---
title: "Visualising simulated data"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Visualising simulated data}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 8,
  fig.height = 5
)
```

This vignette gives an overview of the ways to plot the line list and contacts data output from the `sim_linelist()` and `sim_outbreak()` functions.

Plotting can be useful to identify certain transmission dynamics and patterns in the simulated data, or just to check that the simulated data looks as expected given how the simulation was parameterised.

```{r setup}
library(simulist)
library(epiparameter)
library(incidence2)
library(ggplot2)
library(epicontacts)
library(tidyr)
library(dplyr)
library(ggplot2)
```

First we load the required delay distributions using the {epiparameter} package.

```{r, read-delay-dists}
contact_distribution <- epiparameter(
  disease = "COVID-19",
  epi_name = "contact distribution",
  prob_distribution = create_prob_distribution(
    prob_distribution = "pois",
    prob_distribution_params = c(mean = 3)
  )
)

infectious_period <- epiparameter(
  disease = "COVID-19",
  epi_name = "infectious period",
  prob_distribution = create_prob_distribution(
    prob_distribution = "gamma",
    prob_distribution_params = c(shape = 3, scale = 2)
  )
)

onset_to_hosp <- epiparameter(
  disease = "COVID-19",
  epi_name = "onset to hospitalisation",
  prob_distribution = create_prob_distribution(
    prob_distribution = "lnorm",
    prob_distribution_params = c(meanlog = 1, sdlog = 0.5)
  )
)

# get onset to death from {epiparameter} database
onset_to_death <- epiparameter_db(
  disease = "COVID-19",
  epi_name = "onset to death",
  single_epiparameter = TRUE
)
```

Setting the seed ensures we have the same output each time the vignette is rendered. When using {simulist}, setting the seed is not required unless you need to simulate the same line list multiple times.

```{r, set-seed}
set.seed(123)
```

Using a simple line list simulation with the factory default settings:

```{r sim-linelist} 
linelist <- sim_linelist(
  contact_distribution = contact_distribution,
  infectious_period = infectious_period,
  prob_infection = 0.33,
  onset_to_hosp = onset_to_hosp,
  onset_to_death = onset_to_death,
  outbreak_size = c(500, 1e4)
)
```

This line list contains `r nrow(linelist)` cases.

## Visualising incidence of onset, hospitalisation and death

::: {.alert .alert-info}

This section of the vignette is heavily based upon examples given in the [An introduction to {incidence2} package vignette](https://www.reconverse.org/incidence2/doc/incidence2.html). It is highly recommended to read the documentation supplied in the [{incidence2} package](https://CRAN.R-project.org/package=incidence2) to explore the full range of functionality.

:::

To visualise the number of cases with onset on a particular day, the {incidence2} package, and its dedicated class (`<incidence2>`) are used for handling and plotting this data.

Currently {simulist} outputs dates that are not rounded to the nearest day, i.e. it can be half way through a day. This is not obvious as R prints dates to the nearest day by default, and only by removing the date class (using `unclass()`) can you see the decimals (as R stores dates internally as the number of days since 1970-01-01).

::: {.alert .alert-warning}

{simulist} stores `<Date>`s as precise doubles and not as integer days. This can be misleading as R prints `<Date>`s to the nearest day. By default {incidence2} does not aggregate to the nearest day and without specifying an `interval` in `incidence()` it will aggregate to the same precision as the data. When supplied with non-whole `<Date>`s it will produce this warning. 

```{r incidence-date-warn}
# create incidence object
daily <- incidence(
  x = linelist,
  date_index = "date_onset"
)
```

:::

The `interval = "daily"` is required as {incidence2} requires rounded dates to aggregate cases per unit time and specifying the `interval` will do this automatically for us. It is possible that not every date had the onset of symptoms, resulting in some dates missing entries. This is taken care of by setting `complete_dates = TRUE`, alternatively this can be achieved by using `incidence2::complete_dates()` on the `<incidence2>` object.

