Speech update
2026-04-14
MFCC2_COV.1 is really odd. Retest plot is baically a +, unclear how to fix. Reach out.
Import and clean This includes the updated datsaet sent by Vogel in March 2026
Df analysis Also creates themes
Baseline df.baseline.run2 is what use mostly.
#———————
#Same as above, but using cleaned data
Saving and printing plots
variable | r raw data | r clean data |
|---|---|---|
CPP | 0.83 | 0.83 |
F0_COV | 0.54 | 0.52 |
F0_MEAN | 0.79 | 0.84 |
F0_STD | 0.53 | 0.55 |
HNR_COV | 0.14 | 0.24 |
HNR_MEAN | 0.81 | 0.81 |
HNR_STD | 0.62 | 0.62 |
MFCC1_COV | 0.16 | 0.73 |
MFCC1_MEAN | 0.91 | 0.90 |
MFCC1_STD | 0.81 | 0.79 |
MFCC2_COV | 0.00 | 0.00 |
MFCC2_MEAN | 0.92 | 0.92 |
MFCC2_STD | 0.73 | 0.70 |
SPL_COV | 0.01 | 0.75 |
SPL_MEAN | 0.65 | 0.79 |
SPL_STD | 0.49 | 0.79 |
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## [1] "----------------------------------------------------------"Comparison forest plots
Comparison | Outcome | Beta | LCI | UCI | Pvalue |
|---|---|---|---|---|---|
ALS | F0_MEAN.1_z | -1.959 | -2.653 | -1.265 | 0.000 |
ALS | F0_STD.1_z | -1.689 | -2.629 | -0.749 | 0.000 |
ALS | MFCC1_MEAN.1_z | 1.137 | 0.326 | 1.948 | 0.006 |
ALS | CPP.1_z | 0.923 | 0.201 | 1.645 | 0.012 |
CBS | MFCC1_MEAN.1_z | 0.806 | 0.168 | 1.444 | 0.013 |
CBS | CPP.1_z | 0.683 | 0.102 | 1.264 | 0.021 |
MCBI | HNR_STD.1_z | 0.322 | 0.006 | 0.637 | 0.046 |
Other/Psychiatric | HNR_COV.1_z | -0.385 | -0.713 | -0.058 | 0.021 |
PSP | CPP.1_z | -1.299 | -1.874 | -0.724 | 0.000 |
PSP | MFCC1_MEAN.1_z | -1.142 | -1.791 | -0.494 | 0.001 |
PSP | HNR_COV.1_z | 0.084 | 0.030 | 0.139 | 0.003 |
Parkinson's disease | HNR_STD.1_z | 2.255 | 1.101 | 3.410 | 0.000 |
Parkinson's disease | HNR_COV.1_z | 0.132 | 0.024 | 0.240 | 0.017 |
bvFTD | CPP.1_z | 0.477 | 0.122 | 0.832 | 0.009 |
bvFTD | HNR_STD.1_z | -0.353 | -0.685 | -0.021 | 0.037 |
nfvPPA | HNR_STD.1_z | 0.816 | 0.384 | 1.249 | 0.000 |
nfvPPA | CPP.1_z | -0.705 | -1.184 | -0.225 | 0.004 |
svPPA | CPP.1_z | -0.873 | -1.322 | -0.424 | 0.000 |
svPPA | MFCC1_MEAN.1_z | -0.729 | -1.223 | -0.234 | 0.004 |
svPPA | HNR_COV.1_z | 0.060 | 0.015 | 0.105 | 0.009 |
svPPA | HNR_MEAN.1_z | -0.486 | -0.908 | -0.064 | 0.024 |
Signficant: by diagnosis
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## [1] "----------------------------------------------------------"Signficant: by outcome
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## [1] "----------------------------------------------------------"Comparison | Outcome | Beta | LCI | UCI | Pvalue |
|---|---|---|---|---|---|
