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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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10
R/data.R
View File

@ -124,7 +124,7 @@
#'
#' A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa. MO codes can be looked up using \code{\link{as.mo}}.
#' @inheritSection as.mo ITIS
#' @format A \code{\link{data.frame}} with 18,833 observations and 16 variables:
#' @format A \code{\link{data.frame}} with 18,833 observations and 15 variables:
#' \describe{
#' \item{\code{mo}}{ID of microorganism}
#' \item{\code{tsn}}{Taxonomic Serial Number (TSN), as defined by ITIS}
@ -140,8 +140,7 @@
#' \item{\code{gramstain}}{Gram of microorganism, like \code{"Gram negative"}}
#' \item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungi"}}
#' \item{\code{prevalence}}{A rounded integer based on prevalence of the microorganism. Used internally by \code{\link{as.mo}}, otherwise quite meaningless.}
#' \item{\code{authors}}{Author(s) that published this taxonomic name as found in ITIS, see Source}
#' \item{\code{year}}{Year in which the author(s) published this taxonomic name as found in ITIS, see Source}
#' \item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
#' }
#' @source [3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.umcg}}
@ -151,13 +150,12 @@
#'
#' A data set containing old (previously valid or accepted) taxonomic names according to ITIS. This data set is used internally by \code{\link{as.mo}}.
#' @inheritSection as.mo ITIS
#' @format A \code{\link{data.frame}} with 2,383 observations and 5 variables:
#' @format A \code{\link{data.frame}} with 2,383 observations and 4 variables:
#' \describe{
#' \item{\code{tsn}}{Old Taxonomic Serial Number (TSN), as defined by ITIS}
#' \item{\code{name}}{Old taxonomic name of the microorganism as found in ITIS, see Source}
#' \item{\code{tsn_new}}{New Taxonomic Serial Number (TSN), as defined by ITIS}
#' \item{\code{authors}}{Authors responsible for renaming as found in ITIS, see Source}
#' \item{\code{year}}{Year in which the literature was published about the renaming as found in ITIS, see Source}
#' \item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
#' }
#' @source [3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms}}

9
R/freq.R
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@ -517,6 +517,12 @@ diff.frequency_tbl <- function(x, y, ...) {
stop("Both x and y must be a frequency table.")
}
cat("Differences between frequency tables")
if (identical(x, y)) {
cat("\n\nNo differences found.\n")
return(invisible())
}
x.attr <- attributes(x)$opt
# only keep item and count
@ -543,12 +549,11 @@ diff.frequency_tbl <- function(x, y, ...) {
diff.percent,
paste0("+", diff.percent)))
cat("Differences between frequency tables")
print(
knitr::kable(x,
format = x.attr$tbl_format,
col.names = c("Item", "Count #1", "Count #2", "Difference", "Diff. percent"),
align = "lrrrr",
align = paste0(x.attr$column_align[1], "rrrr"),
padding = 1)
)
}

2
R/globals.R
View File

@ -31,6 +31,7 @@ globalVariables(c(".",
"cum_percent",
"date_lab",
"days_diff",
"diff.percent",
"fctlvl",
"first_isolate_row_index",
"Freq",
@ -58,6 +59,7 @@ globalVariables(c(".",
"patient_id",
"prevalence",
"R",
"ref",
"real_first_isolate",
"S",
"septic_patients",

45
R/mo.R
View File

@ -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

13
R/mo_property.R
View File

@ -45,8 +45,7 @@
#' mo_gramstain("E. coli") # "Gram negative"
#' mo_TSN("E. coli") # 285
#' mo_type("E. coli") # "Bacteria"
#' mo_authors("E. coli") # "Castellani and Chalmers"
#' mo_year("E. coli") # 1919
#' mo_ref("E. coli") # "Castellani and Chalmers, 1919"
#'
#'
#' # Abbreviations known in the field
@ -199,14 +198,8 @@ mo_subkingdom <- function(x, ...) {
#' @rdname mo_property
#' @export
mo_authors <- function(x, ...) {
mo_validate(x = x, property = "authors", ...)
}
#' @rdname mo_property
#' @export
mo_year <- function(x, ...) {
mo_validate(x = x, property = "year", ...)
mo_ref <- function(x, ...) {
mo_validate(x = x, property = "ref", ...)
}
#' @rdname mo_property