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AMR
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added prevalence column and alterted as.mo algorith to use it, added ab_name as alias

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dr. M.S. (Matthijs) Berends 2018-09-16 16:43:29 +02:00
parent b0ca49d68d
commit b792a2754e
16 changed files with 101 additions and 79 deletions
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2
NAMESPACE
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@ -41,8 +41,8 @@ export(MDRO)
export(MRGN) export(MRGN)
export(ab_atc) export(ab_atc)
export(ab_certe) export(ab_certe)
export(ab_name)
export(ab_official) export(ab_official)
export(ab_official_nl)
export(ab_property) export(ab_property)
export(ab_tradenames) export(ab_tradenames)
export(ab_trivial_nl) export(ab_trivial_nl)

6
NEWS.md
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@ -37,7 +37,7 @@
mo_fullname("S. group A") # when run on a on a Portuguese system mo_fullname("S. group A") # when run on a on a Portuguese system
# [1] "Streptococcus grupo A" # [1] "Streptococcus grupo A"
``` ```
* Function `ab_property` and its aliases: `ab_official`, `ab_tradenames`, `ab_certe`, `ab_umcg`, `ab_official_nl` and `ab_trivial_nl` * Function `ab_property` and its aliases: `ab_name`, `ab_tradenames`, `ab_certe`, `ab_umcg` and `ab_trivial_nl`
* Introduction to AMR as a vignette * Introduction to AMR as a vignette
#### Changed #### Changed
@ -47,7 +47,7 @@
```r ```r
ab_official("Bactroban") ab_official("Bactroban")
# [1] "Mupirocin" # [1] "Mupirocin"
ab_official(c("Bactroban", "Amoxil", "Zithromax", "Floxapen")) ab_name(c("Bactroban", "Amoxil", "Zithromax", "Floxapen"))
# [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin" # [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"
ab_atc(c("Bactroban", "Amoxil", "Zithromax", "Floxapen")) ab_atc(c("Bactroban", "Amoxil", "Zithromax", "Floxapen"))
# [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05" # [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"
@ -56,7 +56,7 @@
* Function `ratio` is now deprecated and will be removed in a future release, as it is not really the scope of this package * Function `ratio` is now deprecated and will be removed in a future release, as it is not really the scope of this package
* Fix for `as.mic` for values ending in zeroes after a real number * Fix for `as.mic` for values ending in zeroes after a real number
* Small fix where *B. fragilis* would not be found in the `microorganisms.umcg` data set * Small fix where *B. fragilis* would not be found in the `microorganisms.umcg` data set
* Fix for `is.rsi.eligible`, now ignores reading marks * Added `prevalence` column to the `microorganisms` data set
* Added parameters `minimum` and `as_percent` to `portion_df` * Added parameters `minimum` and `as_percent` to `portion_df`
* Support for quasiquotation in the functions series `count_*` and `portions_*`, and `n_rsi`. This allows to check for more than 2 vectors or columns. * Support for quasiquotation in the functions series `count_*` and `portions_*`, and `n_rsi`. This allows to check for more than 2 vectors or columns.
```r ```r

25
R/ab_property.R
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@ -21,6 +21,7 @@
#' Use these functions to return a specific property of an antibiotic from the \code{\link{antibiotics}} data set, based on their ATC code. Get such a code with \code{\link{as.atc}}. #' Use these functions to return a specific property of an antibiotic from the \code{\link{antibiotics}} data set, based on their ATC code. Get such a code with \code{\link{as.atc}}.
#' @param x a (vector of a) valid \code{\link{atc}} code or any text that can be coerced to a valid atc with \code{\link{as.atc}} #' @param x a (vector of a) valid \code{\link{atc}} code or any text that can be coerced to a valid atc with \code{\link{as.atc}}
#' @param property one of the column names of one of the \code{\link{antibiotics}} data set, like \code{"atc"} and \code{"official"} #' @param property one of the column names of one of the \code{\link{antibiotics}} data set, like \code{"atc"} and \code{"official"}
#' @param language language of the returned text, defaults to the systems language. Either one of \code{"en"} (English) or \code{"nl"} (Dutch).
#' @rdname ab_property #' @rdname ab_property
#' @return A vector of values. In case of \code{ab_tradenames}, if \code{x} is of length one, a vector will be returned. Otherwise a \code{\link{list}}, with \code{x} as names. #' @return A vector of values. In case of \code{ab_tradenames}, if \code{x} is of length one, a vector will be returned. Otherwise a \code{\link{list}}, with \code{x} as names.