AD | F0_MEAN.1_z | 0.744 | -0.832 | 2.319 | 0.353 |
AD | MFCC1_STD.1_z | 0.749 | -1.254 | 2.752 | 0.462 |
AD | MFCC1_MEAN.1_z | 0.730 | -1.365 | 2.825 | 0.493 |
AD | MFCC2_STD.1_z | 0.643 | -1.302 | 2.589 | 0.515 |
AD | HNR_STD.1_z | 0.471 | -1.150 | 2.093 | 0.567 |
AD | F0_STD.1_z | 0.601 | -1.726 | 2.928 | 0.611 |
AD | F0_COV.1_z | 0.523 | -1.623 | 2.669 | 0.632 |
AD | HNR_COV.1_z | 0.029 | -0.123 | 0.180 | 0.708 |
AD | MFCC1_COV.1_z | 0.507 | -2.962 | 3.976 | 0.774 |
AD | HNR_MEAN.1_z | 0.163 | -1.593 | 1.920 | 0.855 |
AD | MFCC2_COV.1_z | 0.315 | -3.832 | 4.463 | 0.881 |
AD | MFCC2_MEAN.1_z | -0.134 | -1.940 | 1.671 | 0.884 |
AD | SPL_STD.1_z | 0.238 | -3.075 | 3.552 | 0.887 |
AD | SPL_MEAN.1_z | -0.185 | -3.827 | 3.457 | 0.920 |
AD | SPL_COV.1_z | -0.179 | -5.537 | 5.179 | 0.948 |
AD | CPP.1_z | 0.011 | -1.845 | 1.866 | 0.991 |
ALS | F0_MEAN.1_z | -1.959 | -2.653 | -1.265 | 0.000 |
ALS | F0_STD.1_z | -1.689 | -2.629 | -0.749 | 0.000 |
ALS | MFCC1_MEAN.1_z | 1.137 | 0.326 | 1.948 | 0.006 |
ALS | CPP.1_z | 0.923 | 0.201 | 1.645 | 0.012 |
ALS | F0_COV.1_z | -0.819 | -1.652 | 0.014 | 0.054 |
ALS | MFCC2_STD.1_z | -0.596 | -1.352 | 0.161 | 0.122 |
ALS | MFCC1_COV.1_z | -0.927 | -2.273 | 0.419 | 0.176 |
ALS | HNR_COV.1_z | -0.018 | -0.078 | 0.041 | 0.543 |
ALS | MFCC2_COV.1_z | 0.380 | -1.223 | 1.982 | 0.641 |
ALS | MFCC2_MEAN.1_z | 0.161 | -0.545 | 0.867 | 0.654 |
ALS | SPL_STD.1_z | -0.292 | -1.572 | 0.989 | 0.654 |
ALS | SPL_MEAN.1_z | 0.304 | -1.107 | 1.715 | 0.672 |
ALS | HNR_STD.1_z | -0.132 | -0.766 | 0.501 | 0.681 |
ALS | MFCC1_STD.1_z | -0.152 | -0.927 | 0.624 | 0.701 |
ALS | HNR_MEAN.1_z | 0.030 | -0.673 | 0.733 | 0.933 |
ALS | SPL_COV.1_z | -0.080 | -2.150 | 1.991 | 0.940 |
CBS | MFCC1_MEAN.1_z | 0.806 | 0.168 | 1.444 | 0.013 |
CBS | CPP.1_z | 0.683 | 0.102 | 1.264 | 0.021 |
CBS | F0_COV.1_z | -0.560 | -1.258 | 0.137 | 0.115 |
CBS | HNR_COV.1_z | -0.025 | -0.073 | 0.023 | 0.300 |
CBS | HNR_MEAN.1_z | 0.281 | -0.274 | 0.837 | 0.320 |
CBS | F0_MEAN.1_z | -0.244 | -0.738 | 0.250 | 0.332 |
CBS | F0_STD.1_z | -0.327 | -1.057 | 0.402 | 0.378 |
CBS | MFCC2_MEAN.1_z | -0.225 | -0.795 | 0.346 | 0.439 |
CBS | MFCC1_COV.1_z | -0.306 | -1.366 | 0.754 | 0.570 |
CBS | SPL_MEAN.1_z | 0.313 | -0.794 | 1.420 | 0.578 |
CBS | MFCC2_COV.1_z | 0.349 | -0.909 | 1.606 | 0.586 |
CBS | MFCC2_STD.1_z | -0.165 | -0.773 | 0.442 | 0.592 |
CBS | HNR_STD.1_z | -0.117 | -0.618 | 0.384 | 0.645 |
CBS | MFCC1_STD.1_z | 0.063 | -0.553 | 0.679 | 0.841 |
CBS | SPL_STD.1_z | 0.045 | -0.961 | 1.050 | 0.930 |
CBS | SPL_COV.1_z | -0.014 | -1.639 | 1.610 | 0.986 |
