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fix for empty values in mo_property

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dr. M.S. (Matthijs) Berends 2018-09-05 12:21:27 +02:00
parent e39a9a8b05
commit de36b0be23
4 changed files with 39 additions and 28 deletions
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2
R/mo.R
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@ -146,7 +146,7 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
if (identical(x_trimmed[i], "")) { if (identical(x_trimmed[i], "")) {
# empty values # empty values
x[i] <- NA x[i] <- NA
failures <- c(failures, x_backup[i]) #failures <- c(failures, x_backup[i])
next next
} }
if (x_backup[i] %in% AMR::microorganisms$mo) { if (x_backup[i] %in% AMR::microorganisms$mo) {

42
R/mo_property.R
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@ -28,6 +28,7 @@
#' #'
#' [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}
#' @rdname mo_property #' @rdname mo_property
#' @return Character or logical (only \code{mo_aerobic})
#' @export #' @export
#' @importFrom dplyr %>% left_join pull #' @importFrom dplyr %>% left_join pull
#' @seealso \code{\link{microorganisms}} #' @seealso \code{\link{microorganisms}}
@ -36,7 +37,7 @@
#' mo_family("E. coli") # "Enterobacteriaceae" #' mo_family("E. coli") # "Enterobacteriaceae"
#' mo_genus("E. coli") # "Escherichia" #' mo_genus("E. coli") # "Escherichia"
#' mo_species("E. coli") # "coli" #' mo_species("E. coli") # "coli"
#' mo_subspecies("E. coli") # <NA> #' mo_subspecies("E. coli") # ""
#' mo_fullname("E. coli") # "Escherichia coli" #' mo_fullname("E. coli") # "Escherichia coli"
#' mo_shortname("E. coli") # "E. coli" #' mo_shortname("E. coli") # "E. coli"
#' mo_type("E. coli") # "Bacteria" #' mo_type("E. coli") # "Bacteria"
@ -84,27 +85,32 @@
#' #'
#' #'
#' # Becker classification, see ?as.mo #' # Becker classification, see ?as.mo
#' mo_fullname("S. epidermidis") # "Staphylococcus epidermidis" #' mo_fullname("S. epi") # "Staphylococcus epidermidis"
#' mo_fullname("S. epidermidis", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)" #' mo_fullname("S. epi", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
#' mo_shortname("S. epidermidis") # "S. epidermidis" #' mo_shortname("S. epi") # "S. epidermidis"
#' mo_shortname("S. epidermidis", Becker = TRUE) # "CoNS" #' mo_shortname("S. epi", Becker = TRUE) # "CoNS"
#' #'
#' # Lancefield classification, see ?as.mo #' # Lancefield classification, see ?as.mo
#' mo_fullname("S. pyogenes") # "Streptococcus pyogenes" #' mo_fullname("S. pyo") # "Streptococcus pyogenes"
#' mo_fullname("S. pyogenes", Lancefield = TRUE) # "Streptococcus group A" #' mo_fullname("S. pyo", Lancefield = TRUE) # "Streptococcus group A"
#' mo_shortname("S. pyogenes") # "S. pyogenes" #' mo_shortname("S. pyo") # "S. pyogenes"
#' mo_shortname("S. pyogenes", Lancefield = TRUE) # "GAS" #' mo_shortname("S. pyo", Lancefield = TRUE) # "GAS"
mo_property <- function(x, property = 'fullname', Becker = FALSE, Lancefield = FALSE) { mo_property <- function(x, property = 'fullname', Becker = FALSE, Lancefield = FALSE) {
property <- tolower(property[1]) property <- tolower(property[1])
if (!property %in% colnames(microorganisms)) { if (!property %in% colnames(microorganisms)) {
stop("invalid property: ", property, " - use a column name of the `microorganisms` data set") stop("invalid property: ", property, " - use a column name of the `microorganisms` data set")
} }
x <- as.mo(x = x, Becker = Becker, Lancefield = Lancefield) # this will give a warning if x cannot be coerced result1 <- as.mo(x = x, Becker = Becker, Lancefield = Lancefield) # this will give a warning if x cannot be coerced
suppressWarnings( result2 <- suppressWarnings(
data.frame(mo = x, stringsAsFactors = FALSE) %>% data.frame(mo = result1, stringsAsFactors = FALSE) %>%
left_join(AMR::microorganisms, by = "mo") %>% left_join(AMR::microorganisms, by = "mo") %>%
pull(property) pull(property)
) )
if (property != "aerobic") {
# will else not retain logical class
result2[x %in% c("", NA) | result2 %in% c("", NA, "(no MO)")] <- ""
}
result2
} }
#' @rdname mo_property #' @rdname mo_property
@ -142,7 +148,7 @@ mo_fullname <- function(x, Becker = FALSE, Lancefield = FALSE) {
mo_shortname <- function(x, Becker = FALSE, Lancefield = FALSE) { mo_shortname <- function(x, Becker = FALSE, Lancefield = FALSE) {
if (Becker %in% c(TRUE, "all") | Lancefield == TRUE) { if (Becker %in% c(TRUE, "all") | Lancefield == TRUE) {
res1 <- as.mo(x) res1 <- as.mo(x)
res2 <- as.mo(x, Becker = Becker, Lancefield = Lancefield) res2 <- suppressWarnings(as.mo(x, Becker = Becker, Lancefield = Lancefield))
res2_fullname <- mo_fullname(res2) res2_fullname <- mo_fullname(res2)
res2_fullname[res2_fullname %like% "\\(CoNS\\)"] <- "CoNS" res2_fullname[res2_fullname %like% "\\(CoNS\\)"] <- "CoNS"
res2_fullname[res2_fullname %like% "\\(CoPS\\)"] <- "CoPS" res2_fullname[res2_fullname %like% "\\(CoPS\\)"] <- "CoPS"
@ -151,18 +157,20 @@ mo_shortname <- function(x, Becker = FALSE, Lancefield = FALSE) {
res2_fullname) # turn "Streptococcus group A" to "GAS" res2_fullname) # turn "Streptococcus group A" to "GAS"
res2_fullname[res2_fullname == mo_fullname(x)] <- paste0(substr(mo_genus(res2_fullname), 1, 1), res2_fullname[res2_fullname == mo_fullname(x)] <- paste0(substr(mo_genus(res2_fullname), 1, 1),
". ", ". ",
mo_species(res2_fullname)) suppressWarnings(mo_species(res2_fullname)))
if (sum(res1 == res2, na.rm = TRUE) > 0) { if (sum(res1 == res2, na.rm = TRUE) > 0) {
res1[res1 == res2] <- paste0(substr(mo_genus(res1[res1 == res2]), 1, 1), res1[res1 == res2] <- paste0(substr(mo_genus(res1[res1 == res2]), 1, 1),
". ", ". ",
mo_species(res1[res1 == res2])) suppressWarnings(mo_species(res1[res1 == res2])))
} }
res1[res1 != res2] <- res2_fullname res1[res1 != res2] <- res2_fullname
as.character(res1) result <- as.character(res1)
} else { } else {
# return G. species # return G. species
paste0(substr(mo_genus(x), 1, 1), ". ", mo_species(x)) result <- paste0(substr(mo_genus(x), 1, 1), ". ", suppressWarnings(mo_species(x)))
} }
result[result %in% c(". ")] <- ""
result
} }

