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vandeVijsel_etal_ComplexChannelPatterns_README.txt

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Written by:
Roeland C. van de Vijsel
Royal Netherlands Institute for Sea Research (NIOZ)
www.nioz.nl
V1 - 16 April 2021: first complete version (belonging to dataset uploaded to dataverse.nioz.nl)

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In this README-file, an overview and brief explanation is given of all the data and computer scripts that were used for the following manuscript:

van de Vijsel, R.C., van Belzen, J., Bouma, T.J., van der Wal, D., Borsje, B.W., Temmerman, S., Cornacchia, L., van de Koppel, J. (Submitted). Simple feedback explains complex channel patterns in coastal wetlands.

Whenever you use any part of the data or scripts described in this README-file, make sure to correctly refer to this manuscript and its authors.

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GENERAL EXPLANATION OF DATA STRUCTURE:

The main folder contains several subfolders and subsubfolders, categorised per (sub)figure from the manuscript stated above (van de Vijsel et al.). The main folder location is hereafter denoted as "~", such that the location of subfolder "Fig1" is denoted as ~/Fig1, etc. Whenever the README-file mentions the "manuscript", it refers to this manuscript. Each file name is followed by a brief description.

Green tag (MacOS) = OK (16/04/2021)

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INDEX:

Fig. 1
Fig. 2 
Fig. 3
Fig. 4
Extended Data Fig. 1
Extended Data Fig. 2
Extended Data Fig. 3
Extended Data Fig. 4
Supplementary Fig. 1
Supplementary Fig. 2

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Fig. 1

~/Fig1/Fig1.pdf
Fig.1, composed of the subfigures given in the subfolders listed below.

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Fig. 1a

~/Fig1/Fig1a/DJI_0041_Ketenisse_2016-09-05.JPG
Simple single-scale patterns: regularly interspaced ridges and runnels on a tidal flat (Schelde estuary, Belgium: 51°17'5.58"N, 4°18'43.72"E). Aerial photo taken with a drone (DJI Inspire 1 drone with Zenmuse X3 gimbal and camera) on 2016-09-05 by Jim van Belzen (NIOZ Yerseke). A selection of this aerial photo is used for Fig. 1a.

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Fig. 1b

~/Fig1/Fig1b/Tillingham_large.jpg
Multi-scale regular patterns: branching tidal marsh channels (Tillingham, United Kingdom: 51°40'32.00"N, 0°56'34.41"E). Aerial image (© 2019 Infoterra Ltd & Bluesky) adapted from Google Earth Pro (2020 © Google LLC). 

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Fig. 1c

~/Fig1/Fig1c/Saeftinghe_2016-09-27_ortho.jpg
Complex multi-scale patterns: high-order branching of tidal marsh channels (Verdronken Land van Saeftinghe, The Netherlands: 51°22'10.80"N, 4°11'9.21"E). Aerial image (© 2020 Maxar Technologies) adapted from Google Earth Pro (2020 © Google LLC).

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Fig. 1d

~/Fig1/Fig1d/VanWesenbeeck_Oikos2008_Tussock_photo.png
Scour around vegetated sediment hummock at a tidal flat. Photo adapted from (Van Wesenbeeck et al., 2008 Oikos). Copyright of photo remains with B.K. van Wesenbeeck, who kindly allowed the use of this photograph for the current manuscript.

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Fig. 1e

~/Fig1/Fig1e/Fig1e.pdf
Graphical illustration of the biogeomorphic, scale-dependent feedback induced by scour around vegetation tussock.

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Fig. 1f

~/Fig1/Fig1f/clPy.Saltmarsh2D_FIG1.ipynb
Phython script: numerical model to simulate the formation of tidal channel networks in a tidal marsh. This script should be run on Jupyter Notebook. To run this script, the file "HydroFunctions_iPy.cl" (explained below) should be in the same main folder. A subfolder "Images" is required; output files from the simulation will be stored here.
 
~/Fig1/Fig1f/HydroFunctions_iPy.cl
Functions (e.g., differential and diffusion operators and boundary conditions) are defined in this script. These functions are used in the main model script (clPy.Saltmarsh2D_FIG1.ipynb).

~/Fig1/Fig1f/Images/s_FIG1_SUBRUN0_SUBRUN20.mat
Output file from the Python script mentioned above: sediment elevation [m] at the end of the simulation. This data is used to make Fig. 1f.

