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(v0.7.0.9007) renamed notes fix

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dr. M.S. (Matthijs) Berends
2019-06-12 16:08:20 +02:00
parent 44ab53128e
commit 699e87ab4a
11 changed files with 31 additions and 24 deletions
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10
R/mo.R
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@ -748,7 +748,7 @@ exec_as.mo <- function(x,
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
}
options(mo_renamed = c(getOption("mo_renamed"),
magenta(paste0("Note: ",
magenta(paste0("NOTE: ",
italic("Salmonella"), " ", trimws(gsub("Salmonella", "", x_backup_without_spp[i])),
" was considered ",
italic("Salmonella species"),
@ -760,7 +760,7 @@ exec_as.mo <- function(x,
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
}
options(mo_renamed = c(getOption("mo_renamed"),
magenta(paste0("Note: ",
magenta(paste0("NOTE: ",
italic("Salmonella"), " ", trimws(gsub("Salmonella", "", x_backup_without_spp[i])),
" was considered a subspecies of ",
italic("Salmonella enterica"),
@ -1233,7 +1233,7 @@ exec_as.mo <- function(x,
post_Becker <- c("argensis", "caeli", "cornubiensis", "edaphicus")
if (any(x %in% MOs_staph[species %in% post_Becker, ..property][[1]])) {
warning("Becker ", italic("et al."), " (2014) does not contain species named after their publication: ",
warning("Becker ", italic("et al."), " (2014, 2019) does not contain species named after their publication: ",
italic(paste("S.",
sort(mo_species(unique(x[x %in% MOs_staph[species %in% post_Becker, ..property][[1]]]))),
collapse = ", ")),
@ -1306,7 +1306,7 @@ exec_as.mo <- function(x,
}
notes <- sort(notes)
for (i in 1:length(notes)) {
base::message(blue(paste("Note:", notes[i])))
base::message(blue(paste("NOTE:", notes[i])))
}
}
@ -1336,7 +1336,7 @@ was_renamed <- function(name_old, name_new, ref_old = "", ref_new = "", mo = "")
}
msg <- paste0(italic(name_old), ref_old, " was renamed ", italic(name_new), ref_new, mo)
msg <- gsub("et al.", italic("et al."), msg)
options(mo_renamed = sort(msg))
options(mo_renamed = c(getOption("mo_renamed"), sort(msg)))
}
#' @exportMethod print.mo