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View Code? Open in Web Editor NEWiTURBO2 toolbox for MATLAB
License: MIT License
iTURBO2 toolbox for MATLAB
License: MIT License
################################################ ### iTURBO2 toolbox for MATLAB ################################################ * The original model by Trauth (2013) was adapted for Hülse et al. (2022) Hülse et al. (2022). Assessing the impact of bioturbation on sedimentary isotopic records: a model study. Paleoceanography, XXX, XXX Trauth, M. H. (2013). TURBO2: A MATLAB simulation to study the effects of bioturbation on paleoceanographic time series. Computers & Geosciences, 61:1–10. ################################################ ### How to run experiments shown in the paper ################################################ ** To run all experiments with one function, call the routine run_iturbo2_paper_experiments.m / ** To run just a single experiment select the respective function-calls in run_iturbo2_paper_experiments.m * Run all Hülse et al. (2022) experiments but with fewer model iterations so the experiments are done faster: run_iturbo2_paper_experiments('data/iTURBO2_input_data.xlsx', true) * Run all experiments with the same model iterations as in Hülse et al. (2022): run_iturbo2_paper_experiments('data/iTURBO2_input_data.xlsx', false) * output figures: Are saved in folder ./output and have the general structure: expname,'_',abutxt,'abu_',numbtxt,'carriers_',expstxt,'Exps' with expname : name as specified by the user (see e.g. in file run_iturbo2_paper_experiments.m) abutxt : max number of carriers in the entire core numbtxt : number of carriers to be measured expstxt : number of different experiments * The MATLAB results of the specific experiments are saved in the folder ./output/mat and have the same general structure as the figures ################################################ ### Other / simple iTURBO2 example experiments ################################################ * run_iturbo2_simple_experiments.m run_iturbo2_simple_experiments('data/iTURBO2_input_data.xlsx') Performs two simple iTURBO2 experiments using abudance and isotope changes for only one model simulation. ################################################ ### Description of the MATLAB files: ################################################ run_iturbo2_paper_experiments.m - MATLAB script to run the experiments presented in the paper run_iturbo2_exps_PETM690.m - MATLAB script to run the PETM OPD 690 experiments presented in the paper (is also called from run_iturbo2_paper_experiments.) run_iturbo2_simple_experiments.m - MATLAB script to run simple iTURBO2 experiments where only one simulation is run (isotope & abundance changes simultaneously) iturbo2_plus_TM.m - MATLAB code of iTURBO2, now including the transition matrix (TM) approach iturbo2script_multipleSims.m - MATLAB script to run iTURBO2 using multiple simulations (i.e. with different random mixing realisations) for one biotrbation depths iturbo2script_multipleSims_3zbio.m - MATLAB script to run iTURBO2 using multiple simulations for three different biotrbation depths iturbo2script_4zbio_ASH.m - MATLAB script to run iTURBO2 to simulate the observed ash layers using four different biotrbation depths iturbo2script_3zbio_ASH.m - MATLAB script to run iTURBO2 to simulate the observed ash layers using three different biotrbation depths iturbo2script_multipleSims_dissolution.m - MATLAB script to run iTURBO2 using multiple simulations for three different dissolution scenarios ./PETM690_code/iturbo2_PETM690.m - MATLAB code of iTURBO2 for the PETM 690 experiment (does not include the TM approach) ./PETM690_code/iturbo2script_PETM690.m - MATLAB script to run iTURBO2 to simulate the observed PETM ODP690 record ################################################ ### Description of the data files that contain information for the mixing experiments: ################################################ * in ./data: iTURBO2_input_data.xlsx - Information for experiments (artificial shapes, artificial sinus signal, Laskar solution, isotope & abundace change for cold and waRM species) iTURBO2_input_ash_experiment.xlsx - Information for the ash experiments iTURBO2_input_dissolution_experiment.xlsx - Information for the dissolution experiments iTURBO2_input_PETM_690_Exp.xlsx - Information for the PETM 690 experiments Excel files as in ./data just with fewer particles so a test run can be performed faster * in ./data/PETM_690: PETM690.mat - PETM OPD 690 observations zbio_10cm_thermo_0.1_and_1.0_percent_NoDeepMix_v2.mat - iTURBO2 results shown in the paper for measuring n=4 carriers zbio10cm_12carriers_Thermo_0.1_and_1.0_percent_IntermedDeepMix.mat - iTURBO2 results shown in the paper for measuring n=12 carriers ################################################ ### Description of other folders: ################################################ * transmtx: - The transition matrices generated and used for the local (upward) mixing for bioturbation depths of 5, 7, 9, 10, 11, 13 and 20 cm - New, user-specified transition matrices have to be saved in this folder and need to be read and used by the iTURBO2 model in the file iturbo2_plus_TM.m. * utils: - MATLAB utility functions for plotting purposes * output: - Result figures are saved here as .eps files. * output/mat: - MATLAB .mat files are saved here that record the results of the specific experiments so they can be recreated. ################################################ ### Licensing ################################################ Most of the routines included are MIT licensed. But please read details in individual files, as it includes some codes that are not authored by us.
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