Estimates the trophic position of a consumer relative to a baseline species. It implements a Bayesian approach which combines an interface to the 'JAGS' MCMC library of 'rjags' and stable isotopes. Users are encouraged to test the package and send bugs and/or errors to [email protected]
tRophicPosition is a colaborative project of Chris Harrod, Andrew L. Jackson, Claudio Quezada-Romegialli and others. It consists of an R package incorporating a Bayesian model for the calculation of consumer trophic position using stable isotopes with one or two baselines. It uses the powerful approach of Markov Chain Monte Carlo simulations provided by JAGS and the statistical language R.
As of 29th of January 2018, we are releasing the version 0.7.5 of the package, the fourth release version. If you find any error, please send it to [email protected] and/or raise an issue in the GitHub page. Also you can also send a direct email to clquezada at harrodlab.net.
If you are interested in joining the tRophicPosition support group, do it at https://groups.google.com/d/forum/trophicposition-support
The stable version of
tRophicPosition is hosted on CRAN, and is installed like any other package:
Remember to install JAGS for your platform as well.
The development version of
tRophicPosition must be installed from GitHub. For this, install the package devtools, and then use the function
install.packages("devtools")devtools::install_github("clquezada/tRophicPosition", build_vignettes = TRUE)
And then see the vignettes we have prepared to describe how to use the package:
Can be found in GitHub here.
tRophicPosition relies on some code from coda and dispRity. At the moment dispRity is only available through GitHub, so it is not included in Suggests.
tRophicPosition included the Bhattacharrya Coefficient (bhatt.coeff function from dispRity) and plotMCMC (from coda) for convenience.
While the paper describing
tRophicPosition is not published (currently under revision at MEE), to cite the package in publications please use:
Claudio Quezada-Romegialli, Andrew L Jackson and Chris Harrod (2018). tRophicPosition: Bayesian Trophic Position Calculation with Stable Isotopes. R package version 0.7.5. https://cran.r-project.org/package=tRophicPosition doi:10.5281/zenodo.1161826
For previous releases please use the corresponding version and doi when citing:
v0.7.5 (29 January 2018) 10.5281/zenodo.1161826
v0.7.3 (12 October 2017) 10.5281/zenodo.1009571
v0.7.0 (12 June 2017) 10.5281/zenodo.806048
You are encouraged to use
tRophicPosition with your own data, test the package and see if there are any issues or problems. You can send your questions or commentaries to the google group tRophicPosition-support or directly to the email trophicposition-support at googlegroups.com. You can send your questions to http://stackexchange.com/ http://stackoverflow.com/ or even Facebook (stable isotope ecology group).
We are constantly working on future releases of
tRophicPosition, so feedback is very much appreciated.
Things to do in tRophicPosition
First release version submitted to CRAN.