README.md

Compile prediction results

This analysis compiles the output from the second analysis.

Analysis steps

There are only two steps here:

1. Compile the data into a single data.table and write to file
2. Run statistical analyses and create plots

Step (1) loops through the output from the second analysis. Because this is a serial loop, it can take a while to complete. To avoid timeouts, step (1) can be run in the background. screen accomplishes this neatly. So does nohup:

nohup Rscript compile_all_results.R \
    --results-directory ${output_data_dir} \
    --output-directory ${resultsdir} \
    --output-filename ${results_file} \
    > nohup.compile.results.out 2> nohup.compile.results.err &

Step (2) saves plots directly to file, but outputs results from statistical analysis to the console. As in the example above, the results can be redirected and saved to file:

Rscript plot_results.R \
     --results-file ${results_filepath} \
     --output-directory ${plotdir} \
     --plot-filetype ${plot_filetype} \
    > plot.results.out 2> plot.results.err

Running

From a Bourne shell, call the script directly:

./compile_results.sh

References

• Dinno A. (2017) dunn.test: Dunn's Test of Multiple Comparisons Using Rank Sums. R package version 1.3.5. (link)
• Wickham H. (2016) ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York.