vandeVijsel_etal_TidalFlatTransitions_README.txt

================================================================================

Written by:
Roeland C. van de Vijsel
Royal Netherlands Institute for Sea Research (NIOZ)
www.nioz.nl
V1 - 4 August 2021: first complete version (belonging to the dataset uploaded to dataverse.nioz.nl)

--------------------------------------------------------------------------------

In this README-file, an overview and brief explanation is given of all the data and computer scripts that were used for Chapter 5 ("Tidal flat transitions signaled by self-organized algal patterns") of the PhD Thesis of Roeland C. van de Vijsel, i.e.

van de Vijsel, R. C. (2021). Biophysical self-organization of coastal wetlands: Unraveling spatial complexity on tidal flats and marshes, from the Precambrian to today. University of Groningen. https://doi.org/10.33612/diss.160081233

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.

--------------------------------------------------------------------------------

Below, "~" denotes the location of the main directory (i.e. the location of the current README-file). Subfolders are indicated relative to this main directory, e.g. "~/Figure1".

================================================================================
~/Figure1
================================================================================

Fig1a_GoogleEarth_20040608_(C)_2020_Aerodata_International_Surveys.jpg
Aerial image (© 2020 Aerodata International Surveys) of Ketenisse, dating from 8 June 2004. Photo adapted from Google Earth Pro (2020 © Google LLC).

Fig1b_GoogleEarth_20130707.jpg
Aerial image of Ketenisse from 7 July 2013. Photo adapted from Google Earth Pro (2020 © Google LLC).

Fig1c_IMG_0196.jpg
In-situ photograph taken by the corresonding author at Ketenisse mudflat (16 September 2016).

Fig1d_GoogleEarth_20040608_(C)_2020_Aerodata_International_Surveys.jpg
Aerial image (© 2020 Aerodata International Surveys) of Paardenschor, from 8 June 2004. Photo adapted from Google Earth Pro (2020 © Google LLC).

Fig1e_GoogleEarth_20090831_(C)_2020_Maxar_Technologies.jpg
Aerial image (© 2020 Maxar Technologies) from Paardenschor on 31 August 2009. Photo adapted from Google Earth Pro (2020 © Google LLC).

Fig1f_SigmaplanPicture.png
In-situ photo taken (© Vilda/Yves Adams) taken around 2010 at the intertidal flat of Paardenschor (51.334521°N, 4.251750°E).

================================================================================
~/Figure2
================================================================================

(This folder contains no files.)

The photo in the top left of Figure 2 is the same photo as in Figure S1a. Please, see this README-file under "~/FigureS1" for more information.

The photo in the lower right of Figure 2 is the same as Figure 1c. Please, see this README-file under "~/Figure1" for more information.

================================================================================
~/Figure3
================================================================================

Figure3.pptx
Powerpoint file where all information (DTM, DEM, aerial photos) are combined to make Figure 3. See below for explanation of these individual elements.

Figure3.pdf
As Figure3.pptx, but saved as a pdf.

----------------------------------------
~/Figure3/Paardenschor
----------------------------------------

dtm_2010_RD_NAP.tif
Digital Terrain Model (DTM) of Paardenschor, derived from LIDAR measurements obtained in 2010 by De Vlaamse Waterweg nv, as part of the Moneos program. See the manuscript for further information.

Paardenschor_DEM_Analysis.m
Matlab-file that plots the DTM "dtm_2010_RD_NAP.tif". This plot is used for Figure 3a.

cmap_PS.mat
Colormap, used in "Paardenschor_DEM_Analysis.m".

DTM_Paardenschor_2010.pdf
Result of "Paardenschor_DEM_Analysis.m", i.e. plot of the DTM.

For the aerial photo of Paardenschor (Figure 3b), the same Google Earth photo as used for Figure 1e ("~/Figure1/Fig1e_GoogleEarth_20090831_(C)_2020_Maxar_Technologies.jpg") is used here. See "~/Figure1" for further explanation.

----------------------------------------
~/Figure3/Ketenisse
----------------------------------------

Keetenisse2016-12-13_FULL.mat
Digital Elevation Model (DEM) of Ketenisse on 13 December 2016. This DEM has been obtained in a published article (van de Vijsel et al., 2020 - Earth Surface Processes and Landforms) and is resused here with permission; see this article for explanation of methodology.

Art4_v9_Fig5.m
Matlab-file that plots the DEM "Keetenisse2016-12-13_FULL.mat". This plot is used for Figure 3c.

cmap_KET.mat
Colormap, used in "Art4_v9_Fig5.m".

Ket20161213_DEM_crop.pdf
Result of "Art4_v9_Fig5.m", i.e. plot of the DEM.

For the aerial photo of Ketenisse (Figure 3d), the drone photo "~/Figure5/DJI_0020.JPG" is used here. This drone photo is  explained in this README-file, under "~/Figure5".

================================================================================
~/Figure4
================================================================================

PaardenschorSeedlings.csv
The raw data: seedling density counts at different locations at Paardenschor mudflat (see the manuscript for more information). The coordinates are (X,Y)-coordinates in the Dutch Rijksdriehoekstelsel. See "CMConvertor%20v1.1%20wgs-rd.xls" for conversion of these coordinates into the WGS84 system.

