Skip to content
Agent-based model of early oak life history
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
appendices
casestudies
data
figures
.gitignore
JABOWA.nlogo
LICENSE.md
README.md
SOEL.nlogo
run_SOEL.R
utility_functions.R

README.md

SOEL

DOI

SOEL (Simulation of Oak Early Life history) is an individual-based model of the oak lifecycle. SOEL simulates individual acorns, seedlings, saplings, and mature trees and their interactions with animals (including weevil infestation, acorn predation and dispersal by small mammals, and herbivory).

The model (SOEL.nlogo) is implemented in the NetLogo language and can be called from R using the run_SOEL.R script. Data to parameterize the model were primarily collected as part of the Hardwood Ecosystem Experiment, a long-term study of forest ecosystem responses to management.

A description of the model along with several case studies are published in the following paper:

Kellner, Kenneth F.; Swihart, Robert K. 2017. Simulation of oak early life history and interactions with disturbance via an individual-based model, SOEL. PLOS ONE.

A more detailed description of SOEL and how it was developed can be found in the supplementary information (S1 Appendix).

Metadata

appendices: LaTeX code for S1 Appendix and R code for individual parameter regression models (provided in S2 Code).

data: Raw datasets from the HEE used to parameterize the model (see S2 Code).

casestudies: R code to set up and run the case studies in the manuscript and the validation experiments found in S1 Appendix.

figures: Code to generate figures 2-6 in the manuscript and figures 1-6 in S1 Appendix.

JABOWA.nlogo: Source code for JABOWA implementation in NetLogo, used in the validation experiments in S1 Appendix. Can be called in R using run_SOEL.R script. Part of S1 Code.

run_SOEL.R: R script that can call SOEL and the JABOWA implementation from within R using the RNetLogo package. The script can run multiple simulations in parallel.

SOEL.nlogo: Source code for SOEL in the NetLogo language. Part of S1 Code.

utility_functions.R: Functions for formatting and analyzing SOEL output.

You can’t perform that action at this time.