stable# note: from dplyr 1.0.0 on, this will be:
# example_isolates %>%
- # mutate(across(where(is.rsi.eligible), as.rsi))
+ # mutate(across((is.rsi.eligible), as.rsi))
}
# }
diff --git a/docs/reference/atc_online.html b/docs/reference/atc_online.html
index bd5f237ba..fae9e5fe3 100644
--- a/docs/reference/atc_online.html
+++ b/docs/reference/atc_online.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/availability.html b/docs/reference/availability.html
index 4633ad463..6e2f58ce8 100644
--- a/docs/reference/availability.html
+++ b/docs/reference/availability.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html
index 7ee74544f..8c2ed01a4 100644
--- a/docs/reference/bug_drug_combinations.html
+++ b/docs/reference/bug_drug_combinations.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/catalogue_of_life.html b/docs/reference/catalogue_of_life.html
index e18babf37..80a338a47 100644
--- a/docs/reference/catalogue_of_life.html
+++ b/docs/reference/catalogue_of_life.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/catalogue_of_life_version.html b/docs/reference/catalogue_of_life_version.html
index eac244e43..7f271b2ee 100644
--- a/docs/reference/catalogue_of_life_version.html
+++ b/docs/reference/catalogue_of_life_version.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/count.html b/docs/reference/count.html
index feb89c2f4..da71389b8 100644
--- a/docs/reference/count.html
+++ b/docs/reference/count.html
@@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/dosage.html b/docs/reference/dosage.html
index abb625f77..78e3e094b 100644
--- a/docs/reference/dosage.html
+++ b/docs/reference/dosage.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html
index 34753480e..12933c278 100644
--- a/docs/reference/eucast_rules.html
+++ b/docs/reference/eucast_rules.html
@@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/example_isolates.html b/docs/reference/example_isolates.html
index 65bd5cfa4..53a51bb23 100644
--- a/docs/reference/example_isolates.html
+++ b/docs/reference/example_isolates.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/example_isolates_unclean.html b/docs/reference/example_isolates_unclean.html
index 368b6070d..e32d1d966 100644
--- a/docs/reference/example_isolates_unclean.html
+++ b/docs/reference/example_isolates_unclean.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/filter_ab_class.html b/docs/reference/filter_ab_class.html
index 6e6af35fb..3b2da8ec9 100644
--- a/docs/reference/filter_ab_class.html
+++ b/docs/reference/filter_ab_class.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html
index 5e874f1d8..146f35b8e 100644
--- a/docs/reference/first_isolate.html
+++ b/docs/reference/first_isolate.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/g.test.html b/docs/reference/g.test.html
index 14d48ca5b..3470910b9 100644
--- a/docs/reference/g.test.html
+++ b/docs/reference/g.test.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/get_episode.html b/docs/reference/get_episode.html
index 6b425466a..9093c38cc 100644
--- a/docs/reference/get_episode.html
+++ b/docs/reference/get_episode.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/ggplot_pca.html b/docs/reference/ggplot_pca.html
index 0379d1567..03ad375d7 100644
--- a/docs/reference/ggplot_pca.html
+++ b/docs/reference/ggplot_pca.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html
index fbef82f1d..8649d827d 100644
--- a/docs/reference/ggplot_rsi.html
+++ b/docs/reference/ggplot_rsi.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/guess_ab_col.html b/docs/reference/guess_ab_col.html
index ea55ffd12..2db3a2cdb 100644
--- a/docs/reference/guess_ab_col.html
+++ b/docs/reference/guess_ab_col.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/index.html b/docs/reference/index.html
index ceb53d07a..c6d2adc7c 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.5.0.9007
+ 1.5.0.9008
@@ -459,7 +459,7 @@
- isolate_identifier()
+ isolate_identifier() all.equal(<isolate_identifier>)
|
Create Identifier of an Isolate |
diff --git a/docs/reference/intrinsic_resistant.html b/docs/reference/intrinsic_resistant.html
index bfcf90556..3dbaf40dd 100644
--- a/docs/reference/intrinsic_resistant.html
+++ b/docs/reference/intrinsic_resistant.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/isolate_identifier.html b/docs/reference/isolate_identifier.html
index 0aaa012a1..21e7fb583 100644
--- a/docs/reference/isolate_identifier.html
+++ b/docs/reference/isolate_identifier.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
@@ -242,7 +242,10 @@
This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.
