diff --git a/vignettes/epidemics.Rmd b/vignettes/epidemics.Rmd index c1e49095..df51c7ad 100644 --- a/vignettes/epidemics.Rmd +++ b/vignettes/epidemics.Rmd @@ -43,7 +43,7 @@ Prepare population and contact data. ::: {.alert .alert-info} ### Note on social contacts data {-} -**Note that** the social contacts matrices provided by the _socialmixr_[https://CRAN.R-project.org/package=socialmixr] package follow a format wherein the matrix $M_{ij}$ represents [contacts from group $i$ to group $j$](https://epiforecasts.io/socialmixr/articles/socialmixr.html#usage). +**Note that** the social contacts matrices provided by the [_socialmixr_](https://CRAN.R-project.org/package=socialmixr) package follow a format wherein the matrix $M_{ij}$ represents [contacts from group $i$ to group $j$](https://epiforecasts.io/socialmixr/articles/socialmixr.html#usage). However, epidemic models traditionally adopt the notation that $M_{ij}$ defines contacts to $i$ from $j$ [@wallinga2006]. diff --git a/vignettes/modelling_interventions.Rmd b/vignettes/modelling_interventions.Rmd index ba4ef3c4..cb222049 100644 --- a/vignettes/modelling_interventions.Rmd +++ b/vignettes/modelling_interventions.Rmd @@ -37,7 +37,7 @@ Prepare population and contact data. _epidemics_ expects social contacts matrices $M_{ij}$ to represent contacts to $i$ from $j$ [@wallinga2006], such that $q M_{ij} / n_i$ is the probability of infection, where $q$ is a scaling factor dependent on infection transmissibility, and $n_i$ is the population proportion of group $i$. -Social contacts matrices provided by the _socialmixr_[https://CRAN.R-project.org/package=socialmixr] package follow the opposite convention, where $M_{ij}$ represents [contacts from group $i$ to group $j$](https://epiforecasts.io/socialmixr/articles/socialmixr.html#usage). +Social contacts matrices provided by the [_socialmixr_](https://CRAN.R-project.org/package=socialmixr) package follow the opposite convention, where $M_{ij}$ represents [contacts from group $i$ to group $j$](https://epiforecasts.io/socialmixr/articles/socialmixr.html#usage). Thus social contact matrices from _socialmixr_ need to be transposed (using `t()`) before they are used with _epidemics_. :::