vignettes/datasets.Rmd
datasets.RmdNEWS.md
- AMR 1.7.1.9030AMR 1.7.1.9031R/first_isolate.R
first_isolate.RdDetermine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler et al. in 2007 (doi: 10.1086/511864
-). To determine patient episodes not necessarily based on microorganisms, use is_new_episode() that also supports grouping with the dplyr package.
Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler et al. in 2007 (doi: 10.1086/511864
+). To determine patient episodes not necessarily based on microorganisms, use is_new_episode() that also supports grouping with the dplyr package .
first_isolate(
@@ -314,7 +314,7 @@
col_keyantimicrobials
- (only useful when method = "phenotype-based") column name of the key antimicrobials to determine first (weighted) isolates, see key_antimicrobials(). Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use col_keyantimicrobials = FALSE to prevent this. Can also be the output of key_antimicrobials().
(only useful when method = "phenotype-based") column name of the key antimicrobials to determine first isolates, see key_antimicrobials(). Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use col_keyantimicrobials = FALSE to prevent this. Can also be the output of key_antimicrobials().
episode_days
@@ -429,8 +429,8 @@
This is a more reliable method, since it also weighs the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:
-Using type = "points" and argument points_threshold
-This method weighs all antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as 0.5 points, a difference from S to R (or vice versa) counts as 1 point. When the sum of points exceeds points_threshold, which defaults to 2, an isolate will be selected as a first weighted isolate.
+Using type = "points" and argument points_threshold (default)
+This method weighs all antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as 0.5 points, a difference from S to R (or vice versa) counts as 1 point. When the sum of points exceeds points_threshold, which defaults to 2, an isolate will be selected as a first weighted isolate.
All antimicrobials are internally selected using the all_antimicrobials() function. The output of this function does not need to be passed to the first_isolate() function.
Using type = "keyantimicrobials" and argument ignore_I
This method only weighs specific antimicrobial agents, called key antimicrobials. Any difference from S to R (or vice versa) in these key antimicrobials will select an isolate as a first weighted isolate. With ignore_I = FALSE, also differences from I to S or R (or vice versa) will lead to this.
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 4c787440..0fb823ab 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -92,7 +92,7 @@
@@ -393,7 +393,7 @@
- Determine First (Weighted) Isolates
Determine First Isolates
diff --git a/inst/tinytest/test-first_isolate.R b/inst/tinytest/test-first_isolate.R
index e7ddc857..f6e48fcd 100755
--- a/inst/tinytest/test-first_isolate.R
+++ b/inst/tinytest/test-first_isolate.R
@@ -133,9 +133,7 @@ if (AMR:::pkg_is_available("dplyr")) {
first_isolate(info = TRUE))
# groups
- message("get to first isolates L136")
x <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate())
- message("get to first isolates L138")
y <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate(.))
expect_identical(x, y)
diff --git a/man/first_isolate.Rd b/man/first_isolate.Rd
index d37370b1..0e305900 100755
--- a/man/first_isolate.Rd
+++ b/man/first_isolate.Rd
@@ -3,7 +3,7 @@
\name{first_isolate}
\alias{first_isolate}
\alias{filter_first_isolate}
-\title{Determine First (Weighted) Isolates}
+\title{Determine First Isolates}
\source{
Methodology of this function is strictly based on:
\itemize{
@@ -60,7 +60,7 @@ filter_first_isolate(
\item{col_icu}{column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU)}
-\item{col_keyantimicrobials}{(only useful when \code{method = "phenotype-based"}) column name of the key antimicrobials to determine first (weighted) isolates, see \code{\link[=key_antimicrobials]{key_antimicrobials()}}. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use \code{col_keyantimicrobials = FALSE} to prevent this. Can also be the output of \code{\link[=key_antimicrobials]{key_antimicrobials()}}.}
+\item{col_keyantimicrobials}{(only useful when \code{method = "phenotype-based"}) column name of the key antimicrobials to determine first isolates, see \code{\link[=key_antimicrobials]{key_antimicrobials()}}. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use \code{col_keyantimicrobials = FALSE} to prevent this. Can also be the output of \code{\link[=key_antimicrobials]{key_antimicrobials()}}.}
\item{episode_days}{episode in days after which a genus/species combination will be determined as 'first isolate' again. The default of 365 days is based on the guideline by CLSI, see \emph{Source}.}
@@ -90,7 +90,7 @@ filter_first_isolate(
A \code{\link{logical}} vector
}
\description{
-Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler \emph{et al.} in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use \code{\link[=is_new_episode]{is_new_episode()}} that also supports grouping with the \code{dplyr} package.
+Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler \emph{et al.} in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use \code{\link[=is_new_episode]{is_new_episode()}} that also supports \link[dplyr:group_by]{grouping with the \code{dplyr} package} .
}
\details{
To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below.
@@ -147,9 +147,9 @@ This is the most common method to correct for duplicate isolates. Patients are c
This is a more reliable method, since it also \emph{weighs} the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:
\enumerate{
-\item Using \code{type = "points"} and argument \code{points_threshold}
+\item Using \code{type = "points"} and argument \code{points_threshold} (default)
-This method weighs \emph{all} antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as 0.5 points, a difference from S to R (or vice versa) counts as 1 point. When the sum of points exceeds \code{points_threshold}, which defaults to \code{2}, an isolate will be selected as a first weighted isolate.
+This method weighs \emph{all} antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as \code{0.5} points, a difference from S to R (or vice versa) counts as \code{1} point. When the sum of points exceeds \code{points_threshold}, which defaults to \code{2}, an isolate will be selected as a first weighted isolate.
All antimicrobials are internally selected using the \code{\link[=all_antimicrobials]{all_antimicrobials()}} function. The output of this function does not need to be passed to the \code{\link[=first_isolate]{first_isolate()}} function.
\item Using \code{type = "keyantimicrobials"} and argument \code{ignore_I}
diff --git a/tests/tinytest.R b/tests/tinytest.R
index 86f63498..6af3eb90 100644
--- a/tests/tinytest.R
+++ b/tests/tinytest.R
@@ -33,9 +33,13 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
testdir = ifelse(AMR:::dir.exists("inst/tinytest"),
"inst/tinytest",
"tinytest"),
- verbose = FALSE)
- cat(attributes(out)$duration, "\n")
+ verbose = 99,
+ color = FALSE)
+ cat("SUMMARY:\n")
print(summary(out))
+ cat("WARNINGS:\n")
print(warnings())
+ cat(attributes(out)$duration, "\n")
+
}
}