remotes::install_github(
"USGS-R/streamMetabolizer", # soon to be "DOI-USGS/streamMetabolizer"
build_vignettes = TRUE)Installing streamMetabolizer
To install the streamMetabolizer package, use the remotes package (running install.packages('remotes') first if needed). To use remotes::install_github() it is convenient to set a GitHub Personal Access Token (PAT). There are several methods for setting your PATs within R; the simplest is to call `Sys.setenv(GITHUB_PAT=“yyyy”), replacing yyyy with the PAT you established on the GitHub website.
You can install the most cutting edge version of streamMetabolizer with this command:
Software dependencies for Bayesian models
Bayesian models require a Stan backend, provided by either the rstan or cmdstanr packages. Installation of these packages is rarely as simple as a call to install.packages(). See the RStan installation guide or the CmdStanR installation guide for up-to-date instructions, which differ by operating system. Select the backend with specs(..., stan_engine = "rstan") or specs(..., stan_engine = "cmdstanr").
streamMetabolizer caches compiled models outside the installed package so they can be reused when the package library is read-only. Advanced users can override the cache locations with the streamMetabolizer.rstan_cache_dir and streamMetabolizer.cmdstan_cache_dir options.