#' @export #' @export
@ -28,8 +29,8 @@
#' @seealso \code{\link{antibiotics}} #' @seealso \code{\link{antibiotics}}
#' @examples #' @examples
#' ab_atc("amcl") # J01CR02 #' ab_atc("amcl") # J01CR02
#' ab_official("amcl") # Amoxicillin and beta-lactamase inhibitor #' ab_name("amcl") # Amoxicillin and beta-lactamase inhibitor
#' ab_official_nl("amcl") # Amoxicilline met enzymremmer #' ab_name("amcl", "nl") # Amoxicilline met enzymremmer
#' ab_trivial_nl("amcl") # Amoxicilline/clavulaanzuur #' ab_trivial_nl("amcl") # Amoxicilline/clavulaanzuur
#' ab_certe("amcl") # amcl #' ab_certe("amcl") # amcl
#' ab_umcg("amcl") # AMCL #' ab_umcg("amcl") # AMCL
@ -56,15 +57,25 @@ ab_atc <- function(x) {
#' @rdname ab_property #' @rdname ab_property
#' @export #' @export
ab_official <- function(x) { ab_official <- function(x, language = NULL) {
ab_property(x, "official")
if (is.null(language)) {
language <- Sys.locale()
} else {
language <- tolower(language[1])
}
if (language %in% c("en", "")) {
ab_property(x, "official")
} else if (language == "nl") {
ab_property(x, "official_nl")
} else {
stop("Unsupported language: '", language, "' - use one of: 'en', 'nl'", call. = FALSE)
}
} }
#' @rdname ab_property #' @rdname ab_property
#' @export #' @export
ab_official_nl <- function(x) { ab_name <- ab_official
ab_property(x, "official_nl")
}
#' @rdname ab_property #' @rdname ab_property
#' @export #' @export

5
R/data.R
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@ -122,8 +122,8 @@
#' Data set with human pathogenic microorganisms #' Data set with human pathogenic microorganisms
#' #'
#' A data set containing 2,630 (potential) human pathogenic microorganisms. MO codes can be looked up using \code{\link{guess_mo}}. #' A data set containing (potential) human pathogenic microorganisms. MO codes can be looked up using \code{\link{guess_mo}}.
#' @format A \code{\link{tibble}} with 2,630 observations and 10 variables: #' @format A \code{\link{tibble}} with 2,642 observations and 11 variables:
#' \describe{ #' \describe{
#' \item{\code{mo}}{ID of microorganism} #' \item{\code{mo}}{ID of microorganism}
#' \item{\code{bactsys}}{Bactsyscode of microorganism} #' \item{\code{bactsys}}{Bactsyscode of microorganism}
@ -135,6 +135,7 @@
#' \item{\code{aerobic}}{Logical whether bacteria is aerobic} #' \item{\code{aerobic}}{Logical whether bacteria is aerobic}
#' \item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungus/yeast"}} #' \item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungus/yeast"}}
#' \item{\code{gramstain}}{Gram of microorganism, like \code{"Negative rods"}} #' \item{\code{gramstain}}{Gram of microorganism, like \code{"Negative rods"}}
#' \item{\code{prevalence}}{A rounded integer based on prevalence of the microorganism. Used internally by \code{\link{as.mo}}, otherwise quite meaningless.}
#' } #' }
# source MOLIS (LIS of Certe) - \url{https://www.certe.nl} # source MOLIS (LIS of Certe) - \url{https://www.certe.nl}
# new <- microorganisms %>% filter(genus == "Bacteroides") %>% .[1,] # new <- microorganisms %>% filter(genus == "Bacteroides") %>% .[1,]

1
R/globals.R
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@ -47,6 +47,7 @@ globalVariables(c(".",
"Pasted", "Pasted",
"patient_id", "patient_id",
"Percentage", "Percentage",
"prevalence",
"R", "R",
"real_first_isolate", "real_first_isolate",
"S", "S",

14
R/misc.R
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@ -155,6 +155,20 @@ tbl_parse_guess <- function(tbl,
tbl tbl
} }
#' @importFrom dplyr case_when
Sys.locale <- function() {
sys <- base::Sys.getlocale()
case_when(
sys %like% '(Deutsch|German|de_)' ~ "de",
sys %like% '(Nederlands|Dutch|nl_)' ~ "nl",
sys %like% '(Espa.ol|Spanish|es_)' ~ "es",
sys %like% '(Fran.ais|French|fr_)' ~ "fr",
sys %like% '(Portugu.s|Portuguese|pt_)' ~ "pt",
sys %like% '(Italiano|Italian|it_)' ~ "it",
TRUE ~ "en"
)
}
# transforms date format like "dddd d mmmm yyyy" to "%A %e %B %Y" # transforms date format like "dddd d mmmm yyyy" to "%A %e %B %Y"
date_generic <- function(format) { date_generic <- function(format) {
