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move object assignment to AMR_env

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-14 13:02:50 +02:00
parent dfae4c7e7d
commit 76bcd3528c
18 changed files with 116 additions and 127 deletions
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6
R/italicise_taxonomy.R
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@ -71,7 +71,7 @@ italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
search_strings <- gsub("[^a-zA-Z-]", "", s_split)
ind_species <- search_strings != "" &
search_strings %in% MO_lookup[which(MO_lookup$rank %in% c(
search_strings %in% AMR_env$MO_lookup[which(AMR_env$MO_lookup$rank %in% c(
"family",
"genus",
"species",
@ -85,7 +85,7 @@ italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
ind_fullname <- search_strings != "" &
search_strings %in% c(
MO_lookup[which(MO_lookup$rank %in% c(
AMR_env$MO_lookup[which(AMR_env$MO_lookup$rank %in% c(
"family",
"genus",
"species",
@ -96,7 +96,7 @@ italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
"fullname",
drop = TRUE
],
MO_lookup[which(MO_lookup$rank %in% c(
AMR_env$MO_lookup[which(AMR_env$MO_lookup$rank %in% c(
"family",
"genus",
"species",