protoDist: Compute distances between prototypes
In SOMbrero: SOM Bound to Realize Euclidean and Relational Outputs
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
Compute distances, either between all prototypes
(mode = "complete") or only between prototypes' neighbours
(mode = "neighbors").
Usage
1
Arguments
object
a somRes object.
mode
Specifies which distances should be computed (default to
"complete").
radius
Radius used to fetch the neighbors (default to 1). The distance
used to compute the neighbors is the Euclidean distance.
...
Not used.
Details
When mode="complete", distances between all prototypes are
computed. When mode="neighbors", distances are computed only between
the prototypes and their neighbors. If the data were preprocessed during the
SOM training procedure, the distances are computed on the normalized values
of the prototypes.
Value
When mode = "complete", the function returns a square matrix
which dimensions are equal to the product of the grid dimensions.
When mode = "neighbors", the function returns a list which length is
equal to the product of the grid dimensions; the length of each item is equal
to the number of neighbors. Neurons are considered to have 8 neighbors at
most (i.e., two neurons are neighbors if they have an Euclidean
distance smaller than radius. Natural choice for radius is
1 for hexagonal topology and 1 or sqrt(2) for square
topology (4 and 8 neighbors respectively).
Author(s)
Madalina Olteanu olteanu@ceremade.dauphine.fr
Nathalie Vialaneix nathalie.vialaneix@inrae.fr
See Also
Examples
1
2
3
Example output
Loading required package: igraph
Attaching package: ‘igraph’
The following objects are masked from ‘package:stats’:
decompose, spectrum
The following object is masked from ‘package:base’:
union
Loading required package: markdown
***********************************************************
This is 'SOMbrero' package, v 1.3.1
Citation details with citation('SOMbrero')
Further information with help(SOMbrero)...
Use sombreroGUI() to start the Graphical Interface.
***********************************************************
1 2 3 4 5 6 7
1 0.0000000 0.3178170 0.7408293 1.1873168 1.5535594 0.4242205 0.2704839
2 0.3178170 0.0000000 0.4241642 0.8716052 1.2385739 0.6765640 0.3694890
3 0.7408293 0.4241642 0.0000000 0.4476473 0.8148699 1.0539550 0.7145318
4 1.1873168 0.8716052 0.4476473 0.0000000 0.3673269 1.4750979 1.1335358
5 1.5535594 1.2385739 0.8148699 0.3673269 0.0000000 1.8273535 1.4873385
6 0.4242205 0.6765640 1.0539550 1.4750979 1.8273535 0.0000000 0.3420686
7 0.2704839 0.3694890 0.7145318 1.1335358 1.4873385 0.3420686 0.0000000
8 0.5694140 0.3115716 0.2962500 0.6786450 1.0298408 0.7984145 0.4577351
9 1.0335849 0.7289397 0.3318952 0.2241131 0.5448079 1.2840738 0.9449666
10 1.4308620 1.1205963 0.7028318 0.2747054 0.1693646 1.6836295 1.3459022
11 1.0348050 1.2591381 1.5837690 1.9594793 2.2823774 0.6110457 0.8924930
12 0.7578400 0.9369763 1.2376949 1.6078411 1.9314759 0.3694616 0.5677968
13 0.5971279 0.5923354 0.7778170 1.1147570 1.4322971 0.5125970 0.3277878
14 0.8660063 0.6286171 0.4404700 0.5973509 0.8831257 1.0088492 0.6943626
15 1.2589775 0.9673679 0.5901318 0.3271829 0.4486932 1.4632733 1.1347884
16 1.6408078 1.8534736 2.1486381 2.4903603 2.7871109 1.2173883 1.4842460
17 1.3755262 1.5681803 1.8490598 2.1855254 2.4818605 0.9584404 1.1992039
18 1.0340019 1.1585036 1.3881543 1.7019917 1.9917703 0.6777154 0.8048885
19 0.8791876 0.8215290 0.8852633 1.1225141 1.3897981 0.7751266 0.6129033
20 1.0814771 0.8567636 0.6390679 0.6586858 0.8605283 1.1772881 0.8866896
21 2.0544193 2.2609021 2.5412032 2.8642276 3.1453950 1.6313879 1.8916124
22 1.8606525 2.0561706 2.3273826 2.6460001 2.9259879 1.4403025 1.6874070