~/Fig1/Fig1f/Plot_FIG1.ipynb
Python script used to plot the output (.mat) mentioned above. Needs to be loaded with Jupyter Notebook.

~/Fig1/Fig1f/FIG1_500dpi.pdf
Output of the above-mentioned plotting script. Plot is used for Fig. 1f.

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Fig. 2

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~/Fig2/Intermediates/FIG25/input/s_FIG25_SUBRUN0_SUBRUN20.mat
Output file (sediment elevation map), obtained with model script "clPy.Saltmarsh2D_FIG25.ipynb" (see ED Fig. 3a for script and explanation). This output file is loaded into the script "ExtractNetwork_Fig2b_NEW.ipynb" (explained hereafter).

~/Fig2/ExtractNetwork_Fig2b_NEW.ipynb
Jupyter Notebook used to extract the creek networks from the sediment elevation map "s_FIG25_SUBRUN0_SUBRUN20.mat". Output of this analysis is stored in the folder "~/Fig2/Intermediates/FIG25/output".

~/Fig2/Intermediates/FIG25/output/DEM_array_FIG25_SUBRUN0_SUBRUN20_t0_SMOOTH=2.mat
~/Fig2/Intermediates/FIG25/output/dist2out_array_FIG25_SUBRUN0_SUBRUN20_t0_SMOOTH=2.mat
~/Fig2/Intermediates/FIG25/output/D8FlowAcc_array_FIG25_SUBRUN0_SUBRUN20_t0_SMOOTH=2.mat
~/Fig2/Intermediates/FIG25/output/HackSO_array_FIG25_SUBRUN0_SUBRUN20_t0_SMOOTH=2.mat
~/Fig2/Intermediates/FIG25/output/filled_accum_array_FIG25_SUBRUN0_SUBRUN20_t0_SMOOTH=2.mat
The 5 most important output files of the creek network analysis done in "ExtractNetwork_Fig2b_NEW.ipynb". What each output file means can be found in this latter .ipynb-script and in the manuscript. These output files are loaded into the Matlab script "ExtractNetwork_Fig2b.m" in order to make the plots used for Fig. 2a+b.

~/Fig2/ExtractNetwork_Fig2b.m
Matlab script used to create Fig. 2a+b from the 5 matrices "..._SMOOTH=2.mat" described above. 

~/Fig2/Fig2a.png
~/Fig2/Fig2b_inset.png
~/Fig2/Fig2b_noline.png
~/Fig2/Fig2b.png
Separate parts of the combined Fig. 2a+b (output from "ExtractNetwork_Fig2b.m").

~/Fig2/Fig2.pptx
In this powerpoint file, the different components that make up Fig. 2a+b are combined (parts adapted from Rinaldo et al. (WRR, 1999) and the plots generated in "ExtractNetwork_Fig2b.m").

~/Fig2/Fig2.pdf
Final Fig. 2a+b.

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Fig. 3

~/Fig3/Plot_FIG2.ipynb
Python script used to make Fig. 3 from the output of the model simulations in subfolder ~/Fig3/Fig3a and ~/Fig3/Fig3b (described below).

~/Fig3/FIG2_500dpi.pdf
Result of the plotting script, i.e. this is Fig. 3 as it appears in the manuscript.

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Fig. 3a

~/Fig3/Fig3a/clPy.Saltmarsh2D_FIG27.ipynb
Numerical model (Jupyter Notebook) used to compute the "gradient simulation" shown in Fig. 3a.

~/Fig3/Fig3a/HydroFunctions_iPy.cl
Model functions used in "clPy.Saltmarsh2D_FIG27.ipynb". 

~/Fig3/Fig3a/Images/s_FIG27_SUBRUN0_SUBRUN20.mat
Output (sediment elevation matrix) of the numerical model "clPy.Saltmarsh2D_FIG27.ipynb". This output is used to plot Fig. 3a in the script "Plot_FIG2.ipynb".

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Fig. 3b

~/Fig3/Fig3b/clPy.Saltmarsh2D_FIG25.ipynb
Numerical model (Jupyter Notebook) used to compute the simulations (channel network formation) shown in Fig. 3b.

~/Fig3/Fig3b/HydroFunctions_iPy.cl
Model functions used in "clPy.Saltmarsh2D_FIG25.ipynb".

