michebio/EEB_Model

Model, associated files and analysis scripts for model described in: Boult, V.L., Quaife, T., Fishlock, V., Moss, C.J., Lee, P.C. & Sibly, R.M, 2018. Individual-based modelling of elephant population dynamics using remote sensing to estimate food availability. Ecological Modelling, 387, pp. 187-195.

Elephant Energy Budget Model and Analysis

Author: Vicky Boult
Date: 25th September 2018
For more info: vlboult93@hotmail.com

Files relating to:

Boult, V.L., Quaife, T., Fishlock, V., Moss, C.J., Lee, P.C. & Sibly, R.M, 2018. Individual-based modelling of elephant population dynamics using remote sensing to estimate food availability. Ecological Modelling, 387, pp. 187-195. https://doi.org/10.1016/j.ecolmodel.2018.09.010

File Directory

FOLDER: EEB_Manuscript

Accepted Version - accepted version of manuscript Boult et al 2018 Ecol Mod 
EEB_TRACE.doc    - Details model development, testing, calibration and validation

FOLDER: EEB_Model (*called by EEB_240418.nlogo)

EEB_240418.nlogo  - Elephant energy budget individual-based model in NetLogo 
*XX_setup.txt     - Starting population for each modelled family (IB, LB, VA and WA). Columns are: individual name, mother's name,
                    age in years, age in days since last birthday, sex, pregnancy status (T/F), days since conception, 
                    lactation status (T/F), days since parturition of lactating calf
*NDVI_ILVW_HR.csv - Time-series of median NDVI value for modelled area (across combined home ranges of modelled families)
*asc_nos.csv      - List of ticks on which NDVI value updated

FOLDER: EEB_Validation (*called by EEB_240418_validation.nlogo)

EEB_240418_validation.nlogo  - Validation version of EEB_240418.nlogo adjusted for resident families
*RES_setup.txt               - Starting population of resident elephant families. Columns are individual variables as of 1st March 2000: name, mother's name,
                               family, sex, age in years, age in days since last birthday, pregnancy status (T/F), days since conception, 
                               lactation status (T/F), days since parturition of lactating calf 
*NDVI_RES.csv                - Time-series of median NDVI value for modelled area (across combined home ranges of resident families)
*asc_nos.csv                 - List of ticks on which NDVI value updated

FOLDER: EEB_Analysis > ABC (*called by EEB_ABC.R)

EEB_ABC.R                   - Script to run approximate Bayesian computation to calibrate model parameters
*ABC_simulation.R           - Simulation function to run EEB_240418.nlogo with prior parameters (returns model output annually)
*ABC_parameter_estimation.R - Function to accept posterior parameter distributions
*ABC_plotting.R             - Creates plots of data, best fitting simulation and accepted results for population dynamic data
*EEB_ILVW_data.txt          - Empirical population data for modelled families

FOLDER: EEB_Analysis > Sensitivity (*called by EEB_SA.R)

EEB_SA.R         - Script to run local sensitivity analysis 
*SA_simulation   - Simulation function to run EEB_240418.nlogo (returns model output once at end of model period)
*best1priors.csv - Best fitting parameter set generated by EEB_ABC.R

FOLDER: EEB_Analysis > Validation (*called by EEB_validation.R)

EEB_validation       - Script to run model validation (EEB_240418_validation.nlogo)
*Validation_plot     - Creates plots of population data and 30 simulations
*best30priors        - 30 accepted parameter sets generated by EEB_ABC.R
*EEB_validation_data - Empirical population data for resident families

FOLDER: EEB_Analysis > Scenarios (*called by EEB_scenarios.R)

EEB_scenarios.R             - Script to run hypothetical range reduction scenarios through EEB_240418.nlogo
*EEB_simulation_scenarios.R - Simulattion function to run EEB_240418.nlogo with reduced range
*EEB_ILVW_data.txt          - Empirical population data for modelled families
*best30priors.csv           - 30 accepted parameter sets generated by EEB_ABC.R

FOLDER: EEB_Analysis > Results

ABC_priors.txt         - prior parameter sets for ABC (100,000 sets of 11 parameters)
ABC_results.txt        - population dynamic model results (100,000 sets of 68 data points)
best1priors.csv        - parameter set producing output best fitting population data (1 set of 11 parameters)
best30priors.csv       - accepted parameter sets (30 closest)
best1res.csv           - best fitting model output (1 set of 68 data points)
best30res.csv          - accepted model output (30 closest)
SA_runs.csv            - population data output during sensitivity simulations
SA_table.csv           - table of sensitivites and SE
scenario50_results.txt - population size with 50% range reduction (30 simulations)
scenario90_results.txt - population size with 10% range reduction (30 simulations)
validation_results.txt - population data output for model validation (30 simulations)

Instructions

TO RUN NETLOGO MODEL (EEB_240418.nlogo):

• Must have NetLogo installed (available: https://ccl.northwestern.edu/netlogo/download.shtml)
• Assuming .nlogo file and associated files in same folder, simply press setup and go
• All plots are enabled, but can be turned-off to speed up model (right click on plot > Edit and put ';' in front of 'Pen update commands'
• Underlying code can be seen by clicking 'Code' tab in top-left