update vignette and readme

README.md

@@ -1,9 +1,22 @@
 # epikinetics
 [![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip) [![R-CMD-check](https://github.com/seroanalytics/epikinetics/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/seroanalytics/epikinetics/actions/workflows/check-standard.yaml) [![codecov](https://codecov.io/gh/seroanalytics/epikinetics/graph/badge.svg?token=5MZYYDUZYH)](https://codecov.io/gh/seroanalytics/epikinetics)
 
-`epikinetics` is an R package for Bayesian hierarchical modelling of antibody kinetics. 
+`epikinetics` is an R package for Bayesian hierarchical modelling of antibody kinetics.
 
 The underlying model is taken from [Russell TW et al., Real-time estimation of immunological responses against emerging SARS-CoV-2 variants in the UK: a mathematical modelling study.](#References)
+See the [case study vignette](https://seroanalytics.org/epikinetics/articles/biokinetics.html) for a replication of some key figures from the paper using `epikinetics`.
+
+Three publicly available datasets from the above paper are also installed with the package and 
+can be used as test input data:
+
+```{r}
+delta <- data.table::fread(system.file("delta_full.rds", package = "epikinetics"))
+ba2 <- data.table::fread(system.file("ba2_full.rds", package = "epikinetics"))
+xbb <- data.table::fread(system.file("xbb_full.rds", package = "epikinetics"))
+```
+
+If running the model with your own data, see the [data vignette](https://seroanalytics.org/epikinetics/articles/data.html) for 
+an explanation of the input format. 
 
 # Installing
 
@@ -24,7 +37,8 @@ remotes::install_github("seroanalytics/epikinetics")
 Alternatively, you can run `epikinetics` via a Docker image, mounting a working directory which contains your input data files:
 
 ```
-docker run -v /workdir:/ -it seroanalytics/epikinetics:main
+docker pull seroanalytics/epikinetics:main
+docker run -v /path/to/local/workdir:/workdir -it seroanalytics/epikinetics:main
 ```
 
 # Developing

vignettes/data.Rmd

@@ -20,14 +20,19 @@ The model requires a data table containing the following columns:
 
 ### pid
 A unique numeric id to identify a person across observations
+
 ### date
 The date of the observation
+
 ### last_exp_date
 The last date on which the person was exposed
+
 ### titre_type
 The name of the titre
+
 ### value
 The value of the titre
+
 ### censored
 Whether this observation should be censored: -1 for lower, 1 for upper, 0 for none