Standardized results for transmissibility analyses

[thibautjombart]

It would help to standardize the results produced by the different methods for estimating transmissibility.

Here are proposed outputs but all ideas welcome.

General principles

All estimates should include:

• mean estimate
• 95% confidence interval (95% CI) or credibility interval (95% CrI)
• (optional, if possible): median, other quantiles, sd
• the time window and data used for the estimation

All graphs should report:

• the central estimate
• the 95% CI or CrI
• the "neutral point": r = 0 or R = 1

Global estimates

Analyses made on the complete dataset, i.e. without stratification.

• (optional, if possible) transmissibility over time: graph
• (optional, if possible) transmissibility over time: table of the last 14 days
• most recent estimate of transmissibility: graph
• (only if not included in table of the last 14 day) most recent estimate of transmissibility: table

Stratified estimates

• (optional, if possible) transmissibility over time: graph
• most recent estimate of transmissibility: graph
• most recent estimate of transmissibility: table

[rozeggo]

Need to make sure the type of interval is stored.
Also for credible intervals would be good to have the option to store posterior samples (although could get large).
For graphs, the capacity to plot 50%, 75% and 95% centiles would be good too.

[Bisaloo]

Current structures

EpiNow2

epinow object with:

• estimates: estimate_infections object with
  • samples: data.table with variable estimates over time repeated over the number of samples
  • summarised: data.table with variable estimates over time summarised
  • fit: stanfit
  • args: args in initial call
  • observations: copy of reported_cases input
• estimated_reported_cases: list of
  • samples: data.table with estimated cases over time repeated over the number of samples
  • summarised: data.table with estimated cases over time summarised
• summary: nicely formatted table with easy to read results
• plots: list of:
  • infections: ggplot
  • reports: ggplot
  • R: ggplot
  • growth_rate: ggplot
  • summary: ggplot
• timing: double

EpiEstim

estimate_R object with:

• R: data_frame with summarised estimates over time
• method: character; copy of arg passed to method
• si_distr: named numeric vector: copy of arg passed to config
• SI.Moments
• dates: copy of dates from incid input
• I: copy of I from incid input
• I_local: copy of I_local from incid input
• I_imported: copy of I_imported from incid input