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In gauseR: Lotka-Volterra Models for Gause's 'Struggle for Existence'

gauseR: Simple methods for fitting Lotka-Volterra models describing Gause's "Struggle for Existence"

Description

A collection of tools and data for analyzing the Gause microcosm experiments, and for fitting Lotka-Volterra models to time series data. Includes methods for fitting single-species logistic growth, and multi-species interaction models, e.g. of competition, predator/prey relationships, or mutualism. See documentation for individual functions for examples. In general, see the lv_optim() function for examples of how to fit parameter values in multi-species systems.

Authors

Adam Clark, Lina Muehlbauer, and Maximilienne Schulze.

Applications

Note that the general methods applied here, as well as the form of the differential equations that we use, are described in detail in the Quantitative Ecology textbook by Lehman et al., cited below. Using the default functions, species dynamics therefore follow the form:

dni/dt = ni * (ri + aii * ni + sum_j(aij * nj))

Source

Clarence Lehman, Shelby Loberg, and Adam T. Clark. (2019). Quantitative Ecology: A New Unified Approach. University of Minnesota Libraries Publishing. University of Minnesota Digital Conservancy, http://hdl.handle.net/11299/204551

Lina K. Muehlbauer, Maximilienne Schulze, W. Stanley Harpole, and Adam T. Clark. "gauseR: Simple methods for fitting Lotka-Volterra models describing Gause's 'Struggle for Existence'." Ecology and Evolution.

Examples

#primary wrapper function
?gause_wrapper        # automatically runs functions to get starting values and fit
                      # paramter vales using simulated ODE dynamics.

#individual functions
?get_lag              # generate time-lagged variables for estimating per-capita growth
?percap_growth        # generate estimates of per-capita growth rates for species
?get_logistic         # logistic growth function
?lv_interaction       # function for simulating Lotka-Voterra ODE models
?lv_interaction_log   # a version of the lv_interaction computed in log abundance space,
                      # which typically works better for optimization
?lv_optim             # methods for fitting complex n-species models
?test_goodness_of_fit # tests goodness of fit of model results, with an R2-like statistic
?ode_prediction       # generic function for simulating time series,
                      # to be used with other optimizers

gauseR documentation built on Oct. 23, 2023, 1:08 a.m.