diff --git a/README.md b/README.md index 9ebbb77..db25fb8 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ There are 3 central R-packages to these analyses that are not on CRAN: 1. The `lazymcmc` R package, which is used for the MCMC procedure. This is easy to do with `devtools::install_github("jameshay218/lazymcmc")`. *However*, for many of the analyses, a separate branch implementing parallel tempering is needed. I'd recommend you set this up as follows: - Install the `lazymcmc` base package using `devtools::install_github` as above. Any time this version is used, `library(lazymcmc)` is called. - Clone the `parallel_tempering` branch from [here](https://github.com/jameshay218/lazymcmc/tree/parallel_tempering). Whenever this version is needed, then `devtools::load_all("PATH TO LAZYMCMC PARALLEL TEMPERING REPO")` is called instead. -2. The `virosolver` R-package, containing all of the Ct models and associated functions used here. This is the R-package you would use for your own datasets. As above, simply install with `devtools::install_github("jameshay218/virosolver")`. +2. The `virosolver` R-package, containing all of the Ct models and associated functions used here. This is the R-package you would use for your own datasets. As above, simply install with `devtools::install_github("jameshay218/virosolver")`. Documentation for this package is available [here](https://jameshay218.github.io/virosolver/index.html). 3. The `EpiNow2` R-package. This is available with instructions at [here](https://github.com/epiforecasts/EpiNow2), maintained and developed by colleagues at LSHTM. This package is simply used to generate R(t) estimates for the various comparisons throughout the paper. Note that this uses [RStan](https://mc-stan.org/users/interfaces/rstan). A number of generic R packages are also used throughout: