diff --git a/DESCRIPTION b/DESCRIPTION
old mode 100755
new mode 100644
index e69de29b..83bdcb56
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -0,0 +1,70 @@
+Package: AMR
+Version: 0.5.0.9009
+Date: 2019-01-06
+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/R/deprecated.R b/R/deprecated.R
index dae2e7c6..a5559954 100644
--- a/R/deprecated.R
+++ b/R/deprecated.R
@@ -48,7 +48,7 @@ ratio <- function(x, ratio) {
}
#' @rdname AMR-deprecated
-#' @exported
+#' @export
guess_mo <- function(...) {
.Deprecated(new = "as.mo", package = "AMR")
as.mo(...)
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 0858e93e..76aa269a 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -75,8 +75,8 @@ reference:
desc: >
Some pages about our package and its external sources.
contents:
- - 'AMR'
- - itis
+ - '`AMR`'
+ - '`itis`'
- title: Cleaning your data
desc: >
Functions for cleaning and optimising your data, to be able
diff --git a/docs/news/index.html b/docs/news/index.html
index e0e827b8..84f0a3e9 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -240,6 +240,7 @@
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/docs/reference/AMR-deprecated.html b/docs/reference/AMR-deprecated.html
index 99cca00b..2797d1a9 100644
--- a/docs/reference/AMR-deprecated.html
+++ b/docs/reference/AMR-deprecated.html
@@ -220,7 +220,9 @@
-
ratio(x, ratio)
+ ratio(x, ratio)
+
+guess_mo(...)
Read more on our website!
diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html
index f2329d1e..40722c4f 100644
--- a/docs/reference/as.mo.html
+++ b/docs/reference/as.mo.html
@@ -223,10 +223,7 @@
as.mo(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
reference_df = NULL)
-is.mo(x)
-
-guess_mo(x, Becker = FALSE, Lancefield = FALSE,
- allow_uncertain = TRUE, reference_df = NULL)
+is.mo(x)
Arguments
@@ -292,7 +289,6 @@
"S. aureus - please mind: MRSA". The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result Staphylococcus aureus (B_STPHY_AUR) needs review.
"D. spartina". This is the abbreviation of an old taxonomic name: Didymosphaeria spartinae (the last "e" was missing from the input). This fungus was renamed to Leptosphaeria obiones, so a warning will be thrown that this result (F_LPTSP_OBI) needs review.
- guess_mo is an alias of as.mo.
Source
@@ -341,12 +337,11 @@ The mo_property functions (like 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`
@@ -362,16 +357,16 @@ The mo_property functions (like # the select function of tidyverse is also supported:
library(dplyr)
df$mo <- df %>%
- select(microorganism_name) %>%
+ select(microorganism_name) %>%
as.mo()
# and can even contain 2 columns, which is convenient for genus/species combinations:
df$mo <- df %>%
- select(genus, species) %>%
+ select(genus, species) %>%
as.mo()
# although this works easier and does the same:
df <- df %>%
- mutate(mo = as.mo(paste(genus, species)))
+ mutate(mo = as.mo(paste(genus, species)))
# }