read_4D

man/read_4D.Rd

@@ -0,0 +1,104 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_4d.R
+\name{read_4D}
+\alias{read_4D}
+\title{Read data from 4D database}
+\usage{
+read_4D(file, header = TRUE, sep = "\\t", quote = "\\"'",
+  dec = ",", na.strings = c("NA", "", "."), skip = 2,
+  check.names = TRUE, strip.white = TRUE, fill = TRUE,
+  blank.lines.skip = TRUE, stringsAsFactors = FALSE,
+  fileEncoding = "UTF-8", encoding = "UTF-8")
+}
+\arguments{
+\item{file}{the name of the file which the data are to be read from.
+    Each row of the table appears as one line of the file.  If it does
+    not contain an \emph{absolute} path, the file name is
+    \emph{relative} to the current working directory,
+    \code{\link{getwd}()}. Tilde-expansion is performed where supported.
+    This can be a compressed file (see \code{\link{file}}).
+
+    Alternatively, \code{file} can be a readable text-mode
+    \link{connection} (which will be opened for reading if
+    necessary, and if so \code{\link{close}}d (and hence destroyed) at
+    the end of the function call).  (If \code{\link{stdin}()} is used,
+    the prompts for lines may be somewhat confusing.  Terminate input
+    with a blank line or an EOF signal, \code{Ctrl-D} on Unix and
+    \code{Ctrl-Z} on Windows.  Any pushback on \code{stdin()} will be
+    cleared before return.)
+
+    \code{file} can also be a complete URL.  (For the supported URL
+    schemes, see the \sQuote{URLs} section of the help for
+    \code{\link{url}}.)
+  }
+
+\item{header}{a logical value indicating whether the file contains the
+    names of the variables as its first line.  If missing, the value is
+    determined from the file format: \code{header} is set to \code{TRUE}
+    if and only if the first row contains one fewer field than the
+    number of columns.}
+
+\item{sep}{the field separator character.  Values on each line of the
+    file are separated by this character.  If \code{sep = ""} (the
+    default for \code{read.table}) the separator is \sQuote{white space},
+    that is one or more spaces, tabs, newlines or carriage returns.}
+
+\item{quote}{the set of quoting characters. To disable quoting
+    altogether, use \code{quote = ""}.  See \code{\link{scan}} for the
+    behaviour on quotes embedded in quotes.  Quoting is only considered
+    for columns read as character, which is all of them unless
+    \code{colClasses} is specified.}
+
+\item{dec}{the character used in the file for decimal points.}
+
+\item{na.strings}{a character vector of strings which are to be
+    interpreted as \code{\link{NA}} values.  Blank fields are also
+    considered to be missing values in logical, integer, numeric and
+    complex fields.  Note that the test happens \emph{after} 
+    white space is stripped from the input, so \code{na.strings} 
+    values may need their own white space stripped in advance.}
+
+\item{skip}{integer: the number of lines of the data file to skip before
+    beginning to read data.}
+
+\item{check.names}{logical.  If \code{TRUE} then the names of the
+    variables in the data frame are checked to ensure that they are
+    syntactically valid variable names.  If necessary they are adjusted
+    (by \code{\link{make.names}}) so that they are, and also to ensure
+    that there are no duplicates.}
+
+\item{strip.white}{logical. Used only when \code{sep} has
+    been specified, and allows the stripping of leading and trailing
+    white space from unquoted \code{character} fields (\code{numeric} fields
+    are always stripped).  See \code{\link{scan}} for further details
+    (including the exact meaning of \sQuote{white space}),
+    remembering that the columns may include the row names.}
+
+\item{fill}{logical. If \code{TRUE} then in case the rows have unequal
+    length, blank fields are implicitly added.  See \sQuote{Details}.}
+
+\item{blank.lines.skip}{logical: if \code{TRUE} blank lines in the
+    input are ignored.}
+
+\item{stringsAsFactors}{logical: should character vectors be converted
+    to factors?  Note that this is overridden by \code{as.is} and
+    \code{colClasses}, both of which allow finer control.}
+
+\item{fileEncoding}{character string: if non-empty declares the
+    encoding used on a file (not a connection) so the character data can
+    be re-encoded.  See the \sQuote{Encoding} section of the help for
+    \code{\link{file}}, the \sQuote{R Data Import/Export Manual} and
+    \sQuote{Note}.
+  }
+
+\item{encoding}{encoding to be assumed for input strings.  It is
+    used to mark character strings as known to be in
+    Latin-1 or UTF-8 (see \code{\link{Encoding}}): it is not used to
+    re-encode the input, but allows \R to handle encoded strings in
+    their native encoding (if one of those two).  See \sQuote{Value}
+    and \sQuote{Note}.
+  }
+}
+\description{
+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 data set to English, transform the \code{mo} with \code{\link{as.mo}} and transform all antimicrobial columns with \code{\link{as.rsi}}.
+}