Data from: Fitting functional responses: direct parameter estimation by simulating differential equations

Rosenbaum B, Rall BC

Date Published: June 22, 2018

DOI: https://doi.org/10.5061/dryad.kb76qj8

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Title Data from Archer et al. (unpublished) for main publication and manual supplement
Downloaded 1 time
Description Functional 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.
Download data_archer_manual.csv (220 bytes)
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Title Data from Fussmann et al. (2017) for main publication and manual supplement
Description Functional 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!
Download data_fussman_manual.csv (10.33 Kb)
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Title Data from Sentis et al. (2015) for main publication
Description Functional 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.
Download data_sentis.csv (502 bytes)
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Title Data from Uszko et al. (2017) for main publication and manual supplement
Description “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.”
Download data_uszko_manual_2.csv (1.887 Kb)
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Title Data from Vucic-Pestic et al. (2010) for main publication and manual supplement
Description Data 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!
Download data_vucic-pestic_manual.csv (299 bytes)
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Title Main R-file including main code
Description This 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.
Download main_fr_manual.r (12.19 Kb)
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Title Source R-file including nll functions
Description This 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.
Download source_fr_manual.r (6.603 Kb)
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Title Source R-file including speedy odeintr code
Description This 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.
Download source_fr_odeintr_manual.r (2.209 Kb)
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When using this data, please cite the original publication:

Rosenbaum B, Rall BC (2018) Fitting functional responses: direct parameter estimation by simulating differential equations. Methods in Ecology and Evolution, online in advance of print. https://doi.org/10.1111/2041-210x.13039

Additionally, please cite the Dryad data package:

Rosenbaum B, Rall BC (2018) Data from: Fitting functional responses: direct parameter estimation by simulating differential equations. Dryad Digital Repository. https://doi.org/10.5061/dryad.kb76qj8
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