Improving flowcharts docs/

[melodiemonod]

Hi! Looking at the flowcharts in docs/

1/ I'm wondering if we should specify the folder where the data and script are

2/ Could you change the color of the text because it is impossible to read the boxes in grey and yellow ...

3/ Maybe we want to find more informative name than preprocessing stage 1 and 2? First Flowchart: "Estimate HIV status and prevalence" and you just show the first row of your flowchanrt

Second flowchart: "Estimate ART use" And you just show the second and third row of your flow chart

Third flowchart: "Estimate Viral suppression" And you just show the fourth and fifth row of your flow chart

Fourth flowchart: "Estimate treatment cascade" The flowchart you have as stage 2 now

4/ We might want to rethink the sensitivity analysis one. It's a lot of info because you're summarising the two first flowcharts into one. Maybe we could have multiple tabs one "main analysis" and then others for the sensitivity. and the flow charts would change dependig on the analysis chosen? Should be the same code just the name of the file would change depending on the analysis. What do you think?

[ShozenD]

• [x] Write a section in README describing where the data and scripts are
• [x] Change the colour of the text to make file names more readable
• [x] A more informative name for the preprocessing stages
• [x] Redo flowchart for sensitivity analysis

[ShozenD]

Hi @melodiemonod, I added more documentation to docs/README for the RCCS surveillance analysis.

I also separated and changed the colours of the flow charts. I hope they are easier to read now. Each section was given the more informative names you suggested.

I decided not to include a flowchart for the sensitivity analysis because Ollie said it is unimportant for people other than ourselves.