~/Fig3/Fig3b/Images/u_FIG25_SUBRUN{0-35}_SUBRUN20.mat
~/Fig3/Fig3b/Images/v_FIG25_SUBRUN{0-35}_SUBRUN20.mat
~/Fig3/Fig3b/Images/h_FIG25_SUBRUN{0-35}_SUBRUN20.mat
~/Fig3/Fig3b/Images/s_FIG25_SUBRUN{0-35}_SUBRUN20.mat
~/Fig3/Fig3b/Images/d_FIG25_SUBRUN{0-35}_SUBRUN20.mat
Output (u,v are velocity fields in x,y directions, h is water layer thickness, s is sediment elevation, d is vegetation density) for all the model runs done with the model "clPy.Saltmarsh2D_FIG25.ipynb". These output files are used in "DrainageEfficiency_Fig2b.m" to compute "FIG25_dmean.mat", FIG25_QXY.mat and "FIG25_smean.mat".

~/Fig3/Fig3b/DrainageEfficiency_Fig2b.m
Matlab script used to calculate drainage flow velocity (FIG25_QXY.mat), domain-averaged sediment elevation (FIG25_smean.mat) and domain-averaged vegetation density (FIG25_dmean.mat) for each of the above simulations.

~/Fig3/Fig3b/Intermediates/FIG25/output/FIG25_dmean.mat
~/Fig3/Fig3b/Intermediates/FIG25/output/FIG25_QXY.mat
~/Fig3/Fig3b/Intermediates/FIG25/output/FIG25_smean.mat
Output from script "DrainageEfficiency_Fig2b.m". These output files are used to make Fig. 3b in the script ~/Fig3/Plot_FIG2.ipynb.

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Fig. 4

~/Fig4/Fig4def/Art2_v7_Fig4.pptx
Powerpoint file where the model results (Fig. 4abc) and field photos (Fig. 4def) are combined into one Figure.

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Fig. 4abc

~/Fig4/Fig4abc/clPy.Saltmarsh2D_FIG31.ipynb
~/Fig4/Fig4abc/clPy.Saltmarsh2D_FIG3100.ipynb
Numerical models (Jupyter Notebook) used to compute the simulations shown in Fig. 4a-c. Channel network formation with idealized model (i.e. with periodic boundary conditions and local water infiltration term).

~/Fig4/Fig4abc/HydroFunctions_iPy.cl
Model functions used in clPy.Saltmarsh2D_FIG31.ipynb and clPy.Saltmarsh2D_FIG3100.ipynb

~/Fig4/Fig4abc/Images/ss_FIG31_SUBRUN2_SUBRUN20.mat
~/Fig4/Fig4abc/Images/ss_FIG3100_SUBRUN2_SUBRUN20.mat
Model output (sediment elevation for each timestep) of clPy.Saltmarsh2D_FIG31.ipynb and clPy.Saltmarsh2D_FIG3100.ipynb, resp.

~/Fig4/Fig4abc/Plot_FIG3ac.ipynb
Script to make Fig. 4a-c from the model output described above.

~/Fig4/Fig4abc/FIG3a_500dpi_nocolorbar.pdf
Output of the above plotting script (i.e. Fig. 4a-c)

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Fig. 4def

~/Fig4/Fig4def/KET_2004.jpg
~/Fig4/Fig4def/KET_2013.jpg
~/Fig4/Fig4def/IMG_0185.jpg
Time series of channel development on a tidal flat (51°17'04.3"N, 4°18'45.1"E) in 2004 ( = KET_2004.jpg) and 2013 (KET_2013.jpg) and in 2016 (IMG_0185.jpg). Fotos for 2004 and 2013 are aerial images, adapted from Google Earth Pro, 2020 © Google LLC). Aerial image from 2004: © 2020 Aerodata International Surveys.  Photo for 2016 is in-situ photo, taken at Ketenisse mudflat, approximately at the location and in the direction of the yellow arrows, see Art2_v7_Fig4.pptx or the manuscript. 

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Extended Data Fig. 1

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~/EDFig1/clPy.Saltmarsh2D_FIG1.ipynb
Jupyter Notebook script used to do the simulations for ED Fig.1.

~/EDFig1/HydroFunctions_iPy.cl
Accompanying model functions (should be in same folder as the .ipynb script mentioned above).

