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README.txt
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Date: 19 December 2019

Dataset creator and contact person:
Roeland C. van de Vijsel
roeland.van.de.vijsel[at]nioz.nl
NIOZ Royal Netherlands Institute for Sea Research (www.nioz.nl)
Yerseke, The Netherlands

This file, i.e. “README.txt”, belongs to the dataset that can be downloaded from the NIOZ Data Repository (https://dataverse.nioz.nl) and/or can be found as DOI: 10.25850/nioz/7b.b.m (https://doi.org/10.25850/nioz/7b.b.m). 

This dataset is part of the following publication:
van de Vijsel, R.C., van Belzen, J., Bouma, T.J., van der Wal, D., Cusseddu, V., Purkis, S.J., Rietkerk, M. & van de Koppel, J. (2019). Estuarine biofilm patterns: Modern analogues for Precambrian self-organization. Earth Surface Processes and Landforms. DOI: 10.1002/esp.4783 (https://doi.org/10.1002/esp.4783).

Whenever any of these data (scripts, figures, raw and processed data) are used elsewhere, please refer correctly to this publication and its authors and please cite the dataset. Options for citing the dataset can be found on https://dataverse.nioz.nl. Dataset and publication published under the Creative Commons Attribution License.

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The current file, i.e. “README.txt”, consists of three parts:
A. Checks before starting downloading the dataset
B. Instructions for downloading and structuring the dataset
C. Overview of dataset contents
 
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A. Checks before starting downloading the dataset

Before starting to download the dataset, please check that all files are present on https://dataverse.nioz.nl (https://doi.org/10.25850/nioz/7b.b.m):

The following files should be present (update: 19/12/2019):

AutoCorrelations_output_part1of3.zip
AutoCorrelations_output_part2of3.zip
AutoCorrelations_output_part3of3.zip
AutoCorrelations_README_and_scripts.zip
DEM_processed.zip
DEM_RAW.zip
DEM_VDVI_Comparison.zip
Figure1.zip
Figure2.zip
Figure3.zip
Figure4_and_FigureSI2.zip
Figure5.zip
Figure6.zip
Figure7.zip
FigureSI1.zip
FigureSI3.zip
FigureSI4.zip
FigureSI5.zip
FigureSI7.zip
FigureSI8.zip
FigureSI9.zip
GoogleEarth.zip
GrowthPotential.zip
Keetenisse 2015-08-11.riproject.zip
Keetenisse 2016-04-18.riproject.zip
Keetenisse 2016-08-26.riproject.zip
Keetenisse 2016-12-13.riproject.zip
Keetenisse 2017-04-07.riproject.zip
Keetenisse 2017-09-19.riproject.zip
Keetenisse 2018-02-08.riproject.zip
Keetenisse2015-08-11.zip
Keetenisse2016-12-13.zip
Keetenisse2017-09-19.zip
Lamination.zip
PenetrationResistance.zip
README.txt.zip (and/or just “README.txt”, i.e. the current file and/or its zipped version)
SiteDescriptions.zip

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B. Instructions for downloading and structuring the dataset

In order to upload and store the entire dataset on dataverse.nioz.nl, the original/designated folder-subfolder structure had to be reorganised somewhat. However, because of this reorganisation, the scripts included in the dataset cannot be used readily (because they are linked to file locations from the original/designated folder structure). Therefore, after downloading all the files from dataverse.nioz.nl, but prior to using the data and its corresponding computation scripts, the original folder-subfolder structure should be restored. Please follow the instructions given below (steps 1-9) in order to do so:

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1) Home folder: “~”
1.1) Make one “home” folder where all files from the dataverse will be downloaded. Here, this “home” directory will be denoted by “~”. 
1.2) Please make sure to download all (zip) files (listed above, at part A.) individually from https://dataverse.nioz.nl. Downloading the entire data set at once might not capture all downloadable files. The most convenient order to download and restructure the dataset will be explained below (steps 2-9).

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2) AutoCorrelations
2.1) Make a new subfolder in the home directory: ~/AutoCorrelations
2.2) Download the following zip-file from dataverse.nioz.nl:
	AutoCorrelations_README_and_scripts.zip
2.3) Unzip this zip-file and move its contents only (i.e. without the overarching folder “AutoCorrelations_README_and_scripts”) to the folder “~/AutoCorrelations”.
2.4) Make a new subfolder: ~/AutoCorrelations/output
2.5) Download the following 3 zip-files from dataverse.nioz.nl:
	AutoCorrelations_output_part1of3.zip
	AutoCorrelations_output_part2of3.zip
	AutoCorrelations_output_part3of3.zip
2.6) Unzip these 3 zip-files and move their contents only (i.e. without the overarching folders “AutoCorrelations_output_part1of3”, “AutoCorrelations_output_part2of3” and “AutoCorrelations_output_part3of3”) to the newly created folder “~/AutoCorrelations/output”
2.7) See “AutoCorrelations_README.txt” in “~/AutoCorrelations” for further information about the individual files.

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3) DEM_VDVI_Comparison
3.1) Download from dataverse.nioz.nl the following zip-file:
	DEM_VDVI_Comparison.zip
3.2) Unzip this zip-file and move the unzipped folder to the “home” directory, i.e. “~”. Hence this becomes a new folder, i.e. “~/DEM_VDVI_Comparison”, which should already contain a large number of subfolders and files.
3.3) Download from dataverse.nioz.nl the following zip-file:
	DEM_processed.zip
3.4) Unzip this zip-file and move it to the folder “~/DEM_VDVI_Comparison/DEM”. In other words, there should now be a new folder “~/DEM_VDVI_Comparison/DEM/DEM_processed”.
3.5) Check that this latter folder contains the following 8 files:
	DEM_processed_README.txt
	Keetenisse2015-08-11.txt
	Keetenisse2016-04-18.txt
	Keetenisse2016-08-26.txt
	Keetenisse2016-12-13.txt
	Keetenisse2017-04-07.txt
	Keetenisse2017-09-19.txt
	Keetenisse2018-02-08.txt
3.6) Download from dataverse.nioz.nl the following zip-file:
	DEM_RAW.zip
3.7) Unzip this zip-file and move it to the folder “~/DEM_VDVI_Comparison/DEM”. In other words, there should now be a new folder “~/DEM_VDVI_Comparison/DEM/DEM_RAW”.
3.8) Check that this latter folder contains the following files:
	DEM_RAW_README.txt
	Keetenisse GLCS.txt
	Keetenisse PRCS.txt
	and a subfolder “backup” with the zipped versions of the latter two text-files.
3.9) Download from dataverse.nioz.nl the following 7 zip-files:
	Keetenisse 2015-08-11.riproject.zip
	Keetenisse 2016-04-18.riproject.zip
	Keetenisse 2016-08-26.riproject.zip
	Keetenisse 2016-12-13.riproject.zip
	Keetenisse 2017-04-07.riproject.zip
	Keetenisse 2017-09-19.riproject.zip
	Keetenisse 2018-02-08.riproject.zip
3.10) Unzip these 7 zip-files and move the 7 unzipped files “Keetenisse YYYY-MM-DD.riproject” to the directory “~/DEM_VDVI_Comparison/DEM/DEM_RAW“ that was created in step 3.7.
3.11) Download from dataverse.nioz.nl the following three zip-files:
	Keetenisse2015-08-11.zip
	Keetenisse2016-12-13.zip
	Keetenisse2017-09-19.zip
3.12) Unzip these 3 zip-files and move the three unzipped folders to “~/DEM_VDVI_Comparison/Drone/Drone_RAW”.

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4) Figures
4.1) Download from dataverse.nioz.nl the following 14 zip-files:
	Figure1.zip
	Figure2.zip
	Figure3.zip
	Figure4_and_FigureSI2.zip
	Figure5.zip
	Figure6.zip
	Figure7.zip
	FigureSI1.zip
	FigureSI3.zip
	FigureSI4.zip
	FigureSI5.zip
	FigureSI7.zip
	FigureSI8.zip
	FigureSI9.zip
4.2) Unzip these 14 zip-files and place the unzipped folders in the main directory, i.e. “~”.

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5) GoogleEarth
5.1) Download from dataverse.nioz.nl the following zip-file:
	GoogleEarth.zip
5.2) Unzip this zip-file and move the entire unzipped folder to the main directory, i.e. “~”. 

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6) GrowthPotential
6.1) Download from dataverse.nioz.nl the following zip-file:
	GrowthPotential.zip
6.2) Unzip this zip-file and move the entire unzipped folder to the main directory, i.e. “~”.

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7) Lamination
7.1) Download from dataverse.nioz.nl the following zip-file:
	Lamination.zip
7.2) Unzip this zip-file and move the entire unzipped folder to the main directory, i.e. “~”. 

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8) PenetrationResistance
8.1) Download from dataverse.nioz.nl the following zip-file:
	PenetrationResistance.zip
8.2) Unzip this zip-file and move the entire unzipped folder to the main directory, i.e. “~”. 

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9) SiteDescriptions
9.1) Download from dataverse.nioz.nl the following zip-file:
	SiteDescriptions.zip
9.2) Unzip this zip-file and move the entire unzipped folder to the main directory, i.e. “~”. 

