Read data from 4D database

This function is only useful for the MMB department of the UMCG. Use this function to import data by just defining the file parameter. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the MO codes with as.mo() and transform all antimicrobial columns with as.rsi().

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

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 absolute path, the file name is relative to the current working directory, getwd(). Tilde-expansion is performed where supported. This can be a compressed file (see file). Alternatively, file can be a readable text-mode connection (which will be opened for reading if necessary, and if so closed (and hence destroyed) at the end of the function call). (If stdin() is used, the prompts for lines may be somewhat confusing. Terminate input with a blank line or an EOF signal, Ctrl-D on Unix and Ctrl-Z on Windows. Any pushback on stdin() will be cleared before return.) file can also be a complete URL. (For the supported URL schemes, see the ‘URLs’ section of the help for url.)
info	a logical to indicate whether info about the import should be printed, defaults to TRUE in interactive sessions
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: header is set to TRUE if and only if the first row contains one fewer field than the number of columns.
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 row.names is missing, the rows are numbered. Using row.names = NULL forces row numbering. Missing or NULL row.names generate row names that are considered to be ‘automatic’ (and not preserved by as.matrix).
sep	the field separator character. Values on each line of the file are separated by this character. If sep = "" (the default for read.table) the separator is ‘white space’, that is one or more spaces, tabs, newlines or carriage returns.
quote	the set of quoting characters. To disable quoting altogether, use quote = "". See scan for the behaviour on quotes embedded in quotes. Quoting is only considered for columns read as character, which is all of them unless colClasses is specified.
dec	the character used in the file for decimal points.
na.strings	a character vector of strings which are to be interpreted as NA values. Blank fields are also considered to be missing values in logical, integer, numeric and complex fields. Note that the test happens after white space is stripped from the input, so na.strings values may need their own white space stripped in advance.
skip	integer: the number of lines of the data file to skip before beginning to read data.
check.names	logical. If 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 make.names) so that they are, and also to ensure that there are no duplicates.
strip.white	logical. Used only when sep has been specified, and allows the stripping of leading and trailing white space from unquoted character fields (numeric fields are always stripped). See scan for further details (including the exact meaning of ‘white space’), remembering that the columns may include the row names.
fill	logical. If TRUE then in case the rows have unequal length, blank fields are implicitly added. See ‘Details’.
blank.lines.skip	logical: if TRUE blank lines in the input are ignored.
stringsAsFactors	logical: should character vectors be converted to factors? Note that this is overridden by as.is and colClasses, both of which allow finer control.
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 ‘Encoding’ section of the help for file, the ‘R Data Import/Export Manual’ and ‘Note’.
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 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 ‘Value’ and ‘Note’.

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.

Dormant lifecycle

The lifecycle of this function is 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.

Read more on our website!

On our website https://msberends.gitlab.io/AMR you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.