~/EDFig1/Images/s_FIG1_SUBRUN0_SUBRUN20.mat
~/EDFig1/Images/u_FIG1_SUBRUN0_SUBRUN20.mat
~/EDFig1/Images/v_FIG1_SUBRUN0_SUBRUN20.mat
~/EDFig1/Images/h_FIG1_SUBRUN0_SUBRUN20.mat
~/EDFig1/Images/d_FIG1_SUBRUN0_SUBRUN20.mat
Model output of clPy.Saltmarsh2D_FIG1.ipynb, used to make the plots with Plot_EDFIG1.ipynb.

~/EDFig1/Plot_EDFIG1.ipynb
Plotting script.

~/EDFig1/EDFIG1_500dpi.pdf
Result of plotting script, i.e. ED Fig.1.

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Extended Data Fig. 2

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~/EDFig2/clPy.Saltmarsh2D_FIG1.ipynb
Jupyter Notebook script used to do the simulations for ED Fig.2.

~/EDFig2/HydroFunctions_iPy.cl
Accompanying model functions (should be in same folder as the .ipynb script mentioned above).

~/EDFig2/Images/ss_FIG1_SUBRUN0_SUBRUN20.mat
Model output of clPy.Saltmarsh2D_FIG1.ipynb, used to make the plots with Plot_EDFIG2.ipynb.

~/EDFig2/Plot_EDFIG2.ipynb
Plotting script.

~/EDFig2/EDFIG2_500dpi.pdf
Result of plotting script, i.e. ED Fig.2.

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Extended Data Fig. 3

~/EDFig3/Plot_EDFIG3.ipynb
Plotting script to make ED Fig. 3 (with the output files mentioned below).

~/EDFig3/EDFIG3_500dpi.pdf
Result of plotting script, i.e. ED Fig. 3.

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Extended Data Fig. 3a

~/EDFig3/EDFig3a/clPy.Saltmarsh2D_FIG25.ipynb
Jupyter Notebook script used to do the simulations for ED Fig. 3a.

~/EDFig3/EDFig3a/HydroFunctions_iPy.cl
Accompanying model functions (should be in same folder as the .ipynb script mentioned above).

~/EDFig3/EDFig3a/Images/s_FIG25_SUBRUN0_SUBRUN20.mat
Model output of clPy.Saltmarsh2D_FIG25.ipynb, used to make the plots with Plot_EDFIG3.ipynb.

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Extended Data Fig. 3b

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~/EDFig3/EDFig3b/clPy.Saltmarsh2D_FIG26.ipynb
Jupyter Notebook script used to do the simulations for ED Fig. 3b.

~/EDFig3/EDFig3b/HydroFunctions_iPy.cl
Accompanying model functions (should be in same folder as the .ipynb script mentioned above).

~/EDFig3/EDFig3b/Images/s_FIG26_SUBRUN0_SUBRUN20.mat
Model output of clPy.Saltmarsh2D_FIG26.ipynb, used to make the plots with Plot_EDFIG3.ipynb.

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Extended Data Fig. 4

~/EDFig4/EDFig3.4.pdf
Illustration of model setup and modelled variables.

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Supplementary Fig. 1

~/SFig1/SFig1.pdf
Final figure, composed of the different parts explained below.

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Supplementary Fig. 1a

~/SFig1/SFig1a/clPy.Saltmarsh2D_FIG200.ipynb
~/SFig1/SFig1a/HydroFunctions_iPy.cl
~/SFig1/SFig1a/Images/ss_FIG200_SUBRUN0_SUBRUN20.mat
~/SFig1/SFig1a/DATA.mat (= equal to previous)
Respectively: Jupyter Notebook script used to do the simulations for SFig1a, accompanying model functions, model output (sediment bed elevation as a function of simulated time). DATA.mat is a copy of the latter output file (renamed for convenience for subsequent analyses).

~/SFig1/SFig1a/CreekTools_ModelFinetuning_SuppFig1a.ipynb
Jupyter Notebook used to extract the creek networks from the sediment elevation map "ss_FIG200_SUBRUN0_SUBRUN20.mat". Output of this analysis is stored in the current folder.

