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Give up on table crosslink
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athowes committed Nov 21, 2024
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18 changes: 9 additions & 9 deletions vignettes/epidist.Rmd
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Expand Up @@ -288,13 +288,8 @@ In particular, we use the the No-U-Turn Sampler (NUTS) Markov chain Monte Carlo
fit <- epidist(data = data, chains = 2, cores = 2, refresh = 0)
```

The `fit` object is a `brmsfit` object containing MCMC samples from each of the parameters (Table \@ref(tab:pars)) in the model.
Users familiar with Stan and `brms`, can work with `fit` directly.
Any tool that supports `brms` fitted model objects will be compatible with `fit`.

**Note that here we use the default `rstan` backend but we generally recommend using the `cmdstanr` backend for faster sampling and additional features. This can be set using `backend = "cmdstanr"` after following the installing `cmdstan` instructions in the README.**

(ref:pars) All of the parameters that are included in the model. Many of these parameters (e.g. `swindow` and `pwindow`) are the so called latent variables in the model, and have lengths corresponding to the `sample_size`. We extracted the model parameters using `brms::variables()` and removed the indices.
The `fit` object is a `brmsfit` object containing MCMC samples from each of the parameters in the model, shown in the table below.
Many of these parameters (e.g. `swindow` and `pwindow`) are the so called latent variables, and have lengths corresponding to the `sample_size`.

```{r pars}
pars <- fit |>
Expand All @@ -304,10 +299,15 @@ pars <- fit |>
data.frame(
Parameter = unique(pars), Length = table(pars)
) |>
gt() |>
tab_caption("(ref:pars)")
gt()
```

Users familiar with Stan and `brms`, can work with `fit` directly.
Any tool that supports `brms` fitted model objects will be compatible with `fit`.

**Note that here we use the default `rstan` backend but we generally recommend using the `cmdstanr` backend for faster sampling and additional features.**
**This can be set using `backend = "cmdstanr"` after following the installing CmdStan instructions in the README.**

The `epidist` package also provides functions to make common post-processing tasks easy.
For example, individual predictions of the lognormal delay parameters can be extracted using:

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