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website update

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dr. M.S. (Matthijs) Berends
2019-01-12 19:31:30 +01:00
parent 3661df7365
commit cda7087722
8 changed files with 57 additions and 39 deletions
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2
man/guess_ab_col.Rd
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@ -14,7 +14,7 @@ guess_ab_col(tbl = NULL, col = NULL, verbose = FALSE)
\item{verbose}{a logical to indicate whether additional info should be printed}
}
\description{
This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set. You can look for an antibiotic (trade) of abbreviation and it will search the data for any column containing a name or ATC code of that antibiotic.
This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set. You can look for an antibiotic (trade) name or abbreviation and it will search the \code{data.frame} for any column containing a name or ATC code of that antibiotic.
}
\section{Read more on our website!}{

20
man/resistance_predict.Rd
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@ -21,9 +21,9 @@ rsi_predict(tbl, col_ab, col_date, year_min = NULL, year_max = NULL,
\item{col_date}{column name of the date, will be used to calculate years if this column doesn't consist of years already}
\item{year_min}{lowest year to use in the prediction model, dafaults the lowest year in \code{col_date}}
\item{year_min}{lowest year to use in the prediction model, dafaults to the lowest year in \code{col_date}}
\item{year_max}{highest year to use in the prediction model, defaults to 15 years after today}
\item{year_max}{highest year to use in the prediction model, defaults to 10 years after today}
\item{year_every}{unit of sequence between lowest year found in the data and \code{year_max}}
@ -31,22 +31,22 @@ rsi_predict(tbl, col_ab, col_date, year_min = NULL, year_max = NULL,
\item{model}{the statistical model of choice. Valid values are \code{"binomial"} (or \code{"binom"} or \code{"logit"}) or \code{"loglin"} or \code{"linear"} (or \code{"lin"}).}
\item{I_as_R}{treat \code{I} as \code{R}}
\item{I_as_R}{a logical to indicate whether values \code{I} should be treated as \code{R}}
\item{preserve_measurements}{logical to indicate whether predictions of years that are actually available in the data should be overwritten with the original data. The standard errors of those years will be \code{NA}.}
\item{preserve_measurements}{a logical to indicate whether predictions of years that are actually available in the data should be overwritten by the original data. The standard errors of those years will be \code{NA}.}
\item{info}{print textual analysis with the name and \code{\link{summary}} of the model.}
\item{info}{a logical to indicate whether textual analysis should be printed with the name and \code{\link{summary}} of the statistical model.}
}
\value{
\code{data.frame} with columns:
\itemize{
\item{\code{year}}
\item{\code{value}, the same as \code{estimated} when \code{preserve_measurements = FALSE}, and a combination of \code{observed} and \code{estimated} otherwise}
\item{\code{se_min}, the lower bound of the standard error with a minimum of \code{0}}
\item{\code{se_max} the upper bound of the standard error with a maximum of \code{1}}
\item{\code{observations}, the total number of observations, i.e. S + I + R}
\item{\code{observed}, the original observed values}
\item{\code{estimated}, the estimated values, calculated by the model}
\item{\code{se_min}, the lower bound of the standard error with a minimum of \code{0} (so the standard error will never go below 0\%)}
\item{\code{se_max} the upper bound of the standard error with a maximum of \code{1} (so the standard error will never go above 100\%)}
\item{\code{observations}, the total number of available observations in that year, i.e. S + I + R}
\item{\code{observed}, the original observed resistant percentages}
\item{\code{estimated}, the estimated resistant percentages, calculated by the model}
}
}
\description{