries from existing microorganisms data set
|
||||
taxonomy <- taxonomy %>%
|
||||
bind_rows(AMR::microorganisms %>%
|
||||
select(all_of(colnames(taxonomy))) %>%
|
||||
filter(!paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname),
|
||||
# these will be added later:
|
||||
source != "manually added")) %>%
|
||||
select(all_of(colnames(taxonomy))) %>%
|
||||
filter(
|
||||
!paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname),
|
||||
# these will be added later:
|
||||
source != "manually added"
|
||||
)) %>%
|
||||
arrange(fullname) %>%
|
||||
filter(fullname != "")
|
||||
|
||||
@ -602,9 +604,10 @@ taxonomy <- taxonomy %>%
|
||||
source = "manually added"
|
||||
) %>%
|
||||
filter(!paste(kingdom, rank) %in% paste(taxonomy$kingdom, taxonomy$rank)) %>%
|
||||
left_join(current_gbif %>%
|
||||
select(kingdom, rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
|
||||
by = c("kingdom", "rank")
|
||||
left_join(
|
||||
current_gbif %>%
|
||||
select(kingdom, rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
|
||||
by = c("kingdom", "rank")
|
||||
) %>%
|
||||
mutate(source = ifelse(!is.na(gbif), "GBIF", source))
|
||||
)
|
||||
@ -625,17 +628,18 @@ for (i in 2:6) {
|
||||
source = "manually added"
|
||||
) %>%
|
||||
filter(!paste(kingdom, .[[ncol(.) - 4]], rank) %in% paste(taxonomy$kingdom, taxonomy[[i + 1]], taxonomy$rank)) %>%
|
||||
# get GBIF identifier where available
|
||||
left_join(current_gbif %>%
|
||||
select(kingdom, all_of(i_name), rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
|
||||
by = c("kingdom", "rank", i_name)
|
||||
) %>%
|
||||
mutate(source = ifelse(!is.na(gbif), "GBIF", source))
|
||||
# get GBIF identifier where available
|
||||
left_join(
|
||||
current_gbif %>%
|
||||
select(kingdom, all_of(i_name), rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
|
||||
by = c("kingdom", "rank", i_name)
|
||||
) %>%
|
||||
mutate(source = ifelse(!is.na(gbif), "GBIF", source))
|
||||
message("n = ", nrow(to_add))
|
||||
if (is.null(taxonomy_all_missing)) {
|
||||
taxonomy_all_missing <- to_add
|
||||
} else {
|
||||
taxonomy_all_missing <- taxonomy_all_missing %>%
|
||||
taxonomy_all_missing <- taxonomy_all_missing %>%
|
||||
bind_rows(to_add)
|
||||
}
|
||||
}
|
||||
@ -645,20 +649,24 @@ taxonomy <- taxonomy %>%
|
||||
bind_rows(taxonomy_all_missing)
|
||||
|
||||
# fix for duplicate fullnames within a kingdom (such as Nitrospira which is the name of the genus AND its class)
|
||||
taxonomy <- taxonomy %>%
|
||||
mutate(rank_index = case_when(rank == "subspecies" ~ 1,
|
||||
rank == "species" ~ 2,
|
||||
rank == "genus" ~ 3,
|
||||
rank == "family" ~ 4,
|
||||
rank == "order" ~ 5,
|
||||
rank == "class" ~ 6,
|
||||
TRUE ~ 7),
|
||||
fullname_rank = paste0(fullname, " {", rank, "}")) %>%
|
||||
