updated according to template

README.md

@@ -1,28 +1,24 @@
 # CarboStratPalEvo
 
-Repository for "Identification of the mode of evolution in incomplete carbonate successions".
+Repository for the manuscript "Identification of the mode of evolution in incomplete carbonate successions".
 
 ## Authors
 
-__Niklas Hohmann__
+__Niklas Hohmann__ 
 Utrecht University 
-email: n.hohmann [at] uu.nl 
-Web page: [uu.nl/staff/NHohmann](uu.nl/staff/NHohmann) 
-Orcid: [0000-0003-1559-1838](https://orcid.org/0000-0003-1559-1838)
+email: n.h.hohmann [at] uu.nl 
+Web page: [www.uu.nl/staff/NHohmann](https://www.uu.nl/staff/NHHohmann) 
+ORCID: [0000-0003-1559-1838](https://orcid.org/0000-0003-1559-1838)
 
 __Jan Roel Koelewijn__ 
 Utrecht University 
-Orcid: [0000-0002-4668-3797](https://orcid.org/0000-0002-4668-3797)
+ORCID: [0000-0002-4668-3797](https://orcid.org/0000-0002-4668-3797)
 
 __Emilia Jarochowska__ 
 Utrecht University 
 email: e.b.jarochowska [at] uu.nl 
-Web page: [uu.nl/staff/EBJarochowska](https://www.uu.nl/staff/EBJarochowska) 
-Orcid: [0000-0001-8937-9405](https://orcid.org/0000-0001-8937-9405)
-
-## License
-
-Apache 2.0, see LICENSE file for full license text
+Web page: [www.uu.nl/staff/EBJarochowska](https://www.uu.nl/staff/EBJarochowska) 
+ORCID: [0000-0001-8937-9405](https://orcid.org/0000-0001-8937-9405)
 
 ## Software requirements
 
@@ -42,9 +38,10 @@ This will install all required packages and their dependencies needed in the pro
 ## Repository Structure
 
 * _README.md_ : Readme file
+* _REPRODUCEME.md_ : Instructions for repetition of the study
 * _LICENSE_ : Apache 2.0 license text
 * _.gitignore_ : Files not tracked by git
-* _Stratigraphy_paper.Rproj_ : Rstudio project file
+* _CarbonateStratPalEvo.Rproj_ : Rstudio project file
 * _renv_ : Folder generated by _renv_ package
 * _data_ : Folder for data
  * _matlab_outputs_ : Folder with raw data generated by CarboCATLite in Matlab
@@ -64,31 +61,15 @@ This will install all required packages and their dependencies needed in the pro
 * _figs_ : Folder with figures
 * _tables_ : Folder with tables
 
-## Old README File
-
-This document describes how to the used in the publication INSERT TITLE HERE
-
-REPEATABILITY OF DATA GENERATION
-Below is a description of the pipeline uses to generate the data used in the publication.
-Note that all data generated by the following steps, including test results, are already provided.
-The aim of the following description is reproducability
-
-1. Run basin simulations:
-Go into the folder scenarioX (where X=A or B), open the file“carboCATGUI.m” in Matlab and run it. In the window that appears, first click “initialize”.
-Once the window shows the initial platform parameters, click “run CA model”. The run itself can take a while. Once it is done, a file “scenarioXMatlabOutputs.mat” will appear in
-the folder. It contains all model outputs.
-2. Extract age-depth models from model outputs:
-Copy the files “scenarioXMatlabOutputs.mat” into the main folder. Open the file
-“extractADMFromCarboCAT.m” in Matlab and run it. It extracts age-depth models from the
-model outputs, and stores them in a file named “scenariosAandBMatlabToR.mat”.
-3. Import age-depth models into R:
-Open the file “importADMToR.R” in R, and run it.
-It will import the age-depth models into R and save them as a workspace named “scenariosAandB.Rdata”.
-This workspace contains all age-depth models used.
-4. Test modes of evolution
-Open the file "testModesOfEvolution.R" in R and run it.
-It will test how well the different modes of evolution are recognized in the different scenarios, and save the results as a workspace named "resultsTestModesOfEvo.Rdata".
-
-## Funding
-
-Co-funded by the European Union (ERC, MindTheGap, StG project no 101041077). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them.
+## Copyright
+
+Copyright 2023 Netherlands eScience Center and Utrecht University
+
+## License
+
+Apache 2.0 License, see LICENSE file for license text.
+
+## Funding information
+
+Funded by the European Union (ERC, MindTheGap, StG project no 101041077). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them.
+![European Union and European Research Council logos](https://erc.europa.eu/sites/default/files/2023-06/LOGO_ERC-FLAG_FP.png)

REPRODUCEME.md

@@ -16,13 +16,13 @@ Below it is described how to reproduce the study. Data generated by the individu
 
 ### 1. Get Age-Depth Models
 
-#### 1.1 Generate Carbonate Platforms 
+#### 1.1 Generate Carbonate Platforms
 
-1. Clone the scenarioA branch of the CarboCAT lite repository from [here](https://github.com/MindTheGap-ERC/CarboCATLite/tree/scenarioA).
-2. Run the file "carbocatGUI.m"in Matlab. This will open a GUI
-3. Click initialize. The GUI output after initialization is saved under "figs/matlab/scenarioA_initial_conditions.pdf" and serves as the basis for fig S1.
-3. Click "Run CA model". This will start the model run, progress is displayed in the console.
-4. After the run, save your Matlab worspace. Once the console outputs indicate hte run is finished, save your worspace. The data is identical to the data saved under "data/matlab_output_scenarioA_matlab_outputs.mat". It constains all the raw data generated by CarboCAT.
+1. Clone the "scenarioA" branch of the CarboCAT lite repository from [here](https://github.com/MindTheGap-ERC/CarboCATLite/tree/scenarioA).
+2. Run the file "carbocatGUI.m" in Matlab
+3. Click initialize in the GUI. The GUI after initialization is saved under "figs/matlab/scenarioA_initial_conditions.pdf" and serves as the basis for fig S1.
+4. Click "Run CA model". This will start the model run, progress is displayed in the console.
+5. Once the console outputs indicates the run is finished, save your workspace. The generated data is identical to the data saved under "data/matlab_output_scenarioA_matlab_outputs.mat". It constains all the raw data generated by CarboCAT.
 5. Click "Plot run" to generate the chronostratigraphic chart and dip section saved under "figs/matlab/scenarioA_dip_section_and_chronostrat.pdf". This might take a while.
 
 Repeat for the branch _scenarioB_ to generate the data for scenario B.