```{r create-incidence}
# create incidence object
daily <- incidence(
  x = linelist,
  date_index = "date_onset",
  interval = "daily",
  complete_dates = TRUE
)
```

```{r plot-daily}
#| fig.alt: >
#|   Histogram of incidence (epicurve) showing the daily incidence of cases
#|   from symptom onset including days with zero cases. The plot shows the
#|   outbreak increasing in incidence and then declining, similar to a normal
#|   distribution.
plot(daily)
```

Alternatively, incidence can be plotting weekly:

```{r prep-weekly}
weekly <- incidence(linelist, date_index = "date_onset", interval = "isoweek")
```

```{r plot-weekly}
#| fig.alt: >
#|   Histogram of incidence (epicurve) showing the weekly incidence of cases
#|   from symptom onset including days with zero cases. The plot shows the
#|   outbreak increasing in incidence and then declining, with some weeks late
#|   in the outbreak have noticably high case counts.
plot(weekly)
```

In order to check differences between a group in the line list data, for example sex, the `<incidence2>` data object can be recreated, specifying which columns to group by.

```{r, group-by-sex}
weekly <- incidence(
  linelist,
  date_index = "date_onset",
  interval = "isoweek",
  groups = "sex"
)
```

```{r plot-group-by-sex}
#| fig.alt: >
#|   Two histograms, in a single row, of incidence (epicurve) showing the
#|   weekly incidence of cases from symtom onset including days with zero
#|   cases, facetted by sex (left female, right male). The plot shows the
#|   outbreak increasing in incidence and then declining, with epidemic curves
#|   similar between sexes.
plot(weekly)
```
 
::: {.alert .alert-info}
The simulated data plotted above used the default equal probability of each contact and case being male or female. To adjust the probability that each contact/case is male/female adjust `prob_male` in the `config` argument (see `create_config()` for details).
:::
 
To visualise the onset, hospitalisation and death incidence in the same plot they can be jointly specified to the `date_index` argument of `incidence2::incidence()`. 

First the outcome data needs to be pivoted from long data to wide data to be input into `incidence2::incidence()`.

### Reshape line list data {.tabset}

#### Base R

```{r, reshape-linelist-base-r, eval=FALSE}
# this can also be achieved with the reshape() function but the user interface
# for that function is complicated so here we just create the columns manually
linelist$date_death <- linelist$date_outcome
linelist$date_death[linelist$outcome == "recovered"] <- NA
linelist$date_recovery <- linelist$date_outcome
linelist$date_recovery[linelist$outcome == "died"] <- NA
```

#### Tidyverse

```{r, reshape-linelist-tidyverse, message=FALSE}
linelist <- linelist |>
  tidyr::pivot_wider(
    names_from = outcome,
    values_from = date_outcome
  ) |>
  dplyr::rename(
    date_death = died,
    date_recovery = recovered
  )
```

## {-}
 
```{r, prep-onset-hospitalisation}
daily <- incidence(
  linelist,
  date_index = c(
    onset = "date_onset",
    hospitalisation = "date_admission",
    death = "date_death"
  ),
  interval = "daily",
  groups = "sex",
  complete_dates = TRUE
)
```

```{r plot-onset-hospitalisation}
#| fig.alt: >
#|   Six histograms, in a grid of two columns and three rows, of incidence
#|   (epicurves) showing the daily incidence of cases from symtom onset
#|   (bottom row), hospital admission (middle row), and death (top row).
#|   The data is facetted by sex (left female, right male) and incidence event
#|   (rows). The plot shows the outbreak fluctuating, with many fewer
#|   hospital admissions and deaths than cases.
plot(daily)
```

## Visualising individual line list events through time

Instead of plotting the aggregated number of cases, deaths, or other events on a particular day, we can plot each individual's timeline events over the course of their infection.

We start by simulating a line list. We include an onset-to-recovery delay distribution so all cases have an outcome (died or recovered) date, a reporting delay so the date cases are reported is after their symptom onset date, and set a high risk of hospitalisation to get many hospital admission events. We subset to the first 10 cases so the events on the plot are clear, however, this subsetting is not required.

