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read.4D improvements

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dr. M.S. (Matthijs) Berends
2018-11-15 12:42:35 +01:00
parent 5cb8f3cf72
commit fab64e6728
10 changed files with 89 additions and 51 deletions
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36
man/read_4D.Rd → man/read.4D.Rd
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@ -1,13 +1,13 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/read_4d.R
\name{read_4D}
\alias{read_4D}
% 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,
read.4D(file, info = interactive(), header = TRUE, row.names = NULL,
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{
@ -32,12 +32,29 @@ read_4D(file, header = TRUE, sep = "\\t", quote = "\\"'",
\code{\link{url}}.)
}
\item{info}{a logical to indicate whether info about the import should be printed, defaults to \code{TRUE} in interactive sessions}
\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{row.names}{a vector of row names. This can be a vector giving
the actual row names, or a single number giving the column of the
table which contains the row names, or character string giving the
name of the table column containing the row names.
If there is a header and the first row contains one fewer field than
the number of columns, the first column in the input is used for the
row names. Otherwise if \code{row.names} is missing, the rows are
numbered.
Using \code{row.names = NULL} forces row numbering. Missing or
\code{NULL} \code{row.names} generate row names that are considered
to be \sQuote{automatic} (and not preserved by \code{\link{as.matrix}}).
}
\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},
@ -100,5 +117,8 @@ read_4D(file, header = TRUE, sep = "\\t", quote = "\\"'",
}
}
\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}}.
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 \code{mo} with \code{\link{as.mo}} and transform all antimicrobial columns with \code{\link{as.rsi}}.
}
\details{
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.
}