+ | ampc_cephalosporin_resistance |
+ a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to NA. Currently only works when version_expertrules is 3.2; 'EUCAST Expert Rules v3.2 on Enterobacterales' states that susceptible (S) results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these agents. A value of NA for this argument will remove results for these agents, while e.g. a value of "R" will make the results for these agents resistant. Use NULL to not alter the results for AmpC de-repressed cephalosporin-resistant mutants.
For EUCAST Expert Rules v3.2, this rule applies to: Enterobacter, Klebsiella aerogenes, Citrobacter freundii, Hafnia alvei, Serratia, Morganella morganii, Providencia. |
+
| ... |
column name of an antibiotic, please see section Antibiotics below |
diff --git a/docs/reference/get_episode.html b/docs/reference/get_episode.html
index 9d14c8cd..2c7c1684 100644
--- a/docs/reference/get_episode.html
+++ b/docs/reference/get_episode.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.4.0.9046
+ 1.4.0.9048
@@ -275,7 +275,7 @@
Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least episode_days days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least episode_days days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.
The first_isolate() function is a wrapper around the is_new_episode() function, but is more efficient for data sets containing microorganism codes or names.
-The dplyr package is not required for these functions to work, but these functions support variable grouping and work conveniently inside dplyr verbs such as filter(), mutate() and summarise().
+The dplyr package is not required for these functions to work, but these functions support variable grouping and work conveniently inside dplyr verbs such as filter(), mutate() and summarise().
Stable lifecycle
@@ -299,7 +299,7 @@ The lifecycle of this function is stableget_episode(example_isolates$date, episode_days = 60)
is_new_episode(example_isolates$date, episode_days = 60)
-# filter on results from the third 60-day episode using base R
+# filter on results from the third 60-day episode only, using base R
example_isolates[which(get_episode(example_isolates$date, 60) == 3), ]
# \donttest{
@@ -307,23 +307,23 @@ The lifecycle of this function is stable# is_new_episode() can also be used in dplyr verbs to determine patient
# episodes based on any (combination of) grouping variables:
example_isolates %>%
- mutate(condition = sample(x = c("A", "B", "C"),
+ mutate(condition = sample(x = c("A", "B", "C"),
size = 2000,
replace = TRUE)) %>%
- group_by(condition) %>%
- mutate(new_episode = is_new_episode(date, 365))
+ group_by(condition) %>%
+ mutate(new_episode = is_new_episode(date, 365))
example_isolates %>%
- group_by(hospital_id, patient_id) %>%
- transmute(date,
+ group_by(hospital_id, patient_id) %>%
+ transmute(date,
patient_id,
new_index = get_episode(date, 60),
new_logical = is_new_episode(date, 60))
example_isolates %>%
- group_by(hospital_id) %>%
- summarise(patients = n_distinct(patient_id),
+ group_by(hospital_id) %>%
+ summarise(patients = n_distinct(patient_id),
n_episodes_365 = sum(is_new_episode(date, episode_days = 365)),
n_episodes_60 = sum(is_new_episode(date, episode_days = 60)),
n_episodes_30 = sum(is_new_episode(date, episode_days = 30)))
@@ -332,19 +332,19 @@ The lifecycle of this function is stable# grouping on patients and microorganisms leads to the same results
# as first_isolate():
x <- example_isolates %>%
- filter(first_isolate(., include_unknown = TRUE))
+ filter(first_isolate(., include_unknown = TRUE))
y <- example_isolates %>%
- group_by(patient_id, mo) %>%
- filter(is_new_episode(date, 365))
+ group_by(patient_id, mo) %>%
+ filter(is_new_episode(date, 365))
identical(x$patient_id, y$patient_id)
# but is_new_episode() has a lot more flexibility than first_isolate(),
# since you can now group on anything that seems relevant:
example_isolates %>%
- group_by(patient_id, mo, hospital_id, ward_icu) %>%
- mutate(flag_episode = is_new_episode(date, 365))
+ group_by(patient_id, mo, hospital_id, ward_icu) %>%
+ mutate(flag_episode = is_new_episode(date, 365))
}
# }
diff --git a/docs/reference/index.html b/docs/reference/index.html
index a0f7e853..d84f7781 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9047
+ 1.4.0.9048
diff --git a/docs/survey.html b/docs/survey.html
index 47f325b4..7c11af22 100644
--- a/docs/survey.html
+++ b/docs/survey.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9047
+ 1.4.0.9048
diff --git a/man/eucast_rules.Rd b/man/eucast_rules.Rd
index cd129781..89d571db 100644
--- a/man/eucast_rules.Rd
+++ b/man/eucast_rules.Rd
@@ -23,6 +23,7 @@ eucast_rules(
verbose = FALSE,
version_breakpoints = 10,
version_expertrules = 3.2,
+ ampc_cephalosporin_resistance = NA,
...