21
man/mo_property.Rd
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@ -54,6 +54,9 @@ mo_aerobic(x)
\item{language}{language of the returned text, either one of \code{"en"} (English), \code{"de"} (German) or \code{"nl"} (Dutch)} \item{language}{language of the returned text, either one of \code{"en"} (English), \code{"de"} (German) or \code{"nl"} (Dutch)}
} }
\value{
Character or logical (only \code{mo_aerobic})
}
\description{ \description{
Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set. All input values will be evaluated internally with \code{\link{as.mo}}. Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set. All input values will be evaluated internally with \code{\link{as.mo}}.
} }
@ -62,7 +65,7 @@ Use these functions to return a specific property of a microorganism from the \c
mo_family("E. coli") # "Enterobacteriaceae" mo_family("E. coli") # "Enterobacteriaceae"
mo_genus("E. coli") # "Escherichia" mo_genus("E. coli") # "Escherichia"
mo_species("E. coli") # "coli" mo_species("E. coli") # "coli"
mo_subspecies("E. coli") # <NA> mo_subspecies("E. coli") # ""
mo_fullname("E. coli") # "Escherichia coli" mo_fullname("E. coli") # "Escherichia coli"
mo_shortname("E. coli") # "E. coli" mo_shortname("E. coli") # "E. coli"
mo_type("E. coli") # "Bacteria" mo_type("E. coli") # "Bacteria"
@ -110,16 +113,16 @@ mo_aerobic("B. fragilis") # FALSE
# Becker classification, see ?as.mo # Becker classification, see ?as.mo
mo_fullname("S. epidermidis") # "Staphylococcus epidermidis" mo_fullname("S. epi") # "Staphylococcus epidermidis"
mo_fullname("S. epidermidis", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)" mo_fullname("S. epi", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
mo_shortname("S. epidermidis") # "S. epidermidis" mo_shortname("S. epi") # "S. epidermidis"
mo_shortname("S. epidermidis", Becker = TRUE) # "CoNS" mo_shortname("S. epi", Becker = TRUE) # "CoNS"
# Lancefield classification, see ?as.mo # Lancefield classification, see ?as.mo
mo_fullname("S. pyogenes") # "Streptococcus pyogenes" mo_fullname("S. pyo") # "Streptococcus pyogenes"
mo_fullname("S. pyogenes", Lancefield = TRUE) # "Streptococcus group A" mo_fullname("S. pyo", Lancefield = TRUE) # "Streptococcus group A"
mo_shortname("S. pyogenes") # "S. pyogenes" mo_shortname("S. pyo") # "S. pyogenes"
mo_shortname("S. pyogenes", Lancefield = TRUE) # "GAS" mo_shortname("S. pyo", Lancefield = TRUE) # "GAS"
} }
\seealso{ \seealso{
\code{\link{microorganisms}} \code{\link{microorganisms}}

2
tests/testthat/test-mo_property.R
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@ -4,7 +4,7 @@ test_that("mo_property works", {
expect_equal(mo_family("E. coli"), "Enterobacteriaceae") expect_equal(mo_family("E. coli"), "Enterobacteriaceae")
expect_equal(mo_genus("E. coli"), "Escherichia") expect_equal(mo_genus("E. coli"), "Escherichia")
expect_equal(mo_species("E. coli"), "coli") expect_equal(mo_species("E. coli"), "coli")
expect_equal(mo_subspecies("E. coli"), NA_character_) expect_equal(mo_subspecies("E. coli"), "")
expect_equal(mo_fullname("E. coli"), "Escherichia coli") expect_equal(mo_fullname("E. coli"), "Escherichia coli")
expect_equal(mo_type("E. coli"), "Bacteria") expect_equal(mo_type("E. coli"), "Bacteria")
expect_equal(mo_gramstain("E. coli"), "Negative rods") expect_equal(mo_gramstain("E. coli"), "Negative rods")