+ download data from osf

MindTheGap-ERC · Dec 14, 2023 · 19005d9 · 19005d9
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diff --git a/REPRODUCEME.md b/REPRODUCEME.md
@@ -37,29 +37,29 @@ For a description of the data generated by Matlab, see _codebook.md_ in the _dat
 
 ### 1.2 Extract age-depth models from CarboCATLite
 
-Run _data/matlab_outputs/get_adm_from_carbocat_outputs.m" in matlab. This extracts age-depth information from the CarboCATLite outputs and generates the file "scenarioA_and_B_matlab_to_R.mat", which can be read into R.
+Run _data/matlab_outputs/get_adm_from_carbocat_outputs.m" in Matlab. This extracts age-depth information from the CarboCATLite outputs and generates the file "scenarioA_and_B_matlab_to_R.mat", which can be read into R.
 
 ### 1.3 Run analyses in R
 
 Open the R Project in Rstudio as described in _README_. Then run
 
-```{R}
+```r
 source("code/process_adm_from_matlab.R")
 ```
 
 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
 
-```{R}
+```r
 source("code/parameters_for_tests.R")
 ```
 
 to load the parameters for the sets, and save them under "data/R_outputs/parameters_for_tests.Rdata". See _codebook.md_ in the same folder for a description of the data saved.
 
 Last, run
 
-```{R}
+```r
 source("code/simulate_and_test_modes_of_evolution.R")
 ```
 
@@ -69,15 +69,22 @@ From here, you can continue to inspect the generated data or generate the plots
 
 ## 2. Inspection of provided data
 
-All produced data is in the folder _/data/_. For a detailed description of the data structure and contents see the file _/data/R_outputs/codebook.md_ (for outputs from R) and _/data/matlab_outputs/codebook.md_ (for outputs from matlab).
+First, download the supporting data from the Open Science Framework (OSF) by running the following code in R
+
+```r
+source("code/utils.R")
+get_data_from_osf(link = "https://osf.io/zbpwa/")
+```
+
+All downloaded data is in the folder _/data/_. For a detailed description of the data structure and contents see the file _/data/R_outputs/codebook.md_ (for outputs from R) and _/data/matlab_outputs/codebook.md_ (for outputs from matlab).
 
 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 described 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_, download the data as described in the section above, and run
 
-```{R}
+```r
 source("code/make_plots.R")
 ```
 

diff --git a/renv.lock b/renv.lock
@@ -1,6 +1,6 @@
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