arrange(kingdom, fullname, rank_index) %>%
|
||||
group_by(kingdom, fullname) %>%
|
||||
mutate(fullname = if_else(row_number() > 1, fullname_rank, fullname)) %>%
|
||||
ungroup() %>%
|
||||
select(-fullname_rank, -rank_index) %>%
|
||||
taxonomy <- taxonomy %>%
|
||||
mutate(
|
||||
rank_index = case_when(
|
||||
rank == "subspecies" ~ 1,
|
||||
rank == "species" ~ 2,
|
||||
rank == "genus" ~ 3,
|
||||
rank == "family" ~ 4,
|
||||
rank == "order" ~ 5,
|
||||
rank == "class" ~ 6,
|
||||
TRUE ~ 7
|
||||
),
|
||||
fullname_rank = paste0(fullname, " {", rank, "}")
|
||||
) %>%
|
||||
arrange(kingdom, fullname, rank_index) %>%
|
||||
group_by(kingdom, fullname) %>%
|
||||
mutate(fullname = if_else(row_number() > 1, fullname_rank, fullname)) %>%
|
||||
ungroup() %>%
|
||||
select(-fullname_rank, -rank_index) %>%
|
||||
arrange(fullname)
|
||||
|
||||
# now also add missing species (requires combination with genus)
|
||||
@ -676,12 +684,13 @@ taxonomy <- taxonomy %>%
|
||||
) %>%
|
||||
filter(!paste(kingdom, genus, species, rank) %in% paste(taxonomy$kingdom, taxonomy$genus, taxonomy$species, taxonomy$rank)) %>%
|
||||
# get GBIF identifier where available
|
||||
left_join(current_gbif %>%
|
||||
select(kingdom, genus, species = specificEpithet, rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
|
||||
by = c("kingdom", "rank", "genus", "species")
|
||||
left_join(
|
||||
current_gbif %>%
|
||||
select(kingdom, genus, species = specificEpithet, rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
|
||||
by = c("kingdom", "rank", "genus", "species")
|
||||
) %>%
|
||||
mutate(source = ifelse(!is.na(gbif), "GBIF", source))
|
||||
)
|
||||
)
|
||||
|
||||
|
||||
# remove NAs from taxonomy again, and keep unique full names
|
||||
@ -702,7 +711,7 @@ manually_added <- AMR::microorganisms %>%
|
||||
filter(source == "manually added", !paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname)) %>%
|
||||
select(fullname:subspecies, ref, source, rank)
|
||||
|
||||
manually_added <- manually_added %>%
|
||||
manually_added <- manually_added %>%
|
||||
bind_rows(salmonellae)
|
||||
|
||||
# get latest taxonomy for those entries
|
||||
@ -805,76 +814,83 @@ taxonomy <- taxonomy %>%
|
||||
pathogens <- read_excel(file_bartlett, sheet = "Tab 6 Full List")
|
||||
|
||||
# get all established, both old and current taxonomic names
|
||||
established <- pathogens %>%
|
||||
filter(status == "established") %>%
|
||||
established <- pathogens %>%
|
||||
filter(status == "established") %>%
|
||||
mutate(fullname = paste(genus, species)) %>%
|
||||
pull(fullname) %>%
|
||||
c(unlist(mo_current(.)),
|
||||
unlist(mo_synonyms(., keep_synonyms = FALSE))) %>%
|
||||
strsplit(" ", fixed = TRUE) %>%
|
||||
sapply(function(x) ifelse(length(x) == 1, x, paste(x[1], x[2]))) %>%
|
