Appendix 16

 

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Appendix 16
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Appendix 16 – SIFR PLS-DA model outputs

 Appendix 16 reproduces the outputs of the PLS-DA modelling performed in Section 5.3.2.1. A list of the outputs is as follows:  

16.1

:

SIFR-PLS-DA-UK1 - Model overview plot.

16.2

:

SIFR-PLS-DA-UK1 – Cross permutation validation plot – class 1.

16.3

:

SIFR-PLS-DA-UK1 – Cross permutation validation plot – class 2.

16.4

:

SIFR-PLS-DA-UK1 – Model membership probabilities and YPredPS values.

16.5

:

SIFR-PLS-DA-UK2 - Model overview plot.

16.6

:

SIFR-PLS-DA-UK2 – Cross permutation validation plot – class 1.

16.7

:

SIFR-PLS-DA-UK2 – Cross permutation validation plot – class 2.

16.8

:

SIFR-PLS-DA-UK2 – Cross permutation validation plot – class 3.

16.9

:

SIFR-PLS-DA-UK2 – Model membership probabilities and YPredPS values.

16.10

:

SIFR-PLS-DA-SE1 - Model overview plot.

16.11

:

SIFR-PLS-DA-SE1 – Cross permutation validation plot – class 1.

16.12

:

SIFR-PLS-DA-SE1 – Cross permutation validation plot – class 2.

16.13

:

SIFR-PLS-DA-SE1 – Model membership probabilities and YPredPS values.

16.14

:

SIFR-PLS-DA-US1 - Model overview plot.

16.15

:

SIFR-PLS-DA-US1 – Cross permutation validation plot – class 1.

16.16

:

SIFR-PLS-DA-US1 – Cross permutation validation plot – class 2.

16.17

:

SIFR-PLS-DA-US1 – Model membership probabilities and YPredPS values.

16.1 – SIFR-PLS-DA-UK1  - Model overview plot

16.2 – SIFR-PLS-DA-UK1 – Cross permutation validation plot – class 1

 

16.3 – SIFR-PLS-DA-UK1 – Cross permutation validation plot – class 2

Primary ID

Model Membership Probability

Actual Class

YPredPS

Class 1

YPredPS

Class 2

UK1

0.67

Class 1

1.02

-0.02

UK2

0.23

Class 2

0.01

0.99

UK3

0.81

Class 1

0.95

0.05

UK4

0.29

Class 1

1.00

-0.01

UK5

0.33

Class 1

0.98

0.02

UK6

0.24

Class 2

0.00

1.00

UK7

0.82

Class 1

1.06

-0.06

UK8

0.88

Class 1

0.94

0.06

UK10

0.56

Class 1

1.03

-0.03

 

16.4 – SIFR-PLS-DA-UK1 Model membership probabilities and YPredPS values

 

16.5 – SIFR-PLS-DA-UK2 - Model overview plot

 

 

16.6 – SIFR-PLS-DA-UK2 Cross validation permutation – class 1

16.7  - SIFR-PLS-DA-UK2 Cross validation permutation – class 2

 

16.8 – SIFR-PLS-DA-UK2 Cross validation permutation – class 3

  

Primary ID

Model Membership Probability

Actual Class

YPredPS

Class 1

YPredPS

Class 2

YpredPS Class 3

UK1

0.42

Class 2

0.16

0.80

0.04

UK2

0.06

Class 3

0.16

0.03

0.81

UK3

0.87

Class 1

0.92

-0.04

0.13

UK4

0.94

Class 1

1.02

0.02

-0.03

UK5

0.62

Class 2

-0.08

1.13

-0.05

UK6

0.43

Class 3

-0.12

0.00

1.12

UK7

0.63

Class 1

0.96

0.10

-0.05

UK8

0.78

Class 2

0.12

0.84

0.04

UK10

0.27

Class 2

-0.13

1.12

0.01

 

16.9 – SIFR-PLS-UK2 Model membership probabilities and YPredPS values

16.10 – SIFR-PLS-DA-SE1 - Model overview plot

 

 

16.11 – SIFR-PLS-DA-SE1 – Cross permutation validation plot – class 1

 

16.12 – SIFR-PLS-DA-SE1 – Cross permutation validation plot – class 2

Primary ID

Model Membership Probability

Actual Class

YPredPS

Class 1

YPredPS

Class 2

SE1

0.98

Class 2

-0.06

1.06

SE2

0.38

Class 1

1.02

-0.02

SE3

0.06

Class 1

0.98

0.02

SE4

0.77

Class 1

1.02

-0.02

SE5

0.84

Class 1

0.98

0.02

SE6

0.97

Class 1

1.01

-0.01

SE7

0.81

Class 1

1.07

-0.07

SE9

0.77

Class 2

0.10

0.90

SE10

0.11

Class 1

1.00

0.00

SE11

0.15

Class 1

0.87

0.13

 

 

16.13  – SE-SIFR PLS-SE1 Model membership probabilities and YPredPS values

 

16.14 – SIFR-PLS-DA-US1 - Model overview plot

 

 

 

16.15 – SIFR-PLS-DA-US1 – Cross permutation validation plot – class 1

  

16.16 – SIFR-PLS-DA-US1 – Cross permutation validation plot – class 2

 

Primary ID

Model Membership Probability

Actual Class

YPredPS

Class 1

YPredPS

Class 2

US1

0.53

1

0.86

0.14

US2

0.19

2

0.45

0.55

US4

0.94

2

-0.17

1.17

US5

0.32

1

0.84

0.16

US6

0.75

1

1.03

-0.03

  

16.17  – SIFR-PLS-DA-US1 – Model membership probabilities and YPredPS values