Added tibble printing support for classes rsi, mic, ab and mo. When using tibbles containing antibiotic columns, values S will print in green, values I will print in yellow and values R will print in red:
@@ -239,7 +239,7 @@
col_icu = NULL, col_keyantibiotics = NULL, episode_days = 365,
testcodes_exclude = NULL, icu_exclude = FALSE,
specimen_group = NULL, type = "keyantibiotics", ignore_I = TRUE,
- points_threshold = 2, info = TRUE, ...)
+ points_threshold = 2, info = TRUE, include_unknown = FALSE, ...)
filter_first_isolate(x, col_date = NULL, col_patient_id = NULL,
col_mo = NULL, ...)
@@ -285,7 +285,7 @@
| episode_days |
- episode in days after which a genus/species combination will be determined as 'first isolate' again |
+ 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 Source. |
| testcodes_exclude |
@@ -315,6 +315,10 @@
info |
print progress |
+
+ | include_unknown |
+ logical to determine whether 'unknown' microorganisms should be included too, i.e. microbial code "UNKNOWN", which defaults to FALSE. For WHONET users, this means that all records with organism code "con" (contamination) will be excluded at default. |
+
| ... |
parameters passed on to the first_isolate function |
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 5aec4a66..ff6bb240 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -78,7 +78,7 @@
AMR (for R)
- 0.7.1.9030
+ 0.7.1.9031
diff --git a/git_merge.sh b/git_merge.sh
index cc6755f7..69ff7fe8 100755
--- a/git_merge.sh
+++ b/git_merge.sh
@@ -10,15 +10,15 @@
# git stash --quiet
# go to master
-git add .
-git commit -a -m "website update" --quiet
git checkout master --quiet
echo "• changed branch to master"
+
# import everything from premaster
git merge premaster --quiet
# and send it to git
git push --quiet
echo "• pushed changes to master"
+
# return to premaster
git checkout premaster --quiet
echo "• changed branch back to premaster"
diff --git a/man/first_isolate.Rd b/man/first_isolate.Rd
index 47d8435d..fa95c148 100755
--- a/man/first_isolate.Rd
+++ b/man/first_isolate.Rd
@@ -14,7 +14,7 @@ first_isolate(x, col_date = NULL, col_patient_id = NULL,
col_icu = NULL, col_keyantibiotics = NULL, episode_days = 365,
testcodes_exclude = NULL, icu_exclude = FALSE,
specimen_group = NULL, type = "keyantibiotics", ignore_I = TRUE,
- points_threshold = 2, info = TRUE, ...)
+ points_threshold = 2, info = TRUE, include_unknown = FALSE, ...)
filter_first_isolate(x, col_date = NULL, col_patient_id = NULL,
col_mo = NULL, ...)
@@ -40,7 +40,7 @@ filter_first_weighted_isolate(x, col_date = NULL,
\item{col_keyantibiotics}{column name of the key antibiotics to determine first \emph{weighted} isolates, see \code{\link{key_antibiotics}}. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' (case insensitive). Use \code{col_keyantibiotics = FALSE} to prevent this.}
-\item{episode_days}{episode in days after which a genus/species combination will be determined as 'first isolate' again}
+\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 Source.}
\item{testcodes_exclude}{character vector with test codes that should be excluded (case-insensitive)}
@@ -56,6 +56,8 @@ filter_first_weighted_isolate(x, col_date = NULL,
\item{info}{print progress}
+\item{include_unknown}{logical to determine whether 'unknown' microorganisms should be included too, i.e. microbial code \code{"UNKNOWN"}, which defaults to \code{FALSE}. For WHONET users, this means that all records with organism code \code{"con"} (\emph{contamination}) will be excluded at default. Isolates with a microbial ID of \code{NA} will always be excluded as first isolate.}
+
\item{...}{parameters passed on to the \code{first_isolate} function}
}
\value{
@@ -68,6 +70,8 @@ Determine first (weighted) isolates of all microorganisms of every patient per e
\strong{WHY THIS IS SO IMPORTANT} \cr
To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode \href{https://www.ncbi.nlm.nih.gov/pubmed/17304462}{[1]}. If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all \emph{S. aureus} isolates would be overestimated, because you included this MRSA more than once. It would be \href{https://en.wikipedia.org/wiki/Selection_bias}{selection bias}.
+All isolates with a microbial ID of \code{NA} will be excluded as first isolate.
+
The functions \code{filter_first_isolate} and \code{filter_first_weighted_isolate} are helper functions to quickly filter on first isolates. The function \code{filter_first_isolate} is essentially equal to:
\preformatted{
x \%>\%
diff --git a/tests/testthat/test-first_isolate.R b/tests/testthat/test-first_isolate.R
index bd2283c0..8572f2f2 100755
--- a/tests/testthat/test-first_isolate.R
+++ b/tests/testthat/test-first_isolate.R
@@ -187,5 +187,25 @@ test_that("first isolates work", {
info = TRUE),
na.rm = TRUE),
1322)
+
+ # unknown MOs
+ expect_equal(septic_patients %>%
+ mutate(mo = ifelse(mo == "B_ESCHR_COL", "UNKNOWN", mo)) %>%
+ mutate(first = first_isolate(., include_unknown = FALSE)) %>%
+ .$first %>%
+ sum(),
+ 1062)
+ expect_equal(septic_patients %>%
+ mutate(mo = ifelse(mo == "B_ESCHR_COL", "UNKNOWN", mo)) %>%
+ mutate(first = first_isolate(., include_unknown = TRUE)) %>%
+ .$first %>%
+ sum(),
+ 1529)
+ expect_equal(septic_patients %>%
+ mutate(mo = ifelse(mo == "B_ESCHR_COL", NA, mo)) %>%
+ mutate(first = first_isolate(.)) %>%
+ .$first %>%
+ sum(),
+ 1062)
})