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https://github.com/msberends/AMR.git
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renamed year columns to ref
This commit is contained in:
parent
3119a221e5
commit
ed17db0263
@ -90,7 +90,6 @@ export(labels_rsi_count)
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export(left_join_microorganisms)
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export(like)
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export(mo_TSN)
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export(mo_authors)
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export(mo_class)
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export(mo_family)
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export(mo_fullname)
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@ -99,13 +98,13 @@ export(mo_gramstain)
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export(mo_order)
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export(mo_phylum)
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export(mo_property)
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export(mo_ref)
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export(mo_shortname)
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export(mo_species)
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export(mo_subkingdom)
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export(mo_subspecies)
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export(mo_taxonomy)
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export(mo_type)
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export(mo_year)
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export(n_rsi)
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export(p.symbol)
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export(portion_I)
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8
NEWS.md
8
NEWS.md
@ -6,7 +6,7 @@
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* Taxonomic names: `mo_phylum`, `mo_class`, `mo_order`, `mo_family`, `mo_genus`, `mo_species`, `mo_subspecies`
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* Semantic names: `mo_fullname`, `mo_shortname`
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* Microbial properties: `mo_type`, `mo_gramstain`
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* Author information: `mo_author`, `mo_year`
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* Author and year: `mo_ref`
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They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:
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```r
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@ -20,11 +20,11 @@
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# [1] "Streptococcus grupo A"
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```
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Furthermore, old taxonomic names will give a note about the current taxonomic name:
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Furthermore, former taxonomic names will give a note about the current taxonomic name:
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```r
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mo_gramstain("Escherichia blattae")
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mo_gramstain("Esc blattae")
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# Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)
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# [1] "Gram negative
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# [1] "Gram negative"
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```
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* Functions `count_R`, `count_IR`, `count_I`, `count_SI` and `count_S` to selectively count resistant or susceptible isolates
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* Extra function `count_df` (which works like `portion_df`) to get all counts of S, I and R of a data set with antibiotic columns, with support for grouped variables
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10
R/data.R
10
R/data.R
@ -124,7 +124,7 @@
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#'
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#' 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}}.
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#' @inheritSection as.mo ITIS
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#' @format A \code{\link{data.frame}} with 18,833 observations and 16 variables:
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#' @format A \code{\link{data.frame}} with 18,833 observations and 15 variables:
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#' \describe{
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#' \item{\code{mo}}{ID of microorganism}
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#' \item{\code{tsn}}{Taxonomic Serial Number (TSN), as defined by ITIS}
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@ -140,8 +140,7 @@
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#' \item{\code{gramstain}}{Gram of microorganism, like \code{"Gram negative"}}
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#' \item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungi"}}
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#' \item{\code{prevalence}}{A rounded integer based on prevalence of the microorganism. Used internally by \code{\link{as.mo}}, otherwise quite meaningless.}
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#' \item{\code{authors}}{Author(s) that published this taxonomic name as found in ITIS, see Source}
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#' \item{\code{year}}{Year in which the author(s) published this taxonomic name as found in ITIS, see Source}
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#' \item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
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#' }
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#' @source [3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
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#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.umcg}}
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@ -151,13 +150,12 @@
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#'
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#' 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}}.
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#' @inheritSection as.mo ITIS
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#' @format A \code{\link{data.frame}} with 2,383 observations and 5 variables:
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#' @format A \code{\link{data.frame}} with 2,383 observations and 4 variables:
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#' \describe{
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#' \item{\code{tsn}}{Old Taxonomic Serial Number (TSN), as defined by ITIS}
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#' \item{\code{name}}{Old taxonomic name of the microorganism as found in ITIS, see Source}
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#' \item{\code{tsn_new}}{New Taxonomic Serial Number (TSN), as defined by ITIS}
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#' \item{\code{authors}}{Authors responsible for renaming as found in ITIS, see Source}
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#' \item{\code{year}}{Year in which the literature was published about the renaming as found in ITIS, see Source}
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#' \item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
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#' }
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#' @source [3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
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#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms}}
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9
R/freq.R
9
R/freq.R
@ -517,6 +517,12 @@ diff.frequency_tbl <- function(x, y, ...) {
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stop("Both x and y must be a frequency table.")