CMConvertor%20v1.1%20wgs-rd.xls
Conversion table from coordinates in Rijksdriehoekstelsel (column "RD") to WGS84.

PaardenschorSeedlings_statistics.r
R-script where statistical analysis of the data in "PaardenschorSeedlings.csv" are performed. Statistical output is stored in the subfolder "~/Figure4/output".

Art4_v7_Fig4.m
Matlab-script where the statistical results of the R-script (see subfolder "~/Figure4/output") are used to make a barplot for Figure 4.

Art4_v7_Fig4_SeedDens.pdf
Barplot (output from "Art4_v7_Fig4.m").

Art4_v7_Fig4_SeedDens_Significance.png
Barplot, where the statistical significance of the differences between bars is indicated. Graphical illustrations are also added to explain the different substrate type. This is the final Figure 4.

----------------------------------------
~/Figure4/output
----------------------------------------
SeedDens_anova.csv
SeedDens_boxplot.pdf
SeedDens_dunn.csv
SeedDens_hist.pdf
SeedDens_levene.csv
SeedDens_qq.pdf
SeedDens_shapiro_pvalue.csv
SeedDens_summary.csv
SeedDens_tHSD.csv
SeedDens_tHSDplot.pdf
The results of the statistical analysis done in "PaardenschorSeedlings_statistics.r". See this script for more information.

================================================================================
~/Figure5
================================================================================

DJI_0020.JPG
DJI_0164.JPG
DJI_0031.JPG
DJI_0095.JPG
DJI_0041.JPG
Five drone photos taken by (and retaining copyright) Jim van Belzen (NIOZ Yerseke, The Netherlands) on 5 September 2016 at Ketenisse mudflat (see the manuscript for explanation of the methods). These drone photos are used in Figure5.pptx to create Figure 5a-d, as explained hereafter.

Figure5.pptx
Powerpoint file where 4 rectangular areas are selected from drone photos. These photo selections are used for Figure 5a-d.

Figure5.pdf
Same as Figure5.pptx, but exported as pdf.

The 4 model simulations shown in Figure 5e-h are taken from "~/Figure6/ART4_FIG105_SUBRUN214_bifurc_logplot=0_std_plot3.png". See the information under "~/Figure6" (below) for further explanation.

================================================================================
~/Figure6
================================================================================

ART4_FIG105_SUBRUN214_bifurc_logplot=0_std_plot3.png
Output from Matlab-script "ART4_Plants_to_Algae_bifurc_FIG105.m", i.e. algal pattern at different values of bifurcation parameter H_in. The values noted above each panel indicate Mudflat elevation relative to MHWS [m], as calculated from each value for H_in. This Matlab-script can be found in folder "~/Figure7/Images". An explanation of this Matlab-script is given below, under the explanation of Figure 7.

ART4_FIG105_SUBRUN214_bifurc_logplot=0_abs.png
Output from Matlab-script "ART4_Plants_to_Algae_bifurc_FIG105.m", used to create Figure 6a. See ~/Figure7/Images for the Matlab script and see further below in the current README-file for an explanation of this Matlab-script.

ART4_FIG105_SUBRUN214_bifurc_logplot=0_std.png
Output from Matlab-script "ART4_Plants_to_Algae_bifurc_FIG105.m", used to create Figure 6b. See ~/Figure7/Images for the Matlab script and see further below in the current README-file for an explanation of this Matlab-script.

Art4_v9_Fig6.pptx
This Powerpoint file creates Figure 6 by combining the lower subplot from "ART4_FIG105_SUBRUN214_bifurc_logplot=0_abs.png" with the upper subplot from "ART4_FIG105_SUBRUN214_bifurc_logplot=0_std.png" and a selection of the panels in "ART4_FIG105_SUBRUN214_bifurc_logplot=0_std_plot3.png" (every second panel of the top and bottom row, i.e. at mudflat elevation -3.41, -3.04, ..., -0.41, -0.03 m).

================================================================================
~/Figure7
================================================================================

clPy.Saltmarsh2D_FIG105.ipynb
The main model code. This Python script (Jupyter Notebook) simulates the formation of channel patterns on algal-covered mudflats, as described in the manuscript. By varying the value of "SUBRUN2" (line 1 in code block 3), different parameter settings are chosen. For the 6 parameter settings used in Figure 7, we selected SUBRUN2 = 1, 2, 4, 11, 12 and 14 (as further explained below in subfolder "Images"). Output of this model, i.e. plots (.png) and model output files (.mat), are stored in the subfolder "Images".

HydroFunctions_iPy.cl
Auxiliary model file, containing (amongst others) the definition of differential operators and boundary conditions. This file should be placed in the same location as main model code "clPy.Saltmarsh2D_FIG105.ipynb".

