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fix for empty values in mo_property
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R/mo.R
2
R/mo.R
@ -146,7 +146,7 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
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if (identical(x_trimmed[i], "")) {
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# empty values
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x[i] <- NA
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failures <- c(failures, x_backup[i])
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#failures <- c(failures, x_backup[i])
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next
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}
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if (x_backup[i] %in% AMR::microorganisms$mo) {
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@ -28,6 +28,7 @@
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#'
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#' [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}
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#' @rdname mo_property
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#' @return Character or logical (only \code{mo_aerobic})
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#' @export
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#' @importFrom dplyr %>% left_join pull
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#' @seealso \code{\link{microorganisms}}
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@ -36,7 +37,7 @@
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#' mo_family("E. coli") # "Enterobacteriaceae"
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#' mo_genus("E. coli") # "Escherichia"
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#' mo_species("E. coli") # "coli"
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#' mo_subspecies("E. coli") # <NA>
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#' mo_subspecies("E. coli") # ""
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#' mo_fullname("E. coli") # "Escherichia coli"
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#' mo_shortname("E. coli") # "E. coli"
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#' mo_type("E. coli") # "Bacteria"
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@ -84,27 +85,32 @@
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#'
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#'
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#' # Becker classification, see ?as.mo
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#' mo_fullname("S. epidermidis") # "Staphylococcus epidermidis"
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#' mo_fullname("S. epidermidis", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
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#' mo_shortname("S. epidermidis") # "S. epidermidis"
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#' mo_shortname("S. epidermidis", Becker = TRUE) # "CoNS"
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#' mo_fullname("S. epi") # "Staphylococcus epidermidis"
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#' mo_fullname("S. epi", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
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#' mo_shortname("S. epi") # "S. epidermidis"
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#' mo_shortname("S. epi", Becker = TRUE) # "CoNS"
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#'
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#' # Lancefield classification, see ?as.mo
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#' mo_fullname("S. pyogenes") # "Streptococcus pyogenes"
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#' mo_fullname("S. pyogenes", Lancefield = TRUE) # "Streptococcus group A"
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#' mo_shortname("S. pyogenes") # "S. pyogenes"
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#' mo_shortname("S. pyogenes", Lancefield = TRUE) # "GAS"
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#' mo_fullname("S. pyo") # "Streptococcus pyogenes"
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#' mo_fullname("S. pyo", Lancefield = TRUE) # "Streptococcus group A"
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#' mo_shortname("S. pyo") # "S. pyogenes"
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#' mo_shortname("S. pyo", Lancefield = TRUE) # "GAS"
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mo_property <- function(x, property = 'fullname', Becker = FALSE, Lancefield = FALSE) {
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property <- tolower(property[1])
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if (!property %in% colnames(microorganisms)) {
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stop("invalid property: ", property, " - use a column name of the `microorganisms` data set")
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}
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x <- as.mo(x = x, Becker = Becker, Lancefield = Lancefield) # this will give a warning if x cannot be coerced
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suppressWarnings(
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data.frame(mo = x, stringsAsFactors = FALSE) %>%
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result1 <- as.mo(x = x, Becker = Becker, Lancefield = Lancefield) # this will give a warning if x cannot be coerced
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result2 <- suppressWarnings(
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data.frame(mo = result1, stringsAsFactors = FALSE) %>%
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left_join(AMR::microorganisms, by = "mo") %>%
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pull(property)
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)
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if (property != "aerobic") {
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# will else not retain logical class
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result2[x %in% c("", NA) | result2 %in% c("", NA, "(no MO)")] <- ""
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}
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result2
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}
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#' @rdname mo_property
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@ -142,7 +148,7 @@ mo_fullname <- function(x, Becker = FALSE, Lancefield = FALSE) {
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mo_shortname <- function(x, Becker = FALSE, Lancefield = FALSE) {
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if (Becker %in% c(TRUE, "all") | Lancefield == TRUE) {
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res1 <- as.mo(x)
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res2 <- as.mo(x, Becker = Becker, Lancefield = Lancefield)
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res2 <- suppressWarnings(as.mo(x, Becker = Becker, Lancefield = Lancefield))