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}
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cat("Differences between frequency tables")
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if (identical(x, y)) {
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cat("\n\nNo differences found.\n")
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return(invisible())
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}
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x.attr <- attributes(x)$opt
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# only keep item and count
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@ -543,12 +549,11 @@ diff.frequency_tbl <- function(x, y, ...) {
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diff.percent,
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paste0("+", diff.percent)))
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cat("Differences between frequency tables")
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print(
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knitr::kable(x,
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format = x.attr$tbl_format,
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col.names = c("Item", "Count #1", "Count #2", "Difference", "Diff. percent"),
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align = "lrrrr",
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align = paste0(x.attr$column_align[1], "rrrr"),
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padding = 1)
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)
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}
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@ -31,6 +31,7 @@ globalVariables(c(".",
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"cum_percent",
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"date_lab",
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"days_diff",
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"diff.percent",
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"fctlvl",
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"first_isolate_row_index",
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"Freq",
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@ -58,6 +59,7 @@ globalVariables(c(".",
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"patient_id",
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"prevalence",
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"R",
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"ref",
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"real_first_isolate",
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"S",
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"septic_patients",
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45
R/mo.R
45
R/mo.R
@ -244,13 +244,11 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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x <- gsub(" ", ".*", x, fixed = TRUE)
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# add start en stop regex
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x <- paste0('^', x, '$')
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x_withspaces_all <- x_withspaces
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x_withspaces_start <- paste0('^', x_withspaces)
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x_withspaces <- paste0('^', x_withspaces, '$')
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# cat(paste0('x "', x, '"\n'))
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# cat(paste0('x_species "', x_species, '"\n'))
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# cat(paste0('x_withspaces_all "', x_withspaces_all, '"\n'))
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# cat(paste0('x_withspaces_start "', x_withspaces_start, '"\n'))
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# cat(paste0('x_withspaces "', x_withspaces, '"\n'))
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# cat(paste0('x_backup "', x_backup, '"\n'))
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@ -522,16 +520,15 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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MOs_old <- as.data.table(AMR::microorganisms.old)
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setkey(MOs_old, name, tsn_new)
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}
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found <- MOs_old[tolower(name) == tolower(x_backup[i]) |
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tsn == x_trimmed[i],]
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found <- MOs_old[tolower(name) == tolower(x_backup[i])
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| tsn == x_trimmed[i]
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| name %like% x_withspaces[i],]
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if (NROW(found) > 0) {
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x[i] <- MOs[tsn == found[1, tsn_new], ..property][[1]]
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renamed_note(name_old = found[1, name],
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name_new = MOs[tsn == found[1, tsn_new], fullname],
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authors_old = found[1, authors],
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authors_new = MOs[tsn == found[1, tsn_new], authors],
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year_old = found[1, year],
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year_new = MOs[tsn == found[1, tsn_new], year])
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ref_old = found[1, ref],
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ref_new = MOs[tsn == found[1, tsn_new], ref])
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next
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}
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@ -548,10 +545,8 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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call. = FALSE, immediate. = TRUE)
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renamed_note(name_old = found[1, name],
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name_new = MOs[tsn == found[1, tsn_new], fullname],
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authors_old = found[1, authors],
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authors_new = MOs[tsn == found[1, tsn_new], authors],
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year_old = found[1, year],
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year_new = MOs[tsn == found[1, tsn_new], year])
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ref_old = found[1, ref],
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ref_new = MOs[tsn == found[1, tsn_new], ref])
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next
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}
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@ -666,20 +661,18 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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}
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#' @importFrom dplyr case_when
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renamed_note <- function(name_old, name_new,
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authors_old = "", authors_new = "",
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year_old = "", year_new = "") {