MCBI | HNR_STD.1_z | 0.322 | 0.006 | 0.637 | 0.046 |
MCBI | MFCC2_STD.1_z | 0.251 | -0.105 | 0.607 | 0.167 |
MCBI | F0_MEAN.1_z | 0.210 | -0.100 | 0.520 | 0.184 |
MCBI | MFCC2_COV.1_z | -0.259 | -0.956 | 0.438 | 0.465 |
MCBI | F0_STD.1_z | 0.146 | -0.294 | 0.587 | 0.513 |
MCBI | CPP.1_z | -0.093 | -0.435 | 0.249 | 0.594 |
MCBI | SPL_STD.1_z | -0.144 | -0.705 | 0.416 | 0.612 |
MCBI | MFCC2_MEAN.1_z | 0.074 | -0.248 | 0.396 | 0.653 |
MCBI | SPL_MEAN.1_z | 0.123 | -0.494 | 0.739 | 0.696 |
MCBI | HNR_COV.1_z | 0.004 | -0.023 | 0.031 | 0.754 |
MCBI | HNR_MEAN.1_z | 0.050 | -0.276 | 0.375 | 0.763 |
MCBI | MFCC1_MEAN.1_z | -0.040 | -0.422 | 0.342 | 0.836 |
MCBI | SPL_COV.1_z | 0.074 | -0.826 | 0.973 | 0.872 |
MCBI | MFCC1_STD.1_z | 0.029 | -0.332 | 0.389 | 0.874 |
MCBI | F0_COV.1_z | 0.009 | -0.376 | 0.395 | 0.962 |
MCBI | MFCC1_COV.1_z | -0.001 | -0.601 | 0.599 | 0.997 |
Other/Psychiatric | HNR_COV.1_z | -0.385 | -0.713 | -0.058 | 0.021 |
Other/Psychiatric | MFCC1_MEAN.1_z | -0.226 | -0.584 | 0.132 | 0.214 |
Other/Psychiatric | CPP.1_z | -0.195 | -0.517 | 0.128 | 0.236 |
Other/Psychiatric | F0_COV.1_z | 0.198 | -0.188 | 0.584 | 0.314 |
Other/Psychiatric | MFCC2_STD.1_z | 0.158 | -0.181 | 0.497 | 0.360 |
Other/Psychiatric | F0_MEAN.1_z | -0.103 | -0.366 | 0.159 | 0.439 |
Other/Psychiatric | F0_STD.1_z | 0.146 | -0.268 | 0.560 | 0.489 |
Other/Psychiatric | HNR_MEAN.1_z | -0.098 | -0.419 | 0.222 | 0.546 |
Other/Psychiatric | MFCC2_COV.1_z | -0.196 | -0.868 | 0.476 | 0.566 |
Other/Psychiatric | SPL_COV.1_z | 0.203 | -0.663 | 1.069 | 0.645 |
Other/Psychiatric | SPL_STD.1_z | -0.126 | -0.668 | 0.416 | 0.649 |
Other/Psychiatric | SPL_MEAN.1_z | 0.109 | -0.485 | 0.702 | 0.719 |
Other/Psychiatric | MFCC2_MEAN.1_z | -0.042 | -0.354 | 0.271 | 0.794 |
Other/Psychiatric | HNR_STD.1_z | 0.026 | -0.254 | 0.306 | 0.856 |
Other/Psychiatric | MFCC1_COV.1_z | -0.052 | -0.623 | 0.519 | 0.858 |
Other/Psychiatric | MFCC1_STD.1_z | -0.029 | -0.381 | 0.323 | 0.872 |
PSP | CPP.1_z | -1.299 | -1.874 | -0.724 | 0.000 |
PSP | MFCC1_MEAN.1_z | -1.142 | -1.791 | -0.494 | 0.001 |
PSP | HNR_COV.1_z | 0.084 | 0.030 | 0.139 | 0.003 |
PSP | HNR_MEAN.1_z | -0.504 | -1.065 | 0.058 | 0.078 |
PSP | F0_MEAN.1_z | 0.431 | -0.079 | 0.940 | 0.097 |
PSP | MFCC1_STD.1_z | -0.431 | -1.055 | 0.193 | 0.175 |
PSP | F0_COV.1_z | -0.374 | -1.042 | 0.293 | 0.270 |
PSP | SPL_MEAN.1_z | -0.620 | -1.738 | 0.499 | 0.276 |
PSP | MFCC1_COV.1_z | -0.328 | -1.414 | 0.758 | 0.552 |
PSP | MFCC2_MEAN.1_z | 0.166 | -0.395 | 0.727 | 0.561 |