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res2_fullname <- mo_fullname(res2)
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res2_fullname[res2_fullname %like% "\\(CoNS\\)"] <- "CoNS"
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res2_fullname[res2_fullname %like% "\\(CoPS\\)"] <- "CoPS"
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@ -151,18 +157,20 @@ mo_shortname <- function(x, Becker = FALSE, Lancefield = FALSE) {
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res2_fullname) # turn "Streptococcus group A" to "GAS"
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res2_fullname[res2_fullname == mo_fullname(x)] <- paste0(substr(mo_genus(res2_fullname), 1, 1),
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". ",
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mo_species(res2_fullname))
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suppressWarnings(mo_species(res2_fullname)))
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if (sum(res1 == res2, na.rm = TRUE) > 0) {
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res1[res1 == res2] <- paste0(substr(mo_genus(res1[res1 == res2]), 1, 1),
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". ",
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mo_species(res1[res1 == res2]))
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suppressWarnings(mo_species(res1[res1 == res2])))
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}
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res1[res1 != res2] <- res2_fullname
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as.character(res1)
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result <- as.character(res1)
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} else {
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# return G. species
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paste0(substr(mo_genus(x), 1, 1), ". ", mo_species(x))
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result <- paste0(substr(mo_genus(x), 1, 1), ". ", suppressWarnings(mo_species(x)))
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}
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result[result %in% c(". ")] <- ""
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result
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}
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@ -54,6 +54,9 @@ mo_aerobic(x)
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\item{language}{language of the returned text, either one of \code{"en"} (English), \code{"de"} (German) or \code{"nl"} (Dutch)}
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}
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\value{
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Character or logical (only \code{mo_aerobic})
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}
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\description{
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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}}.
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}
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@ -62,7 +65,7 @@ Use these functions to return a specific property of a microorganism from the \c
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mo_family("E. coli") # "Enterobacteriaceae"
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mo_genus("E. coli") # "Escherichia"
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mo_species("E. coli") # "coli"
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mo_subspecies("E. coli") # <NA>
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mo_subspecies("E. coli") # ""
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mo_fullname("E. coli") # "Escherichia coli"
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mo_shortname("E. coli") # "E. coli"
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mo_type("E. coli") # "Bacteria"
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@ -110,16 +113,16 @@ mo_aerobic("B. fragilis") # FALSE
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# Becker classification, see ?as.mo
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mo_fullname("S. epidermidis") # "Staphylococcus epidermidis"
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mo_fullname("S. epidermidis", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
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mo_shortname("S. epidermidis") # "S. epidermidis"
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mo_shortname("S. epidermidis", Becker = TRUE) # "CoNS"
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mo_fullname("S. epi") # "Staphylococcus epidermidis"
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mo_fullname("S. epi", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
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mo_shortname("S. epi") # "S. epidermidis"
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mo_shortname("S. epi", Becker = TRUE) # "CoNS"
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# Lancefield classification, see ?as.mo
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mo_fullname("S. pyogenes") # "Streptococcus pyogenes"
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mo_fullname("S. pyogenes", Lancefield = TRUE) # "Streptococcus group A"
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mo_shortname("S. pyogenes") # "S. pyogenes"
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mo_shortname("S. pyogenes", Lancefield = TRUE) # "GAS"
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mo_fullname("S. pyo") # "Streptococcus pyogenes"
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mo_fullname("S. pyo", Lancefield = TRUE) # "Streptococcus group A"
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mo_shortname("S. pyo") # "S. pyogenes"
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mo_shortname("S. pyo", Lancefield = TRUE) # "GAS"
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}
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\seealso{
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\code{\link{microorganisms}}
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@ -4,7 +4,7 @@ test_that("mo_property works", {
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expect_equal(mo_family("E. coli"), "Enterobacteriaceae")
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expect_equal(mo_genus("E. coli"), "Escherichia")
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expect_equal(mo_species("E. coli"), "coli")
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expect_equal(mo_subspecies("E. coli"), NA_character_)
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expect_equal(mo_subspecies("E. coli"), "")
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expect_equal(mo_fullname("E. coli"), "Escherichia coli")
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expect_equal(mo_type("E. coli"), "Bacteria")
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expect_equal(mo_gramstain("E. coli"), "Negative rods")
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