if (!grepl('%', format, fixed = TRUE)) { if (!grepl('%', format, fixed = TRUE)) {

49
R/mo.R
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@ -33,12 +33,12 @@
#' #'
#' Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples. #' Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
#' #'
#' Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. These are: #' Thus function uses Artificial Intelligence (AI) to help getting more logical results, based on type of input and known prevalence of human pathogens. For example:
#' \itemize{ #' \itemize{
#' \item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first} #' \item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first}
#' \item{\code{"H. influenzae"} will return the ID of \emph{Haemophilus influenzae} and not \emph{Haematobacter influenzae}} #' \item{\code{"H. influenzae"} will return the ID of \emph{Haemophilus influenzae} and not \emph{Haematobacter influenzae} for the same reason}
#' \item{Something like \code{"p aer"} will return the ID of \emph{Pseudomonas aeruginosa} and not \emph{Pasteurella aerogenes}} #' \item{Something like \code{"p aer"} will return the ID of \emph{Pseudomonas aeruginosa} and not \emph{Pasteurella aerogenes}}
#' \item{Something like \code{"stau"} or \code{"staaur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}} #' \item{Something like \code{"stau"} or \code{"S aur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}}
#' } #' }
#' Moreover, this function also supports ID's based on only Gram stain, when the species is not known. \cr #' Moreover, this function also supports ID's based on only Gram stain, when the species is not known. \cr
#' For example, \code{"Gram negative rods"} and \code{"GNR"} will both return the ID of a Gram negative rod: \code{GNR}. #' For example, \code{"Gram negative rods"} and \code{"GNR"} will both return the ID of a Gram negative rod: \code{GNR}.
@ -47,7 +47,7 @@
#' #'
#' [2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571} #' [2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
#' @export #' @export
#' @importFrom dplyr %>% pull left_join #' @importFrom dplyr %>% pull left_join arrange
#' @return Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}. #' @return Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.
#' @seealso \code{\link{microorganisms}} for the dataframe that is being used to determine ID's. #' @seealso \code{\link{microorganisms}} for the dataframe that is being used to determine ID's.
#' @examples #' @examples
@ -118,7 +118,10 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
} }
} }
MOs <- AMR::microorganisms %>% filter(!mo %like% '^_FAM') # dont search in those MOs <- AMR::microorganisms %>%
arrange(prevalence) %>% # more expected result on multiple findings
filter(!mo %like% '^_FAM', # don't search in those
(nchar(mo) > 3 | mo %in% c("GNR", "GPR", "GNC", "GPC"))) # no genera
failures <- character(0) failures <- character(0)
x_input <- x x_input <- x
@ -144,11 +147,11 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
x_withspaces_start <- paste0('^', x_withspaces) x_withspaces_start <- paste0('^', x_withspaces)
x_withspaces <- paste0('^', x_withspaces, '$') x_withspaces <- paste0('^', x_withspaces, '$')
# print(x) # cat(paste0('x "', x, '"\n'))
# print(x_withspaces_all) # cat(paste0('x_withspaces_all "', x_withspaces_all, '"\n'))
# print(x_withspaces_start) # cat(paste0('x_withspaces_start "', x_withspaces_start, '"\n'))
# print(x_withspaces) # cat(paste0('x_withspaces "', x_withspaces, '"\n'))
# print(x_backup) # cat(paste0('x_backup "', x_backup, '"\n'))
for (i in 1:length(x)) { for (i in 1:length(x)) {
if (identical(x_trimmed[i], "")) { if (identical(x_trimmed[i], "")) {
@ -201,7 +204,7 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
next next
} }
if (toupper(x_trimmed[i]) == 'VRE') { if (toupper(x_trimmed[i]) == 'VRE') {
x[i] <- 'ENC' x[i] <- 'ENCSPP'
next next
} }
if (toupper(x_trimmed[i]) == 'MRPA') { if (toupper(x_trimmed[i]) == 'MRPA') {
