load.tables: Load tables from an export and distinguish between...

In SwissClinicalTrialOrganisation/DM_secuTrial_R: Handling of secuTrial related data

Description

If is.rt is TRUE then only the decode.rt.visitlabels and silent parameters are used. If is.rt is FALSE then all other parameters including silent are interpreted. The argument tables can handle four distinguished cases:

• tables=NULL: there is variable called 'table.list' e.g. created from dossier-specific package and all tables should be loaded. Definition: table.list <- list(data.frame.name=list(filename=<filename in the export>, tablename=<internal table name>), ...). The latter is only relevant for queries.

• tables=c(tablename1,tablename2,...): there is a 'table.list', but only some tables should be loaded.

• tables=c(filename1,filename2,...): the user specifies the files that should be loaded.

• tables="all" loads all files in the zip-archive or directory.

The optional pre-processing steps are: identification of date columns and conversion to objects of the class 'Date', conversion of unknown dates to NA and renaming of column names (remove '_' and capital letters, see new.names). The study specific date formats and unknown date strings are specified in load.study.options.

Usage

load.tables(data.dir, tables = "all", convert.dates = FALSE,
  convert.unknown.date.to.na = FALSE, rename.headers = FALSE,
  add.pat.id = TRUE, add.center = FALSE, silent = FALSE,
  is.rt = FALSE, add.id.name = NULL, decode.rt.visitlabels = TRUE)

Arguments

data.dir	location of the export directory (or zip file) containing the csv/xls files
tables	vector of tables to be loaded (if a table.list exists, the corresponding table names can be given)
convert.dates	identify and convert date columns
convert.unknown.date.to.na	convert unknown date strings (e.g 1900-01-01) to NA
rename.headers	rename column names
add.pat.id	adding study ID pat.id to the first column
add.center	adding center information
silent	hide output
is.rt	specifies if export is in rectangular table format
add.id.name	This string needs to be specified if your Add-ID name has been changed in the AdminTool Design setting
decode.rt.visitlabels	specifies whether to decode the visit labels in the rectangular table

Value

(Pre-processed) tables in tables as data frames

References

http://stackoverflow.com/questions/3640925/global-variable-in-r-function

See Also

read.DB.table, load.table.list (used in dossier-specific packages), load.study.options

Examples

## non rectangular table
load.tables(data.dir=system.file("extdata", "s_export_CSV-xls_BMD.zip", package = "secuTrial"))
## rectangular table
load.tables(system.file("extdata", "s_export_rt-CSV-xls_BMD.zip", package = "secuTrial"),
            decode.rt.visitlabels = TRUE)

SwissClinicalTrialOrganisation/DM_secuTrial_R documentation built on May 21, 2019, 10:16 a.m.