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The dataset’s original/designated folder-subfolder structure is now completely restored. The computational scripts included in the dataset can now be used to process raw data and to make Figures etc.

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C. Overview of dataset contents

The main folder is named “~” in the instructions (part A and B) above and in any README-files throughout the dataset. This main folder contains all (raw) data, computation scripts and figures that were used in the corresponding published article (van de Vijsel et al., 2019).

For further details on each of these subfolders, please see the README-files in each subfolder and the explanations given in the actual computation scripts.

Please find all individual Article Figures, and explanation about which data they were obtained from, in the corresponding folders “Figure ##”. “SI” refers to “Supplementary Information”.

Below, an overview is given of the data/Figures shown in the Manuscript and how to derive them:

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o All information about Ketenisse and Paardenschor that was deduced from the reference Van den Neucker et al. (2007) and is described in Methods subsection “Study area” is summarised in “~/SiteDescriptions/Ketenisse_Paardenschor_SiteDescriptions.xlsx”.

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o Digital Elevation Models (DEM) and green intensity maps (VDVI, a measure for algal cover) are derived from laserscan resp. drone data. These analyses are done in the folder “~/DEM_VDVI_Comparison”:		

	+ DEMs are obtained from raw (or processed) laserscan data in “~/DEM_VDVI_Comparison/DEM” using the scripts “AerialPicture_DEM_Overlay_YYYYMMDD.m” 

	+  Raw drone data and orthomosaics derived from these can be found in “~/DEM_VDVI_Comparison/Drone”. The orthomosaics are converted into VDVI-data in the scripts “AerialPicture_DEM_Overlay_YYYYMMDD.m”.

	+ DEM and VDVI data are overlayed and georeferenced in the script “AerialPicture_DEM_Overlay_YYYYMMDD.m” as well.

	+ A rectangular selection (44x49.5m), i.e. the focus area, is taken from the georeferenced DEM and VDVI-data, in the scripts “AerialPicture_DEM_SelectPlot.m” and “AerialPicture_DEM_SelectPlot_20170919.m”. 

	+ The distinction between ridges/runnels and creek levees/creeks is made in “~/DEM_VDVI_Comparison/Ketenisse_Bedform_Amplitude_and_RidgeRunnel_vs_Channel.m”. Here, the elevation difference between ridges and runnels is computed as well.

	+ The statement that Ketenisse mudflat slopes down towards 359.05 degrees, i.e. almost to the north, was computed in section 2.2 of “~/DEM_VDVI_Comparison/AerialPicture_DEM_SelectPlot.m”.

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o Google Earth aerial images of Ketenisse mudflat are georeferenced in “~/GoogleEarth/LoadGoogleEarthImages.m”.

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o X-radiographs of the sampled sediment cores are analysed in “~/Lamination/AnalyseXradiographs.m” and plotted in “~/Lamination/PlotXradiographs.m”.

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o All spatial auto-correlations and cross-correlations and linear correlation coefficients (Pearson’s r) are computed using “~/AutoCorrelations/PermutationTest_Pearson_AutoCrossCorr.m”. 
	
	+ For spatial auto-/cross-correlations and Pearson’s r-values of the laserscan-derived DEMs and drone-derived VDVI-maps, input data is imported from the folder “~/DEM_VDVI_Comparison”.
	
	+ For spatial auto-/cross-correlations of the Google Earth image-derived VDVI-maps, input data is imported from the folder “~/GoogleEarth”.
	
	+ For spatial auto-correlations of the X-radiographs of the sediment cores, input data is imported from the folder “~/Lamination”.

	+ Pattern wavelengths (measured as the distance of maximal auto-correlation) and idem the spanwise pattern displacement (measured as distance of maximal cross-correlation) are stored in the folder “~/AutoCorrelations/output/“ as “PermutationTest_AutoCorr_DEM-VDVI_Wavelengths.txt”, “PermutationTest_CrossCorr_DEM-VDVI_Wavelengths.txt”, “PermutationTest_AutoCorr_GoogleEarth_Wavelengths.txt”, “PermutationTest_CrossCorr_GoogleEarth_Wavelengths.txt” and “PermutationTest_AutoCorr_Xray_Wavelengths.txt”. The order of numbers given in these files correspond to the order in the legends of the corresponding Figures.

	+ Annual mean accretion rates along the northern and southern edges of the 44x49.5m focus area are computed in “~/Figure4_and_SI2/PlatformRiseAnnually.m”.

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o Results of the algal growth potential tests (Supplementary Information SI3) can be found in the folder “~/GrowthPotential”.

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o Penetration Resistance measurements (INSTRON) are analysed in the folder “~/PenetrationResistance”.

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(End of the file “README.txt”)

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