P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-13 02:32:07 +02:00
Code Releases Activity

(v1.5.0.9016) only_rsi_columns update, documentation

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-02-08 14:18:42 +01:00
parent 8fda473e49
commit 4a84894f79
88 changed files with 654 additions and 375 deletions
Download Patch File Download Diff File Expand all files Collapse all files

16
man/first_isolate.Rd
View File

@ -12,7 +12,7 @@ Methodology of this function is strictly based on:
}
\usage{
first_isolate(
x,
x = NULL,
col_date = NULL,
col_patient_id = NULL,
col_mo = NULL,
@ -33,7 +33,7 @@ first_isolate(
)
filter_first_isolate(
x,
x = NULL,
col_date = NULL,
col_patient_id = NULL,
col_mo = NULL,
@ -41,7 +41,7 @@ filter_first_isolate(
)
filter_first_weighted_isolate(
x,
x = NULL,
col_date = NULL,
col_patient_id = NULL,
col_mo = NULL,
@ -50,7 +50,7 @@ filter_first_weighted_isolate(
)
}
\arguments{
\item{x}{a \link{data.frame} containing isolates. Can be left blank for automatic determination.}
\item{x}{a \link{data.frame} containing isolates. Can be left blank for automatic determination, see \emph{Examples}.}
\item{col_date}{column name of the result date (or date that is was received on the lab), defaults to the first column with a date class}
@ -130,7 +130,7 @@ There are two ways to determine whether isolates can be included as first weight
Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With \code{ignore_I = FALSE}, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the \code{\link[=key_antibiotics]{key_antibiotics()}} function.
\item Using \code{type = "points"} and argument \code{points_threshold}
A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, which default to \code{2}, an isolate will be (re)selected as a first weighted isolate.
A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, which defaults to \code{2}, an isolate will be (re)selected as a first weighted isolate.
}
}
@ -151,10 +151,12 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.
# basic filtering on first isolates
example_isolates[first_isolate(), ]
example_isolates[first_isolate(example_isolates), ]
\donttest{
# faster way, only works in R 3.2 and later:
example_isolates[first_isolate(), ]
# get all first Gram-negatives
example_isolates[which(first_isolate() & mo_is_gram_negative()), ]