guess_mo deprecation

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

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

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(...)
+}

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
+#' as.mo("S. epidermidis")                 # will remain species: B_STPHY_EPI
-#' guess_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. epidermidis", Becker = TRUE)  # will not remain species: B_STPHY_CNS
 #'
-#' guess_mo("S. pyogenes")                    # will remain species: B_STRPTC_PYO
+#' as.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", 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

_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: >

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(as.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(as.mo("S. epidermidis", Becker = TRUE)),  "B_STPHY_CNS")
-  expect_identical(as.character(guess_mo("STAEPI",         Becker = TRUE)),  "B_STPHY_CNS")
+  expect_identical(as.character(as.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(as.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(as.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(as.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("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(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AUR")
-  expect_identical(as.character(guess_mo("STAAUR", Becker = TRUE)),  "B_STPHY_AUR")
+  expect_identical(as.character(as.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 = "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(as.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(as.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(as.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(as.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(as.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(as.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. 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(as.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(as.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(as.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(as.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(as.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(as.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(as.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(as.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("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))),