mirror of https://github.com/msberends/AMR.git
149 lines
6.9 KiB
R
149 lines
6.9 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/read.4d.R
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\name{read.4D}
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\alias{read.4D}
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\title{Read data from 4D database}
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\usage{
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read.4D(
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file,
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info = interactive(),
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header = TRUE,
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row.names = NULL,
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sep = "\\t",
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quote = "\\"'",
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dec = ",",
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na.strings = c("NA", "", "."),
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skip = 2,
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check.names = TRUE,
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strip.white = TRUE,
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fill = TRUE,
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blank.lines.skip = TRUE,
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stringsAsFactors = FALSE,
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fileEncoding = "UTF-8",
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encoding = "UTF-8"
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)
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}
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\arguments{
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\item{file}{the name of the file which the data are to be read from.
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Each row of the table appears as one line of the file. If it does
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not contain an \emph{absolute} path, the file name is
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\emph{relative} to the current working directory,
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\code{\link{getwd}()}. Tilde-expansion is performed where supported.
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This can be a compressed file (see \code{\link{file}}).
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Alternatively, \code{file} can be a readable text-mode
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\link{connection} (which will be opened for reading if
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necessary, and if so \code{\link{close}}d (and hence destroyed) at
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the end of the function call). (If \code{\link{stdin}()} is used,
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the prompts for lines may be somewhat confusing. Terminate input
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with a blank line or an EOF signal, \code{Ctrl-D} on Unix and
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\code{Ctrl-Z} on Windows. Any pushback on \code{stdin()} will be
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cleared before return.)
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\code{file} can also be a complete URL. (For the supported URL
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schemes, see the \sQuote{URLs} section of the help for
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\code{\link{url}}.)
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}
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\item{info}{a logical to indicate whether info about the import should be printed, defaults to \code{TRUE} in interactive sessions}
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\item{header}{a logical value indicating whether the file contains the
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names of the variables as its first line. If missing, the value is
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determined from the file format: \code{header} is set to \code{TRUE}
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if and only if the first row contains one fewer field than the
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number of columns.}
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\item{row.names}{a vector of row names. This can be a vector giving
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the actual row names, or a single number giving the column of the
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table which contains the row names, or character string giving the
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name of the table column containing the row names.
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If there is a header and the first row contains one fewer field than
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the number of columns, the first column in the input is used for the
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row names. Otherwise if \code{row.names} is missing, the rows are
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numbered.
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Using \code{row.names = NULL} forces row numbering. Missing or
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\code{NULL} \code{row.names} generate row names that are considered
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to be \sQuote{automatic} (and not preserved by \code{\link{as.matrix}}).
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}
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\item{sep}{the field separator character. Values on each line of the
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file are separated by this character. If \code{sep = ""} (the
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default for \code{read.table}) the separator is \sQuote{white space},
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that is one or more spaces, tabs, newlines or carriage returns.}
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\item{quote}{the set of quoting characters. To disable quoting
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altogether, use \code{quote = ""}. See \code{\link{scan}} for the
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behaviour on quotes embedded in quotes. Quoting is only considered
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for columns read as character, which is all of them unless
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\code{colClasses} is specified.}
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\item{dec}{the character used in the file for decimal points.}
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\item{na.strings}{a character vector of strings which are to be
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interpreted as \code{\link{NA}} values. Blank fields are also
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considered to be missing values in logical, integer, numeric and
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complex fields. Note that the test happens \emph{after}
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white space is stripped from the input, so \code{na.strings}
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values may need their own white space stripped in advance.}
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\item{skip}{integer: the number of lines of the data file to skip before
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beginning to read data.}
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\item{check.names}{logical. If \code{TRUE} then the names of the
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variables in the data frame are checked to ensure that they are
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syntactically valid variable names. If necessary they are adjusted
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(by \code{\link{make.names}}) so that they are, and also to ensure
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that there are no duplicates.}
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\item{strip.white}{logical. Used only when \code{sep} has
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been specified, and allows the stripping of leading and trailing
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white space from unquoted \code{character} fields (\code{numeric} fields
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are always stripped). See \code{\link{scan}} for further details
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(including the exact meaning of \sQuote{white space}),
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remembering that the columns may include the row names.}
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\item{fill}{logical. If \code{TRUE} then in case the rows have unequal
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length, blank fields are implicitly added. See \sQuote{Details}.}
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\item{blank.lines.skip}{logical: if \code{TRUE} blank lines in the
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input are ignored.}
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\item{stringsAsFactors}{logical: should character vectors be converted
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to factors? Note that this is overridden by \code{as.is} and
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\code{colClasses}, both of which allow finer control.}
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\item{fileEncoding}{character string: if non-empty declares the
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encoding used on a file (not a connection) so the character data can
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be re-encoded. See the \sQuote{Encoding} section of the help for
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\code{\link{file}}, the \sQuote{R Data Import/Export Manual} and
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\sQuote{Note}.
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}
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\item{encoding}{encoding to be assumed for input strings. It is
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used to mark character strings as known to be in
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Latin-1 or UTF-8 (see \code{\link{Encoding}}): it is not used to
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re-encode the input, but allows \R to handle encoded strings in
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their native encoding (if one of those two). See \sQuote{Value}
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and \sQuote{Note}.
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}
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}
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\description{
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This function is only useful for the MMB department of the UMCG. Use this function to \strong{import data by just defining the \code{file} parameter}. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the MO codes with \code{\link[=as.mo]{as.mo()}} and transform all antimicrobial columns with \code{\link[=as.rsi]{as.rsi()}}.
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}
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\details{
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Column names will be transformed, but the original column names are set as a "label" attribute and can be seen in e.g. RStudio Viewer.
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}
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\section{Dormant lifecycle}{
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\if{html}{\figure{lifecycle_dormant.svg}{options: style=margin-bottom:5px} \cr}
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The \link[AMR:lifecycle]{lifecycle} of this function is \strong{dormant}. A dormant function is currently not under active development and has not reached a stable phase. We might return to it in the future. As with experimental functions, you are best off waiting until a function is more mature before you use it in production code.
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}
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\section{Read more on our website!}{
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On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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}
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