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authorship_old <- case_when(
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!authors_old %in% c("", NA) & !year_old %in% c("", NA) ~ paste0(" (", authors_old, ", ", year_old, ")"),
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!authors_old %in% c("", NA) ~ paste0(" (", authors_old, ")"),
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!year_old %in% c("", NA) ~ paste0(" (", year_old, ")"),
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TRUE ~ "")
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authorship_new <- case_when(
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!authors_new %in% c("", NA) & !year_new %in% c("", NA) ~ paste0(" (", authors_new, ", ", year_new, ")"),
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!authors_new %in% c("", NA) ~ paste0(" (", authors_new, ")"),
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!year_new %in% c("", NA) ~ paste0(" (", year_new, ")"),
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TRUE ~ "")
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base::message(paste0("Note: '", name_old, "'", authorship_old, " was renamed '", name_new, "'", authorship_new))
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renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "") {
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if (!is.na(ref_old)) {
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ref_old <- paste0(" (", ref_old, ")")
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} else {
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ref_old <- ""
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}
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if (!is.na(ref_new)) {
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ref_new <- paste0(" (", ref_new, ")")
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} else {
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ref_new <- ""
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}
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base::message(paste0("Note: '", name_old, "'", ref_old, " was renamed '", name_new, "'", ref_new))
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}
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#' @exportMethod print.mo
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@ -45,8 +45,7 @@
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#' mo_gramstain("E. coli") # "Gram negative"
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#' mo_TSN("E. coli") # 285
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#' mo_type("E. coli") # "Bacteria"
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#' mo_authors("E. coli") # "Castellani and Chalmers"
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#' mo_year("E. coli") # 1919
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#' mo_ref("E. coli") # "Castellani and Chalmers, 1919"
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#'
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#'
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#' # Abbreviations known in the field
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@ -199,14 +198,8 @@ mo_subkingdom <- function(x, ...) {
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#' @rdname mo_property
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#' @export
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mo_authors <- function(x, ...) {
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mo_validate(x = x, property = "authors", ...)
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}
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#' @rdname mo_property
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#' @export
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mo_year <- function(x, ...) {
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mo_validate(x = x, property = "year", ...)
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mo_ref <- function(x, ...) {
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mo_validate(x = x, property = "ref", ...)
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}
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#' @rdname mo_property
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Binary file not shown.
Binary file not shown.
@ -119,7 +119,7 @@ years <- format(years)
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# print a histogram of numeric values
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septic_patients \%>\%
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freq(age) \%>\%
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hist() # prettier: ggplot(septic_patients, aes(age)) + geom_histogram()
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hist()
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# or print all points to a regular plot
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septic_patients \%>\%
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@ -147,6 +147,10 @@ table(septic_patients$gender,
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septic_patients$age) \%>\%
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freq(sep = " **sep** ")
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# check differences between frequency tables
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diff(freq(septic_patients$trim),
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freq(septic_patients$trsu))
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\dontrun{
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# send frequency table to clipboard (e.g. for pasting in Excel)
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septic_patients \%>\%
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@ -4,7 +4,7 @@
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\name{microorganisms}
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\alias{microorganisms}
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\title{Data set with taxonomic data from ITIS}
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\format{A \code{\link{data.frame}} with 18,833 observations and 16 variables:
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\format{A \code{\link{data.frame}} with 18,833 observations and 15 variables:
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\describe{
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\item{\code{mo}}{ID of microorganism}
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\item{\code{tsn}}{Taxonomic Serial Number (TSN), as defined by ITIS}
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@ -20,8 +20,7 @@
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\item{\code{gramstain}}{Gram of microorganism, like \code{"Gram negative"}}
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\item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungi"}}
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\item{\code{prevalence}}{A rounded integer based on prevalence of the microorganism. Used internally by \code{\link{as.mo}}, otherwise quite meaningless.}
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\item{\code{authors}}{Author(s) that published this taxonomic name as found in ITIS, see Source}
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\item{\code{year}}{Year in which the author(s) published this taxonomic name as found in ITIS, see Source}
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\item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