@ -234,6 +237,13 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
next next
} }
# try any match with genus, keeping spaces, not ending with $ ----
found <- MOs[which(MOs$genus %like% x_withspaces_start[i] & MOs$mo %like% 'SPP$'),]$mo
if (length(found) > 0) {
x[i] <- found[1L]
next
}
# try any match keeping spaces, not ending with $ ---- # try any match keeping spaces, not ending with $ ----
found <- MOs[which(MOs$fullname %like% x_withspaces_start[i]),]$mo found <- MOs[which(MOs$fullname %like% x_withspaces_start[i]),]$mo
if (length(found) > 0) { if (length(found) > 0) {
@ -297,19 +307,6 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
} }
# avoid detection of Staphylococcus auricularis in case of S. aureus ----
x[x == "STAAUC" & toupper(x_backup) != "STAAUC" & !x_backup %like% 'auri'] <- "STAAUR"
# avoid detection of Entamoeba coli in case of E. coli ----
x[x == "ENMCOL" & toupper(x_backup) != "ENMCOL" & !x_backup %like% '^ent?'] <- "ESCCOL"
# avoid detection of Haematobacter influenzae in case of H. influenzae ----
x[x == "HABINF" & toupper(x_backup) != "HABINF" & !x_backup %like% '^haema'] <- "HAEINF"
# avoid detection of Pasteurella aerogenes in case of P. aeruginosa ----
x[x == "PASAER" & toupper(x_backup) != "PASAER" & !(x_backup %like% '^pas?' | x_backup %like% 'aero')] <- "PSEAER"
# avoid detection of Legionella non pneumophila in case of Legionella pneumophila ----
x[x == "LEGNON" & toupper(x_backup) != "LEGNON" & !x_backup %like% 'non'] <- "LEGPNE"
# avoid detection of Streptobacillus in case of Streptococcus ----
x[x == "STB" & toupper(x_backup) != "STB" & !x_backup %like% 'streptob'] <- "STC"
failures <- failures[!failures %in% c(NA, NULL, NaN)] failures <- failures[!failures %in% c(NA, NULL, NaN)]
if (length(failures) > 0) { if (length(failures) > 0) {
warning("These ", length(failures) , " values could not be coerced to a valid mo: ", warning("These ", length(failures) , " values could not be coerced to a valid mo: ",
@ -376,7 +373,9 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
# for the returned genera without species, add species ---- # for the returned genera without species, add species ----
# like "ESC" -> "ESCSPP", but only where the input contained it # like "ESC" -> "ESCSPP", but only where the input contained it
indices <- unique(x_input) %like% "[A-Z]{3}SPP" & !x %like% "[A-Z]{3}SPP" indices <- nchar(unique(x)) == 3 & !x %like% "[A-Z]{3}SPP" & !x %in% c("GNR", "GPR", "GNC", "GPC",
"GNS", "GPS", "GNK", "GPK")
indices <- indices[!is.na(indices)]
x[indices] <- paste0(x[indices], 'SPP') x[indices] <- paste0(x[indices], 'SPP')
# left join the found results to the original input values (x_input) # left join the found results to the original input values (x_input)

16
R/mo_property.R
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@ -207,7 +207,7 @@ mo_property <- function(x, property = 'fullname', Becker = FALSE, Lancefield = F
#' @importFrom dplyr %>% case_when #' @importFrom dplyr %>% case_when
mo_translate <- function(x, language) { mo_translate <- function(x, language) {
if (is.null(language)) { if (is.null(language)) {
language <- mo_getlangcode() language <- Sys.locale()
} else { } else {
language <- tolower(language[1]) language <- tolower(language[1])
} }
@ -350,17 +350,3 @@ mo_translate <- function(x, language) {
) )
} }
#' @importFrom dplyr case_when
mo_getlangcode <- function() {
sys <- base::Sys.getlocale()
case_when(
sys %like% '(Deutsch|German|de_)' ~ "de",
sys %like% '(Nederlands|Dutch|nl_)' ~ "nl",
sys %like% '(Espa.ol|Spanish|es_)' ~ "es",
sys %like% '(Fran.ais|French|fr_)' ~ "fr",
sys %like% '(Portugu.s|Portuguese|pt_)' ~ "pt",
sys %like% '(Italiano|Italian|it_)' ~ "it",
TRUE ~ "en"
)
}

4
README.md
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@ -56,7 +56,7 @@ This `AMR` package basically does four important things:
* You can also identify first *weighted* isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them. * You can also identify first *weighted* isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.