~/SFig1/SFig1a/HackSO_array_t99_SMOOTH=2.mat
~/SFig1/SFig1a/D8FlowAcc_array_t99_SMOOTH=2.mat
~/SFig1/SFig1a/DEM_array_t99_SMOOTH=2.mat
~/SFig1/SFig1a/dist2out_array_t99_SMOOTH=2.mat
~/SFig1/SFig1a/filled_accum_array_t99_SMOOTH=2.mat
The 5 most important output files of the creek network analysis done in "CreekTools_ModelFinetuning_SuppFig1a.ipynb". What each output file means can be found in this latter .ipynb-script and in the manuscript. These output files are loaded into the Matlab script "CreekToolBox_matlab_SupplFig1a.m" in order to make the plots used for Suppl. Fig. 1a.

~/SFig1/SFig1a/CreekToolBox_matlab_SupplFig1a.m
~/SFig1/SFig1a/SupplFig1a_StreamLength_vs_FillAcc_Color.png
~/SFig1/SFig1a/SupplFig1a_DEM.png
Respectively: Matlab script used to do further analyses on the output files "..._SMOOTH=2.mat" and to make the two png-plots. These plots are used to make the final figure.

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Supplementary Fig. 1b

~/SFig1/SFig1b/clPy.Saltmarsh2D_FIG3100.ipynb
~/SFig1/SFig1b/HydroFunctions_iPy.cl
~/SFig1/SFig1b/Images/ss_FIG3100_SUBRUN2_SUBRUN20.mat
~/SFig1/SFig1b/DATA.mat (= equal to previous)
Respectively: Jupyter Notebook script used to do the simulations for SFig1b, accompanying model functions, model output (sediment bed elevation as a function of simulated time). DATA.mat is a copy of the latter output file (renamed for convenience for subsequent analyses).

~/SFig1/SFig1b/CreekTools_ModelFinetuning_SuppFig1b.ipynb
See SFig.1a for explanation.

~/SFig1/SFig1b/D8FlowAcc_array_t99_SMOOTH=2.mat
~/SFig1/SFig1b/DEM_array_t99_SMOOTH=2.mat
~/SFig1/SFig1b/dist2out_array_t99_SMOOTH=2.mat
~/SFig1/SFig1b/filled_accum_array_t99_SMOOTH=2.mat
~/SFig1/SFig1b/HackSO_array_t99_SMOOTH=2.mat
See SFig.1a for explanation.

~/SFig1/SFig1b/CreekToolBox_matlab_SupplFig1b.m
~/SFig1/SFig1b/SupplFig1b_DEM.png
~/SFig1/SFig1b/SupplFig1b_StreamLength_vs_FillAcc_Color.png\
See SFig.1a for explanation.

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Supplementary Fig. 2

~/SFig1/SFig2.pdf
Final figure, composed of the different parts explained below.

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Supplementary Fig. 2a

~/SFig2/SFig2a/clPy.Saltmarsh2D_FIG3100.ipynb
~/SFig2/SFig2a/HydroFunctions_iPy.cl
~/SFig2/SFig2a/Images/ss_FIG3100_SUBRUN2_SUBRUN20.mat
~/SFig2/SFig2a/DATA.mat (= equal to previous)
Respectively: Jupyter Notebook script used to do the simulations for SFig2a, accompanying model functions, model output (sediment bed elevation as a function of simulated time). DATA.mat is a copy of the latter output file (renamed for convenience for subsequent analyses).

~/SFig2/SFig2a/CreekTools_ModelFinetuning_SuppFig2a.ipynb
~/SFig2/SFig2a/D8FlowAcc_array_t0_SMOOTH=2.mat
~/SFig2/SFig2a/DEM_array_t0_SMOOTH=2.mat
~/SFig2/SFig2a/dist2out_array_t0_SMOOTH=2.mat
~/SFig2/SFig2a/filled_accum_array_t0_SMOOTH=2.mat
~/SFig2/SFig2a/HackSO_array_t0_SMOOTH=2.mat
See SFig1a for explanation.

~/SFig2/SFig2a/CreekToolBox_matlab_SupplFig2a.m
~/SFig2/SFig2a/SupplFig2a_DEM.png
~/SFig2/SFig2a/SupplFig2a_StreamLength_vs_FillAcc_Color.png
See SFig1a for explanation.