```{r, sim-subset-linelist}
set.seed(123)

onset_to_recovery <- epiparameter(
  disease = "COVID-19",
  epi_name = "onset to recovert",
  prob_distribution = create_prob_distribution(
    prob_distribution = "lnorm",
    prob_distribution_params = c(meanlog = 2, sdlog = 0.5)
  )
)

reporting_delay <- epiparameter(
  disease = "COVID-19",
  epi_name = "reporting delay",
  prob_distribution = create_prob_distribution(
    prob_distribution = "lnorm",
    prob_distribution_params = c(meanlog = 1, sdlog = 0.5)
  )
)

linelist <- sim_linelist(
  onset_to_recovery = onset_to_recovery,
  reporting_delay = reporting_delay,
  hosp_risk = 0.8
)
linelist <- linelist[1:10, ]
```

We need to reshape the line list to _tidy_ data in order to easily plot it with {ggplot2}.

```{r, prep-events}
tidy_linelist <- linelist |>
  pivot_longer(
    cols = c("date_onset", "date_reporting", "date_admission", "date_outcome")
  ) |>
  mutate(
    ordering_value = ifelse(name == "date_onset", value, NA),
    case_name = reorder(case_name, ordering_value, min, na.rm = TRUE)
)

tidy_linelist$name <- factor(
  tidy_linelist$name,
  levels = c("date_onset", "date_reporting", "date_admission", "date_outcome")
)
```

Here we plot the line list with each case on its own row and the timeline of the outbreak on the x-axis. For clarity, we'll just plot the first 10 cases in the line list.

```{r, plot-events}
#| fig.alt: >
#|   Case timelines showing key epidemiological events for individual cases.
#|   Each horizontal line represents one case, ordered by date of onset. Points
#|   mark four event types recorded in the line list: date of onset (red
#|   squares), date of reporting (blue circles), date of admission (green
#|   triangles), and date of outcome (purple diamonds). The temporal spacing of
#|   these markers illustrates variation in delays between symptom onset,
#|   healthcare seeking, reporting, and eventual outcomes across cases.
ggplot(data = tidy_linelist) +
  geom_line(
    mapping = aes(x = value, y = case_name),
    linewidth = 0.25
  ) +
  geom_point(
    mapping = aes(
      x = value,
      y = case_name,
      shape = name,
      col = name
    ),
    size = 2
  ) +
  scale_x_date(name = "Event date", date_breaks = "week") +
  scale_y_discrete(name = "Case name") +
  scale_color_brewer(
    palette = "Set1",
    name = "Event type",
    labels = c("Date Onset", "Date Reporting", "Date Admission", "Date Outcome")
  ) +
  scale_shape_manual(
    name = "Event type",
    labels = c(
      "Date Onset", "Date Reporting", "Date Admission", "Date Outcome"
    ),
    values = c(15, 16, 17, 18)
  ) +
  theme_bw() +
  theme(
    legend.position = "bottom",
    axis.text.x = element_text(
      angle = 45,
      vjust = 1,
      hjust = 1
    )
  )
```

## Demographic data

Please see the [Age-structured population vignette](age-struct-pop.html) for examples of how to plot the distribution of ages within a line list data set, including age pyramids. 

The plotting code in vignettes is hidden by default, click the Code button with arrow to reveal the plotting code.

## Visualising contact data

::: {.alert .alert-info}

This section of the vignette is based upon examples from the [{epicontacts} R package documentation](https://www.repidemicsconsortium.org/epicontacts/index.html) and the examples provided in the [The Epidemiological R Handbook chapter on transmission chains](https://www.epirhandbook.com/en/new_pages/transmission_chains.html). We recommend going to the documentation of the {epicontacts} R package to see the all plotting and data wrangling functionality.

:::

Just as we utilised the `<incidence2>` class from the {incidence2} package to handle and plot incidence data, we are going to use the `<epicontacts>` class from the {epicontacts} R package to handle and plot epidemiological contact data.

::: {.alert .alert-success}

The benefit of using {epicontacts} is the same as {incidence2}, in the fact that a default plotting method is supplied by the package.

_Advanced_

Additionally, {epicontacts} provides access to network plotting from JavaScript libraries via the [{visNetwork}](https://CRAN.R-project.org/package=visNetwork) and [{threejs}](https://CRAN.R-project.org/package=threejs) R packages.

:::

The {epicontacts} function `make_epicontacts()` requires both the line list and contacts table, so we will run the `sim_outbreak()` function to produce both. We will use the same epidemiological delay distributions that we used to simulate a line list above, but reduce the mean number of contacts in the contact distribution to 2.

