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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-01-23 15:01:21 +01:00
parent af139a3c82
commit 19fd0ef121
57 changed files with 2864 additions and 2739 deletions
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59
R/italicise_taxonomy.R
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@ -73,41 +73,44 @@ italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
search_strings <- gsub("[^a-zA-Z-]", "", s_split)
ind_species <- search_strings != "" &
search_strings %in% AMR_env$MO_lookup[which(AMR_env$MO_lookup$rank %in% c(
"family",
"genus",
search_strings %in% AMR_env$MO_lookup[
which(AMR_env$MO_lookup$rank %in% c(
"family",
"genus",
"species",
"subspecies",
"infraspecies",
"subsp."
)),
"species",
"subspecies",
"infraspecies",
"subsp."
)),
"species",
drop = TRUE
drop = TRUE
]
ind_fullname <- search_strings != "" &
search_strings %in% c(
AMR_env$MO_lookup[which(AMR_env$MO_lookup$rank %in% c(
"family",
"genus",
"species",
"subspecies",
"infraspecies",
"subsp."
)),
"fullname",
drop = TRUE
AMR_env$MO_lookup[
which(AMR_env$MO_lookup$rank %in% c(
"family",
"genus",
"species",
"subspecies",
"infraspecies",
"subsp."
)),
"fullname",
drop = TRUE
],
AMR_env$MO_lookup[which(AMR_env$MO_lookup$rank %in% c(
"family",
"genus",
"species",
AMR_env$MO_lookup[
which(AMR_env$MO_lookup$rank %in% c(
"family",
"genus",
"species",
"subspecies",
"infraspecies",
"subsp."
)),
"subspecies",
"infraspecies",
"subsp."
)),
"subspecies",
drop = TRUE
drop = TRUE
]
)