23 1.5406395 1.7032690 1.9462413 2.2496035 2.5238369 1.1366351 1.3396851
24 1.1838512 1.2604531 1.4294616 1.6941465 1.9544154 0.8675581 0.9329772
25 1.0367296 0.9561532 0.9633482 1.1401936 1.3723707 0.9349396 0.7728872
8 9 10 11 12 13 14
1 0.5694140 1.0335849 1.4308620 1.0348050 0.7578400 0.5971279 0.8660063
2 0.3115716 0.7289397 1.1205963 1.2591381 0.9369763 0.5923354 0.6286171
3 0.2962500 0.3318952 0.7028318 1.5837690 1.2376949 0.7778170 0.4404700
4 0.6786450 0.2241131 0.2747054 1.9594793 1.6078411 1.1147570 0.5973509
5 1.0298408 0.5448079 0.1693646 2.2823774 1.9314759 1.4322971 0.8831257
6 0.7984145 1.2840738 1.6836295 0.6110457 0.3694616 0.5125970 1.0088492
7 0.4577351 0.9449666 1.3459022 0.8924930 0.5677968 0.3277878 0.6943626
8 0.0000000 0.4877645 0.8894063 1.2963087 0.9473204 0.4818723 0.3170686
9 0.4877645 0.0000000 0.4019441 1.7461652 1.3943448 0.8977335 0.3735323
10 0.8894063 0.4019441 0.0000000 2.1234045 1.7731703 1.2734218 0.7204601
11 1.2963087 1.7461652 2.1234045 0.0000000 0.3520920 0.8507098 1.4045566
12 0.9473204 1.3943448 1.7731703 0.3520920 0.0000000 0.4999031 1.0554554
13 0.4818723 0.8977335 1.2734218 0.8507098 0.4999031 0.0000000 0.5562842
14 0.3170686 0.3735323 0.7204601 1.4045566 1.0554554 0.5562842 0.0000000
15 0.6930269 0.2605406 0.2795068 1.8675400 1.5199832 1.0217625 0.4658817
16 1.8543146 2.2697204 2.6219613 0.6064133 0.9191366 1.3806551 1.9067395
17 1.5538600 1.9645613 2.3167698 0.3685392 0.6314393 1.0775414 1.6012172
18 1.0924176 1.4796176 1.8261178 0.4265197 0.3142711 0.6105852 1.1127605
19 0.6157947 0.8989165 1.2224726 0.9640214 0.6460432 0.2879389 0.5254610
20 0.5454165 0.4585732 0.6915596 1.5004032 1.1630602 0.6842219 0.2290312
21 2.2455574 2.6416398 2.9783114 1.0206097 1.3242334 1.7663328 2.2726587
22 2.0315129 2.4232193 2.7588385 0.8338946 1.1197287 1.5511985 2.0537610
23 1.6506389 2.0263130 2.3563541 0.5826310 0.7832137 1.1688552 1.6551531
24 1.1405811 1.4706616 1.7862895 0.6350482 0.5219592 0.6752231 1.0973415
25 0.7190423 0.9209502 1.2036693 1.0723852 0.7767204 0.4503646 0.5572813
15 16 17 18 19 20 21
1 1.2589775 1.6408078 1.3755262 1.0340019 0.8791876 1.0814771 2.0544193
2 0.9673679 1.8534736 1.5681803 1.1585036 0.8215290 0.8567636 2.2609021
3 0.5901318 2.1486381 1.8490598 1.3881543 0.8852633 0.6390679 2.5412032
4 0.3271829 2.4903603 2.1855254 1.7019917 1.1225141 0.6586858 2.8642276
5 0.4486932 2.7871109 2.4818605 1.9917703 1.3897981 0.8605283 3.1453950
6 1.4632733 1.2173883 0.9584404 0.6777154 0.7751266 1.1772881 1.6313879
7 1.1347884 1.4842460 1.1992039 0.8048885 0.6129033 0.8866896 1.8916124
8 0.6930269 1.8543146 1.5538600 1.0924176 0.6157947 0.5454165 2.2455574
9 0.2605406 2.2697204 1.9645613 1.4796176 0.8989165 0.4585732 2.6416398
10 0.2795068 2.6219613 2.3167698 1.8261178 1.2224726 0.6915596 2.9783114
11 1.8675400 0.6064133 0.3685392 0.4265197 0.9640214 1.5004032 1.0206097
12 1.5199832 0.9191366 0.6314393 0.3142711 0.6460432 1.1630602 1.3242334
13 1.0217625 1.3806551 1.0775414 0.6105852 0.2879389 0.6842219 1.7663328
14 0.4658817 1.9067395 1.6012172 1.1127605 0.5254610 0.2290312 2.2726587
15 0.0000000 2.3516788 2.0469230 1.5555180 0.9485152 0.4122360 2.7033532
16 2.3516788 0.0000000 0.3056046 0.7963138 1.4048423 1.9543409 0.4143859
17 2.0469230 0.3056046 0.0000000 0.4915611 1.1010452 1.6512356 0.6947122
18 1.5555180 0.7963138 0.4915611 0.0000000 0.6098425 1.1603892 1.1629165
19 0.9485152 1.4048423 1.1010452 0.6098425 0.0000000 0.5506592 1.7562793
20 0.4122360 1.9543409 1.6512356 1.1603892 0.5506592 0.0000000 2.2972550
21 2.7033532 0.4143859 0.6947122 1.1629165 1.7562793 2.2972550 0.0000000
22 2.4838161 0.2485315 0.4883687 0.9454023 1.5367972 2.0777898 0.2195744
