Serial interval changes

[lorecatta]

Hi @ginacuomo @IlariaD

As mentioned, I have restructured the repo a bit. Now

• all analysis scripts are /scripts
• all functions are in /R
• the repo now ignores .png, .tiff and .rds (there is a gitignore file)
• there is an R studio project file which users can use to run the analysis
• all the previous README files have been merged into one single file, which probably needs updating.
• analysis results need to be saved in a csv/rds (final output)

Also, I have not finished running the italy_analysis_script.R script as it was taking long. Needs a final checking.

Lorenzo

[lorecatta]

@IlariaD @ginacuomo

In reply to your points @IlariaD :

1. I have removed the default values from the function definitions
2. I also had noted the hard-coded 10000 value. I am not sure whether the 10000 iterations and the hard-coded 10000 value are actually two different things, e.g. the second 10000 seems to be used for sampling from a dgamma so perhaps independent from the first 10000 used as number of iterations. You can take how many sample you want right? But I will let you and Gina sort this out.
3. final.data.xlsx and parameters.R have been removed
4. Not sure about the conflict. The folder "Logistic_regression" does not exist any more on the branch. Is this a conflict on your local machine? You probably have to resolve it then.

Lorenzo