- isolate_identifier(x, col_mo = NULL, cols_ab = NULL)
+ isolate_identifier(x, col_mo = NULL, cols_ab = NULL)
+
+# S3 method for isolate_identifier
+all.equal(target, current, ignore_empty_results = TRUE, ...)
Arguments
- Maturing Lifecycle
+ Experimental Lifecycle
-
-The lifecycle of this function is maturing. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome to suggest changes at our repository or write us an email (see section 'Contact Us').
+
+The lifecycle of this function is experimental. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this AMR
package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
Read more on Our Website!
diff --git a/docs/reference/join.html b/docs/reference/join.html
index 4bd46665b..b6da0cad7 100644
--- a/docs/reference/join.html
+++ b/docs/reference/join.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/key_antibiotics.html b/docs/reference/key_antibiotics.html
index 39945a9ce..21e512d59 100644
--- a/docs/reference/key_antibiotics.html
+++ b/docs/reference/key_antibiotics.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/kurtosis.html b/docs/reference/kurtosis.html
index 7f841b6df..957c3739d 100644
--- a/docs/reference/kurtosis.html
+++ b/docs/reference/kurtosis.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/lifecycle.html b/docs/reference/lifecycle.html
index 1682ba1a4..2a6e01e47 100644
--- a/docs/reference/lifecycle.html
+++ b/docs/reference/lifecycle.html
@@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/like.html b/docs/reference/like.html
index 08df34844..c8c0afc32 100644
--- a/docs/reference/like.html
+++ b/docs/reference/like.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html
index c793a3bfe..daccc21f9 100644
--- a/docs/reference/mdro.html
+++ b/docs/reference/mdro.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html
index 1932c7ec4..dbf9cc233 100644
--- a/docs/reference/microorganisms.codes.html
+++ b/docs/reference/microorganisms.codes.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html
index 04a6aabee..05c2850a5 100644
--- a/docs/reference/microorganisms.html
+++ b/docs/reference/microorganisms.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html
index 7bccad5cd..7946f46d3 100644
--- a/docs/reference/microorganisms.old.html
+++ b/docs/reference/microorganisms.old.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/mo_matching_score.html b/docs/reference/mo_matching_score.html
index d129ab3c9..187ea1cd1 100644
--- a/docs/reference/mo_matching_score.html
+++ b/docs/reference/mo_matching_score.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html
index 2260754b9..77c4ab8bd 100644
--- a/docs/reference/mo_property.html
+++ b/docs/reference/mo_property.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/mo_source.html b/docs/reference/mo_source.html
index f9e35b02c..9315bec1c 100644
--- a/docs/reference/mo_source.html
+++ b/docs/reference/mo_source.html
@@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/pca.html b/docs/reference/pca.html
index 354cbeb94..2379e238f 100644
--- a/docs/reference/pca.html
+++ b/docs/reference/pca.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/plot.html b/docs/reference/plot.html
index 3a5b8e253..0fd878495 100644
--- a/docs/reference/plot.html
+++ b/docs/reference/plot.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/proportion.html b/docs/reference/proportion.html
index 2c9d9268a..560cc6a25 100644
--- a/docs/reference/proportion.html
+++ b/docs/reference/proportion.html
@@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/random.html b/docs/reference/random.html
index 5058efc8f..18d028732 100644
--- a/docs/reference/random.html
+++ b/docs/reference/random.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html
index ae871da0a..0d5c3d5f8 100644
--- a/docs/reference/resistance_predict.html
+++ b/docs/reference/resistance_predict.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/rsi_translation.html b/docs/reference/rsi_translation.html
index 8fd79c768..2041954ac 100644
--- a/docs/reference/rsi_translation.html
+++ b/docs/reference/rsi_translation.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/skewness.html b/docs/reference/skewness.html
index 35a7ee418..175b74fc7 100644
--- a/docs/reference/skewness.html
+++ b/docs/reference/skewness.html
@@ -83,7 +83,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/reference/translate.html b/docs/reference/translate.html
index 19ddf4e04..72c453f7b 100644
--- a/docs/reference/translate.html
+++ b/docs/reference/translate.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.5.0.9006
+ 1.5.0.9008
diff --git a/docs/survey.html b/docs/survey.html
index b1b9d7cc2..9f0370530 100644
--- a/docs/survey.html
+++ b/docs/survey.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.5.0.9007
+ 1.5.0.9008
diff --git a/man/as.rsi.Rd b/man/as.rsi.Rd
index 2bf0eabe7..61c247c48 100755
--- a/man/as.rsi.Rd
+++ b/man/as.rsi.Rd
@@ -87,15 +87,15 @@ The \code{\link[=as.rsi]{as.rsi()}} function works in four ways:
\item For \strong{cleaning raw / untransformed data}. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as \code{"<0.25; S"} will be coerced to \code{"S"}. Combined interpretations for multiple test methods (as seen in laboratory records) such as \code{"S; S"} will be coerced to \code{"S"}, but a value like \code{"S; I"} will return \code{NA} with a warning that the input is unclear.
