diff --git a/DESCRIPTION b/DESCRIPTION
index 117b5e2a..f5e0783c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: AMR
-Version: 0.7.1.9055
-Date: 2019-08-13
+Version: 0.7.1.9056
+Date: 2019-08-14
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),
@@ -11,6 +11,8 @@ Authors@R: c(
family = "Friedrich", given = c("Alex", "W."), email = "alex.friedrich@umcg.nl", comment = c(ORCID = "0000-0003-4881-038X")),
person(role = c("aut", "ths"),
family = "Sinha", given = c("Bhanu", "N.", "M."), email = "b.sinha@umcg.nl", comment = c(ORCID = "0000-0003-1634-0010")),
+ person(role = c("aut", "ths"),
+ family = "Albers", given = c("Casper", "J."), email = "c.j.albers@rug.nl", comment = c(ORCID = "0000-0002-9213-6743")),
person(role = c("aut", "ths"),
family = "Glasner", given = "Corinna", email = "c.glasner@umcg.nl", comment = c(ORCID = "0000-0003-1241-1328")),
person(role = "ctb",
diff --git a/NAMESPACE b/NAMESPACE
index 7cafc1af..5c9db6c2 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,6 +2,12 @@
S3method("[",ab)
S3method("[",mo)
+S3method("[<-",ab)
+S3method("[<-",mo)
+S3method("[[",ab)
+S3method("[[",mo)
+S3method("[[<-",ab)
+S3method("[[<-",mo)
S3method(as.data.frame,ab)
S3method(as.data.frame,mo)
S3method(as.double,mic)
@@ -13,6 +19,8 @@ S3method(as.rsi,disk)
S3method(as.rsi,mic)
S3method(barplot,mic)
S3method(barplot,rsi)
+S3method(c,ab)
+S3method(c,mo)
S3method(droplevels,mic)
S3method(droplevels,rsi)
S3method(freq,mo)
@@ -172,6 +180,12 @@ export(skewness)
export(theme_rsi)
exportMethods("[.ab")
exportMethods("[.mo")
+exportMethods("[<-.ab")
+exportMethods("[<-.mo")
+exportMethods("[[.ab")
+exportMethods("[[.mo")
+exportMethods("[[<-.ab")
+exportMethods("[[<-.mo")
exportMethods(as.data.frame.ab)
exportMethods(as.data.frame.mo)
exportMethods(as.double.mic)
@@ -179,6 +193,8 @@ exportMethods(as.integer.mic)
exportMethods(as.numeric.mic)
exportMethods(barplot.mic)
exportMethods(barplot.rsi)
+exportMethods(c.ab)
+exportMethods(c.mo)
exportMethods(droplevels.mic)
exportMethods(droplevels.rsi)
exportMethods(freq.mo)
diff --git a/NEWS.md b/NEWS.md
index d84c3818..7a95044b 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 0.7.1.9055
+# AMR 0.7.1.9056
### Breaking
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
@@ -73,7 +73,7 @@
* Classes `ab` and `mo` will now be preserved in any subsetting
#### Other
-* Added Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors
+* Added Prof Dr Casper Albers as doctoral advisor and Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors
# AMR 0.7.1
diff --git a/R/ab.R b/R/ab.R
index 19864eb3..ecac120d 100755
--- a/R/ab.R
+++ b/R/ab.R
@@ -282,10 +282,42 @@ as.data.frame.ab <- function (x, ...) {
#' @exportMethod [.ab
#' @export
#' @noRd
-"[.ab" <- function (x, ...) {
- # this function is needed to preserve the "ab" class for any subsetting, like df %>% filter(...)
+"[.ab" <- function(x, ...) {
y <- NextMethod()
- structure(y, class = "ab")
+ attributes(y) <- attributes(x)
+ y
+}
+#' @exportMethod [<-.ab
+#' @export
+#' @noRd
+"[<-.ab" <- function(value) {
+ y <- NextMethod()
+ attributes(y) <- attributes(value)
+ y
+}
+#' @exportMethod [[.ab
+#' @export
+#' @noRd
+"[[.ab" <- function(x, ...) {
+ y <- NextMethod()
+ attributes(y) <- attributes(x)
+ y
+}
+#' @exportMethod [[<-.ab
+#' @export
+#' @noRd
+"[[<-.ab" <- function(i, j, ..., value) {
+ y <- NextMethod()
+ attributes(y) <- attributes(value)
+ y
+}
+#' @exportMethod c.ab
+#' @export
+#' @noRd
+c.ab <- function(x, ...) {
+ y <- NextMethod()
+ attributes(y) <- attributes(x)
+ y
}
#' @importFrom pillar type_sum
diff --git a/R/first_isolate.R b/R/first_isolate.R
index f9abcd15..50baae75 100755
--- a/R/first_isolate.R
+++ b/R/first_isolate.R
@@ -79,8 +79,8 @@
#' @source Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
#' @inheritSection AMR Read more on our website!
