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@ -73,41 +73,44 @@ italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
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search_strings <- gsub("[^a-zA-Z-]", "", s_split)
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ind_species <- search_strings != "" &
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search_strings %in% AMR_env$MO_lookup[which(AMR_env$MO_lookup$rank %in% c(
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"family",
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"genus",
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search_strings %in% AMR_env$MO_lookup[
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which(AMR_env$MO_lookup$rank %in% c(
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"family",
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"genus",
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"species",
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"subspecies",
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"infraspecies",
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"subsp."
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)),
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"species",
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"subspecies",
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"infraspecies",
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"subsp."
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)),
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"species",
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drop = TRUE
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drop = TRUE
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]
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ind_fullname <- search_strings != "" &
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search_strings %in% c(
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AMR_env$MO_lookup[which(AMR_env$MO_lookup$rank %in% c(
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"family",
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"genus",
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"species",
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"subspecies",
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"infraspecies",
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"subsp."
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)),
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"fullname",
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drop = TRUE
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AMR_env$MO_lookup[
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which(AMR_env$MO_lookup$rank %in% c(
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"family",
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"genus",
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"species",
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"subspecies",
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"infraspecies",
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"subsp."
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)),
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"fullname",
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drop = TRUE
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],
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AMR_env$MO_lookup[which(AMR_env$MO_lookup$rank %in% c(
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"family",
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"genus",
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"species",
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AMR_env$MO_lookup[
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which(AMR_env$MO_lookup$rank %in% c(
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"family",
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"genus",
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"species",
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"subspecies",
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"infraspecies",
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"subsp."
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)),
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"subspecies",
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"infraspecies",
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"subsp."
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)),
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"subspecies",
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drop = TRUE
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drop = TRUE
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]
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)
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