```{r, contact-distribution}
contact_distribution <- epiparameter(
  disease = "COVID-19",
  epi_name = "contact distribution",
  prob_distribution = create_prob_distribution(
    prob_distribution = "pois",
    prob_distribution_params = c(mean = 2)
  )
)
```

```{r, sim-outbreak}
set.seed(1)
outbreak <- sim_outbreak(
  contact_distribution = contact_distribution,
  infectious_period = infectious_period,
  prob_infection = 0.5,
  onset_to_hosp = onset_to_hosp,
  onset_to_death = onset_to_death
)
head(outbreak$linelist)
head(outbreak$contacts)
```

Using the line list and contacts data simulated we can create the `<epicontacts>` object.

```{r, create-epicontacts}
epicontacts <- make_epicontacts(
  linelist = outbreak$linelist,
  contacts = outbreak$contacts,
  id = "case_name",
  from = "from",
  to = "to",
  directed = TRUE
)
```

The `<epicontacts>` object comes with a custom printing feature to see the data.

```{r, print-epicontacts}
epicontacts
```

To plot the contact network we can use the plotting method that is supplied by {epicontacts} and will be automatically recognised if the {epicontacts} package is loaded (as done above with `library(epicontacts)`).

::: {.alert .alert-primary}

If you are viewing this vignette on the web (or on a web browser) the graph below is interactive and will allow you to highlight individuals in the network using the drop-down menu, to zoom in and out of the plot by scrolling, and to move the network using the mouse to drag and drop.

:::

```{r, plot-epicontacts}
#| fig.alt: >
#|   Contact network from infectious disease outbreak. This includes all
#|   contacts, i.e. individuals that were infected and not infected. Each
#|   individual is shown as a circle with a name tag, and arrows connecting
#|   the contacts to show directionality of contact.
plot(epicontacts)
```

There is also the option to plot the contacts network in 3D using the `epicontacts::graph3D()`. 

By default the outbreak simulated by `sim_outbreak()` contains contacts of cases that were not infected. These are shown in the previous network plot by terminal nodes that do not pass on infection to other individuals (note that terminal nodes can also be infected individuals that did not infect anybody else, either due to not have any contacts or due to the probabilistic nature of infection transmission). Here we show how to subset the contacts table in order to only plot the transmission network of cases from the outbreak. 

### Subset contact network to transmission network {.tabset}

#### Base R

```{r, subset-linelist-base-r}
outbreak$contacts <- outbreak$contacts[outbreak$contacts$was_case, ]
```

#### Tidyverse

```{r, subset-linelist-tidyverse, echo=2}
# nolint start: one_call_pipe_linter.
outbreak$contacts <- outbreak$contacts |>
  dplyr::filter(was_case)
# nolint end
```

## {-}

```{r, inspect-data}
head(outbreak$linelist)
head(outbreak$contacts)
```

```{r, create-cases-epicontacts}
epicontacts <- make_epicontacts(
  linelist = outbreak$linelist,
  contacts = outbreak$contacts,
  id = "case_name",
  from = "from",
  to = "to",
  directed = TRUE
)
```

```{r, print-cases-epicontacts}
epicontacts
```

```{r, plot-cases-epicontacts}
#| fig.alt: >
#|   Transmission chain from infectious disease outbreak. This includes only
#|   individuals that were infected, including confirmed, probable and
#|   suspected cases. Each individual is shown as a circle with a name tag,
#|   and arrows connecting the cases to show directionality of transmission.
plot(epicontacts)
```

## Visualising other line list information

If there are other aspects of line list data that can be plotted and you would like to them added to this vignette please make an [issue](https://github.com/epiverse-trace/simulist/issues) or [pull request](https://github.com/epiverse-trace/simulist/pulls).