Use {epiparameter} in documentation

DESCRIPTION

@@ -39,6 +39,7 @@ Suggests:
     distcrete,
     distributional,
     dplyr,
+    epiparameter,
     forcats,
     ggplot2,
     incidence2,

NEWS.md

@@ -1,5 +1,7 @@
 # cfr (development version)
 
+* Added examples using _epiparameter_ to the `delay_distributions.Rmd` vignette. _epiparameter_ is added as a suggested dependency (#191, @joshwlambert).
+
 # cfr 0.2.0
 
 ## New features

README.Rmd

@@ -175,6 +175,6 @@ _cfr_ functionality overlaps with that of some other packages, including
 - [_coarseDataTools_](https://cran.r-project.org/package=coarseDataTools) is an R package that allows estimation of relative case fatality risk between covariate groups while accounting for delays due to survival time, when numbers of deaths and recoveries over time are known. _cfr_ uses simpler methods from @nishiura2009 that can be applied when only cases and deaths over time are known, generating estimates based on all data to date, as well as time-varying estimates. _cfr_ can also convert estimates of cases with known outcomes over time into an estimate of under-ascertainment, if a baseline estimate of fatality risk is available from the literature (e.g. from past outbreaks). 
 - [_EpiNow2_](https://cran.r-project.org/package=EpiNow2) is an R package that can allow estimation of case fatality risk if it is defined as a secondary observation of cases. In particular, it allows for estimation that accounts for the smooth underlying epidemic process, but this requires additional computational effort. A comparison of these methods is planned for a future release.
 
-_cfr_ is in future expected to benefit from the functionality of the forthcoming [_epiparameter_ package](https://epiverse-trace.github.io/epiparameter/), which is also developed by Epiverse-TRACE. _epiparameter_ aims to provide a library of epidemiological parameters to parameterise delay density functions, as well as the convenient `<epiparameter>` class to store, access, and pass these parameters for delay correction.
+_cfr_ benefits from the functionality of the [_epiparameter_ package](https://epiverse-trace.github.io/epiparameter/), which is also developed by Epiverse-TRACE. _epiparameter_ aims to provide a library of epidemiological parameters to parameterise delay density functions, as well as the convenient `<epiparameter>` class to store, access, and pass these parameters for delay correction.
 
 ## References

README.md

@@ -208,8 +208,7 @@ By contributing to this project, you agree to abide by its terms.
   process, but this requires additional computational effort. A
   comparison of these methods is planned for a future release.
 
-*cfr* is in future expected to benefit from the functionality of the
-forthcoming [*epiparameter*
+*cfr* benefits from the functionality of the [*epiparameter*
 package](https://epiverse-trace.github.io/epiparameter/), which is also
 developed by Epiverse-TRACE. *epiparameter* aims to provide a library of
 epidemiological parameters to parameterise delay density functions, as

vignettes/cfr.Rmd

@@ -82,7 +82,7 @@ The onset-to-death distribution is considered to be Gamma distributed, with a sh
 **Note also** that we use the central estimates for each distribution parameter, and by ignoring uncertainty in these parameters the uncertainty in the resulting CFR is likely to be underestimated. 
 :::
 
-The forthcoming [_epiparameter_ package](https://epiverse-trace.github.io/epiparameter/) aims to be a library of epidemiological delay distributions, which can be accessed easily from within workflows.
+The [_epiparameter_ package](https://epiverse-trace.github.io/epiparameter/) aims to be a library of epidemiological delay distributions, which can be accessed easily from within workflows.
 See the [vignette on using delay distributions](delay_distributions.html) for more information on how to use this and other distribution objects supported by R to prepare delay density functions.
 
 ## Estimate disease severity

vignettes/delay_distributions.Rmd

@@ -156,16 +156,36 @@ Further, _cfr_ functions tally estimated death counts (calculated by convolving
 
 While users can pass functions from _stats_, and can manage distribution parameters using specialised packages and classes, it may be convenient to be able to access parameters reported in the epidemiological literature from a curated library.
 
-The forthcoming [_epiparameter_ package](https://epiverse-trace.github.io/epiparameter/) aims to be such a library of epidemiological delay distributions.
+The [_epiparameter_ package](https://epiverse-trace.github.io/epiparameter/) aims to be such a library of epidemiological delay distributions.
 The dedicated `<epiparameter>` class is expected to have similar functionality to other distribution classes, allowing easy definition of density functions that can be passed to _cfr_.
 
-The pseudo-code below shows how this might work.
+Here is an example of how this works:
 
-```r
-# NOTE: this is pseudo-code
-EPIPARAMETER_OBJECT <- ACCESS_DISTRIBUTION(disease, study)
+```{r}
+ebola_onset_to_death <- epiparameter::epiparameter_db(
+  disease = "Ebola",
+  epi_name = "onset-to-death",
+  single_epiparameter = TRUE
+)
+
+cfr_static(data = ebola1976, delay_density = function(x) {
+  density(ebola_onset_to_death, at = x)
+ }
+)
+```
+
+This works with other functions that have the `delay_density` argument.
+
+Another way to use `<epiparameter>` objects with _cfr_ is to convert them into a function and pass that to the `cfr_*()` function:
+
+```{r}
+# using the same Ebola onset-to-death delay distribution as the previous example
+ebola_onset_to_death_func <- as.function(
+  ebola_onset_to_death,
+  func_type = "density"
+)
 
-cfr_*(data = data, delay_density = function(x) density(<EPIPARAMETER_OBJECT>, x))
+cfr_static(data = ebola1976, delay_density = ebola_onset_to_death_func)
 ```
 
 ## References