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replace vis_epicontacts with plot #250

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Oct 24, 2025
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replace vis_epicontacts with plot #250

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6 changes: 3 additions & 3 deletions episodes/superspreading-estimate.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -108,14 +108,14 @@ With the argument `directed = TRUE` we configure a directed graph. These directi

```{r,eval=FALSE}
# visualise contact network
epicontacts::vis_epicontacts(epi_contacts)
plot(epi_contacts)
```

```{r,echo=FALSE}
withr::with_envvar(c(OPENSSL_CONF = file.path("/dev", "null")), {
# visualise contact network
network <-
vis_epicontacts(epi_contacts) %>%
plot(epi_contacts) %>%
visNetwork::visPhysics(solver = "barnesHut")
fname <- "network.html"
visNetwork::visSave(network, fname)
Expand Down Expand Up @@ -334,7 +334,7 @@ Calculate the distribution of secondary cases for Ebola using the `ebola_sim_cle

:::::::::::::::::: hint

⚠️ **Optional step:** This dataset has `r nrow(ebola_sim_clean$linelist)` cases. Running `epicontacts::vis_epicontacts()` may take several minutes and use significant memory for large outbreaks such as the Ebola linelist. If you're on an older or slower computer, you can skip this step.
⚠️ **Optional step:** This dataset has `r nrow(ebola_sim_clean$linelist)` cases. Running `plot(<epicontacts>)` may take several minutes and use significant memory for large outbreaks such as the Ebola linelist. If you're on an older or slower computer, you can skip this step.

::::::::::::::::::

Expand Down
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