PSP | MFCC2_COV.1_z | -0.374 | -1.645 | 0.896 | 0.562 |
PSP | MFCC2_STD.1_z | 0.139 | -0.472 | 0.750 | 0.655 |
PSP | HNR_STD.1_z | -0.092 | -0.594 | 0.410 | 0.719 |
PSP | F0_STD.1_z | -0.111 | -0.844 | 0.621 | 0.765 |
PSP | SPL_STD.1_z | -0.151 | -1.167 | 0.866 | 0.771 |
PSP | SPL_COV.1_z | -0.009 | -1.650 | 1.632 | 0.991 |
Parkinson's disease | HNR_STD.1_z | 2.255 | 1.101 | 3.410 | 0.000 |
Parkinson's disease | HNR_COV.1_z | 0.132 | 0.024 | 0.240 | 0.017 |
Parkinson's disease | CPP.1_z | -0.762 | -2.083 | 0.560 | 0.257 |
Parkinson's disease | HNR_MEAN.1_z | -0.623 | -1.875 | 0.629 | 0.328 |
Parkinson's disease | MFCC2_MEAN.1_z | -0.632 | -1.919 | 0.655 | 0.334 |
Parkinson's disease | F0_STD.1_z | -0.337 | -1.995 | 1.320 | 0.689 |
Parkinson's disease | MFCC1_STD.1_z | -0.275 | -1.702 | 1.151 | 0.704 |
Parkinson's disease | F0_MEAN.1_z | 0.205 | -0.918 | 1.329 | 0.719 |
Parkinson's disease | F0_COV.1_z | -0.265 | -1.794 | 1.264 | 0.733 |
Parkinson's disease | MFCC1_MEAN.1_z | -0.251 | -1.744 | 1.242 | 0.741 |
Parkinson's disease | SPL_MEAN.1_z | 0.304 | -2.289 | 2.897 | 0.818 |
Parkinson's disease | MFCC2_STD.1_z | -0.123 | -1.509 | 1.264 | 0.862 |
Parkinson's disease | MFCC1_COV.1_z | -0.164 | -2.635 | 2.307 | 0.896 |
Parkinson's disease | SPL_STD.1_z | -0.145 | -2.505 | 2.214 | 0.903 |
Parkinson's disease | MFCC2_COV.1_z | 0.038 | -2.915 | 2.992 | 0.980 |
Parkinson's disease | SPL_COV.1_z | 0.027 | -3.787 | 3.842 | 0.989 |
bvFTD | CPP.1_z | 0.477 | 0.122 | 0.832 | 0.009 |
bvFTD | HNR_STD.1_z | -0.353 | -0.685 | -0.021 | 0.037 |
bvFTD | F0_MEAN.1_z | -0.252 | -0.553 | 0.048 | 0.099 |
bvFTD | MFCC1_STD.1_z | -0.283 | -0.681 | 0.114 | 0.162 |
bvFTD | F0_STD.1_z | -0.235 | -0.692 | 0.222 | 0.313 |
bvFTD | F0_COV.1_z | -0.217 | -0.649 | 0.215 | 0.323 |
bvFTD | MFCC2_COV.1_z | 0.314 | -0.429 | 1.058 | 0.406 |
bvFTD | MFCC1_MEAN.1_z | 0.097 | -0.307 | 0.501 | 0.637 |
bvFTD | SPL_STD.1_z | 0.063 | -0.533 | 0.660 | 0.834 |
bvFTD | SPL_MEAN.1_z | 0.060 | -0.595 | 0.716 | 0.856 |
bvFTD | MFCC2_MEAN.1_z | -0.026 | -0.374 | 0.323 | 0.885 |
bvFTD | MFCC1_COV.1_z | -0.042 | -0.673 | 0.589 | 0.895 |
bvFTD | MFCC2_STD.1_z | 0.020 | -0.346 | 0.386 | 0.915 |
bvFTD | HNR_COV.1_z | 0.001 | -0.028 | 0.029 | 0.958 |
bvFTD | HNR_MEAN.1_z | 0.001 | -0.334 | 0.335 | 0.997 |
bvFTD | SPL_COV.1_z | 0.001 | -0.959 | 0.960 | 0.999 |
lvPPA | CPP.1_z | -0.643 | -1.976 | 0.689 | 0.343 |
lvPPA | MFCC2_MEAN.1_z | -0.492 | -1.786 | 0.801 | 0.454 |
lvPPA | MFCC2_COV.1_z | -0.916 | -3.883 | 2.052 | 0.544 |
lvPPA | MFCC1_MEAN.1_z | -0.460 | -1.959 | 1.039 | 0.546 |
