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fix reference_df endless loop

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dr. M.S. (Matthijs) Berends
2023-06-26 13:52:02 +02:00
parent 1d9ee39cc7
commit 2d97cca6d9
29 changed files with 215 additions and 200 deletions
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10
man/as.sir.Rd
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@ -43,7 +43,7 @@ is_sir_eligible(x, threshold = 0.05)
reference_data = AMR::clinical_breakpoints,
include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
ecoff = getOption("AMR_ecoff", FALSE),
breakpoint_type = getOption("AMR_breakpoint_type", FALSE),
...
)
@ -57,7 +57,7 @@ is_sir_eligible(x, threshold = 0.05)
reference_data = AMR::clinical_breakpoints,
include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
ecoff = getOption("AMR_ecoff", FALSE),
breakpoint_type = getOption("AMR_breakpoint_type", FALSE),
...
)
@ -72,7 +72,7 @@ is_sir_eligible(x, threshold = 0.05)
reference_data = AMR::clinical_breakpoints,
include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
ecoff = getOption("AMR_ecoff", FALSE)
breakpoint_type = getOption("AMR_breakpoint_type", FALSE)
)
sir_interpretation_history(clean = FALSE)
@ -102,7 +102,7 @@ sir_interpretation_history(clean = FALSE)
\item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_include_PKPD}}.}
\item{ecoff}{a \link{logical} to indicate that ECOFF (Epidemiological Cut-Off) values must be used \strong{instead} of other clinical breakpoints - the default is \code{FALSE}. Can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_ecoff}}.}
\item{breakpoint_type}{the type of breakpoints to use, either "". ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_breakpoint_type}}.}
\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
@ -114,6 +114,8 @@ Ordered \link{factor} with new class \code{sir}
\description{
Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing SIR values. This transforms the input to a new class \code{\link{sir}}, which is an ordered \link{factor} with levels \verb{S < I < R}.
Currently available \strong{breakpoint guidelines} are EUCAST 2011-2023 and CLSI 2011-2023, and available \strong{breakpoint types} are "".
All breakpoints used for interpretation are publicly available in the \link{clinical_breakpoints} data set.
}
\details{

4
man/microorganisms.Rd
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@ -3,9 +3,9 @@
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data Set with 52 151 Microorganisms}
\title{Data Set with 52 158 Microorganisms}
\format{
A \link[tibble:tibble]{tibble} with 52 151 observations and 23 variables:
A \link[tibble:tibble]{tibble} with 52 158 observations and 23 variables:
\itemize{
\item \code{mo}\cr ID of microorganism as used by this package
\item \code{fullname}\cr Full name, like \code{"Escherichia coli"}. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon.

4
man/microorganisms.codes.Rd
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@ -3,9 +3,9 @@
\docType{data}
\name{microorganisms.codes}
\alias{microorganisms.codes}
\title{Data Set with 4 942 Common Microorganism Codes}
\title{Data Set with 4 946 Common Microorganism Codes}
\format{
A \link[tibble:tibble]{tibble} with 4 942 observations and 2 variables:
A \link[tibble:tibble]{tibble} with 4 946 observations and 2 variables:
\itemize{
\item \code{code}\cr Commonly used code of a microorganism
\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set