reorganize folders

.gitignore

@@ -44,4 +44,7 @@ vignettes/*.pdf
 # figures
 *.pdf
 
+# data folder
+data/*
+
 

REPRODUCEME.md

@@ -28,12 +28,12 @@ Each point is described separately, and can be performed independentof the other
 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".
 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 the _glob_ variable in your workspace. The generated data is identical to the data saved under "data/matlab_output/scenarioA_glob_matlab_outputs.mat". It constains all the raw data generated by CarboCAT.
-6. Click "Plot run" to generate the chronostratigraphic chart and dip section. This figure is saved under "figs/matlab/scenarioA_dip_section_and_chronostrat.pdf". This might take a while.
+5. Once the console outputs indicates the run is finished, save the _glob_ variable in your workspace. The generated data is identical to the data saved under "data/matlab_outputs/scenarioA_glob_matlab_outputs.mat". It constains all the raw data generated by CarboCAT.
+6. Click "Plot run" to generate the chronostratigraphic chart and dip section. This figure is saved under "data/matlab_outputs/figs/scenarioA_dip_section_and_chronostrat.pdf". This might take a while.
 
-Repeat for the branch _scenarioB_, which is available [here](https://github.com/MindTheGap-ERC/CarboCATLite/tree/scenarioB). The generated data is available in "data/matlab_output/scenarioB_glob_matlab_outputs.mat", the figures are "figs/matlab/scenarioB_initial_conditions.pdf" and "figs/matlab/scenarioB_dip_section_and_chronostrat.pdf"
+Repeat for the branch _scenarioB_, which is available [here](https://github.com/MindTheGap-ERC/CarboCATLite/tree/scenarioB). The generated data is available in "data/matlab_outputs/scenarioB_glob_matlab_outputs.mat", the figures are "data/matlab_outputs/figs/scenarioB_initial_conditions.pdf" and "data/matlab_outputs/figs/scenarioB_dip_section_and_chronostrat.pdf"
 
-For a description of the data generated by Matlab, see _codebook.md_ in the _data/matlab_output/_ folder.
+For a description of the data generated by Matlab, see _codebook.md_ in the _data/matlab_outputs/_ folder.
 
 ### 1.2 Extract age-depth models from CarboCATLite
 
@@ -47,7 +47,7 @@ Open the R Project in Rstudio as described in _README_. Then run
 source("code/process_adm_from_matlab.R")
 ```
 
-in R. This importa the age-depth models into R, calculates hiatus durations and (in)completeness, and saves the results in "data/R_outputs/ageDepthModelsScenariosAandB.Rdata". See _codebook.md_ in the same folder for a description of the data saved.
+in R. This imports the age-depth models into R, calculates hiatus durations and (in)completeness, and saves the results in "data/R_outputs/ageDepthModelsScenariosAandB.Rdata". See _codebook.md_ in the same folder for a description of the data saved.
 
 Next, run
 
@@ -63,7 +63,7 @@ Last, run
 source("code/simulate_and_test_modes_of_evolution.R")
 ```
 
-tu run the tests based on the specified parameters and age-depth models. Runtime is multiple hours! The results are saved under under "data/R_outputs/results_modes_of_evolution.Rdata". See _codebook.md_ in the same folder for a description of the data saved.
+to run the tests based on the specified parameters and age-depth models. Runtime is multiple hours! The results are saved under under "data/R_outputs/results_modes_of_evolution.Rdata". See _codebook.md_ in the same folder for a description of the data saved.
 
 From here, you can continue to inspect the generated data or generate the plots as described below.
 
@@ -75,7 +75,7 @@ R outputs can be visualized using the scripts in _code/visualize_data.R_.
 
 ## 3. Reproduction of figures
 
-To reproduce the figures in the main test and supplementary material, open the R project ad describedn in the _README_, and run
+To reproduce the figures in the main test and supplementary material, open the R project ad described in the _README_, and run
 
 ```{R}
 source("code/make_plots.R")