BASEmetab

Code accompanying Grace et al. (2015) Fast processing of diel oxygen curves: estimating stream metabolism with BASE (BAyesian Single-station Estimation). Limnology and Oceanography: Methods, 13, 103–114 http://onlinelibrary.wiley.com/doi/10.1002/lom3.10011/full

Currently the BASEmetab package contains just a single user function bayesmetab, which performs the above analysis.

See vignette and run ?bayesmetab for details. https://github.com/dgiling/BASEmetab/blob/master/vignettes/BASEmetab.pdf

Installation

The parameter estimation is performed with the JAGS software, which must be separately installed (Plummer 2003; http://mcmc-jags.sourceforge.net/). To install the BASEmetab package run the following code:

  # install devtools package
  install.packages(c("devtools"))

  # install BASEmetab package
    devtools::install_github("dgiling/BASEmetab")

    # Remove the package zip after installation
    unlink("BASEmetab.zip")

    #load library
    library(BASEmetab)

    #load R2jags to connect to JAGS
    library(R2jags)

Example

See the help file associated with bayesmetab.

Developer

Technical code prepared by Darren Giling darren.giling@canberra.edu.au Packaged by Nick Bond n.bond@latrobe.edu.au