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Merged
avallecam merged 2 commits into from
Mar 20, 2026
Merged

Update 24 packages #259

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666d15f
[actions] update 24 packages
Bisaloo Mar 3, 2026
9d3d71c
replace deprecated epinow()$plots with plot() for EpiNow2 1.8.0
avallecam Mar 20, 2026
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4 changes: 2 additions & 2 deletions episodes/quantify-transmissibility.Rmd
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Expand Up @@ -98,7 +98,7 @@

Refer to the prior probability distribution and the [posterior probability](https://en.wikipedia.org/wiki/Posterior_probability) distribution.

In the ["`Expected change in reports`" callout](#expected-change-in-daily-cases), by "the posterior probability that $R_t < 1$", we refer specifically to the [area under the posterior probability distribution curve](https://www.nature.com/articles/nmeth.3368/figures/1).

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 [missing anchor]: [" Expected change in reports " callout](#expected-change-in-daily-cases)

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We can extract and visualise estimates of the effective reproduction number through time:

```{r}
estimates$plots$R
plot(estimates, type = "R")
```

The uncertainty in the estimates increases through time. This is because estimates are informed by data in the past - within the delay periods. This difference in uncertainty is categorised into **Estimate** (green) utilises all data and **Estimate based on partial data** (orange) estimates that are based on less data (because infections that happened at the time are more likely to not have been observed yet) and therefore have increasingly wider intervals towards the date of the last data point. Finally, the **Forecast** (purple) is a projection ahead of time.

We can also visualise the growth rate estimate through time:
```{r}
estimates$plots$growth_rate
plot(estimates, type = "growth_rate")
```

To extract a summary of the key transmission metrics at the *latest date* in the data:
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estimates_regional$summary$plots$R
```

![](fig/quantify-transmissibility-regional.png)

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 [image missing alt-text]: fig/quantify-transmissibility-regional.png

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4 changes: 2 additions & 2 deletions locale/es/episodes/quantify-transmissibility.Rmd
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Expand Up @@ -466,15 +466,15 @@ EpiNow2::epinow(
Podemos extraer y visualizar estimaciones del número de reproducción efectivo a lo largo del tiempo:

```{r}
estimates$plots$R
plot(estimates, type = "R")
```

La incertidumbre de las estimaciones aumenta con el tiempo. Esto se debe a que las estimaciones se basan en datos del pasado, dentro de los periodos de retraso. Esta diferencia de incertidumbre se clasifica en **Estimación** (verde) utiliza todos los datos y **Estimación basada en datos parciales** (naranja) estimaciones que se basan en menos datos (porque es más probable que las infecciones que se produjeron en su momento no se hayan observado todavía), por este motivo, tienen intervalos cada vez más amplios hacia la fecha del último punto de datos. Por último, el **Pronóstico** (morado) es una proyección a futuro.

También podemos visualizar la estimación de la tasa de crecimiento a lo largo del tiempo:

```{r}
estimates$plots$growth_rate
plot(estimates, type = "growth_rate")
```

Para extraer un resumen de las métricas clave de transmisión en la *última fecha* de los datos:
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