'Opal' Data Repository Client and 'DataSHIELD' Utils

Data integration Web application for biobanks by 'OBiBa'. 'Opal' is the core database application for biobanks. Participant data, once collected from any data source, must be integrated and stored in a central data repository under a uniform model. 'Opal' is such a central repository. It can import, process, validate, query, analyze, report, and export data. 'Opal' is typically used in a research center to analyze the data acquired at assessment centres. Its ultimate purpose is to achieve seamless data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal' web services and to perform operations on the R server side. 'DataSHIELD' administration tools are also provided.


Build Status

Opal R Client

Usage:

library(opalr)
o <- opal.login('username', 'passwd', 'http://localhost:8080')
# Assign one variable to a R symbol
opal.assign(o, 'VAR1', 'datasource.table:VAR1')
opal.execute(o, 'summary(VAR1)')
# Assign some variables as a data.frame to a R symbol
opal.assign(o, 'TABLE', 'datasource.table', variables=list('VAR1','VAR2'))
opal.execute(o, 'summary(TABLE$VAR1)')
opal.execute(o, 'summary(TABLE$VAR2)')
opal.logout(o)

DataSHIELD Client

See DSOpal.

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Reference manual

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install.packages("opalr")

1.2.0 by Yannick Marcon, 4 months ago


https://www.obiba.org/ https://www.obiba.org/pages/products/opal/ https://doi.org/10.1093/ije/dyx180 http://www.datashield.ac.uk/


Report a bug at https://github.com/obiba/opalr


Browse source code at https://github.com/cran/opalr


Authors: Yannick Marcon [aut, cre] , Amadou Gaye [ctb] , OBiBa group [cph]


Documentation:   PDF Manual  


GPL-3 license


Imports xml2, jsonlite, mime

Depends on httr

Suggests e1071, knitr, knitrBootstrap, rmarkdown


See at CRAN