||||
sort() %>%
|
||||
pull(fullname) %>%
|
||||
c(
|
||||
unlist(mo_current(.)),
|
||||
unlist(mo_synonyms(., keep_synonyms = FALSE))
|
||||
) %>%
|
||||
strsplit(" ", fixed = TRUE) %>%
|
||||
sapply(function(x) ifelse(length(x) == 1, x, paste(x[1], x[2]))) %>%
|
||||
sort() %>%
|
||||
unique()
|
||||
|
||||
# get all putative, both old and current taxonomic names
|
||||
putative <- pathogens %>%
|
||||
filter(status == "putative") %>%
|
||||
putative <- pathogens %>%
|
||||
filter(status == "putative") %>%
|
||||
mutate(fullname = paste(genus, species)) %>%
|
||||
pull(fullname) %>%
|
||||
c(unlist(mo_current(.)),
|
||||
unlist(mo_synonyms(., keep_synonyms = FALSE))) %>%
|
||||
strsplit(" ", fixed = TRUE) %>%
|
||||
sapply(function(x) ifelse(length(x) == 1, x, paste(x[1], x[2]))) %>%
|
||||
sort() %>%
|
||||
pull(fullname) %>%
|
||||
c(
|
||||
unlist(mo_current(.)),
|
||||
unlist(mo_synonyms(., keep_synonyms = FALSE))
|
||||
) %>%
|
||||
strsplit(" ", fixed = TRUE) %>%
|
||||
sapply(function(x) ifelse(length(x) == 1, x, paste(x[1], x[2]))) %>%
|
||||
sort() %>%
|
||||
unique()
|
||||
|
||||
established <- established[established %unlike% "unknown"]
|
||||
putative <- putative[putative %unlike% "unknown"]
|
||||
|
||||
established_genera <- established %>%
|
||||
strsplit(" ", fixed = TRUE) %>%
|
||||
sapply(function(x) x[1]) %>%
|
||||
sort() %>%
|
||||
established_genera <- established %>%
|
||||
strsplit(" ", fixed = TRUE) %>%
|
||||
sapply(function(x) x[1]) %>%
|
||||
sort() %>%
|
||||
unique()
|
||||
|
||||
putative_genera <- putative %>%
|
||||
strsplit(" ", fixed = TRUE) %>%
|
||||
sapply(function(x) x[1]) %>%
|
||||
sort() %>%
|
||||
putative_genera <- putative %>%
|
||||
strsplit(" ", fixed = TRUE) %>%
|
||||
sapply(function(x) x[1]) %>%
|
||||
sort() %>%
|
||||
unique()
|
||||
|
||||
nonbacterial_genera <- AMR:::MO_PREVALENT_GENERA %>%
|
||||
c(unlist(mo_current(.)),
|
||||
unlist(mo_synonyms(., keep_synonyms = FALSE))) %>%
|
||||
strsplit(" ", fixed = TRUE) %>%
|
||||
sapply(function(x) x[1]) %>%
|
||||
sort() %>%
|
||||
nonbacterial_genera <- AMR:::MO_PREVALENT_GENERA %>%
|
||||
c(
|
||||
unlist(mo_current(.)),
|
||||
unlist(mo_synonyms(., keep_synonyms = FALSE))
|
||||
) %>%
|
||||
strsplit(" ", fixed = TRUE) %>%
|
||||
sapply(function(x) x[1]) %>%
|
||||
sort() %>%
|
||||
unique()
|
||||
nonbacterial_genera <- nonbacterial_genera[nonbacterial_genera %unlike% "unknown"]
|
||||
|
||||
# update prevalence based on taxonomy (following the recent and thorough work of Bartlett et al., 2022)
|
||||
# see https://doi.org/10.1099/mic.0.001269
|
||||
taxonomy <- taxonomy %>%
|
||||
taxonomy <- taxonomy %>%
|
||||
mutate(prevalence = case_when(
|
||||
# 'established' means 'have infected at least three persons in three or more references'
|
