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athowes committed May 20, 2024
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13 changes: 6 additions & 7 deletions vignettes/epidist.Rmd
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Expand Up @@ -19,7 +19,7 @@ vignette: >
```{r setup, include=FALSE}
# exclude compile warnings from cmdstanr
knitr::opts_chunk$set(
fig.path = "figures/getting-started-nowcasting-",
fig.path = "figures/epidist-",
cache = TRUE,
collapse = TRUE,
comment = "#>",
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# Fit the model {#fit}

If we had access to `obs`, then it would be simple to estimate the delay distribution
However, with only access to `obs_cens_trunc_samp`, we must use a more sophisticated statistical model to make sure that our estimates are not severely biased!
If we had access to `obs`, then it would be simple to estimate the delay distribution.
However, with only access to `obs_cens_trunc_samp`, we must use a statistical model to avoid severely biased estimates!

The primary modelling function in `epidist` is `latent_truncation_censoring_adjusted_delay`.
In a future vignette, we will explain in more detail the structure of the model.

The parameters of the model are inferred using Bayesian inference.
The main model function in `epidist` is `latent_truncation_censoring_adjusted_delay`.
<!-- In a future vignette, we will explain in more detail the structure of the model. -->
The parameters of this model are inferred using Bayesian inference.
In particular, we use the the No-U-Turn Sampler (NUTS) Markov chain Monte Carlo (MCMC) algorithm via the `brms` R package.

```{r}
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