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episodes/superspreading-estimate.Rmd

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@@ -158,7 +158,9 @@ epi_contacts %>%
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But this output only contains the number of secondary cases for reported infectors in the contact data, not for **all** the individuals in the whole `<epicontacts>` object.
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Instead, from `{epicontacts}` we can use the function `epicontacts::get_degree()`. The argument `type = "out"` get the **out-degree** of each **node** in the contact network from the `<epicontacts>` class object. In a directed network, the out-degree is the number of outgoing edges (infectees) emanating from a node (infector) ([Nykamp DQ, accessed: 2025](https://mathinsight.org/definition/node_degree)). Also, the argument `only_linelist = TRUE` include individuals in contacts and linelist data frames.
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Instead, from `{epicontacts}` we can use the function `epicontacts::get_degree()`. The argument `type = "out"` gets the **out-degree** of each **node** in the contact network from the `<epicontacts>` class object. In a directed network, the out-degree is the number of outgoing edges (infectees) emanating from a node (infector) ([Nykamp DQ, accessed: 2025](https://mathinsight.org/definition/node_degree)).
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Also, the argument `only_linelist = TRUE` will only include individuals in the linelist data frame. During outbreak investigations, we expect a registry of **all** the observed infected individuals in the linelist data. However, anyone not linked with a potential infector or infectee will not appear in the contact data. Thus, the argument `only_linelist = TRUE` will protect us against missing this later set of individuals when counting the number of secondary cases caused by all the observed infected individuals. They will appear in the `<integer>` vector output as `0` secondary cases.
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```{r,message=FALSE,warning=FALSE}
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# Count secondary cases per subject in contacts and linelist
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which includes individuals in contacts and linelist data frames.
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This assumption may not work for all situations.
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If you need to consider only the individuals from the contact data,
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For example, if during the registry of observed infections,
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the contact data included more subjects than the ones available in the linelist data,
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then you need to consider only the individuals from the contact data.
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In that situation,
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at `epicontacts::get_degree()` we use the `only_linelist = FALSE` argument.
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@@ -288,7 +293,7 @@ Calculate the distribution of secondary cases for Ebola using the `ebola_sim_cle
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**Note:** This dataset has `r nrow(ebola_sim_clean$linelist)` cases. Running `epicontacts::vis_epicontacts()` may overload your session! Try to avoid this step.
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⚠️ **Optional step:** This dataset has `r nrow(ebola_sim_clean$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.
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