P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 01:42:08 +02:00
Code Releases Activity

(v2.1.1.9254) fix antimicrobial synonyms

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-04-26 16:23:14 +02:00
parent 4e7fca3b38
commit 92316d5ddc
15 changed files with 114 additions and 74 deletions
Download Patch File Download Diff File Expand all files Collapse all files

26
man/as.sir.Rd
View File

@ -33,7 +33,7 @@ is.sir(x)
is_sir_eligible(x, threshold = 0.05)
\method{as.sir}{default}(x, S = "^(S|U)+$", I = "^(I)+$", R = "^(R)+$",
NI = "^(N|NI|V)+$", SDD = "^(SDD|D|H)+$", info = TRUE, ...)
NI = "^(N|NI|V)+$", SDD = "^(SDD|D|H)+$", info = interactive(), ...)
\method{as.sir}{mic}(x, mo = NULL, ab = deparse(substitute(x)),
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
@ -44,7 +44,8 @@ is_sir_eligible(x, threshold = 0.05)
FALSE), include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
verbose = FALSE, info = TRUE, conserve_capped_values = NULL, ...)
verbose = FALSE, info = interactive(), conserve_capped_values = NULL,
...)
\method{as.sir}{disk}(x, mo = NULL, ab = deparse(substitute(x)),
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
@ -54,7 +55,7 @@ is_sir_eligible(x, threshold = 0.05)
FALSE), include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
verbose = FALSE, info = TRUE, ...)
verbose = FALSE, info = interactive(), ...)
\method{as.sir}{data.frame}(x, ..., col_mo = NULL,
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
@ -65,8 +66,8 @@ is_sir_eligible(x, threshold = 0.05)
FALSE), include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
verbose = FALSE, info = TRUE, parallel = FALSE, max_cores = -1,
conserve_capped_values = NULL)
verbose = FALSE, info = interactive(), parallel = FALSE,
max_cores = -1, conserve_capped_values = NULL)
sir_interpretation_history(clean = FALSE)
}
@ -79,7 +80,7 @@ sir_interpretation_history(clean = FALSE)
\item{S, I, R, NI, SDD}{A case-independent \link[base:regex]{regular expression} to translate input to this result. This regular expression will be run \emph{after} all non-letters and whitespaces are removed from the input.}
\item{info}{A \link{logical} to print information about the process.}
\item{info}{A \link{logical} to print information about the process, defaults to \code{TRUE} only in \link[base:interactive]{interactive sessions}.}
\item{mo}{A vector (or column name) with \link{character}s that can be coerced to valid microorganism codes with \code{\link[=as.mo]{as.mo()}}, can be left empty to determine it automatically.}
@ -292,7 +293,17 @@ df_long <- data.frame(
guideline = c("EUCAST 2021", "EUCAST 2022", "EUCAST 2023", "EUCAST 2024")
)
# most basic application:
as.sir(df_wide)
# return a 'logbook' about the results:
sir_interpretation_history()
\donttest{
# using parallel computing, which is available in base R:
as.sir(df_wide, parallel = TRUE, info = TRUE)
## Using dplyr -------------------------------------------------
if (require("dplyr")) {
# approaches that all work without additional arguments:
@ -406,6 +417,9 @@ as.sir(df_wide)
# return a 'logbook' about the results:
sir_interpretation_history()
# using parallel computing, which is available in base R
as.sir(df_wide, parallel = TRUE)
# for single values
as.sir(
x = as.mic(2),