||||
paste(genus, species) %in% established & rank %in% c("species", "subspecies") ~ 1.0,
|
||||
# other genera in the 'established' group
|
||||
genus %in% established_genera & rank == "genus" ~ 1.0,
|
||||
|
||||
|
||||
# 'putative' means 'fewer than three known cases'
|
||||
paste(genus, species) %in% putative & rank %in% c("species", "subspecies") ~ 1.25,
|
||||
# other genera in the 'putative' group
|
||||
genus %in% putative_genera & rank == "genus" ~ 1.25,
|
||||
|
||||
|
||||
# species and subspecies in 'established' and 'putative' groups
|
||||
genus %in% c(established_genera, putative_genera) & rank %in% c("species", "subspecies") ~ 1.5,
|
||||
# other species from a genus in either group
|
||||
genus %in% nonbacterial_genera & rank %in% c("genus", "species", "subspecies") ~ 1.5,
|
||||
# we keep track of prevalent genera too of non-bacterial species
|
||||
genus %in% AMR:::MO_PREVALENT_GENERA & kingdom != "Bacteria" & rank %in% c("genus", "species", "subspecies") ~ 1.5,
|
||||
|
||||
|
||||
# all others
|
||||
TRUE ~ 2.0))
|
||||
TRUE ~ 2.0
|
||||
))
|
||||
|
||||
table(taxonomy$prevalence, useNA = "always")
|
||||
# (a lot will be removed further below)
|
||||
@ -909,13 +925,14 @@ mo_kingdom <- taxonomy %>%
|
||||
mo_phylum <- taxonomy %>%
|
||||
filter(rank == "phylum") %>%
|
||||
distinct(kingdom, phylum) %>%
|
||||
left_join(AMR::microorganisms %>%
|
||||
filter(rank == "phylum") %>%
|
||||
transmute(kingdom,
|
||||
phylum = fullname,
|
||||
mo_old = gsub("[A-Z]{1,2}_", "", as.character(mo))
|
||||
),
|
||||
by = c("kingdom", "phylum")
|
||||
left_join(
|
||||
AMR::microorganisms %>%
|
||||
filter(rank == "phylum") %>%
|
||||
transmute(kingdom,
|
||||
phylum = fullname,
|
||||
mo_old = gsub("[A-Z]{1,2}_", "", as.character(mo))
|
||||
),
|
||||
by = c("kingdom", "phylum")
|
||||
) %>%
|
||||
group_by(kingdom) %>%
|
||||
mutate(
|
||||
@ -935,13 +952,14 @@ mo_phylum <- mo_phylum %>%
|
||||
mo_class <- taxonomy %>%
|
||||
filter(rank == "class") %>%
|
||||
distinct(kingdom, class) %>%
|
||||
left_join(AMR::microorganisms %>%
|
||||
filter(rank == "class") %>%
|
||||
transmute(kingdom,
|
||||
class = fullname,
|
||||
mo_old = gsub("[A-Z]{1,2}_", "", as.character(mo))
|
||||
),
|
||||
by = c("kingdom", "class")
|
||||
left_join(
|
||||
AMR::microorganisms %>%
|
||||
filter(rank == "class") %>%
|
||||
transmute(kingdom,
|
||||
class = fullname,
|
||||
mo_old = gsub("[A-Z]{1,2}_", "", as.character(mo))
|
||||
),
|
||||
by = c("kingdom", "class")
|
||||
) %>%
|
||||
group_by(kingdom) %>%
|
||||
mutate(
|
||||
@ -961,13 +979,14 @@ mo_class <- mo_class %>%
|
||||
mo_order <- taxonomy %>%
|
||||
filter(rank == "order") %>%
|
||||
distinct(kingdom, order) %>%
|
||||
left_join(AMR::microorganisms %>%
|
||||
filter(rank == "order") %>%
|
||||
