epiforecasts / forecast.vocs

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.

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In this PR:

Update the internal model configuration to be non-vectorised so that the case AR(1) process can be easily generalised to an AR(P) process. This funcationality has not yet been exposed to users via the control interface.
Added new functionality to delay case reporting and sequence reporting by some probability mass function. This funcationality has not yet been exposed to users via the control interface.
Made piecewise constant growth rates backwards looking from the last available data rather than forward looking as was previously the case. This means that forecasts are made using a full window of data to estimate the growth rate but also means that the precise dates of steps change as new data is added.
Add a new argument r_forecast which controls if the growth rate is allowed to vary outside the range of the data.
Add optional adjustment for periodic case data based on a random effect. This can be used to account for day of the week or month effects.

Adds model features required for #68 and #69 but does not expose to the user as some interface decisions to be made + some potential initialisation issues.

Codecov Report

Merging #109 (1f656d5) into main (6cb7c98) will decrease coverage by 1.48%. The diff coverage is 59.45%.

@@            Coverage Diff             @@
##             main     #109      +/-   ##
==========================================
- Coverage   94.63%   93.14%   -1.49%     
==========================================
  Files          14       14              
  Lines         894      919      +25     
==========================================
+ Hits          846      856      +10     
- Misses         48       63      +15

Impacted Files	Coverage Δ
R/preprocess.R	`78.26% <0.00%> (-21.74%)`	:arrow_down:
R/utils.R	`75.75% <75.00%> (-0.91%)`	:arrow_down:
R/model.R	`95.58% <77.77%> (-2.83%)`	:arrow_down:
R/forecast.R	`93.50% <100.00%> (+0.26%)`	:arrow_up:
R/postprocess.R	`98.64% <100.00%> (-0.01%)`	:arrow_down:

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epiforecasts / forecast.vocs

Feature : day of week + internal convolutions #109

Codecov Report