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(v2.1.1.9126) implemented WISCA! Also added top_n_microorganisms() and fixed Python wrapper

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dr. M.S. (Matthijs) Berends
2025-01-26 23:01:17 +01:00
parent 92c4fc0f94
commit 66833b4f5a
46 changed files with 1786 additions and 1842 deletions
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53
man/resistance_predict.Rd
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@ -8,51 +8,22 @@
\alias{autoplot.resistance_predict}
\title{Predict Antimicrobial Resistance}
\usage{
resistance_predict(
x,
col_ab,
col_date = NULL,
year_min = NULL,
year_max = NULL,
year_every = 1,
minimum = 30,
model = NULL,
I_as_S = TRUE,
preserve_measurements = TRUE,
info = interactive(),
...
)
resistance_predict(x, col_ab, col_date = NULL, year_min = NULL,
year_max = NULL, year_every = 1, minimum = 30, model = NULL,
I_as_S = TRUE, preserve_measurements = TRUE, info = interactive(), ...)
sir_predict(
x,
col_ab,
col_date = NULL,
year_min = NULL,
year_max = NULL,
year_every = 1,
minimum = 30,
model = NULL,
I_as_S = TRUE,
preserve_measurements = TRUE,
info = interactive(),
...
)
sir_predict(x, col_ab, col_date = NULL, year_min = NULL, year_max = NULL,
year_every = 1, minimum = 30, model = NULL, I_as_S = TRUE,
preserve_measurements = TRUE, info = interactive(), ...)
\method{plot}{resistance_predict}(x, main = paste("Resistance Prediction of", x_name), ...)
\method{plot}{resistance_predict}(x, main = paste("Resistance Prediction of",
x_name), ...)
ggplot_sir_predict(
x,
main = paste("Resistance Prediction of", x_name),
ribbon = TRUE,
...
)
ggplot_sir_predict(x, main = paste("Resistance Prediction of", x_name),
ribbon = TRUE, ...)
\method{autoplot}{resistance_predict}(
object,
main = paste("Resistance Prediction of", x_name),
ribbon = TRUE,
...
)
\method{autoplot}{resistance_predict}(object,
main = paste("Resistance Prediction of", x_name), ribbon = TRUE, ...)
}
\arguments{
\item{x}{a \link{data.frame} containing isolates. Can be left blank for automatic determination, see \emph{Examples}.}