added feature set.

.gitignore

@@ -1,5 +1,4 @@
 ## ignore the following
 TODO_for_paper.org
 data/change_c_codes.sh
-data/subset_features_v*csv
 .Rhistory

README.md

@@ -1,7 +1,11 @@
 Code for manuscript:
 
-`O'Toole JM, Pavlidis E, Korotchikova I, Boylan GB, Stevenson NJ, Temporal evolution of
-quantitative EEG within 3 days of birth in early preterm infants, 2018, under review`
+
+O'Toole JM, Pavlidis E, Korotchikova I, Boylan GB, Stevenson NJ, Temporal evolution of
+quantitative EEG within 3 days of birth in early preterm infants, Scientific Reports,
+41227, [DOI: 10.1038/s41598-019-41227-9](https://doi.org/10.1038/s41598-019-41227-9)
+(2019)
+
 
 
 Please cite the above reference if using this code or data to generate new results. 
@@ -23,7 +27,6 @@ also available [on github](https://github.com/otoolej/burst_detector)). See
 [references](#references) [1,2] for more details on these.
 
 
-__*NB: feature set (as .csv file) will be included after publication.*__
 
 
 ## Require packages

data/coeffs_fixedEffects_MM_v1.csv

@@ -1,35 +1,35 @@
- # feature, intercept, Ici1, Ici2, time, Tci1, Tci2, GA, Gci1, Gci2, time:GA, TGci1, TGci2 
-spectral_power..1.,-180.1,-1436.3, 952.6,1229.0,  655.5,1835.1,  18.4,  -22.3,  62.5, -38.7,  -60.0, -17.8
-spectral_power..2.,29.829,-30.06,85.2787,33.480,  7.13,58.0620,-0.359, -2.38, 1.8432,-1.032, -1.90,-0.0827
-spectral_power..3.,4.79,3.695,5.86,1.08,0.575,1.63,,,,,,
-spectral_power..4.,1.622,1.13,2.090,0.589,0.23,0.913,,,,,,
+# feature, intercept, Ici1, Ici2, time, Tci1, Tci2, GA, Gci1, Gci2, time:GA, TGci1, TGci2 
+spectral_power..1.,-180.1,-1457.4,1105.6,1229.0,  603.3,1833.7,  18.4,  -27.1,  64.1, -38.7,  -60.0, -16.1
+spectral_power..2.,29.822,-33.76,90.94,33.483,  9.45,59.88,-0.359, -2.60, 1.88,-1.032, -1.94,-0.16
+spectral_power..3.,4.79,3.743,5.77,1.08,0.574,1.65,,,,,,
+spectral_power..4.,1.622,1.122,2.119,0.589,0.235,0.959,,,,,,
 spectral_relative_power..1.,93.5,92.9,94,,,,,,,,,
-spectral_relative_power..2., 5.12, 4.507, 5.8287,-0.38,-0.709,-0.0537,,,,,,
-spectral_relative_power..3., 1.14669,-0.9815, 3.437,-1.71700,-3.3462,-0.188, 0.00728,-0.0734, 0.082, 0.05774, 0.0037, 0.115
-spectral_relative_power..4.,-0.6856,-1.3447,-0.0487,,,, 0.0407, 0.0181, 0.0648,,,
+spectral_relative_power..2., 5.12, 4.442, 5.7630,-0.38,-0.704,-0.0315,,,,,,
+spectral_relative_power..3., 1.14669,-1.14211, 3.5818,-1.71699,-3.44362,-0.1466, 0.00728,-0.07919, 0.0872, 0.05774, 0.00249, 0.1182
+spectral_relative_power..4.,-0.6856,-1.2993,-0.0947,,,, 0.0407, 0.0196, 0.0624,,,
 spectral_flatness..1.,0.269,0.26,0.278,,,,,,,,,
-spectral_flatness..2.,0.54401,0.38920,0.6831,0.00950,0.00329,0.0156,0.00695,0.00208,0.0125,,,
-spectral_flatness..3.,0.62048,0.55645,0.68533,0.00955,0.00273,0.01603,0.00723,0.00480,0.00949,,,
+spectral_flatness..2.,0.54401,0.40131,0.7055,0.00950,0.00351,0.0152,0.00695,0.00132,0.0122,,,
+spectral_flatness..3.,0.62048,0.55691,0.68516,0.00955,0.00281,0.01612,0.00723,0.00489,0.00947,,,
 spectral_flatness..4.,0.665,0.656,0.676,,,,,,,,,
-spectral_edge_frequency, 6.2846, 1.11000,12.0275,-3.6348,-7.12350,-0.3179,-0.0992,-0.30037, 0.0852, 0.1235, 0.00545, 0.2436
-FD,0.9775,0.81649,1.133,,,,0.0124,0.00688,0.018,,,
-amplitude_skew..1., 0.610522,-0.2937, 1.54206, 0.723368, 0.1407, 1.28159,-0.000956,-0.0332, 0.03255,-0.026347,-0.0460,-0.00609
-amplitude_skew..2., 0.6013, 0.4763, 0.71880,-0.0145,-0.0254,-0.00390,-0.0144,-0.0185,-0.00983,,,
-amplitude_skew..3., 0.15206, 0.12859, 0.17766,,,,-0.00423,-0.00511,-0.00341,,,
-amplitude_skew..4., 0.8910, 0.694, 1.088,,,,-0.0231,-0.030,-0.016,,,
-amplitude_kurtosis..1.,25.688,19.614,31.296,,,,-0.622,-0.818,-0.411,,,
-amplitude_kurtosis..2.,78.35,61.22,94.61,-2.52,-4.10,-1.01,-1.94,-2.53,-1.37,,,
-amplitude_kurtosis..3.,85.87,66.8,105.51,,,,-2.31,-3.0, -1.65,,,
-amplitude_kurtosis..4.,82.67,62.44,103.46,,,,-2.23,-2.99, -1.51,,,
-connectivity_coh_mean..1., 0.4481, 0.3140, 0.5807,,,,-0.0106,-0.0153,-0.0059,,,
-connectivity_coh_mean..2., 0.4209, 0.3275, 0.51374,,,,-0.0103,-0.0136,-0.00704,,,
-connectivity_coh_mean..3., 0.38125, 0.2755, 0.48207,,,,-0.00964,-0.0132,-0.00588,,,
-connectivity_coh_mean..4., 0.25549, 0.17111, 0.33142,,,,-0.00568,-0.00834,-0.00278,,,
-rEEG_median,23.72,20.17,27.57, 5.17, 3.17, 7.05,,,,,,
-rEEG_lower_margin,-7.513,-16.729,1.367, 1.189,  0.255,2.104, 0.578,  0.252,0.902,,,
-rEEG_upper_margin, 92.665,-147.61,336.51,175.866,  51.71,298.13,  0.978,  -7.74,  9.43, -5.901, -10.31, -1.54
-rEEG_asymmetry, 1.4456, 1.1805, 1.7330,-0.0372,-0.0593,-0.0157,-0.0267,-0.0363,-0.0171,,,
-IBI_length_max,34.813,22.92,47.131,-0.994,-1.92,-0.108,-0.807,-1.23,-0.393,,,
-IBI_length_median, 6.219, 3.764, 8.5497,,,,-0.116,-0.201,-0.0324,,,
-IBI_burst_prc,3.50,-34.800,41.80,5.77,  2.803, 8.77,2.26,  0.908, 3.59,,,
-IBI_burst_number,514.9,370.0,665.53,-26.9,-42.9,-10.73,-10.0,-15.3, -4.85,,,
+spectral_edge_frequency, 6.2866, 1.08161,11.9100,-3.6358,-7.09981,-0.2256,-0.0993,-0.29630, 0.0856, 0.1235, 0.00557, 0.2462
+FD,0.9775,0.82034,1.1373,,,,0.0124,0.00677,0.0178,,,
+amplitude_skew..1., 0.610531,-0.3586, 1.57228, 0.723401, 0.1558, 1.31125,-0.000957,-0.0358, 0.03391,-0.026349,-0.0467,-0.00674
+amplitude_skew..2., 0.6013, 0.4701, 0.72481,-0.0145,-0.0266,-0.00321,-0.0144,-0.0187,-0.00996,,,
+amplitude_skew..3., 0.15206, 0.12790, 0.17617,,,,-0.00423,-0.00507,-0.00339,,,
+amplitude_skew..4., 0.8910, 0.6857, 1.1050,,,,-0.0231,-0.0307,-0.0158,,,
+amplitude_kurtosis..1.,25.687,19.615,32.12,,,,-0.622,-0.851,-0.41,,,
+amplitude_kurtosis..2.,78.34,62.11,96.959,-2.52,-4.08,-0.998,-1.94,-2.61,-1.378,,,
+amplitude_kurtosis..3.,85.87,65.47,105.9,,,,-2.31,-3.02, -1.6,,,
+amplitude_kurtosis..4.,82.67,61.47,104.30,,,,-2.23,-3.01, -1.47,,,
+connectivity_coh_mean..1., 0.4481, 0.3133, 0.5747,,,,-0.0106,-0.0152,-0.0058,,,
+connectivity_coh_mean..2., 0.4209, 0.3355, 0.50647,,,,-0.0103,-0.0133,-0.00723,,,
+connectivity_coh_mean..3., 0.38125, 0.2713, 0.48090,,,,-0.00964,-0.0132,-0.00583,,,
+connectivity_coh_mean..4., 0.25549, 0.17544, 0.33723,,,,-0.00568,-0.00852,-0.00283,,,
+rEEG_median,23.72,20.37,27.19, 5.17, 3.36, 7.05,,,,,,
+rEEG_lower_margin,-7.513,-16.647,1.456, 1.189,  0.307,2.123, 0.578,  0.269,0.915,,,
+rEEG_upper_margin, 92.661,-166.38,352.15,175.870,  52.90,295.09,  0.979,  -8.15, 10.29, -5.901, -10.24, -1.47
+rEEG_asymmetry, 1.4457, 1.1376, 1.7084,-0.0372,-0.0587,-0.0158,-0.0267,-0.0360,-0.0159,,,
+IBI_length_max,34.813,23.31,46.9330,-0.994,-1.88,-0.0665,-0.807,-1.23,-0.3921,,,
+IBI_length_median, 6.219, 3.764, 8.5181,,,,-0.116,-0.198,-0.0281,,,
+IBI_burst_prc,3.50,-31.733,40.11,5.77,  2.894, 8.76,2.26,  0.918, 3.52,,,
+IBI_burst_number,514.9,365.1,666.25,-26.9,-42.9,-10.02,-10.0,-15.8, -4.66,,,