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renamed year columns to ref

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dr. M.S. (Matthijs) Berends
2018-10-01 14:44:40 +02:00
parent 3119a221e5
commit ed17db0263
16 changed files with 78 additions and 66 deletions
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45
R/mo.R
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@ -244,13 +244,11 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
x <- gsub(" ", ".*", x, fixed = TRUE)
# add start en stop regex
x <- paste0('^', x, '$')
x_withspaces_all <- x_withspaces
x_withspaces_start <- paste0('^', x_withspaces)
x_withspaces <- paste0('^', x_withspaces, '$')
# cat(paste0('x "', x, '"\n'))
# cat(paste0('x_species "', x_species, '"\n'))
# cat(paste0('x_withspaces_all "', x_withspaces_all, '"\n'))
# cat(paste0('x_withspaces_start "', x_withspaces_start, '"\n'))
# cat(paste0('x_withspaces "', x_withspaces, '"\n'))
# cat(paste0('x_backup "', x_backup, '"\n'))
@ -522,16 +520,15 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
MOs_old <- as.data.table(AMR::microorganisms.old)
setkey(MOs_old, name, tsn_new)
}
found <- MOs_old[tolower(name) == tolower(x_backup[i]) |
tsn == x_trimmed[i],]
found <- MOs_old[tolower(name) == tolower(x_backup[i])
| tsn == x_trimmed[i]
| name %like% x_withspaces[i],]
if (NROW(found) > 0) {
x[i] <- MOs[tsn == found[1, tsn_new], ..property][[1]]
renamed_note(name_old = found[1, name],
name_new = MOs[tsn == found[1, tsn_new], fullname],
authors_old = found[1, authors],
authors_new = MOs[tsn == found[1, tsn_new], authors],
year_old = found[1, year],
year_new = MOs[tsn == found[1, tsn_new], year])
ref_old = found[1, ref],
ref_new = MOs[tsn == found[1, tsn_new], ref])
next
}
@ -548,10 +545,8 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
call. = FALSE, immediate. = TRUE)
renamed_note(name_old = found[1, name],
name_new = MOs[tsn == found[1, tsn_new], fullname],
authors_old = found[1, authors],
authors_new = MOs[tsn == found[1, tsn_new], authors],
year_old = found[1, year],
year_new = MOs[tsn == found[1, tsn_new], year])
ref_old = found[1, ref],
ref_new = MOs[tsn == found[1, tsn_new], ref])
next
}
@ -666,20 +661,18 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
}
#' @importFrom dplyr case_when
renamed_note <- function(name_old, name_new,
authors_old = "", authors_new = "",
year_old = "", year_new = "") {
authorship_old <- case_when(
!authors_old %in% c("", NA) & !year_old %in% c("", NA) ~ paste0(" (", authors_old, ", ", year_old, ")"),
!authors_old %in% c("", NA) ~ paste0(" (", authors_old, ")"),
!year_old %in% c("", NA) ~ paste0(" (", year_old, ")"),
TRUE ~ "")
authorship_new <- case_when(
!authors_new %in% c("", NA) & !year_new %in% c("", NA) ~ paste0(" (", authors_new, ", ", year_new, ")"),
!authors_new %in% c("", NA) ~ paste0(" (", authors_new, ")"),
!year_new %in% c("", NA) ~ paste0(" (", year_new, ")"),
TRUE ~ "")
base::message(paste0("Note: '", name_old, "'", authorship_old, " was renamed '", name_new, "'", authorship_new))
renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "") {
if (!is.na(ref_old)) {
ref_old <- paste0(" (", ref_old, ")")
} else {
ref_old <- ""
}
if (!is.na(ref_new)) {
ref_new <- paste0(" (", ref_new, ")")
} else {
ref_new <- ""
}
base::message(paste0("Note: '", name_old, "'", ref_old, " was renamed '", name_new, "'", ref_new))
}
#' @exportMethod print.mo