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}}
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\source{
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[3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
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@ -4,13 +4,12 @@
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\name{microorganisms.old}
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\alias{microorganisms.old}
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\title{Data set with old taxonomic data from ITIS}
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\format{A \code{\link{data.frame}} with 2,383 observations and 5 variables:
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\format{A \code{\link{data.frame}} with 2,383 observations and 4 variables:
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\describe{
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\item{\code{tsn}}{Old Taxonomic Serial Number (TSN), as defined by ITIS}
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\item{\code{name}}{Old taxonomic name of the microorganism as found in ITIS, see Source}
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\item{\code{tsn_new}}{New Taxonomic Serial Number (TSN), as defined by ITIS}
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\item{\code{authors}}{Authors responsible for renaming as found in ITIS, see Source}
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\item{\code{year}}{Year in which the literature was published about the renaming as found in ITIS, see Source}
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\item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
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}}
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\source{
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[3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
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@ -12,8 +12,7 @@
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\alias{mo_class}
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\alias{mo_phylum}
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\alias{mo_subkingdom}
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\alias{mo_authors}
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\alias{mo_year}
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\alias{mo_ref}
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\alias{mo_type}
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\alias{mo_TSN}
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\alias{mo_gramstain}
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@ -40,9 +39,7 @@ mo_phylum(x, ...)
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mo_subkingdom(x, ...)
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mo_authors(x, ...)
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mo_year(x, ...)
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mo_ref(x, ...)
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mo_type(x, language = NULL, ...)
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@ -103,8 +100,7 @@ mo_shortname("E. coli") # "E. coli"
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mo_gramstain("E. coli") # "Gram negative"
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mo_TSN("E. coli") # 285
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mo_type("E. coli") # "Bacteria"
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mo_authors("E. coli") # "Castellani and Chalmers"
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mo_year("E. coli") # 1919
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mo_ref("E. coli") # "Castellani and Chalmers, 1919"
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# Abbreviations known in the field
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@ -112,5 +112,19 @@ test_that("frequency table works", {
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expect_error(septic_patients %>% freq(peni, oxac, clox, amox, amcl,
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ampi, pita, czol, cfep, cfur))
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# run diff
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expect_output(print(
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diff(freq(septic_patients$amcl),
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freq(septic_patients$amox))
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))
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expect_output(print(
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diff(freq(septic_patients$age),
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freq(septic_patients$age)) # same
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))
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expect_error(print(
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diff(freq(septic_patients$amcl),
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"Just a string") # not a freq tbl
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))
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})
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@ -158,4 +158,14 @@ test_that("as.mo works", {
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expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = TRUE))), "B_ESCHR_COL")
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expect_warning(as.mo("esco extra_text", allow_uncertain = TRUE))
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# predefined reference_df
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expect_equal(as.character(as.mo("TestingOwnID",
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reference_df = data.frame(a = "TestingOwnID", b = "B_ESCHR_COL"))),
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"B_ESCHR_COL")
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expect_equal(as.character(as.mo(c("TestingOwnID", "E. coli"),
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reference_df = data.frame(a = "TestingOwnID", b = "B_ESCHR_COL"))),
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c("B_ESCHR_COL", "B_ESCHR_COL"))
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expect_warning(as.character(as.mo("TestingOwnID",
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reference_df = NULL)))
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})
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@ -15,8 +15,8 @@ test_that("mo_property works", {
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expect_equal(class(mo_taxonomy("E. coli")), "list")
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expect_equal(names(mo_taxonomy("E. coli")), c("subkingdom", "phylum", "class", "order",
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"family", "genus", "species", "subspecies"))
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expect_equal(mo_authors("E. coli"), "Castellani and Chalmers")
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expect_equal(mo_year("E. coli"), 1919)
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expect_equal(mo_ref("E. coli"), "Castellani and Chalmers, 1919")
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expect_equal(mo_shortname("MRSA"), "S. aureus")
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expect_equal(mo_shortname("MRSA", Becker = TRUE), "S. aureus")
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