\item For \strong{interpreting minimum inhibitory concentration (MIC) values} according to EUCAST or CLSI. You must clean your MIC values first using \code{\link[=as.mic]{as.mic()}}, that also gives your columns the new data class \code{\link{mic}}. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the \code{mo} argument.
\itemize{
-\item Using \code{dplyr}, R/SI interpretation can be done very easily with either:\preformatted{your_data \%>\% mutate_if(is.mic, as.rsi) # until dplyr 1.0.0
-your_data \%>\% mutate(across(where(is.mic), as.rsi)) # since dplyr 1.0.0
+\item Using \code{dplyr}, R/SI interpretation can be done very easily with either:\preformatted{your_data \%>\% mutate_if(is.mic, as.rsi) # until dplyr 1.0.0
+your_data \%>\% mutate(across((is.mic), as.rsi)) # since dplyr 1.0.0
}
\item Operators like "<=" will be stripped before interpretation. When using \code{conserve_capped_values = TRUE}, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (\code{conserve_capped_values = FALSE}) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
}
\item For \strong{interpreting disk diffusion diameters} according to EUCAST or CLSI. You must clean your disk zones first using \code{\link[=as.disk]{as.disk()}}, that also gives your columns the new data class \code{\link{disk}}. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the \code{mo} argument.
\itemize{
-\item Using \code{dplyr}, R/SI interpretation can be done very easily with either:\preformatted{your_data \%>\% mutate_if(is.disk, as.rsi) # until dplyr 1.0.0
-your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
+\item Using \code{dplyr}, R/SI interpretation can be done very easily with either:\preformatted{your_data \%>\% mutate_if(is.disk, as.rsi) # until dplyr 1.0.0
+your_data \%>\% mutate(across((is.disk), as.rsi)) # since dplyr 1.0.0
}
}
\item For \strong{interpreting a complete data set}, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running \code{as.rsi(data)}.
@@ -193,7 +193,7 @@ as.rsi(x = as.disk(18),
if (require("dplyr")) {
df \%>\% mutate_if(is.mic, as.rsi)
df \%>\% mutate_if(function(x) is.mic(x) | is.disk(x), as.rsi)
- df \%>\% mutate(across(where(is.mic), as.rsi))
+ df \%>\% mutate(across((is.mic), as.rsi))
df \%>\% mutate_at(vars(AMP:TOB), as.rsi)
df \%>\% mutate(across(AMP:TOB, as.rsi))
@@ -238,7 +238,7 @@ if (require("dplyr")) {
# note: from dplyr 1.0.0 on, this will be:
# example_isolates \%>\%
- # mutate(across(where(is.rsi.eligible), as.rsi))
+ # mutate(across((is.rsi.eligible), as.rsi))
}
}
}
diff --git a/man/isolate_identifier.Rd b/man/isolate_identifier.Rd
index c6d2c3e76..4c95e4873 100644
--- a/man/isolate_identifier.Rd
+++ b/man/isolate_identifier.Rd
@@ -2,9 +2,12 @@
% Please edit documentation in R/isolate_identifier.R
\name{isolate_identifier}
\alias{isolate_identifier}
+\alias{all.equal.isolate_identifier}
\title{Create Identifier of an Isolate}
\usage{
isolate_identifier(x, col_mo = NULL, cols_ab = NULL)
+
+\method{all.equal}{isolate_identifier}(target, current, ignore_empty_results = TRUE, ...)
