mirror of https://github.com/msberends/AMR.git
guess_mo deprecation
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DESCRIPTION
70
DESCRIPTION
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Package: AMR
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Version: 0.5.0.9009
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Date: 2019-01-05
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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given = c("Matthijs", "S."),
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family = "Berends",
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email = "m.s.berends@umcg.nl",
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role = c("aut", "cre"),
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comment = c(ORCID = "0000-0001-7620-1800")),
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person(
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given = c("Christian", "F."),
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family = "Luz",
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email = "c.f.luz@umcg.nl",
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role = c("aut", "rev"),
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comment = c(ORCID = "0000-0001-5809-5995")),
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person(
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given = c("Erwin", "E.", "A."),
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family = "Hassing",
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email = "e.hassing@certe.nl",
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role = "ctb"),
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person(
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given = "Corinna",
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family = "Glasner",
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email = "c.glasner@umcg.nl",
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role = c("aut", "ths"),
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comment = c(ORCID = "0000-0003-1241-1328")),
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person(
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given = c("Alex", "W."),
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family = "Friedrich",
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email = "alex.friedrich@umcg.nl",
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role = c("aut", "ths"),
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comment = c(ORCID = "0000-0003-4881-038X")),
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person(
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given = c("Bhanu", "N.", "M."),
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family = "Sinha",
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email = "b.sinha@umcg.nl",
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role = c("aut", "ths"),
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comment = c(ORCID = "0000-0003-1634-0010")))
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Description: Functions to simplify the analysis and prediction of Antimicrobial
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Resistance (AMR) and to work with microbial and antimicrobial properties by
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using evidence-based methods.
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Depends:
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R (>= 3.1.0)
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Imports:
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backports,
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curl,
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crayon (>= 1.3.0),
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data.table (>= 1.9.0),
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dplyr (>= 0.7.0),
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hms,
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knitr (>= 1.0.0),
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rlang (>= 0.2.0),
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rvest (>= 0.3.2),
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tidyr (>= 0.7.0),
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xml2 (>= 1.0.0)
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Suggests:
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covr (>= 3.0.1),
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ggplot2,
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rmarkdown,
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rstudioapi,
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testthat (>= 1.0.2)
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VignetteBuilder: knitr
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URL: https://msberends.gitlab.io/AMR, https://gitlab.com/msberends/AMR
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BugReports: https://gitlab.com/msberends/AMR/issues
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License: GPL-2 | file LICENSE
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 6.1.1
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1
NEWS.md
1
NEWS.md
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@ -28,6 +28,7 @@
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* 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.
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#### Changed
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* Function `guess_mo()` is now deprecated in favour of `as.mo()` and will be remover in future versions
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* Fixed a critical bug in `eucast_rules()` where some rules that depend on previous applied rules would not be applied adequately
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* Improvements for `as.mo()`:
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* Finds better results when input is in other languages
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@ -46,3 +46,10 @@ ratio <- function(x, ratio) {
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}
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sum(x, na.rm = TRUE) * (ratio / sum(ratio, na.rm = TRUE))
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}
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#' @rdname AMR-deprecated
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#' @exported
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guess_mo <- function(...) {
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.Deprecated(new = "as.mo", package = "AMR")
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as.mo(...)
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}
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14
R/mo.R
14
R/mo.R
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@ -76,7 +76,6 @@
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#' \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.}
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#' }
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#'
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#' \code{guess_mo} is an alias of \code{as.mo}.
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#' @inheritSection itis ITIS
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# (source as a section, so it can be inherited by other man pages)
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#' @section Source:
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@ -109,12 +108,11 @@
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#' as.mo("GAS") # Group A Streptococci
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#' as.mo("GBS") # Group B Streptococci
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#'
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#' # guess_mo is an alias of as.mo and works the same
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#' guess_mo("S. epidermidis") # will remain species: B_STPHY_EPI
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#' guess_mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
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#' as.mo("S. epidermidis") # will remain species: B_STPHY_EPI
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#' as.mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
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#'
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#' guess_mo("S. pyogenes") # will remain species: B_STRPTC_PYO
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#' guess_mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
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#' as.mo("S. pyogenes") # will remain species: B_STRPTC_PYO
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#' as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
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#'
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#' # Use mo_* functions to get a specific property based on `mo`
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#' Ecoli <- as.mo("E. coli") # returns `B_ESCHR_COL`
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@ -154,10 +152,6 @@ is.mo <- function(x) {
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identical(class(x), "mo")
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}
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#' @rdname as.mo
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#' @export
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guess_mo <- as.mo
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#' @importFrom dplyr %>% pull left_join n_distinct progress_estimated
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#' @importFrom data.table data.table as.data.table setkey
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#' @importFrom crayon magenta red italic
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@ -71,6 +71,12 @@ navbar:
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href: 'LICENSE-text.html'
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reference:
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- title: Backround information
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desc: >
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Some pages about our package and its external sources.
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contents:
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- 'AMR'
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- itis
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- title: Cleaning your data
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desc: >
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Functions for cleaning and optimising your data, to be able
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@ -79,6 +85,7 @@ reference:
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contents:
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- starts_with("as.")
