diff --git a/README.Rmd b/README.Rmd index 9e53d920..bfbe2807 100644 --- a/README.Rmd +++ b/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 `` class to store, access, and pass these parameters for delay correction. +_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 `` class to store, access, and pass these parameters for delay correction. ## References diff --git a/README.md b/README.md index 8884d0ea..d38339df 100644 --- a/README.md +++ b/README.md @@ -213,7 +213,7 @@ 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 `` class to store, access, and pass +well as the convenient `` class to store, access, and pass these parameters for delay correction. ## References diff --git a/vignettes/delay_distributions.Rmd b/vignettes/delay_distributions.Rmd index 3ba0a36b..72b90256 100644 --- a/vignettes/delay_distributions.Rmd +++ b/vignettes/delay_distributions.Rmd @@ -157,15 +157,15 @@ 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 dedicated `` class is expected to have similar functionality to other distribution classes, allowing easy definition of density functions that can be passed to _cfr_. +The dedicated `` 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. ```r # NOTE: this is pseudo-code -EPIDIST_OBJECT <- ACCESS_DISTRIBUTION(disease, study) +EPIPARAMETER_OBJECT <- ACCESS_DISTRIBUTION(disease, study) -cfr_*(data = data, delay_density = function(x) density(, x)) +cfr_*(data = data, delay_density = function(x) density(, x)) ``` ## References