----------------------------------------
~/Figure7/Images
----------------------------------------

This folder contains model output files (.mat) obtained with the model script "clPy.Saltmarsh2D_FIG105.ipynb" (described above). In the list below, run numbers are indicated by ## (= 0 - 40), representing 41 runs with each slightly different values for bifurcation parameter H_in. Files "d_FIG105_..." are model results for algal density; files "s_FIG105_..." are model results for sediment elevation. This folder contains the following 492 (6x2x41) output files:

d_FIG105_SUBRUN##_SUBRUN21.mat
s_FIG105_SUBRUN##_SUBRUN21.mat
Used for grey data points (diatoms) in Fig. 7a, i.e. pD = 0.00 and D0 = D0x1000 = 1e-4 m2/s.

d_FIG105_SUBRUN##_SUBRUN22.mat
s_FIG105_SUBRUN##_SUBRUN22.mat
Used for grey data points (diatoms) in Fig. 7b, i.e. pD = 0.00 and D0 = D0x100 = 1e-5 m2/s.

d_FIG105_SUBRUN##_SUBRUN24.mat
s_FIG105_SUBRUN##_SUBRUN24.mat
Used for grey data points (diatoms) in Fig. 7c, i.e. pD = 0.00 and D0 = D0x1 = 1e-7 m2/s.

d_FIG105_SUBRUN##_SUBRUN211.mat
s_FIG105_SUBRUN##_SUBRUN211.mat
Used for colored data points (Vaucheria) in Fig. 7a, i.e. pD = 0.99 and D0 = D0x1000 = 1e-4 m2/s.

d_FIG105_SUBRUN##_SUBRUN212.mat
s_FIG105_SUBRUN##_SUBRUN212.mat
Used for colored data points (Vaucheria) in Fig. 7b, i.e. pD = 0.99 and D0 = D0x100 = 1e-5 m2/s.

d_FIG105_SUBRUN##_SUBRUN214.mat
s_FIG105_SUBRUN##_SUBRUN214.mat
Used for colored data points (Vaucheria) in Fig. 7c, i.e. pD = 0.99 and D0 = D0x1 = 1e-7 m2/s.

--------------------

ART4_Plants_to_Algae_bifurc_FIG105.m
This is the Matlab-script used to make the plots for in Figures 6 and 7. This Matlab-script uses the model output (.mat) in the same folder as input files. A selection of the resulting plots are listed in the subfolder "output", as described below.

----------------------------------------
~/Figure7/output
----------------------------------------

This folder contains a selection of the plots generated by Matlab-script "ART4_Plants_to_Algae_bifurc_FIG105.m", i.e.:

ART4_FIG105_SUBRUN21_bifurc_logplot=0_std.png
Result from Matlab-script "ART4_Plants_to_Algae_bifurc_FIG105.m". Used for grey data points (diatoms) in Fig. 7a, i.e. pD = 0.00 and D0 = D0x1000 = 1e-4 m2/s.

ART4_FIG105_SUBRUN22_bifurc_logplot=0_std.png
Result from Matlab-script "ART4_Plants_to_Algae_bifurc_FIG105.m". Used for grey data points (diatoms) in Fig. 7b, i.e. pD = 0.00 and D0 = D0x100 = 1e-5 m2/s.

ART4_FIG105_SUBRUN24_bifurc_logplot=0_std.png
Result from Matlab-script "ART4_Plants_to_Algae_bifurc_FIG105.m". Used for grey data points (diatoms) in Fig. 7c, i.e. pD = 0.00 and D0 = D0x1 = 1e-7 m2/s.

ART4_FIG105_SUBRUN211_bifurc_logplot=0_std.png
Result from Matlab-script "ART4_Plants_to_Algae_bifurc_FIG105.m". Used for colored data points (Vaucheria) in Fig. 7a, i.e. pD = 0.99 and D0 = D0x1000 = 1e-4 m2/s.

ART4_FIG105_SUBRUN212_bifurc_logplot=0_std.png
Result from Matlab-script "ART4_Plants_to_Algae_bifurc_FIG105.m". Used for colored data points (Vaucheria) in Fig. 7b, i.e. pD = 0.99 and D0 = D0x100 = 1e-5 m2/s.

ART4_FIG105_SUBRUN214_bifurc_logplot=0_std.png
Result from Matlab-script "ART4_Plants_to_Algae_bifurc_FIG105.m". Used for colored data points (Vaucheria) in Fig. 7c, i.e. pD = 0.99 and D0 = D0x1 = 1e-7 m2/s.

Art4_v7_Fig7.pptx
In this Powerpoint presentation, the 6 plots in this same subfolder are combined to create Figure 7.

Art4_v7_Fig7.pdf
Same as "Art4_v7_Fig7.pptx", but saved as a pdf.

================================================================================
~/FigureS1
================================================================================

IMG_0185.jpg
In-situ photo taken by the corresponding author at Ketenisse mudflat on 16 September 2016. Photo used for Figure S1c.

IMG_2091.jpg
IMG_2123.jpg
IMG_2118.jpg
In-situ photos taken by the corresponding author at Ketenisse mudflat on 13 December 2016. Photos used for Figure S1a,b,d.

================================================================================
END OF README-FILE
================================================================================