* Use `MDRO` (abbreviation of Multi Drug Resistant Organisms) to check your isolates for exceptional resistance with country-specific guidelines or EUCAST rules. Currently, national guidelines for Germany and the Netherlands are supported. * Use `MDRO` (abbreviation of Multi Drug Resistant Organisms) to check your isolates for exceptional resistance with country-specific guidelines or EUCAST rules. Currently, national guidelines for Germany and the Netherlands are supported.
* The data set `microorganisms` contains the family, genus, species, subspecies, colloquial name and Gram stain of almost 3,000 potential human pathogenic microorganisms (bacteria, fungi/yeasts and parasites). This enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like `mo_genus`, `mo_family` or `mo_gramstain`. As they use `as.mo` internally, they also use artificial intelligence. For example, `mo_genus("MRSA")` and `mo_genus("S. aureus")` will both return `"Staphylococcus"`. They also come with support for German, Dutch, French, Italian, Spanish and Portuguese. These functions can be used to add new variables to your data. * The data set `microorganisms` contains the family, genus, species, subspecies, colloquial name and Gram stain of almost 3,000 potential human pathogenic microorganisms (bacteria, fungi/yeasts and parasites). This enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like `mo_genus`, `mo_family` or `mo_gramstain`. As they use `as.mo` internally, they also use artificial intelligence. For example, `mo_genus("MRSA")` and `mo_genus("S. aureus")` will both return `"Staphylococcus"`. They also come with support for German, Dutch, French, Italian, Spanish and Portuguese. These functions can be used to add new variables to your data.
* The data set `antibiotics` contains the ATC code, LIS codes, official name, trivial name and DDD of both oral and parenteral administration. It also contains a total of 298 trade names. Use functions like `ab_official` and `ab_tradenames` to look up values. As the `mo_*` functions use `as.mo` internally, the `ab_*` functions use `as.atc` internally so it uses AI to guess your expected result. For example, `ab_official("Fluclox")`, `ab_official("Floxapen")` and `ab_official("J01CF05")` will all return `"Flucloxacillin"`. These functions can again be used to add new variables to your data. * The data set `antibiotics` contains the ATC code, LIS codes, official name, trivial name and DDD of both oral and parenteral administration. It also contains a total of 298 trade names. Use functions like `ab_name` and `ab_tradenames` to look up values. As the `mo_*` functions use `as.mo` internally, the `ab_*` functions use `as.atc` internally so it uses AI to guess your expected result. For example, `ab_name("Fluclox")`, `ab_name("Floxapen")` and `ab_name("J01CF05")` will all return `"Flucloxacillin"`. These functions can again be used to add new variables to your data.
3. It **analyses the data** with convenient functions that use well-known methods. 3. It **analyses the data** with convenient functions that use well-known methods.
@ -388,7 +388,7 @@ antibiotics # A tibble: 423 x 18
# Dataset with bacteria codes and properties like gram stain and # Dataset with bacteria codes and properties like gram stain and
# aerobic/anaerobic # aerobic/anaerobic
microorganisms # A tibble: 2,630 x 10 microorganisms # A tibble: 2,642 x 11
``` ```
## Copyright ## Copyright

BIN
data/microorganisms.rda
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12
man/ab_property.Rd
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@ -4,7 +4,7 @@
\alias{ab_property} \alias{ab_property}
\alias{ab_atc} \alias{ab_atc}
\alias{ab_official} \alias{ab_official}
\alias{ab_official_nl} \alias{ab_name}
\alias{ab_trivial_nl} \alias{ab_trivial_nl}
\alias{ab_certe} \alias{ab_certe}
\alias{ab_umcg} \alias{ab_umcg}
@ -15,9 +15,9 @@ ab_property(x, property = "official")
ab_atc(x) ab_atc(x)
ab_official(x) ab_official(x, language = NULL)
ab_official_nl(x) ab_name(x, language = NULL)
ab_trivial_nl(x) ab_trivial_nl(x)
@ -31,6 +31,8 @@ ab_tradenames(x)
\item{x}{a (vector of a) valid \code{\link{atc}} code or any text that can be coerced to a valid atc with \code{\link{as.atc}}} \item{x}{a (vector of a) valid \code{\link{atc}} code or any text that can be coerced to a valid atc with \code{\link{as.atc}}}
\item{property}{one of the column names of one of the \code{\link{antibiotics}} data set, like \code{"atc"} and \code{"official"}} \item{property}{one of the column names of one of the \code{\link{antibiotics}} data set, like \code{"atc"} and \code{"official"}}
\item{language}{language of the returned text, defaults to the systems language. Either one of \code{"en"} (English) or \code{"nl"} (Dutch).}
} }
\value{ \value{
A vector of values. In case of \code{ab_tradenames}, if \code{x} is of length one, a vector will be returned. Otherwise a \code{\link{list}}, with \code{x} as names. A vector of values. In case of \code{ab_tradenames}, if \code{x} is of length one, a vector will be returned. Otherwise a \code{\link{list}}, with \code{x} as names.