transmute(kingdom,
|
||||
order = fullname,
|
||||
mo_old = gsub("[A-Z]{1,2}_", "", as.character(mo))
|
||||
),
|
||||
by = c("kingdom", "order")
|
||||
left_join(
|
||||
AMR::microorganisms %>%
|
||||
filter(rank == "order") %>%
|
||||
transmute(kingdom,
|
||||
order = fullname,
|
||||
mo_old = gsub("[A-Z]{1,2}_", "", as.character(mo))
|
||||
),
|
||||
by = c("kingdom", "order")
|
||||
) %>%
|
||||
group_by(kingdom) %>%
|
||||
mutate(
|
||||
@ -987,13 +1006,14 @@ mo_order <- mo_order %>%
|
||||
mo_family <- taxonomy %>%
|
||||
filter(rank == "family") %>%
|
||||
distinct(kingdom, family) %>%
|
||||
left_join(AMR::microorganisms %>%
|
||||
filter(rank == "family") %>%
|
||||
transmute(kingdom,
|
||||
family = fullname,
|
||||
mo_old = gsub("[A-Z]{1,2}_", "", as.character(mo))
|
||||
),
|
||||
by = c("kingdom", "family")
|
||||
left_join(
|
||||
AMR::microorganisms %>%
|
||||
filter(rank == "family") %>%
|
||||
transmute(kingdom,
|
||||
family = fullname,
|
||||
mo_old = gsub("[A-Z]{1,2}_", "", as.character(mo))
|
||||
),
|
||||
by = c("kingdom", "family")
|
||||
) %>%
|
||||
group_by(kingdom) %>%
|
||||
mutate(
|
||||
@ -1014,11 +1034,12 @@ mo_genus <- taxonomy %>%
|
||||
filter(rank == "genus") %>%
|
||||
distinct(kingdom, genus) %>%
|
||||
# get available old MO codes
|
||||
left_join(AMR::microorganisms %>%
|
||||
filter(rank == "genus") %>%
|
||||
transmute(mo_genus_old = gsub("^[A-Z]+_", "", as.character(mo)), kingdom, genus) %>%
|
||||
distinct(kingdom, genus, .keep_all = TRUE),
|
||||
by = c("kingdom", "genus")
|
||||
left_join(
|
||||
AMR::microorganisms %>%
|
||||
filter(rank == "genus") %>%
|
||||
transmute(mo_genus_old = gsub("^[A-Z]+_", "", as.character(mo)), kingdom, genus) %>%
|
||||
distinct(kingdom, genus, .keep_all = TRUE),
|
||||
by = c("kingdom", "genus")
|
||||
) %>%
|
||||
distinct(kingdom, genus, .keep_all = TRUE) %>%
|
||||
# since kingdom is part of the code, genus abbreviations may be duplicated between kingdoms
|
||||
@ -1060,12 +1081,13 @@ mo_genus <- mo_genus %>%
|
||||
mo_species <- taxonomy %>%
|
||||
filter(rank == "species") %>%
|
||||
distinct(kingdom, genus, species) %>%
|
||||
left_join(AMR::microorganisms %>%
|
||||
filter(rank == "species") %>%
|
||||
transmute(mo_species_old = gsub("^[A-Z]+_[A-Z]+_", "", as.character(mo)), kingdom, genus, species) %>%
|
||||
filter(mo_species_old %unlike% "-") %>%
|
||||
distinct(kingdom, genus, species, .keep_all = TRUE),
|
||||
by = c("kingdom", "genus", "species")
|
||||
left_join(
|
||||
AMR::microorganisms %>%
|
||||
filter(rank == "species") %>%
|
||||
transmute(mo_species_old = gsub("^[A-Z]+_[A-Z]+_", "", as.character(mo)), kingdom, genus, species) %>%
|
||||
filter(mo_species_old %unlike% "-") %>%
|
||||
distinct(kingdom, genus, species, .keep_all = TRUE),
|
||||
