trini_mod: Network model for nitrogen fluxes in Trinidadian streams...
In isotracer: Isotopic Tracer Analysis Using MCMC

trini_mod

R Documentation

Network model for nitrogen fluxes in Trinidadian streams (Collins et al. 2016)

Description

This model is used in the package case study about Trinidadian streams and is based on an original dataset taken from Collins et al. (2016).

Usage

trini_mod

Format

An object of class networkModel (inherits from tbl_df, tbl, data.frame) with 6 rows and 6 columns.

Details

The model is complete, with topology, initial conditions, observations, covariates and priors.

It is ready for an MCMC run as shown in the example. Note that it might be a good idea to relax the priors for uptake rates from seston to Leptonema (e.g. using hcauchy_p(10)), seston being a compartment that is flowing with the stream water and that can be replenished from upstream.

Source

This network model contains data from the original article: Collins, Sarah M., Steven A. Thomas, Thomas Heatherly, Keeley L. MacNeill, Antoine O.H.C. Leduc, Andrés López-Sepulcre, Bradley A. Lamphere, et al. 2016. “Fish Introductions and Light Modulate Food Web Fluxes in Tropical Streams: A Whole-Ecosystem Experimental Approach.” Ecology, <doi:10.1002/ecy.1530>.

This dataset was also used in the paper: López-Sepulcre, Andrés, Matthieu Bruneaux, Sarah M. Collins, Rana El-Sabaawi, Alexander S. Flecker, and Steven A. Thomas. 2020. “A New Method to Reconstruct Quantitative Food Webs and Nutrient Flows from Isotope Tracer Addition Experiments.” The American Naturalist 195 (6): 964–85. <doi:10.1086/708546>.

Examples

trini_mod
ggtopo(trini_mod)

## Not run: 
# Warning: the run below can take quite a long time!
# (about 15 min with 4 cores at 3.3 Ghz).
run <- run_mcmc(trini_mod, iter = 500, chains = 4, cores = 4)

## End(Not run)

isotracer documentation built on Sept. 22, 2023, 1:07 a.m.