labkey.selectRows {Rlabkey}R Documentation

Retrieve data from a labkey database

Description

Import full datasets or selected rows into R. The data can be sorted and filtered prior to import.

Usage

labkey.selectRows(baseUrl, folderPath, schemaName, queryName, 
viewName = NULL, colSelect = NULL, maxRows = NULL, 
rowOffset = NULL, colSort = NULL, colFilter = NULL, showHidden = FALSE)

Arguments

baseUrl a string specifying the baseUrlfor the labkey server
folderPath a string specifying the folderPath
schemaName a string specifying the schemaName for the query
queryName a string specifying the queryName
viewName (optional) a string specifying the viewName
colSelect (optional) a vector of comma separated strings specifying which columns of a dataset or view to import
maxRows (optional) an integer specifying how many rows of data to return. If no value is specified, all rows are returned.
colSort (optional) a string including the name of the column to sort preceeded by a “+” or “-” to indicate sort direction
rowOffset (optional) an integer specifying which row of data should be the first row in the retrieval. If no value is specified, the retrieval starts with the first row.
colFilter (optional) a vector or array object created by the makeFilter function which contains the column name, operator and value of the filter(s) to be applied to the retrieved data.
showHidden (optional) a logical value indicating whether or not to return data columns that would normally be hidden from user view. If no value is specified, the hidden columns are not returned. In versions 0.0.5 and earlier, this argument was called stripAllHidden. The stripAllHidden argument performed the same function as showHidden but with different logic. The change was made for clarity.

Details

A full dataset or any portion of a dataset can be imported into an R data frame using the
labkey.selectRows function. Function arguments are the components of the url that identify the location of the data and what actions should be taken on the data prior to import (ie, sorting, selecting particular columns or maximum number of rows, etc.).

NOTE: Each variable in a dataset has both a column label and a column name. The column label is visible at the top of each column on the web page and is longer and more descriptive. The column name is shorter and is used “behind the scenes” for database manipulation. It is the column name that must be used in the Rlabkey functions when a column name is expected. To identify a particular column name in a dataset on a web site, use the “export to R script” option available as a drop down option under the “views” tab for each dataset.

Value

The requested data are returned in a data frame with column names as they appear on the website.

Author(s)

Valerie Obenchain

References

http://www.omegahat.org/RCurl/,
http://dssm.unipa.it/CRAN/web/packages/rjson/rjson.pdf,
https://www.labkey.org/project/home/begin.view

See Also

labkey.executeSql, makeFilter, labkey.insertRows, labkey.updateRows,
labkey.deleteRows

Examples

## These example datasets are located at 
## https://www.labkey.org/project/home/Study/demo/begin.view?

## Retrieve full HIV Test Results dataset
fulldata <- labkey.selectRows(  
baseUrl="https://www.labkey.org", 
folderPath="/home/Study/demo", 
schemaName="study", 
queryName="HIV Test Results")

## Specifying filters, max rows and selecting columns
myfilters<- makeFilter(c("HIVLoadQuant","GREATER_THAN",500), 
c("HIVRapidTest","EQUAL","Positive"))
smalldata <- labkey.selectRows( 
baseUrl="https://www.labkey.org", 
folderPath="/home/Study/demo", 
schemaName="study",     
queryName="HIV Test Results", 
colSelect=c("ParticipantId","HIVDate","HIVLoadQuant","HIVRapidTest"), 
maxRows=20,
colFilter=myfilters)



[Package Rlabkey version 0.0.7 Index]