by = c("kingdom", "genus", "species")
|
||||
) %>%
|
||||
distinct(kingdom, genus, species, .keep_all = TRUE) %>%
|
||||
group_by(kingdom, genus) %>%
|
||||
@ -1108,12 +1130,13 @@ mo_species <- mo_species %>%
|
||||
mo_subspecies <- taxonomy %>%
|
||||
filter(rank == "subspecies") %>%
|
||||
distinct(kingdom, genus, species, subspecies) %>%
|
||||
left_join(AMR::microorganisms %>%
|
||||
filter(rank %in% c("subspecies", "subsp.", "infraspecies")) %>%
|
||||
transmute(mo_subspecies_old = gsub("^[A-Z]+_[A-Z]+_[A-Z]+_", "", as.character(mo)), kingdom, genus, species, subspecies) %>%
|
||||
filter(mo_subspecies_old %unlike% "-") %>%
|
||||
distinct(kingdom, genus, species, subspecies, .keep_all = TRUE),
|
||||
by = c("kingdom", "genus", "species", "subspecies")
|
||||
left_join(
|
||||
AMR::microorganisms %>%
|
||||
filter(rank %in% c("subspecies", "subsp.", "infraspecies")) %>%
|
||||
transmute(mo_subspecies_old = gsub("^[A-Z]+_[A-Z]+_[A-Z]+_", "", as.character(mo)), kingdom, genus, species, subspecies) %>%
|
||||
filter(mo_subspecies_old %unlike% "-") %>%
|
||||
distinct(kingdom, genus, species, subspecies, .keep_all = TRUE),
|
||||
by = c("kingdom", "genus", "species", "subspecies")
|
||||
) %>%
|
||||
distinct(kingdom, genus, species, subspecies, .keep_all = TRUE) %>%
|
||||
group_by(kingdom, genus, species) %>%
|
||||
@ -1187,20 +1210,26 @@ taxonomy <- taxonomy %>%
|
||||
arrange(fullname)
|
||||
|
||||
# now check these - e.g. Nitrospira is the name of a genus AND its class
|
||||
taxonomy %>% filter(fullname %in% .[duplicated(fullname), "fullname", drop = TRUE]) %>% View()
|
||||
taxonomy %>%
|
||||
filter(fullname %in% .[duplicated(fullname), "fullname", drop = TRUE]) %>%
|
||||
View()
|
||||
taxonomy <- taxonomy %>%
|
||||
mutate(rank_index = case_when(kingdom == "Bacteria" ~ 1,
|
||||
kingdom == "Fungi" ~ 2,
|
||||
kingdom == "Protozoa" ~ 3,
|
||||
kingdom == "Archaea" ~ 4,
|
||||
TRUE ~ 5)) %>%
|
||||
arrange(fullname, rank_index) %>%
|
||||
distinct(fullname, .keep_all = TRUE) %>%
|
||||
select(-rank_index) %>%
|
||||
mutate(rank_index = case_when(
|
||||
kingdom == "Bacteria" ~ 1,
|
||||
kingdom == "Fungi" ~ 2,
|
||||
kingdom == "Protozoa" ~ 3,
|
||||
kingdom == "Archaea" ~ 4,
|
||||
TRUE ~ 5
|
||||
)) %>%
|
||||
arrange(fullname, rank_index) %>%
|
||||
distinct(fullname, .keep_all = TRUE) %>%
|
||||
select(-rank_index) %>%
|
||||
filter(mo != "")
|
||||
|
||||
# this must not exist:
|
||||
taxonomy %>% filter(mo %like% "__") %>% View()
|
||||
taxonomy %>%
|
||||
filter(mo %like% "__") %>%
|
||||
View()
|
||||
taxonomy <- taxonomy %>% filter(mo %unlike% "__")
|
||||
|
||||
|
||||
@ -1214,14 +1243,20 @@ taxonomy <- taxonomy %>% distinct(mo, .keep_all = TRUE)
|
||||
taxonomy %>% filter(fullname %in% .[duplicated(fullname), "fullname", drop = TRUE])