@ -40,8 +42,8 @@ Use these functions to return a specific property of an antibiotic from the \cod
} }
\examples{ \examples{
ab_atc("amcl") # J01CR02 ab_atc("amcl") # J01CR02
ab_official("amcl") # Amoxicillin and beta-lactamase inhibitor ab_name("amcl") # Amoxicillin and beta-lactamase inhibitor
ab_official_nl("amcl") # Amoxicilline met enzymremmer ab_name("amcl", "nl") # Amoxicilline met enzymremmer
ab_trivial_nl("amcl") # Amoxicilline/clavulaanzuur ab_trivial_nl("amcl") # Amoxicilline/clavulaanzuur
ab_certe("amcl") # amcl ab_certe("amcl") # amcl
ab_umcg("amcl") # AMCL ab_umcg("amcl") # AMCL

6
man/as.mo.Rd
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@ -40,12 +40,12 @@ Use this function to determine a valid ID based on a genus (and species). Determ
Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples. Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. These are: Thus function uses Artificial Intelligence (AI) to help getting more logical results, based on type of input and known prevalence of human pathogens. For example:
\itemize{ \itemize{
\item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first} \item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first}
\item{\code{"H. influenzae"} will return the ID of \emph{Haemophilus influenzae} and not \emph{Haematobacter influenzae}} \item{\code{"H. influenzae"} will return the ID of \emph{Haemophilus influenzae} and not \emph{Haematobacter influenzae} for the same reason}
\item{Something like \code{"p aer"} will return the ID of \emph{Pseudomonas aeruginosa} and not \emph{Pasteurella aerogenes}} \item{Something like \code{"p aer"} will return the ID of \emph{Pseudomonas aeruginosa} and not \emph{Pasteurella aerogenes}}
\item{Something like \code{"stau"} or \code{"staaur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}} \item{Something like \code{"stau"} or \code{"S aur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}}
} }
Moreover, this function also supports ID's based on only Gram stain, when the species is not known. \cr Moreover, this function also supports ID's based on only Gram stain, when the species is not known. \cr
For example, \code{"Gram negative rods"} and \code{"GNR"} will both return the ID of a Gram negative rod: \code{GNR}. For example, \code{"Gram negative rods"} and \code{"GNR"} will both return the ID of a Gram negative rod: \code{GNR}.

5
man/microorganisms.Rd
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@ -4,7 +4,7 @@
\name{microorganisms} \name{microorganisms}
\alias{microorganisms} \alias{microorganisms}
\title{Data set with human pathogenic microorganisms} \title{Data set with human pathogenic microorganisms}
\format{A \code{\link{tibble}} with 2,630 observations and 10 variables: \format{A \code{\link{tibble}} with 2,642 observations and 11 variables:
\describe{ \describe{
\item{\code{mo}}{ID of microorganism} \item{\code{mo}}{ID of microorganism}
\item{\code{bactsys}}{Bactsyscode of microorganism} \item{\code{bactsys}}{Bactsyscode of microorganism}
@ -16,12 +16,13 @@
\item{\code{aerobic}}{Logical whether bacteria is aerobic} \item{\code{aerobic}}{Logical whether bacteria is aerobic}
\item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungus/yeast"}} \item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungus/yeast"}}
\item{\code{gramstain}}{Gram of microorganism, like \code{"Negative rods"}} \item{\code{gramstain}}{Gram of microorganism, like \code{"Negative rods"}}
\item{\code{prevalence}}{A rounded integer based on prevalence of the microorganism. Used internally by \code{\link{as.mo}}, otherwise quite meaningless.}
}} }}
\usage{ \usage{
microorganisms microorganisms
} }
\description{ \description{
A data set containing 2,630 (potential) human pathogenic microorganisms. MO codes can be looked up using \code{\link{guess_mo}}. A data set containing (potential) human pathogenic microorganisms. MO codes can be looked up using \code{\link{guess_mo}}.
