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 5th of April 2019, we are releasing the version 0.7.7 of the package, the fifth release version. If you find any error, please send it to trophicposition-support@googlegroups.com 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:
install.packages("tRophicPosition")
Remember to install JAGS for your platform as well. A number of packages are needed, which can be installed with:
install.packages(c("coda", "data.table", "dplyr", "ggplot2", "gridExtra",
"hdrcde", "MCMCglmm", "plyr", "rjags", "knitr", "rmarkdown"))
The development version of tRophicPosition
must be installed from GitHub. For this, install the package devtools, and then use the function install_github()
:
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:
browseVignettes("tRophicPosition")
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.
When citing tRophicPosition
in publications, please cite both the paper describing the method and the package version you used to analyse your data:
Claudio Quezada-Romegialli, Andrew L Jackson, Brian Hayden, Kimmo K Kahilainen, Christelle Lopes and Chris Harrod (2018). tRophicPosition
, an R package for the Bayesian estimation of trophic position from consumer stable isotope ratios. Methods in Ecology and Evolution, 9(6):1592-1599. doi:10.1111/2041-210X.13009
Claudio Quezada-Romegialli, Andrew L Jackson, Brian Hayden, Kimmo K Kahilainen, Christelle Lopes 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.
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