Open thibautjombart opened 1 year ago
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.
Current structures
epinow
object with:
estimates
: estimate_infections
object with
samples
: data.table
with variable estimates over time repeated over the number of samplessummarised
: data.table
with variable estimates over time summarisedfit
: stanfit
args
: args in initial callobservations
: copy of reported_cases
inputestimated_reported_cases
: list of
samples
: data.table
with estimated cases over time repeated over the number of samplessummarised
: data.table
with estimated cases over time summarisedsummary
: nicely formatted table with easy to read resultsplots
: list
of:
infections
: ggplot
reports
: ggplot
R
: ggplot
growth_rate
: ggplot
summary
: ggplot
timing
: double
estimate_R
object with:
R
: data_frame
with summarised estimates over timemethod
: 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
inputI
: copy of I
from incid
inputI_local
: copy of I_local
from incid
inputI_imported
: copy of I_imported
from incid
input
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:
All graphs should report:
Global estimates
Analyses made on the complete dataset, i.e. without stratification.
Stratified estimates