serofoi

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Modify `get_exposure_matrix` to allow multiple serosurveys

8

We may have data from multiple years. The current approach assumes a single survey year. This is linked to #70

ben18785

Remove simulated data and replace (where used in e.g. testing) with code to simulate

3

Including replacing calls to simulated data with code in vignettes.

ben18785

Pass argument from `fit_seromodel()` to `rstan::sampling()` via `...`

2

At the moment, it seems that several arguments are passed from `fit_seromodel()` to `rstan::sampling()` directly, without any transformation. Additionally, some `rstan::sampling()` are hardcoded, even though users might want to adjust...

Bisaloo

* **Please check if the PR fulfills these requirements** - [x] I have read the CONTRIBUTING guidelines - [ ] A new item has been added to `NEWS.md` - [...

ekamau

ntorresd

Add checks on `simdata` and informative error messages to `get_sim_n_seropositive()`

1

This is to address https://github.com/epiverse-trace/serofoi/pull/83#discussion_r1294343451 in a separate PR.

ntorresd

Combine Stan files

11

There are a number of Stan files with very similar structure. This redundancy will make it harder to extend functionality, test etc. So I propose we combine them into a...

ben18785

Verify that parameters have the correct datatype and format

jpavlich

Users may want to perform a quick optimisation to check their fit to data rather than wait for MCMC sampling. I'd propose something like: ``` fit

ben18785

Model initialisation

2

Currently, the MCMC is initialised using arbitrary FOI values etc. which vary according to the specific model being fitted. To make this more robust, I'd suggest the following approach: 1....

ben18785