P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-18 01:23:16 +02:00
Code Releases Activity

(v2.1.1.9252) fix MIC for >= and <=

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-04-25 10:19:40 +02:00
parent 6135805455
commit abee2a954e
11 changed files with 40 additions and 26 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
man/AMR.Rd
View File

@ -28,7 +28,7 @@ A BibTeX entry for LaTeX users is:
\description{
Welcome to the \code{AMR} package.
The \code{AMR} package is a \href{https://amr-for-r.org/#copyright}{free and open-source} R package with \href{https://en.wikipedia.org/wiki/Dependency_hell}{zero dependencies} to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. \strong{Our aim is to provide a standard} for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. \href{https://amr-for-r.org/authors.html}{Many different researchers} from around the globe are continually helping us to make this a successful and durable project!
The \code{AMR} package is a peer-reviewed, \href{https://amr-for-r.org/#copyright}{free and open-source} R package with \href{https://en.wikipedia.org/wiki/Dependency_hell}{zero dependencies} to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. \strong{Our aim is to provide a standard} for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. \href{https://amr-for-r.org/authors.html}{Many different researchers} from around the globe are continually helping us to make this a successful and durable project!
This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).

2
man/as.sir.Rd
View File

@ -403,7 +403,7 @@ as.sir(
)
# For CLEANING existing SIR values ------------------------------------
# For CLEANING existing SIR values -------------------------------------
as.sir(c("S", "SDD", "I", "R", "NI", "A", "B", "C"))
as.sir("<= 0.002; S") # will return "S"

3
man/guess_ab_col.Rd
View File

@ -35,7 +35,6 @@ guess_ab_col(df, "amoxicillin")
guess_ab_col(df, "J01AA07") # ATC code of tetracycline
guess_ab_col(df, "J01AA07", verbose = TRUE)
# NOTE: Using column 'tetr' as input for J01AA07 (tetracycline).
# WHONET codes
df <- data.frame(
@ -44,5 +43,5 @@ df <- data.frame(
)
guess_ab_col(df, "ampicillin")
guess_ab_col(df, "J01CR02")
guess_ab_col(df, as.ab("augmentin"))
guess_ab_col(df, "augmentin")
}