}
\arguments{
\item{x}{data with antibiotic columns, such as \code{amox}, \code{AMX} and \code{AMC}}
@@ -12,14 +15,16 @@ isolate_identifier(x, col_mo = NULL, cols_ab = NULL)
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{cols_ab}{a character vector of column names of \code{x}, or (a combination with) an \href{[ab_class()]}{antibiotic selector function}, such as \code{\link[=carbapenems]{carbapenems()}} and \code{\link[=aminoglycosides]{aminoglycosides()}}}
+
+\item{...}{column name of an antibiotic, see section \emph{Antibiotics} below}
}
\description{
This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.
}
-\section{Maturing Lifecycle}{
+\section{Experimental Lifecycle}{
-\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
+\if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
+The \link[=lifecycle]{lifecycle} of this function is \strong{experimental}. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this \code{AMR} package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
}
\section{Read more on Our Website!}{
diff --git a/pkgdown/extra.css b/pkgdown/extra.css
index 8bf2825fc..11c2f0ad8 100644
--- a/pkgdown/extra.css
+++ b/pkgdown/extra.css
@@ -24,14 +24,6 @@
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
*/
-@media (prefers-color-scheme: dark) {
- .navbar-default {
- background-color: #213730;
- }
- .navbar-default .navbar-nav > .active > a, .navbar-default .navbar-nav > .active > a:hover, .navbar-default .navbar-nav > .active > a:focus {
- background-color: #355951;
- }
-}
/* R for Data Science (r4ds) */
#r4ds a {
@@ -209,16 +201,6 @@ thead ~ tbody {
/* only when it has a header */
border-bottom: 2px solid black;
}
-@media (prefers-color-scheme: dark) {
- thead {
- border-top: 2px solid white;
- border-bottom: 2px solid white;
- }
- thead ~ tbody {
- /* only when it has a header */
- border-bottom: 2px solid white;
- }
-}
thead th {
text-align: inherit;
}
diff --git a/tests/testthat/test-isolate_identifier.R b/tests/testthat/test-isolate_identifier.R
new file mode 100644
index 000000000..fd63bcc3b
--- /dev/null
+++ b/tests/testthat/test-isolate_identifier.R
@@ -0,0 +1,44 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 Berends MS, Luz CF et al. #
+# Developed at the University of Groningen, the Netherlands, in #
+# collaboration with non-profit organisations Certe Medical #
+# Diagnostics & Advice, and University Medical Center Groningen. #
+# #
+# This R package is free software; you can freely use and distribute #
+# it for both personal and commercial purposes under the terms of the #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by #
+# the Free Software Foundation. #
+# We created this package for both routine data analysis and academic #
+# research and it was publicly released in the hope that it will be #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
+# #
+# Visit our website for the full manual and a complete tutorial about #
+# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+context("isolate_identifier.R")
+
+test_that("isolate_identifier works", {
+ x <- suppressMessages(isolate_identifier(example_isolates))
+ expect_s3_class(x, "isolate_identifier")
+ expect_s3_class(x, "character")
+
+ expect_equal(suppressMessages(
+ unique(nchar(isolate_identifier(example_isolates, cols_ab = carbapenems(), col_mo = FALSE)))),
+ 2)
+
+ expect_warning(isolate_identifier(example_isolates[, 1:3, drop = FALSE])) # without mo and without rsi
+ expect_warning(isolate_identifier(example_isolates[, 1:9, drop = FALSE])) # only without rsi
+
+
+ expect_output(print(x))
+ expect_s3_class(unique(c(x, x)), "isolate_identifier")
+
+})
diff --git a/vignettes/SPSS.Rmd b/vignettes/SPSS.Rmd
index 75c8d653e..53eb0cddf 100755
--- a/vignettes/SPSS.Rmd
+++ b/vignettes/SPSS.Rmd
@@ -49,7 +49,7 @@ As said, SPSS is easier to learn than R. But SPSS, SAS and Stata come with major
* **R has a huge community.**
- Many R users just ask questions on websites like [StackOverflow.com](https://stackoverflow.com), the largest online community for programmers. At the time of writing, more than [360,000 R-related questions](https://stackoverflow.com/questions/tagged/r?sort=votes) have already been asked on this platform (which covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.
+ Many R users just ask questions on websites like [StackOverflow.com](https://stackoverflow.com), the largest online community for programmers. At the time of writing, [`r format(suppressWarnings(readr::read_csv("https://data.stackexchange.com/stackoverflow/csv/1674647", col_types = "d")[[1]]), big.mark = ",")` R-related questions](https://stackoverflow.com/questions/tagged/r?sort=votes) have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.
* **R understands any data type, including SPSS/SAS/Stata.**