Opal Reporting with R

In opalr: 'Opal' Data Repository Client and 'DataSHIELD' Utils

This is an example of how to use knitr for producing reports on data stored in Opal.

Procedure

The requirement on client side is to have opal package installed:

install.packages('opalr', repos=c(getOption('repos'), 'https://cloud.r-project.org'), dependencies=TRUE)

The requirements on server side is:

• to have permissions to access to Opal data
• to have permission to send R commands to Opal server
• to have a running R server

The procedure is then the following:

• connect to Opal server
• assign data from Opal to the associated R server
• send to Opal R commands to be executed in R server
• process in R client the data received from these commands

Example

Load the required libraries on client side and login in Opal (credentials and output are hidden)...

library(opalr)
o <- opal.login()

Assign some variables into a data.frame with associated D symbol in R on Opal server side:

opal.assign(o,'D','FNAC.FNAC',variables=c('SVUOSI','SUKUP','PITUUS','PAINO'))

Preview the assigned data.frame:

opal.execute(o,'head(D)')

Summary of the assigned data.frame:

opal.execute(o,'summary(D)')

Histogram figure of the PITUUS variable:

plot(opal.execute(o,'hist(D$PITUUS)'))

Loading ggplot2 library in R on Opal server side... This will fail if ggplot2 is not installed in R server environment.

opal.execute(o, 'library(ggplot2)')

Plot PITUUS vs. PAINO with "lm" smoothing:

opal.execute(o,'qplot(PITUUS,PAINO, data=D) + geom_smooth(method="lm")')

Cleaning the resources on Opal server side...

opal.logout(o)

opalr documentation built on Sept. 18, 2024, 9:11 a.m.