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1_individual_methods_analysis/README.md

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+# Individual and combined methods analysis
+
+This subfolder contains the code and data for analyzing the networks created by the 40 single methods inmplemented in MULAN and molecular biology methods 
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+
+The code to perform the analysis can be found in  `analysis.Rmd`. An rmarkdown .html file is also found within this folder (`analysis.html`)
+
+The `sim` subfolders contain the following files for each simulated network:
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+- Combined_Data_onlyAUC.csv: the area under the reciever operating characteristic (AUROC, abbreviated here as AUC) values for each method for the 50 time series simulations of the network calculated by MULAN
+- Combined_Data_onlyACC.csv: the accuracy (ACC) values for each method for the 50 time series simulations of the network calculated by MULAN
+- Combined_data_sums_onlyAUC: The Row Sums for each  method across the 50 simulated time series using the weight Weight_{AUC=1}, Weight_{ACC=0}
+- Combined_data_sums_onlyACC: The Row Sums for each method across the 50 simulated time series using the weight Weight_{AUC=0}, Weight_{ACC=1}
+- Combined_data_median_onlyAUC: The Median value for each method across the 50 simulated time series using the weight Weight_{AUC=1}, Weight_{ACC=0}
+- Combined_data_median_onlyACC: The Row Sums value for each method across the 50 simulated time series using the weight Weight_{AUC=0}, Weight_{ACC=1}
+- Combined_data_sums_equal: The Row Sums for each method across the 50 simulated time series using the weight Weight_{AUC=0.5}, Weight_{ACC=0.5}
+- Combined_data_median_equal: The Median value for each method across the 50 simulated time series using the weight Weight_{AUC=0.5}, Weight_{ACC=0.5}
+- Combined_data_sums_73: The Row Sums for each method across the 50 simulated time series using the weight Weight_{AUC=0.7}, Weight_{ACC=0.3}
+- Combined_data_median_73: The Median value for each method across the 50 simulated time series using the weight Weight_{AUC=0.7}, Weight_{ACC=0.3}
+- Combined_data_sums_37: The Row Sums for each method across the 50 simulated time series using the weight Weight_{AUC=0.3}, Weight_{ACC=0.7}
+- Combined_data_median_37: The Median value for each method across the 50 simulated time series using the weight Weight_{AUC=0.3}, Weight_{ACC=0.7}
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+The `averages` subfolder contains the values of the averages for each method across all simulated networks for both the row sums and median values under the various weights of AUROC and ACC
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+The heatmap and lineplots that display the row sums and median values can be found in the main folder.