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- '`eucast_rules`'
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- '`guess_ab`'
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- '`read.4D`'
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- title: Adding variables to your data
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desc: >
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@ -102,36 +102,36 @@ test_that("as.mo works", {
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c(NA_character_, NA_character_, "B_STNTR_MAL", "B_KLBSL_PNE_RHI", "B_ESCHR_COL"))
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# check for Becker classification
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expect_identical(as.character(guess_mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPI")
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expect_identical(as.character(guess_mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CNS")
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expect_identical(as.character(guess_mo("STAEPI", Becker = TRUE)), "B_STPHY_CNS")
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expect_identical(as.character(guess_mo("S. intermedius", Becker = FALSE)), "B_STRPTC_INT") # Strep (!) intermedius
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expect_identical(as.character(guess_mo("Sta intermedius",Becker = FALSE)), "B_STPHY_INT")
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expect_identical(as.character(guess_mo("Sta intermedius",Becker = TRUE)), "B_STPHY_CPS")
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expect_identical(as.character(guess_mo("STAINT", Becker = TRUE)), "B_STPHY_CPS")
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expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPI")
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expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CNS")
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expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CNS")
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expect_identical(as.character(as.mo("S. intermedius", Becker = FALSE)), "B_STRPTC_INT") # Strep (!) intermedius
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expect_identical(as.character(as.mo("Sta intermedius",Becker = FALSE)), "B_STPHY_INT")
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expect_identical(as.character(as.mo("Sta intermedius",Becker = TRUE)), "B_STPHY_CPS")
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expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_CPS")
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# aureus must only be influenced if Becker = "all"
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expect_identical(as.character(guess_mo("STAAUR", Becker = FALSE)), "B_STPHY_AUR")
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expect_identical(as.character(guess_mo("STAAUR", Becker = TRUE)), "B_STPHY_AUR")
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expect_identical(as.character(guess_mo("STAAUR", Becker = "all")), "B_STPHY_CPS")
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expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AUR")
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expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AUR")
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expect_identical(as.character(as.mo("STAAUR", Becker = "all")), "B_STPHY_CPS")
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# check for Lancefield classification
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expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = FALSE)), "B_STRPTC_PYO")
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expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = TRUE)), "B_STRPTC_GRA")
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expect_identical(as.character(guess_mo("STCPYO", Lancefield = TRUE)), "B_STRPTC_GRA") # group A
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expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = FALSE)), "B_STRPTC_AGA")
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expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = TRUE)), "B_STRPTC_GRB") # group B
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expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = FALSE)), "B_STRPTC_DYS_EQU")
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expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = TRUE)), "B_STRPTC_GRC") # group C
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expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPTC_PYO")
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expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPTC_GRA")
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expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPTC_GRA") # group A
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expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPTC_AGA")
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expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPTC_GRB") # group B
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expect_identical(as.character(as.mo("S. equisimilis", Lancefield = FALSE)), "B_STRPTC_DYS_EQU")
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expect_identical(as.character(as.mo("S. equisimilis", Lancefield = TRUE)), "B_STRPTC_GRC") # group C
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# Enterococci must only be influenced if Lancefield = "all"
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expect_identical(as.character(guess_mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_IUM")
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expect_identical(as.character(guess_mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_IUM")
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expect_identical(as.character(guess_mo("E. faecium", Lancefield = "all")), "B_STRPTC_GRD") # group D
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expect_identical(as.character(guess_mo("S. anginosus", Lancefield = FALSE)), "B_STRPTC_ANG")
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expect_identical(as.character(guess_mo("S. anginosus", Lancefield = TRUE)), "B_STRPTC_GRF") # group F
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expect_identical(as.character(guess_mo("S. sanguinis", Lancefield = FALSE)), "B_STRPTC_SAN")
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expect_identical(as.character(guess_mo("S. sanguinis", Lancefield = TRUE)), "B_STRPTC_GRH") # group H
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expect_identical(as.character(guess_mo("S. salivarius", Lancefield = FALSE)), "B_STRPTC_SAL")
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expect_identical(as.character(guess_mo("S. salivarius", Lancefield = TRUE)), "B_STRPTC_GRK") # group K
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expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_IUM")
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expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_IUM")
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expect_identical(as.character(as.mo("E. faecium", Lancefield = "all")), "B_STRPTC_GRD") # group D
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expect_identical(as.character(as.mo("S. anginosus", Lancefield = FALSE)), "B_STRPTC_ANG")
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expect_identical(as.character(as.mo("S. anginosus", Lancefield = TRUE)), "B_STRPTC_GRF") # group F
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expect_identical(as.character(as.mo("S. sanguinis", Lancefield = FALSE)), "B_STRPTC_SAN")
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expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPTC_GRH") # group H
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expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPTC_SAL")
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expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPTC_GRK") # group K
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library(dplyr)
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@ -166,7 +166,7 @@ test_that("as.mo works", {
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# helper function
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expect_identical(as.mo("B_ESCHR_COL"),
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guess_mo("B_ESCHR_COL"))
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as.mo("B_ESCHR_COL"))
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# test pull
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expect_equal(nrow(septic_patients %>% mutate(mo = as.mo(mo))),
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