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update document following discussion
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sbfnk committed Oct 29, 2024
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Expand Up @@ -14,24 +14,24 @@ This matches the current default behaviour, introduced in version 1.5.0.

### Accumulation

If instead modelled values on these days should be accumulated onto the next reporting date, the passed `data.frame` must have an additional numeric column, `accumulate`.
If `accumulate` is greater than zero and the value in the data is `NA` then the modelled value of the observed latent variable on that day is not used in the likelihood and instead added to any existing accumulation and stored for later observation.
If the value in the data is not `NA` then the modelled value is multiplied with the value in `accumulate` and added to any stored accumulated variables.
This is then used in the likelihood.
If instead modelled values on these days should be accumulated onto the next reporting date, the passed `data.frame` must have an additional logical column, `accumulate`.
If `accumulate` is TRUE then the modelled value of the observed latent variable on that day is not used in the likelihood and instead added to any existing accumulation and stored for later observation.
If `accumulate` is FALSE modelled value is added to any stored accumulated variables before being used in the likelihood on that day.
Subsequently the stored accumulated variable is rest to zero.

### Example

| date | confirm | accumulate |
|------------|---------|------------|
| 2024-10-23 | NA | 0.5 |
| 2024-10-24 | 10 | 1 |
| 2024-10-26 | NA | 1 |
| 2024-10-27 | NA | 0 |
| 2024-10-28 | 17 | 1 |
| 2024-10-23 | NA | TRUE |
| 2024-10-24 | 10 | FALSE |
| 2024-10-26 | NA | TRUE |
| 2024-10-27 | NA | TRUE |
| 2024-10-28 | 17 | FALSE |

The likelihood is evaluated on two days, 24 October and 28 October.
On 24 October the data (10) is compared to 0.5 * (modelled value on 23 October) + (modelled value on 24 October).
On 28 October the data (17) is compared to (modelled value on 26 October) + (modelled value on 28 October).
On 24 October the data (10) is compared to (modelled value on 23 October) + (modelled value on 24 October).
On 28 October the data (17) is compared to (modelled value on 26 October) + (modelled value on 27 October) + (modelled value on 28 October).

## Helper functions

Expand All @@ -47,24 +47,24 @@ can be converted with `fill_missing_dates(missing = "accumulate", initial = 7)`

| date | confirm | accumulate |
|------------|---------|------------|
| 2024-10-18 | NA | 1 |
| 2024-10-19 | NA | 1 |
| 2024-10-20 | NA | 1 |
| 2024-10-21 | NA | 1 |
| 2024-10-22 | NA | 1 |
| 2024-10-23 | NA | 1 |
| 2024-10-24 | 10 | 1 |
| 2024-10-25 | NA | 1 |
| 2024-10-26 | NA | 1 |
| 2024-10-27 | NA | 1 |
| 2024-10-28 | NA | 1 |
| 2024-10-29 | NA | 1 |
| 2024-10-30 | NA | 1 |
| 2024-10-31 | 17 | 1 |
| 2024-11-01 | NA | 1 |
| 2024-11-02 | NA | 1 |
| 2024-11-03 | NA | 1 |
| 2024-11-04 | NA | 1 |
| 2024-11-05 | NA | 1 |
| 2024-11-06 | NA | 1 |
| 2024-11-07 | 11 | 1 |
| 2024-10-18 | NA | TRUE |
| 2024-10-19 | NA | TRUE |
| 2024-10-20 | NA | TRUE |
| 2024-10-21 | NA | TRUE |
| 2024-10-22 | NA | TRUE |
| 2024-10-23 | NA | TRUE |
| 2024-10-24 | 10 | FALSE |
| 2024-10-25 | NA | TRUE |
| 2024-10-26 | NA | TRUE |
| 2024-10-27 | NA | TRUE |
| 2024-10-28 | NA | TRUE |
| 2024-10-29 | NA | TRUE |
| 2024-10-30 | NA | TRUE |
| 2024-10-31 | 17 | FALSE |
| 2024-11-01 | NA | TRUE |
| 2024-11-02 | NA | TRUE |
| 2024-11-03 | NA | TRUE |
| 2024-11-04 | NA | TRUE |
| 2024-11-05 | NA | TRUE |
| 2024-11-06 | NA | TRUE |
| 2024-11-07 | 11 | TRUE |

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