Saving analyses to file

The following instructions work in the DataSHIELD test environment only.

Write a table to .csv

use the write.csv or write.table R functions to write tables to file


#output to the R console
> ds.table2D(x='D$DIS_DIAB', y='D$GENDER')
#prints to the current working directory into a file called test_table.csv
> write.csv(x=ds.table2D(x='D$DIS_DIAB', y='D$GENDER'), file = "test_table.csv")

Write an image to .png, .pdf, .ps

In R it is possible to print sequential images on sequential pages.

To do this an image writing function such as png(), pdf() or postscript() needs to be opened.
Each file to be written must be put on seperate lines
The print device needs closing.
All images are written to the current working directory in R.


#png example
png(filename = "image_name.png", width = 900, height = 700, units = "px", pointsize = 12,  bg = "white", type = "cairo")
ds.histogram(x='D$LAB_HDL')
dev.off()

The pdf example prints the output of two seperate ds.histogram commands onto seperate pages. Each line is output to a seperate page in the pdf.


# a pdf example
pdf (file="image_name.pdf")
ds.histogram(x='D$LAB_HDL')
ds.histogram(x='D$LAB_HDL', type='split')
dev.off()


# a postscript example
postscript(file= "image_name.ps", paper="special", width = 9, height = 7, onefile = TRUE, horizontal=FALSE)
ds.histogram(x='D$LAB_HDL')
ds.histogram(x='D$LAB_HDL', type='split')
dev.off()

Write the R console screen to file

In some cases the non-disclosive data used to create an image may be required, this can be printed to file using the capture.output R function:


# print to file the non-disclosive data that comprises a histogram
out<-capture.output(ds.histogram(x='D$LAB_HDL'))
cat(out,file="name.txt",sep="\n",append=TRUE)

All arguments to customise the above functions can be found in their respective function manual pages.