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Supplementary Fig. 2b

~/SFig2/SFig2b/clPy.Saltmarsh2D_FIG3100.ipynb
~/SFig2/SFig2b/HydroFunctions_iPy.cl
~/SFig2/SFig2b/Images/ss_FIG3100_SUBRUN2_SUBRUN20.mat
~/SFig2/SFig2b/DATA.mat (= equal to previous)
Respectively: Jupyter Notebook script used to do the simulations for SFig2b, accompanying model functions, model output (sediment bed elevation as a function of simulated time). DATA.mat is a copy of the latter output file (renamed for convenience for subsequent analyses).

~/SFig2/SFig2b/CreekTools_ModelFinetuning_SuppFig2b.ipynb
~/SFig2/SFig2b/D8FlowAcc_array_t99_SMOOTH=2.mat
~/SFig2/SFig2b/DEM_array_t99_SMOOTH=2.mat
~/SFig2/SFig2b/dist2out_array_t99_SMOOTH=2.mat
~/SFig2/SFig2b/filled_accum_array_t99_SMOOTH=2.mat
~/SFig2/SFig2b/HackSO_array_t99_SMOOTH=2.mat
See SFig1a for explanation.

~/SFig2/SFig2b/CreekToolBox_matlab_SupplFig2b.m
~/SFig2/SFig2b/SupplFig2b_StreamLength_vs_FillAcc_Color.png
~/SFig2/SFig2b/SupplFig2b_DEM.png
See SFig1a for explanation.

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Supplementary Fig. 2c

~/SFig2/SFig2c/clPy.Saltmarsh2D_FIG3200.ipynb
~/SFig2/SFig2c/HydroFunctions_iPy.cl
~/SFig2/SFig2c/Images/ss_FIG3200_SUBRUN2_SUBRUN20.mat
~/SFig2/SFig2c/DATA.mat (= equal to previous)
Respectively: Jupyter Notebook script used to do the simulations for SFig2c, accompanying model functions, model output (sediment bed elevation as a function of simulated time). DATA.mat is a copy of the latter output file (renamed for convenience for subsequent analyses).

~/SFig2/SFig2cCreekTools_ModelFinetuning_SuppFig2c.ipynb
~/SFig2/SFig2cD8FlowAcc_array_t99_SMOOTH=2.mat
~/SFig2/SFig2cDEM_array_t99_SMOOTH=2.mat
~/SFig2/SFig2cdist2out_array_t99_SMOOTH=2.mat
~/SFig2/SFig2cfilled_accum_array_t99_SMOOTH=2.mat
~/SFig2/SFig2cHackSO_array_t99_SMOOTH=2.mat
See SFig1a for explanation.

~/SFig2/SFig2cCreekToolBox_matlab_SupplFig2c.m
~/SFig2/SFig2cSupplFig2c_StreamLength_vs_FillAcc_Color.png
~/SFig2/SFig2cSupplFig2c_DEM.png
See SFig1a for explanation.

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Supplementary Fig. 2d

~/SFig2/SFig2d/clPy.Saltmarsh2D_FIG3300.ipynb
~/SFig2/SFig2d/HydroFunctions_iPy.cl
~/SFig2/SFig2d/Images/ss_FIG3300_SUBRUN2_SUBRUN20.mat
~/SFig2/SFig2d/DATA.mat (= equal to previous)
Respectively: Jupyter Notebook script used to do the simulations for SFig2d, accompanying model functions, model output (sediment bed elevation as a function of simulated time). DATA.mat is a copy of the latter output file (renamed for convenience for subsequent analyses).

~/SFig2/SFig2dCreekTools_ModelFinetuning_SuppFig2d.ipynb
~/SFig2/SFig2dD8FlowAcc_array_t99_SMOOTH=2.mat
~/SFig2/SFig2dDEM_array_t99_SMOOTH=2.mat
~/SFig2/SFig2ddist2out_array_t99_SMOOTH=2.mat
~/SFig2/SFig2dfilled_accum_array_t99_SMOOTH=2.mat
~/SFig2/SFig2dHackSO_array_t99_SMOOTH=2.mat
See SFig1a for explanation.

~/SFig2/SFig2dCreekToolBox_matlab_SupplFig2d.m
~/SFig2/SFig2dSupplFig2d_StreamLength_vs_FillAcc_Color.png
~/SFig2/SFig2dSupplFig2d_DEM.png
See SFig1a for explanation.

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END OF README-FILE
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