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new tibble export

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dr. M.S. (Matthijs) Berends
2022-08-27 20:49:37 +02:00
parent 164886f50b
commit 303d61b473
115 changed files with 836 additions and 996 deletions
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44
man/eucast_rules.Rd
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@ -36,7 +36,7 @@ eucast_rules(
eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
}
\arguments{
\item{x}{data with antibiotic columns, such as \code{amox}, \code{AMX} and \code{AMC}}
\item{x}{a data set with antibiotic columns, such as \code{amox}, \code{AMX} and \code{AMC}}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
@ -83,26 +83,26 @@ Custom rules can be created using \code{\link[=custom_eucast_rules]{custom_eucas
AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
eucast_rules(example_isolates, rules = "custom", custom_rules = x, info = FALSE)
#> # A tibble: 2,000 x 49
#> date hospit~1 ward_~2 ward_~3 ward_~4 age gender patie~5 mo
#> * <date> <fct> <lgl> <lgl> <lgl> <dbl> <chr> <chr> <mo>
#> 1 2002-01-02 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI
#> 2 2002-01-03 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI
#> 3 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR
#> 4 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR
#> 5 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR
#> 6 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR
#> 7 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS
#> 8 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS
#> 9 2002-01-16 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR
#> 10 2002-01-17 B TRUE FALSE FALSE 79 F 858515 B_STPHY_EPDR
#> # ... with 1,990 more rows, 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>,
#> # AMX <rsi>, AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>,
#> # CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>,
#> # TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>,
#> # FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>,
#> # TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>,
#> # IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, ...
#> # A tibble: 2,000 x 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> * <date> <chr> <dbl> <chr> <chr> <mo> <rsi> <rsi> <rsi> <rsi>
#> 1 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
#> 2 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
#> 3 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
#> 4 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
#> 5 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
#> 6 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
#> 7 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
#> 8 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
#> 9 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA
#> 10 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA
#> # ... with 1,990 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>,
#> # TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>,
#> # CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>,
#> # TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>,
#> # MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>,
#> # ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>,
#> # CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi>
#> # i Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names
}\if{html}{\out{</div>}}
}
@ -131,7 +131,7 @@ Amikacin (\code{AMK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB06&sho
\section{Reference Data Publicly Available}{
All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this \code{AMR} package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find \href{https://msberends.github.io/AMR/articles/datasets.html}{all download links on our website}, which is automatically updated with every code change.
All data sets in this \code{AMR} package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{