} }
\seealso{ \seealso{
\code{\link{guess_mo}} \code{\link{antibiotics}} \code{\link{microorganisms.umcg}} \code{\link{guess_mo}} \code{\link{antibiotics}} \code{\link{microorganisms.umcg}}

7
tests/testthat/test-ab_property.R
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@ -2,8 +2,9 @@ context("ab_property.R")
test_that("ab_property works", { test_that("ab_property works", {
expect_equal(ab_certe("amox"), "amox") expect_equal(ab_certe("amox"), "amox")
expect_equal(ab_official("amox"), "Amoxicillin") expect_equal(ab_name("amox", language = "en"), "Amoxicillin")
expect_equal(ab_official_nl("amox"), "Amoxicilline") expect_equal(ab_name("amox", language = "nl"), "Amoxicilline")
expect_equal(ab_official("amox", language = "en"), "Amoxicillin")
expect_equal(ab_trivial_nl("amox"), "Amoxicilline") expect_equal(ab_trivial_nl("amox"), "Amoxicilline")
expect_equal(ab_umcg("amox"), "AMOX") expect_equal(ab_umcg("amox"), "AMOX")
expect_equal(class(ab_tradenames("amox")), "character") expect_equal(class(ab_tradenames("amox")), "character")
@ -11,4 +12,6 @@ test_that("ab_property works", {
expect_equal(ab_atc("amox"), as.character(as.atc("amox"))) expect_equal(ab_atc("amox"), as.character(as.atc("amox")))
expect_error(ab_property("amox", "invalid property")) expect_error(ab_property("amox", "invalid property"))
expect_error(ab_name("amox", language = "INVALID"))
expect_output(print(ab_name("amox", language = NULL)))
}) })

26
tests/testthat/test-mo.R
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@ -3,7 +3,7 @@ context("mo.R")
test_that("as.mo works", { test_that("as.mo works", {
library(dplyr) library(dplyr)
MOs <- AMR::microorganisms %>% filter(!is.na(mo)) MOs <- AMR::microorganisms %>% filter(!is.na(mo), nchar(mo) > 3)
expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo))) expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo)))
expect_identical( expect_identical(
@ -12,18 +12,20 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("Escherichia coli")), "ESCCOL") expect_equal(as.character(as.mo("Escherichia coli")), "ESCCOL")
expect_equal(as.character(as.mo("Escherichia coli")), "ESCCOL") expect_equal(as.character(as.mo("Escherichia coli")), "ESCCOL")
expect_equal(as.character(as.mo("Escherichia species")), "ESC") expect_equal(as.character(as.mo("Escherichia species")), "ESCSPP")
expect_equal(as.character(as.mo("Escherichia")), "ESCSPP")
expect_equal(as.character(as.mo(" ESCCOL ")), "ESCCOL") expect_equal(as.character(as.mo(" ESCCOL ")), "ESCCOL")
expect_equal(as.character(as.mo("coli")), "ESCCOL") # not Campylobacter
expect_equal(as.character(as.mo("klpn")), "KLEPNE") expect_equal(as.character(as.mo("klpn")), "KLEPNE")
expect_equal(as.character(as.mo("Klebsiella")), "KLE") expect_equal(as.character(as.mo("Klebsiella")), "KLESPP")
expect_equal(as.character(as.mo("K. pneu rhino")), "KLEPNERH") # K. pneumoniae subspp. rhinoscleromatis expect_equal(as.character(as.mo("K. pneu rhino")), "KLEPNERH") # K. pneumoniae subspp. rhinoscleromatis
expect_equal(as.character(as.mo("Bartonella")), "BAR") expect_equal(as.character(as.mo("Bartonella")), "BARSPP")
expect_equal(as.character(as.mo("C. difficile")), "CLODIF") expect_equal(as.character(as.mo("C. difficile")), "CLODIF")
expect_equal(as.character(as.mo("L. pneumophila")), "LEGPNE") expect_equal(as.character(as.mo("L. pneumophila")), "LEGPNE")
expect_equal(as.character(as.mo("L. non pneumophila")), "LEGNON") expect_equal(as.character(as.mo("L. non pneumophila")), "LEGNON")