|
||||
|
||||
# are all GBIFs available?
|
||||
taxonomy %>% filter(!gbif_parent %in% gbif) %>% count(rank)
|
||||
taxonomy %>%
|
||||
filter(!gbif_parent %in% gbif) %>%
|
||||
count(rank)
|
||||
# try to find the right gbif IDs
|
||||
taxonomy$gbif_parent[which(!taxonomy$gbif_parent %in% taxonomy$gbif & taxonomy$rank == "species")] <- taxonomy$gbif[match(taxonomy$genus[which(!taxonomy$gbif_parent %in% taxonomy$gbif & taxonomy$rank == "species")], taxonomy$genus)]
|
||||
taxonomy$gbif_parent[which(!taxonomy$gbif_parent %in% taxonomy$gbif & taxonomy$rank == "class")] <- taxonomy$gbif[match(taxonomy$phylum[which(!taxonomy$gbif_parent %in% taxonomy$gbif & taxonomy$rank == "class")], taxonomy$phylum)]
|
||||
taxonomy %>% filter(!gbif_parent %in% gbif) %>% count(rank)
|
||||
taxonomy %>%
|
||||
filter(!gbif_parent %in% gbif) %>%
|
||||
count(rank)
|
||||
|
||||
# are all LPSNs available?
|
||||
taxonomy %>% filter(!lpsn_parent %in% lpsn) %>% count(rank)
|
||||
taxonomy %>%
|
||||
filter(!lpsn_parent %in% lpsn) %>%
|
||||
count(rank)
|
||||
# make GBIF refer to newest renaming according to LPSN
|
||||
taxonomy$gbif_renamed_to[which(!is.na(taxonomy$gbif_renamed_to) & !is.na(taxonomy$lpsn_renamed_to))] <- taxonomy$gbif[match(taxonomy$lpsn_renamed_to[which(!is.na(taxonomy$gbif_renamed_to) & !is.na(taxonomy$lpsn_renamed_to))], taxonomy$lpsn)]
|
||||
|
||||
@ -1251,21 +1286,33 @@ taxonomy <- taxonomy %>%
|
||||
|
||||
# no ghost families, orders classes, phyla
|
||||
taxonomy <- taxonomy %>%
|
||||
group_by(kingdom, family) %>% filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom") %>%
|
||||
group_by(kingdom, order) %>% filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom") %>%
|
||||
group_by(kingdom, class) %>% filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom") %>%
|
||||
group_by(kingdom, phylum) %>% filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom") %>%
|
||||
group_by(kingdom, family) %>%
|
||||
filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom") %>%
|
||||
group_by(kingdom, order) %>%
|
||||
filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom") %>%
|
||||
group_by(kingdom, class) %>%
|
||||
filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom") %>%
|
||||
group_by(kingdom, phylum) %>%
|
||||
filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom") %>%
|
||||
ungroup()
|
||||
|
||||
|
||||
message("\nCongratulations! The new taxonomic table will contain ", format(nrow(taxonomy), big.mark = ","), " rows.\n",
|
||||
"This was ", format(nrow(AMR::microorganisms), big.mark = ","), " rows.\n")
|
||||
message(
|
||||
"\nCongratulations! The new taxonomic table will contain ", format(nrow(taxonomy), big.mark = ","), " rows.\n",
|
||||
"This was ", format(nrow(AMR::microorganisms), big.mark = ","), " rows.\n"
|
||||
)
|
||||
|
||||
# these are the new ones:
|
||||
taxonomy %>% filter(!paste(kingdom, fullname) %in% paste(AMR::microorganisms$kingdom, AMR::microorganisms$fullname)) %>% View()
|
||||
taxonomy %>%
|
||||
filter(!paste(kingdom, fullname) %in% paste(AMR::microorganisms$kingdom, AMR::microorganisms$fullname)) %>%
|
||||
View()
|
||||
# these were removed:
|
||||
AMR::microorganisms %>% filter(!paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname)) %>% View()
|
||||
AMR::microorganisms %>% filter(!fullname %in% taxonomy$fullname) %>% View()
|
||||
AMR::microorganisms %>%
|
||||
filter(!paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname)) %>%
|
||||
View()
|
||||
AMR::microorganisms %>%
|
||||
filter(!fullname %in% taxonomy$fullname) %>%
|
||||
View()
|
||||
|
||||
|
||||
# Add SNOMED CT -----------------------------------------------------------
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user