Create REPRODUCEME.md

REPRODUCEME.md

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+# Instructions for Repetition of Study
+
+This file descirbes how to reproduce the analysis of "Identification of the Mode of Evolution in Incomplete Carbonate Successions"
+
+## Authors
+
+__Niklas Hohmann__  
+Utrecht University   
+email: [email protected]  
+Web page: [uu.nl/staff/NHohmann](uu.nl/staff/NHohmann)  
+Orcid: [0000-0003-1559-1838](https://orcid.org/0000-0003-1559-1838)
+
+## Reproducibility
+\
+Below it is described how to reproduce the study. Data generated by the individual steps are also saved under od. fill un here
+
+### 1. Get Age-Depth Models
+
+#### 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.
+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.
+
+#### 1.2 Extract Age-Depth Models from CartboCAT
+
+1. Ïn the folder data -> matlab_outputs, run "get_adm_from_carbocat_outputs.m" in matlab. This generates the file "scenarioA_and_B_matlab_to_R.mat", which can be read into R.
+
+### Run analyses
+Open the project "blblb" in Rstudio