lvPPA | F0_STD.1_z | 0.472 | -1.194 | 2.137 | 0.577 |
lvPPA | F0_COV.1_z | 0.397 | -1.139 | 1.933 | 0.611 |
lvPPA | MFCC1_STD.1_z | -0.351 | -1.784 | 1.082 | 0.630 |
lvPPA | HNR_STD.1_z | 0.279 | -0.887 | 1.446 | 0.637 |
lvPPA | HNR_COV.1_z | -0.018 | -0.127 | 0.090 | 0.740 |
lvPPA | MFCC1_COV.1_z | -0.372 | -2.855 | 2.110 | 0.768 |
lvPPA | SPL_MEAN.1_z | -0.380 | -2.986 | 2.226 | 0.774 |
lvPPA | F0_MEAN.1_z | -0.112 | -1.239 | 1.015 | 0.845 |
lvPPA | MFCC2_STD.1_z | -0.134 | -1.526 | 1.259 | 0.850 |
lvPPA | SPL_STD.1_z | -0.159 | -2.530 | 2.212 | 0.895 |
lvPPA | HNR_MEAN.1_z | 0.054 | -1.203 | 1.310 | 0.933 |
lvPPA | SPL_COV.1_z | 0.108 | -3.725 | 3.941 | 0.956 |
nfvPPA | HNR_STD.1_z | 0.816 | 0.384 | 1.249 | 0.000 |
nfvPPA | CPP.1_z | -0.705 | -1.184 | -0.225 | 0.004 |
nfvPPA | F0_MEAN.1_z | 0.429 | -0.002 | 0.860 | 0.051 |
nfvPPA | HNR_COV.1_z | 0.038 | -0.002 | 0.077 | 0.063 |
nfvPPA | F0_STD.1_z | 0.564 | -0.044 | 1.173 | 0.069 |
nfvPPA | MFCC1_MEAN.1_z | -0.453 | -0.993 | 0.086 | 0.099 |
nfvPPA | F0_COV.1_z | 0.463 | -0.101 | 1.027 | 0.108 |
nfvPPA | HNR_MEAN.1_z | -0.262 | -0.737 | 0.213 | 0.278 |
nfvPPA | MFCC2_COV.1_z | -0.471 | -1.516 | 0.573 | 0.375 |
nfvPPA | MFCC2_STD.1_z | 0.197 | -0.300 | 0.694 | 0.436 |
nfvPPA | SPL_MEAN.1_z | -0.111 | -1.032 | 0.809 | 0.812 |
nfvPPA | MFCC2_MEAN.1_z | 0.056 | -0.414 | 0.527 | 0.814 |
nfvPPA | MFCC1_STD.1_z | 0.053 | -0.464 | 0.569 | 0.841 |
nfvPPA | MFCC1_COV.1_z | 0.082 | -0.796 | 0.961 | 0.853 |
nfvPPA | SPL_STD.1_z | -0.028 | -0.865 | 0.810 | 0.948 |
nfvPPA | SPL_COV.1_z | 0.038 | -1.311 | 1.387 | 0.956 |
svPPA | CPP.1_z | -0.873 | -1.322 | -0.424 | 0.000 |
svPPA | MFCC1_MEAN.1_z | -0.729 | -1.223 | -0.234 | 0.004 |
svPPA | HNR_COV.1_z | 0.060 | 0.015 | 0.105 | 0.009 |
svPPA | HNR_MEAN.1_z | -0.486 | -0.908 | -0.064 | 0.024 |
svPPA | HNR_STD.1_z | 0.359 | -0.050 | 0.768 | 0.085 |
svPPA | F0_COV.1_z | 0.458 | -0.084 | 1.000 | 0.098 |
svPPA | MFCC2_STD.1_z | -0.327 | -0.784 | 0.130 | 0.161 |
svPPA | F0_STD.1_z | 0.289 | -0.281 | 0.858 | 0.319 |
svPPA | MFCC1_STD.1_z | -0.205 | -0.679 | 0.270 | 0.397 |
svPPA | MFCC2_COV.1_z | -0.384 | -1.346 | 0.578 | 0.433 |
svPPA | SPL_STD.1_z | -0.203 | -0.973 | 0.566 | 0.603 |
svPPA | SPL_MEAN.1_z | -0.166 | -1.014 | 0.681 | 0.700 |
svPPA | MFCC2_MEAN.1_z | 0.056 | -0.367 | 0.479 | 0.795 |
svPPA | MFCC1_COV.1_z | 0.042 | -0.766 | 0.849 | 0.919 |
svPPA | F0_MEAN.1_z | -0.011 | -0.395 | 0.373 | 0.956 |
svPPA | SPL_COV.1_z | 0.028 | -1.214 | 1.271 | 0.964 |
All tasks by diagnosis
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