expect_equal(as.character(as.mo("S. beta-haemolytic")), "STCHAE") expect_equal(as.character(as.mo("S. beta-haemolytic")), "STCHAE")
expect_equal(as.character(as.mo("Strepto")), "STC") # not Streptobacillus expect_equal(as.character(as.mo("Strepto")), "STCSPP")
expect_equal(as.character(as.mo("Streptococcus")), "STC") # not Peptostreptoccus expect_equal(as.character(as.mo("Streptococcus")), "STCSPP") # not Peptostreptoccus
expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("STCGRA", "STCGRB")) expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("STCGRA", "STCGRB"))
@ -39,7 +41,7 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("bctfgr")), "BACFRA") expect_equal(as.character(as.mo("bctfgr")), "BACFRA")
expect_equal(as.character(as.mo("MRSE")), "STAEPI") expect_equal(as.character(as.mo("MRSE")), "STAEPI")
expect_equal(as.character(as.mo("VRE")), "ENC") expect_equal(as.character(as.mo("VRE")), "ENCSPP")
expect_equal(as.character(as.mo("MRPA")), "PSEAER") expect_equal(as.character(as.mo("MRPA")), "PSEAER")
expect_equal(as.character(as.mo("PISP")), "STCPNE") expect_equal(as.character(as.mo("PISP")), "STCPNE")
expect_equal(as.character(as.mo("PRSP")), "STCPNE") expect_equal(as.character(as.mo("PRSP")), "STCPNE")
@ -67,8 +69,9 @@ test_that("as.mo works", {
expect_identical(as.character(guess_mo("S. epidermidis", Becker = FALSE)), "STAEPI") expect_identical(as.character(guess_mo("S. epidermidis", Becker = FALSE)), "STAEPI")
expect_identical(as.character(guess_mo("S. epidermidis", Becker = TRUE)), "STACNS") expect_identical(as.character(guess_mo("S. epidermidis", Becker = TRUE)), "STACNS")
expect_identical(as.character(guess_mo("STAEPI", Becker = TRUE)), "STACNS") expect_identical(as.character(guess_mo("STAEPI", Becker = TRUE)), "STACNS")
expect_identical(as.character(guess_mo("S. intermedius", Becker = FALSE)), "STAINT") expect_identical(as.character(guess_mo("S. intermedius", Becker = FALSE)), "STCINT") # Strep (!) intermedius
expect_identical(as.character(guess_mo("S. intermedius", Becker = TRUE)), "STACPS") expect_identical(as.character(guess_mo("Sta intermedius",Becker = FALSE)), "STAINT")
expect_identical(as.character(guess_mo("Sta intermedius",Becker = TRUE)), "STACPS")
expect_identical(as.character(guess_mo("STAINT", Becker = TRUE)), "STACPS") expect_identical(as.character(guess_mo("STAINT", Becker = TRUE)), "STACPS")
# aureus must only be influenced if Becker = "all" # aureus must only be influenced if Becker = "all"
expect_identical(as.character(guess_mo("STAAUR", Becker = FALSE)), "STAAUR") expect_identical(as.character(guess_mo("STAAUR", Becker = FALSE)), "STAAUR")
@ -103,8 +106,9 @@ test_that("as.mo works", {
select(genus) %>% select(genus) %>%
as.mo() %>% as.mo() %>%
as.character(), as.character(),
c("ESC", "ESC", "STA", "STA", "STA", paste0(c("ESC", "ESC", "STA", "STA", "STA",
"STA", "STA", "STA", "STA", "STA")) "STA", "STA", "STA", "STA", "STA"),
"SPP"))
# select with two columns # select with two columns
expect_identical( expect_identical(

2
tests/testthat/test-mo_property.R
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@ -18,7 +18,7 @@ test_that("mo_property works", {
# test integrity # test integrity
library(dplyr) library(dplyr)
MOs <- AMR::microorganisms %>% filter(!is.na(mo)) MOs <- AMR::microorganisms %>% filter(!is.na(mo), nchar(mo) > 3)
expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en")) expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
mo_clean <- MOs$mo mo_clean <- MOs$mo