Contains models and tools to produce short-term forecasts for both case and sequence notifications assuming circulation of either one or two variants. Tools are also provided to allow the evaluation of the use of sequence data for short-term forecasts in both real-world settings and in user generated scenarios.
This PR contains quality of life changes as well as model improvements.
It contains:
Plotting labels have been generalised
Log2 has been made the default case scaling
Logit has been made the fraction voc scaling
r_step has been added which allows growth rates to be piecewise constant..
The two strain model has been updated to consistently make use of a difference AR(1) process significantly simplifying the previous model code in prep for vector autoregressions
Vector and step convolution functions have been added
To do:
[x] Reimplement the pooled model
[ ] Add renewal equation based autoregressive case weighting
[ ] Update model equations
[x] Expand tests to cover piecewise constant models
This PR contains quality of life changes as well as model improvements.
It contains:
r_stephas been added which allows growth rates to be piecewise constant..To do: