Data description
## [1] "Original parameters"
## [1] "meanfreq" "sd"
## [3] "freq.median" "freq.Q25"
## [5] "freq.Q75" "freq.IQR"
## [7] "time.median" "time.Q25"
## [9] "time.Q75" "time.IQR"
## [11] "skew" "kurt"
## [13] "sp.ent" "time.ent"
## [15] "entropy" "sfm"
## [17] "meanfun" "minfun"
## [19] "maxfun" "meandom"
## [21] "mindom" "maxdom"
## [23] "dfrange" "modindx"
## [25] "startdom" "enddom"
## [27] "dfslope" "meanpeakf"
## [29] "peakf" "dfDTW.D1"
## [31] "dfDTW.D2" "dfDTW.D3"
## [33] "dfDTW.D4" "spenDTW.D1"
## [35] "spenDTW.D2" "spenDTW.D3"
## [37] "spenDTW.D4" "ffDTW.D1"
## [39] "ffDTW.D2" "ffDTW.D3"
## [41] "ffDTW.D4" "multiDTW.D1"
## [43] "multiDTW.D2" "multiDTW.D3"
## [45] "multiDTW.D4" "Q1.Freq..Hz."
## [47] "Q1.Freq.Rel." "Q1.Time..s."
## [49] "Q1.Time.Rel." "Q3.Freq..Hz."
## [51] "Q3.Freq.Rel." "Q3.Time..s."
## [53] "Q3.Time.Rel." "Agg.Entropy..bits."
## [55] "Avg.Entropy..bits." "Avg.Power..dB."
## [57] "BW.90...Hz." "Center.Freq..Hz."
## [59] "Center.Time..s." "Center.Time.Rel."
## [61] "Delta.Time..s." "Energy..dB."
## [63] "Freq.5...Hz." "Freq.5..Rel."
## [65] "Freq.95...Hz." "Freq.95..Rel."
## [67] "IQR.BW..Hz." "Max.Entropy..bits."
## [69] "Max.Freq..Hz." "Max.Time..s."
## [71] "Min.Entropy..bits." "Peak.Freq..Hz."
## [73] "PFC.Avg.Slope..Hz.ms." "PFC.Max.Freq..Hz."
## [75] "PFC.Max.Slope..Hz.ms." "PFC.Min.Freq..Hz."
## [77] "PFC.Min.Slope..Hz.ms." "PFC.Num.Inf.Pts"
## [79] "Peak.Time..s." "Peak.Time.Relative"
## [81] "Time.5...s." "Time.5..Rel."
## [83] "Time.95...s." "Time.95..Rel."
## [85] "XC.D1" "XC.D2"
## [87] "XC.D3" "XC.D4"
## [89] "XC.D5" "XC.D6"
## [91] "XC.D7" "XC.D8"
## [93] "XC.D9" "XC.D10"
## [95] "RND1" "RND2"
## [97] "RND3"
Stress of MDS on acoustic structure
## [1] "Removed colinear parameters (r > 0.95"
## [1] "sp.ent" "Max.Freq..Hz." "Time.95...s."
## [4] "Time.5...s." "Q3.Time..s." "Center.Time..s."
## [7] "Max.Time..s." "Peak.Time..s." "Energy..dB."
## [10] "kurt"
## [1] "Removed SNR correlated parameters (abs(r) > 0.2)"
## [1] "Avg.Entropy..bits." "spenDTW.D1"
## [3] "Min.Entropy..bits." "minfun"
## [5] "peakf" "sd"
## [7] "sfm" "BW.90...Hz."
## [9] "Avg.Power..dB." "Energy..dB."
## [11] "sp.ent" "entropy"
## [13] "PFC.Num.Inf.Pts" "modindx"
## [15] "Agg.Entropy..bits." "freq.IQR"
## [17] "Freq.5..Rel." "Max.Entropy..bits."
## [19] "meanfun" "XC.D3"
## [21] "Freq.5...Hz." "PFC.Min.Slope..Hz.ms."
## [23] "spenDTW.D2" "Time.95...s."
## [25] "Q3.Time..s." "Max.Time..s."
## [27] "Peak.Time..s." "Center.Time..s."
## [29] "Q1.Time..s." "Time.5...s."
## [31] "Time.95..Rel." "PFC.Min.Freq..Hz."
## [33] "PFC.Max.Slope..Hz.ms." "time.median"
## [1] "Final parameters"
## [1] "meanfreq" "freq.median"
## [3] "freq.Q25" "freq.Q75"
## [5] "time.Q25" "time.Q75"
## [7] "time.IQR" "skew"
## [9] "kurt" "time.ent"
## [11] "maxfun" "meandom"
## [13] "mindom" "maxdom"
## [15] "dfrange" "startdom"
## [17] "enddom" "dfslope"
## [19] "meanpeakf" "dfDTW.D1"
## [21] "dfDTW.D2" "dfDTW.D3"
## [23] "dfDTW.D4" "spenDTW.D3"
## [25] "spenDTW.D4" "ffDTW.D1"
## [27] "ffDTW.D2" "ffDTW.D3"
## [29] "ffDTW.D4" "multiDTW.D1"
## [31] "multiDTW.D2" "multiDTW.D3"
## [33] "multiDTW.D4" "Q1.Freq..Hz."
## [35] "Q1.Freq.Rel." "Q1.Time.Rel."
## [37] "Q3.Freq..Hz." "Q3.Freq.Rel."
## [39] "Q3.Time.Rel." "Center.Freq..Hz."
## [41] "Center.Time.Rel." "Delta.Time..s."
## [43] "Freq.95...Hz." "Freq.95..Rel."
## [45] "IQR.BW..Hz." "Max.Freq..Hz."
## [47] "Peak.Freq..Hz." "PFC.Avg.Slope..Hz.ms."
## [49] "PFC.Max.Freq..Hz." "Peak.Time.Relative"
## [51] "Time.5..Rel." "XC.D1"
## [53] "XC.D2" "XC.D4"
## [55] "XC.D5" "XC.D6"
## [57] "XC.D7" "XC.D8"
## [59] "XC.D9" "XC.D10"
## [61] "RND1" "RND2"
## [63] "RND3"
Classification
Random forest On training data (with random variables)
## The following object is masked _by_ .GlobalEnv:
##
## asp.trans
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 0.93924466 0.93831848 0.92432482 0.95199637 0.03366174
## AccuracyPValue McnemarPValue
## 0.00000000 NaN
On test data (with random variables)
Proximity matrix
| SUR-E |
0.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
0.9992551 |
1.0000000 |
1.0000000 |
1.0000000 |
0.9561593 |
0.9940300 |
0.9977641 |
1.0000000 |
0.9196332 |
1.0000000 |
| CCE-I |
1.0000000 |
0.0000000 |
0.9992551 |
0.9917851 |
1.0000000 |
0.9925338 |
0.9970180 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
0.9970180 |
0.9992551 |
1.0000000 |
0.9992551 |
| CCL-L |
1.0000000 |
0.9992551 |
0.0000000 |
0.9985098 |
1.0000000 |
0.9774874 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
0.9992551 |
0.9857819 |
1.0000000 |
0.9962716 |
| BR2-A |
1.0000000 |
0.9917851 |
0.9985098 |
0.0000000 |
1.0000000 |
0.9955248 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
0.9992551 |
0.9970180 |
1.0000000 |
1.0000000 |
| SUR-G |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
0.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
0.9917851 |
1.0000000 |
1.0000000 |
0.9797542 |
0.9985098 |
1.0000000 |
1.0000000 |
| LOC-A |
0.9992551 |
0.9925338 |
0.9774874 |
0.9955248 |
1.0000000 |
0.0000000 |
1.0000000 |
0.9992551 |
0.9985098 |
1.0000000 |
1.0000000 |
0.9992551 |
0.9789990 |
1.0000000 |
1.0000000 |
| LOC-D |
1.0000000 |
0.9970180 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
0.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
0.9992551 |
1.0000000 |
0.9977641 |
| BR1-C |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
0.9992551 |
1.0000000 |
0.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
0.9895368 |
1.0000000 |
1.0000000 |
1.0000000 |
| HC2-B |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
0.9917851 |
0.9985098 |
1.0000000 |
1.0000000 |
0.0000000 |
1.0000000 |
0.9985098 |
1.0000000 |
0.9992551 |
0.9992551 |
1.0000000 |
| SUR-K |
0.9561593 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
0.0000000 |
0.9970180 |
1.0000000 |
1.0000000 |
0.9721845 |
1.0000000 |
| HC2-G |
0.9940300 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
0.9985098 |
0.9970180 |
0.0000000 |
1.0000000 |
1.0000000 |
0.9917851 |
1.0000000 |
| SUR-D |
0.9977641 |
0.9970180 |
0.9992551 |
0.9992551 |
0.9797542 |
0.9992551 |
1.0000000 |
0.9895368 |
1.0000000 |
1.0000000 |
1.0000000 |
0.0000000 |
1.0000000 |
0.9992551 |
0.9992551 |
| HC2-A |
1.0000000 |
0.9992551 |
0.9857819 |
0.9970180 |
0.9985098 |
0.9789990 |
0.9992551 |
1.0000000 |
0.9992551 |
1.0000000 |
1.0000000 |
1.0000000 |
0.0000000 |
1.0000000 |
0.9985098 |
| SUR-E |
0.9196332 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
0.9992551 |
0.9721845 |
0.9917851 |
0.9992551 |
1.0000000 |
0.0000000 |
1.0000000 |
| CCL-N |
1.0000000 |
0.9992551 |
0.9962716 |
1.0000000 |
1.0000000 |
1.0000000 |
0.9977641 |
1.0000000 |
1.0000000 |
1.0000000 |
1.0000000 |
0.9992551 |
0.9985098 |
1.0000000 |
0.0000000 |
Random forest On training data no ramdom variables
## The following object is masked _by_ .GlobalEnv:
##
## asp.trans
## The following objects are masked from datasets (pos = 3):
##
## asp.trans, testset, trainset
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 0.93924466 0.93831848 0.92432482 0.95199637 0.03366174
## AccuracyPValue McnemarPValue
## 0.00000000 NaN
On test data
Mantel tests
## [1] "#################"
## [1] "Songs from same song type"
## [1] "mantel R: 0.745"
## [1] "p: 1e-04"
## [1] "#################"
## [1] "Song types from same lek"
## [1] "mantel R: 0.104"
## [1] "p: 1e-04"
## [1] "#################"
## [1] "Song types from same lek in 20th century"
## [1] "mantel R: 0.139"
## [1] "p: 0.0019"
## [1] "#################"
## [1] "Song types from same lek in 21th century"
## [1] "mantel R: 0.283"
## [1] "p: 1e-04"
## [1] "#################"
## [1] "Song types from same lek and decade"
## [1] "mantel R: 0.127"
## [1] "p: 1e-04"
## [1] "#################"
## [1] "Song types from same lek and year"
## [1] "mantel R: 0.025"
## [1] "p: 0.0177"
Acoustic similarity through time
Within leks