#' @examples
-#' # septic_patients is a dataset available in the AMR package. It is true, genuine data.
-#' ?septic_patients
+#' # `septic_patients` is a dataset available in the AMR package. It is true, genuine data.
+#' # See ?septic_patients.
#'
#' library(dplyr)
#' # Filter on first isolates:
@@ -97,7 +97,7 @@
#' # or for first weighted isolates:
#' septic_patients %>%
#' filter_first_weighted_isolate()
-#'
+#'
#' # Now let's see if first isolates matter:
#' A <- septic_patients %>%
#' group_by(hospital_id) %>%
diff --git a/R/key_antibiotics.R b/R/key_antibiotics.R
index 807f729d..f802492f 100755
--- a/R/key_antibiotics.R
+++ b/R/key_antibiotics.R
@@ -48,8 +48,8 @@
#' @seealso \code{\link{first_isolate}}
#' @inheritSection AMR Read more on our website!
#' @examples
-#' # septic_patients is a dataset available in the AMR package
-#' ?septic_patients
+#' # `septic_patients` is a dataset available in the AMR package. It is true, genuine data.
+#' # See ?septic_patients.
#'
#' library(dplyr)
#' # set key antibiotics to a new variable
diff --git a/R/mo.R b/R/mo.R
index db163435..27078825 100755
--- a/R/mo.R
+++ b/R/mo.R
@@ -1723,10 +1723,42 @@ as.data.frame.mo <- function(x, ...) {
#' @exportMethod [.mo
#' @export
#' @noRd
-"[.mo" <- function (x, ...) {
- # this function is needed to preserve the "mo" class for any subsetting, like df %>% filter(...)
+"[.mo" <- function(x, ...) {
y <- NextMethod()
- to_class_mo(y)
+ attributes(y) <- attributes(x)
+ y
+}
+#' @exportMethod [<-.mo
+#' @export
+#' @noRd
+"[<-.mo" <- function(i, j, ..., value) {
+ y <- NextMethod()
+ attributes(y) <- attributes(value)
+ y
+}
+#' @exportMethod [[.mo
+#' @export
+#' @noRd
+"[[.mo" <- function(x, ...) {
+ y <- NextMethod()
+ attributes(y) <- attributes(x)
+ y
+}
+#' @exportMethod [[<-.mo
+#' @export
+#' @noRd
+"[[<-.mo" <- function(value) {
+ y <- NextMethod()
+ attributes(y) <- attributes(value)
+ y
+}
+#' @exportMethod c.mo
+#' @export
+#' @noRd
+c.mo <- function(x, ...) {
+ y <- NextMethod()
+ attributes(y) <- attributes(x)
+ y
}
#' @rdname as.mo
diff --git a/_pkgdown.yml b/_pkgdown.yml
index b230db94..fbeee742 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -172,12 +172,14 @@ authors:
href: https://www.rug.nl/staff/m.s.berends/
Christian F. Luz:
href: https://www.rug.nl/staff/c.f.luz/
- Corinna Glasner:
- href: https://www.rug.nl/staff/c.glasner/
Alex W. Friedrich:
href: https://www.rug.nl/staff/a.w.friedrich/
Bhanu N. M. Sinha:
href: https://www.rug.nl/staff/b.sinha/
+ Casper J. Albers:
+ href: https://www.rug.nl/staff/c.j.albers/
+ Corinna Glasner:
+ href: https://www.rug.nl/staff/c.glasner/
template:
assets: "pkgdown/logos" # use logos in this folder
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index ae2885e7..99df50d3 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -78,7 +78,7 @@
AMR (for R)
- 0.7.1.9055
+ 0.7.1.9056
@@ -513,7 +513,7 @@ END OF TERMS AND CONDITIONS