diff --git a/DESCRIPTION b/DESCRIPTION index f4327adc..e69de29b 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,70 +0,0 @@ -Package: AMR -Version: 0.5.0.9009 -Date: 2019-01-05 -Title: Antimicrobial Resistance Analysis -Authors@R: c( - person( - given = c("Matthijs", "S."), - family = "Berends", - email = "m.s.berends@umcg.nl", - role = c("aut", "cre"), - comment = c(ORCID = "0000-0001-7620-1800")), - person( - given = c("Christian", "F."), - family = "Luz", - email = "c.f.luz@umcg.nl", - role = c("aut", "rev"), - comment = c(ORCID = "0000-0001-5809-5995")), - person( - given = c("Erwin", "E.", "A."), - family = "Hassing", - email = "e.hassing@certe.nl", - role = "ctb"), - person( - given = "Corinna", - family = "Glasner", - email = "c.glasner@umcg.nl", - role = c("aut", "ths"), - comment = c(ORCID = "0000-0003-1241-1328")), - person( - given = c("Alex", "W."), - family = "Friedrich", - email = "alex.friedrich@umcg.nl", - role = c("aut", "ths"), - comment = c(ORCID = "0000-0003-4881-038X")), - person( - given = c("Bhanu", "N.", "M."), - family = "Sinha", - email = "b.sinha@umcg.nl", - role = c("aut", "ths"), - comment = c(ORCID = "0000-0003-1634-0010"))) -Description: Functions to simplify the analysis and prediction of Antimicrobial - Resistance (AMR) and to work with microbial and antimicrobial properties by - using evidence-based methods. -Depends: - R (>= 3.1.0) -Imports: - backports, - curl, - crayon (>= 1.3.0), - data.table (>= 1.9.0), - dplyr (>= 0.7.0), - hms, - knitr (>= 1.0.0), - rlang (>= 0.2.0), - rvest (>= 0.3.2), - tidyr (>= 0.7.0), - xml2 (>= 1.0.0) -Suggests: - covr (>= 3.0.1), - ggplot2, - rmarkdown, - rstudioapi, - testthat (>= 1.0.2) -VignetteBuilder: knitr -URL: https://msberends.gitlab.io/AMR, https://gitlab.com/msberends/AMR -BugReports: https://gitlab.com/msberends/AMR/issues -License: GPL-2 | file LICENSE -Encoding: UTF-8 -LazyData: true -RoxygenNote: 6.1.1 diff --git a/NEWS.md b/NEWS.md index 03ffac5d..7b26b020 100755 --- a/NEWS.md +++ b/NEWS.md @@ -28,6 +28,7 @@ * New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the *G*-test and more. These are also available (and even easier readable) on our website: https://msberends.gitlab.io/AMR. #### Changed +* Function `guess_mo()` is now deprecated in favour of `as.mo()` and will be remover in future versions * Fixed a critical bug in `eucast_rules()` where some rules that depend on previous applied rules would not be applied adequately * Improvements for `as.mo()`: * Finds better results when input is in other languages diff --git a/R/deprecated.R b/R/deprecated.R index 20007026..dae2e7c6 100644 --- a/R/deprecated.R +++ b/R/deprecated.R @@ -46,3 +46,10 @@ ratio <- function(x, ratio) { } sum(x, na.rm = TRUE) * (ratio / sum(ratio, na.rm = TRUE)) } + +#' @rdname AMR-deprecated +#' @exported +guess_mo <- function(...) { + .Deprecated(new = "as.mo", package = "AMR") + as.mo(...) +} diff --git a/R/mo.R b/R/mo.R index 6117680c..666f64c7 100644 --- a/R/mo.R +++ b/R/mo.R @@ -76,7 +76,6 @@ #' \item{\code{"D. spartina"}. This is the abbreviation of an old taxonomic name: \emph{Didymosphaeria spartinae} (the last "e" was missing from the input). This fungus was renamed to \emph{Leptosphaeria obiones}, so a warning will be thrown that this result (\code{F_LPTSP_OBI}) needs review.} #' } #' -#' \code{guess_mo} is an alias of \code{as.mo}. #' @inheritSection itis ITIS # (source as a section, so it can be inherited by other man pages) #' @section Source: @@ -109,12 +108,11 @@ #' as.mo("GAS") # Group A Streptococci #' as.mo("GBS") # Group B Streptococci #' -#' # guess_mo is an alias of as.mo and works the same -#' guess_mo("S. epidermidis") # will remain species: B_STPHY_EPI -#' guess_mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS +#' as.mo("S. epidermidis") # will remain species: B_STPHY_EPI +#' as.mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS #' -#' guess_mo("S. pyogenes") # will remain species: B_STRPTC_PYO -#' guess_mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA +#' as.mo("S. pyogenes") # will remain species: B_STRPTC_PYO +#' as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA #' #' # Use mo_* functions to get a specific property based on `mo` #' Ecoli <- as.mo("E. coli") # returns `B_ESCHR_COL` @@ -154,10 +152,6 @@ is.mo <- function(x) { identical(class(x), "mo") } -#' @rdname as.mo -#' @export -guess_mo <- as.mo - #' @importFrom dplyr %>% pull left_join n_distinct progress_estimated #' @importFrom data.table data.table as.data.table setkey #' @importFrom crayon magenta red italic diff --git a/_pkgdown.yml b/_pkgdown.yml index 774c8984..0858e93e 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -71,6 +71,12 @@ navbar: href: 'LICENSE-text.html' reference: +- title: Backround information + desc: > + Some pages about our package and its external sources. + contents: + - 'AMR' + - itis - title: Cleaning your data desc: > Functions for cleaning and optimising your data, to be able @@ -79,6 +85,7 @@ reference: contents: - starts_with("as.") - '`eucast_rules`' + - '`guess_ab`' - '`read.4D`' - title: Adding variables to your data desc: > diff --git a/tests/testthat/test-mo.R