)
}
@@ -41,6 +42,8 @@ eucast_rules(
\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Currently supported: 3.1, 3.2.}
+\item{ampc_cephalosporin_resistance}{a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2}; '\emph{EUCAST Expert Rules v3.2 on Enterobacterales}' states that susceptible (S) results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these agents. A value of \code{NA} for this argument will remove results for these agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Enterobacter}, \emph{Klebsiella aerogenes}, \emph{Citrobacter freundii}, \emph{Hafnia alvei}, \emph{Serratia}, \emph{Morganella morganii}, \emph{Providencia}.}
+
\item{...}{column name of an antibiotic, please see section \emph{Antibiotics} below}
}
\value{
diff --git a/man/get_episode.Rd b/man/get_episode.Rd
index 9e478c7d..ecab0ae6 100644
--- a/man/get_episode.Rd
+++ b/man/get_episode.Rd
@@ -52,7 +52,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
get_episode(example_isolates$date, episode_days = 60)
is_new_episode(example_isolates$date, episode_days = 60)
-# filter on results from the third 60-day episode using base R
+# filter on results from the third 60-day episode only, using base R
example_isolates[which(get_episode(example_isolates$date, 60) == 3), ]
\donttest{
diff --git a/pkgdown/extra.js b/pkgdown/extra.js
index 78f0d9dd..bc54c5de 100644
--- a/pkgdown/extra.js
+++ b/pkgdown/extra.js
@@ -90,6 +90,7 @@ $(document).ready(function() {
x = x.replace("Judith", "Dr. Judith");
x = x.replace("Gwen", "Dr. Gwen");
x = x.replace("Anthony", "Dr. Anthony");
+ x = x.replace("Rogier", "Dr. Rogier");
}
return(x);
}
diff --git a/tests/testthat/test-eucast_rules.R b/tests/testthat/test-eucast_rules.R
index 7c188867..575ace55 100755
--- a/tests/testthat/test-eucast_rules.R
+++ b/tests/testthat/test-eucast_rules.R
@@ -118,4 +118,24 @@ test_that("EUCAST rules work", {
# check verbose output
expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, rules = "all", info = TRUE)))
+ # AmpC de-repressed cephalo mutants
+ expect_identical(
+ eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
+ cefotax = as.rsi(c("S", "S"))),
+ ampc_derepressed_cephalosporins = "R",
+ info = FALSE)$cefotax,
+ as.rsi(c("S", "R")))
+ expect_identical(
+ eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
+ cefotax = as.rsi(c("S", "S"))),
+ ampc_derepressed_cephalosporins = NA,
+ info = FALSE)$cefotax,
+ as.rsi(c("S", NA)))
+ expect_identical(
+ eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
+ cefotax = as.rsi(c("S", "S"))),
+ ampc_derepressed_cephalosporins = NULL,
+ info = FALSE)$cefotax,
+ as.rsi(c("S", "S")))
+
})