DOI: 10.5061/dryad.kb76qj8
title: Data from: Fitting functional responses: direct parameter estimation by simulating differential equations

description: 1. The feeding functional response is one of the most widespread
 mathematical frameworks in Ecology, Marine Biology, Freshwater Biology,
 Microbiology and related scientific fields describing the
 resource-dependent uptake of a consumer. Since the exact knowledge of its
 parameters is crucial to predict, for example, the efficiency of
 biocontrol agents, population dynamics, food web structure and
 subsequently biodiversity, a trustworthy parameter estimation method is
 highly important for scientists using this framework. Classical approaches
 for estimating functional response parameters lack flexibility and often
 only provide approximations of the correct parameters. 2. Here, we
 combined ordinary differential equation (ODE) models that were numerically
 solved using computer simulations with an iterative maximum likelihood
 fitting approach. We compared our method to classical approaches of
 fitting functional responses using data both with and without additional
 resource growth and mortality. 3. We found that for classical functional
 response models, such as the frequently used type II and type III
 functional responses, the established fitting methods are reliable.
 However, by using more complex and flexible functional responses, our new
 method outperforms the traditional methods. Additionally, our method
 allows the incorporation of side effects such as resource growth and
 background mortality. 4. Our method will enable researchers from different
 scientific fields who are measuring functional responses to calculate more
 accurate parameter estimates. These estimates will enable community
 ecologists to parameterize their models more precisely, thus allowing a
 deeper understanding of complex ecological systems, and will increase the
 quality of ecological prediction models.
description: Data from Archer et al.
 (unpublished) for main publication and manual supplementFunctional response data
 provided by Louise Archer and colleagues. “N0” is the initial prey number
 per arena; “Ndead” is the number of dead prey individuals after the
 experiment; “PredNo” is the number of predators in the experiment (0 ==
 control). These data appear both in the main publication (D7) and are
 needed to perform examples in the supplemental "manual"
 published in MEE.data_archer_manual.csvData from Fussmann et al. (2017) for main publication and manual supplementFunctional response data provided by Katarina Fussmann and colleagues (https://doi.org/10.1101/101675). “N0” is the initial prey density; “Nend” is the remaining prey density after the experiment; “Ndead” is the number of dead prey individuals after the experiment; "T" is the time in minutes, "P" is the number of predators in the experiment (0 == control). These data appear both in the main publication (D8) and are needed to perform examples in the supplemental "manual" published in MEE. Please also refer to the original publication (https://doi.org/10.1101/101675) if you use these data!data_fussman_manual.csvData from Sentis et al. (2015) for main publicationFunctional response data provided by Arnaud Sentis and colleagues (https://doi.org/10.1111/gcb.12931). “Daphnia_density” is the initial prey number; “Daphnia_eaten” is the number of eaten prey individuals after the experiment. Please see the original publication by Sentis et al. (2015, https://doi.org/10.1111/gcb.12931) for details and also cite their paper if using these data! These data appear only in the main publication (D1) published in MEE.data_sentis.csvData from Uszko et al. (2017) for main publication and manual supplement“Subset of the data already published on DRYAD by Uszko W, Diehl S, Englund G, Amarasekare P (https://doi.org/10.5061/dryad.kb00n and https://doi.org/10.1111/ele.12755). Please see the original publication for further details and refer also to them if you use the data! These data appear both in the main publication (D3) and are needed to perform examples in the supplemental "manual" published in MEE.”data_uszko_manual_2.csvData from Vucic-Pestic et al. (2010) for main publication and manual supplementData from Vucic-Pestic and colleagues (https://doi.org/10.1111/j.1365-2656.2009.01622.x). "N0" is the initial prey density; "Neaten" is the number of prey consumed after the experiment. These data appears both in the main publication (D2) and are needed to perform examples in the supplemental "manual" published in MEE. Please see the original publication by Vucic-Pestic et al. (2010, https://doi.org/10.1111/j.1365-2656.2009.01622.x) for details and also cite their paper if using these data!data_vucic-pestic_manual.csvMain R-file including main codeThis r-file contains the main statistical procedures to estimate functional responses following the manual of our paper. Please see the supplemental "manual" published along with the main paper in MEE for further and in-depth instructions.main_fr_manual.rSource R-file including nll functionsThis r-file contains the negative likelihood functions plus some underlying functions needed to perform the code in the file “main_fr_manual.r”. Please see the supplemental "manual" published along with the main paper in MEE for further and in-depth instructions.source_fr_manual.rSource R-file including speedy odeintr codeThis r-file contains the negative likelihood functions plus some underlying functions needed to perform functional response fitting using the faster differential equation solver “odeintr” compared to the one used in “source_fr_manual.r”. Please see the supplemental "manual" published along with the main paper in MEE for further and in-depth instructions.source_fr_odeintr_manual.r