b/tests/testthat/test-mo.R index 4761483c..86e76c19 100644 --- a/tests/testthat/test-mo.R +++ b/tests/testthat/test-mo.R @@ -102,36 +102,36 @@ test_that("as.mo works", { c(NA_character_, NA_character_, "B_STNTR_MAL", "B_KLBSL_PNE_RHI", "B_ESCHR_COL")) # check for Becker classification - expect_identical(as.character(guess_mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPI") - expect_identical(as.character(guess_mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CNS") - expect_identical(as.character(guess_mo("STAEPI", Becker = TRUE)), "B_STPHY_CNS") - expect_identical(as.character(guess_mo("S. intermedius", Becker = FALSE)), "B_STRPTC_INT") # Strep (!) intermedius - expect_identical(as.character(guess_mo("Sta intermedius",Becker = FALSE)), "B_STPHY_INT") - expect_identical(as.character(guess_mo("Sta intermedius",Becker = TRUE)), "B_STPHY_CPS") - expect_identical(as.character(guess_mo("STAINT", Becker = TRUE)), "B_STPHY_CPS") + expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPI") + expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CNS") + expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CNS") + expect_identical(as.character(as.mo("S. intermedius", Becker = FALSE)), "B_STRPTC_INT") # Strep (!) intermedius + expect_identical(as.character(as.mo("Sta intermedius",Becker = FALSE)), "B_STPHY_INT") + expect_identical(as.character(as.mo("Sta intermedius",Becker = TRUE)), "B_STPHY_CPS") + expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_CPS") # aureus must only be influenced if Becker = "all" - expect_identical(as.character(guess_mo("STAAUR", Becker = FALSE)), "B_STPHY_AUR") - expect_identical(as.character(guess_mo("STAAUR", Becker = TRUE)), "B_STPHY_AUR") - expect_identical(as.character(guess_mo("STAAUR", Becker = "all")), "B_STPHY_CPS") + expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AUR") + expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AUR") + expect_identical(as.character(as.mo("STAAUR", Becker = "all")), "B_STPHY_CPS") # check for Lancefield classification - expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = FALSE)), "B_STRPTC_PYO") - expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = TRUE)), "B_STRPTC_GRA") - expect_identical(as.character(guess_mo("STCPYO", Lancefield = TRUE)), "B_STRPTC_GRA") # group A - expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = FALSE)), "B_STRPTC_AGA") - expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = TRUE)), "B_STRPTC_GRB") # group B - expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = FALSE)), "B_STRPTC_DYS_EQU") - expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = TRUE)), "B_STRPTC_GRC") # group C + expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPTC_PYO") + expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPTC_GRA") + expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPTC_GRA") # group A + expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPTC_AGA") + expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPTC_GRB") # group B + expect_identical(as.character(as.mo("S. equisimilis", Lancefield = FALSE)), "B_STRPTC_DYS_EQU") + expect_identical(as.character(as.mo("S. equisimilis", Lancefield = TRUE)), "B_STRPTC_GRC") # group C # Enterococci must only be influenced if Lancefield = "all" - expect_identical(as.character(guess_mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_IUM") - expect_identical(as.character(guess_mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_IUM") - expect_identical(as.character(guess_mo("E. faecium", Lancefield = "all")), "B_STRPTC_GRD") # group D - expect_identical(as.character(guess_mo("S. anginosus", Lancefield = FALSE)), "B_STRPTC_ANG") - expect_identical(as.character(guess_mo("S. anginosus", Lancefield = TRUE)), "B_STRPTC_GRF") # group F - expect_identical(as.character(guess_mo("S. sanguinis", Lancefield = FALSE)), "B_STRPTC_SAN") - expect_identical(as.character(guess_mo("S. sanguinis", Lancefield = TRUE)), "B_STRPTC_GRH") # group H - expect_identical(as.character(guess_mo("S. salivarius", Lancefield = FALSE)), "B_STRPTC_SAL") - expect_identical(as.character(guess_mo("S. salivarius", Lancefield = TRUE)), "B_STRPTC_GRK") # group K + expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_IUM") + expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_IUM") + expect_identical(as.character(as.mo("E. faecium", Lancefield = "all")), "B_STRPTC_GRD") # group D + expect_identical(as.character(as.mo("S. anginosus", Lancefield = FALSE)), "B_STRPTC_ANG") + expect_identical(as.character(as.mo("S. anginosus", Lancefield = TRUE)), "B_STRPTC_GRF") # group F + expect_identical(as.character(as.mo("S. sanguinis", Lancefield = FALSE)), "B_STRPTC_SAN") + expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPTC_GRH") # group H + expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPTC_SAL") + expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPTC_GRK") # group K library(dplyr) @@ -166,7 +166,7 @@ test_that("as.mo works", { # helper function expect_identical(as.mo("B_ESCHR_COL"), - guess_mo("B_ESCHR_COL")) + as.mo("B_ESCHR_COL")) # test pull expect_equal(nrow(septic_patients %>% mutate(mo = as.mo(mo))),