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update data vignette
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@hillalex
hillalex committed Oct 24, 2024
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34 changes: 18 additions & 16 deletions vignettes/data.Rmd
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Expand Up @@ -50,11 +50,11 @@ that users who are already familiar with `cmdstanr` are free to do what they wan
**Important!**
**If you provide data on a natural scale, it will be converted to a base2 log scale before inference is performed. This means that if working
directly with the fitted `CmdStanMCMC` all values will be on this scale. The package provides a helper function for converting
back to the original scale: [convert_log_scale_inverse](../reference/convert_log_scale_inverse.html).**
back to the original scale: [convert_log2_scale_inverse](../reference/convert_log2_scale_inverse.html).**

Three further functions provide model outputs that we think are particularly useful in [data.table](https://cran.r-project.org/web/packages/data.table/) format.
[biokinetics](../reference/biokinetics.html) contains documentation on each of these functions so please read that first; this Vignette provides
guidance on the correct interpretation of each column in the returned tables. (In these functions data is returned on the original scale).
[biokinetics](../reference/biokinetics.html) contains documentation on each of these functions so please read that first; this vignette provides
guidance on the correct interpretation of each column in the returned tables (in these functions data is returned on the original scale).

## simulate_population_trajectories

Expand All @@ -72,7 +72,6 @@ Returned columns are
| lo | numeric | Titre value at the 0.025 quantile |
| hi | numeric | Titre value at the 0.975 quantile |
| titre_type | character | Name of the titre or biomarker |
| censored | -1, 0 or 1 | Whether this observation should be treated as censored: -1 for lower, 1 for upper, 0 for none |

There will also be a column for each covariate in the regression model.

Expand All @@ -83,24 +82,27 @@ Returned columns are
| name | type | description |
|---------------------|---------|------------------------------------|
| time_since_last_exp | integer | Number of days since last exposure |
| t0_pop | numeric | |
| tp_pop | numeric | |
| ts_pop | numeric | |
| m1_pop | numeric | |
| m2_pop | numeric | |
| m3_pop | numeric | |
| beta_t0 | numeric | |
| beta_tp | numeric | |
| beta_ts | numeric | |
| beta_m1 | numeric | |
| beta_m2 | numeric | |
| beta_t3 | numeric | |
| t0_pop | numeric | Titre value at time 0 |
| tp_pop | numeric | Time at peak titre |
| ts_pop | numeric | Time at start of waning |
| m1_pop | numeric | Boosting rate |
| m2_pop | numeric | Plateau rate |
| m3_pop | numeric | Waning rate |
| beta_t0 | numeric | Coefficient to adjust t0 by |
| beta_tp | numeric | Coefficient to adjust tp by |
| beta_ts | numeric | Coefficient to adjust ts by |
| beta_m1 | numeric | Coefficient to adjust m1 by |
| beta_m2 | numeric | Coefficient to adjust m2 by |
| beta_m3 | numeric | Coefficient to adjust m3 by |
| mu | numeric | Titre value |
| .draw | integer | Draw number |
| titre_type | numeric | Name of the titre or biomarker |

There will also be column for each covariate in the hierarchical model.

See the [model vignette](../article/model.html) for more detail about the model
parameters.

## simulate_individual_trajectories

See the documentation for this function [here](../reference/biokinetics.html#method-simulate-individual-trajectories).
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