23 2.0806484 0.3519411 0.2318452 0.5582924 1.1350659 1.6737731 0.6237036
24 1.5091223 0.8823263 0.5978739 0.2235936 0.5720155 1.1001523 1.1989014
25 0.9247886 1.4621966 1.1644495 0.6838115 0.1632056 0.5129428 1.7904188
22 23 24 25
1 1.8606525 1.5406395 1.1838512 1.0367296
2 2.0561706 1.7032690 1.2604531 0.9561532
3 2.3273826 1.9462413 1.4294616 0.9633482
4 2.6460001 2.2496035 1.6941465 1.1401936
5 2.9259879 2.5238369 1.9544154 1.3723707
6 1.4403025 1.1366351 0.8675581 0.9349396
7 1.6874070 1.3396851 0.9329772 0.7728872
8 2.0315129 1.6506389 1.1405811 0.7190423
9 2.4232193 2.0263130 1.4706616 0.9209502
10 2.7588385 2.3563541 1.7862895 1.2036693
11 0.8338946 0.5826310 0.6350482 1.0723852
12 1.1197287 0.7832137 0.5219592 0.7767204
13 1.5511985 1.1688552 0.6752231 0.4503646
14 2.0537610 1.6551531 1.0973415 0.5572813
15 2.4838161 2.0806484 1.5091223 0.9247886
16 0.2485315 0.3519411 0.8823263 1.4621966
17 0.4883687 0.2318452 0.5978739 1.1644495
18 0.9454023 0.5582924 0.2235936 0.6838115
19 1.5367972 1.1350659 0.5720155 0.1632056
20 2.0777898 1.6737731 1.1001523 0.5129428
21 0.2195744 0.6237036 1.1989014 1.7904188
22 0.0000000 0.4045136 0.9798912 1.5714013
23 0.4045136 0.0000000 0.5754035 1.1669217
24 0.9798912 0.5754035 0.0000000 0.5915595
25 1.5714013 1.1669217 0.5915595 0.0000000
SOMbrero documentation built on Jan. 4, 2022, 1:07 a.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
Compute distances, either between all prototypes
(mode = "complete") or only between prototypes' neighbours
(mode = "neighbors").
Usage
1 |
Arguments
object |
a |
mode |
Specifies which distances should be computed (default to
|
radius |
Radius used to fetch the neighbors (default to 1). The distance used to compute the neighbors is the Euclidean distance. |
... |
Not used. |
Details
When mode="complete", distances between all prototypes are
computed. When mode="neighbors", distances are computed only between
the prototypes and their neighbors. If the data were preprocessed during the
SOM training procedure, the distances are computed on the normalized values
of the prototypes.
Value
When mode = "complete", the function returns a square matrix
which dimensions are equal to the product of the grid dimensions.
When mode = "neighbors", the function returns a list which length is
equal to the product of the grid dimensions; the length of each item is equal
to the number of neighbors. Neurons are considered to have 8 neighbors at
most (i.e., two neurons are neighbors if they have an Euclidean
distance smaller than radius. Natural choice for radius is
1 for hexagonal topology and 1 or sqrt(2) for square
topology (4 and 8 neighbors respectively).
Author(s)
Madalina Olteanu olteanu@ceremade.dauphine.fr
Nathalie Vialaneix nathalie.vialaneix@inrae.fr
See Also
Examples
1 2 3 |
Example output
Loading required package: igraph
Attaching package: ‘igraph’
The following objects are masked from ‘package:stats’:
decompose, spectrum
The following object is masked from ‘package:base’:
union
Loading required package: markdown
***********************************************************
This is 'SOMbrero' package, v 1.3.1
Citation details with citation('SOMbrero')
Further information with help(SOMbrero)...
Use sombreroGUI() to start the Graphical Interface.
***********************************************************
1 2 3 4 5 6 7
1 0.0000000 0.3178170 0.7408293 1.1873168 1.5535594 0.4242205 0.2704839
2 0.3178170 0.0000000 0.4241642 0.8716052 1.2385739 0.6765640 0.3694890
3 0.7408293 0.4241642 0.0000000 0.4476473 0.8148699 1.0539550 0.7145318
4 1.1873168 0.8716052 0.4476473 0.0000000 0.3673269 1.4750979 1.1335358
5 1.5535594 1.2385739 0.8148699 0.3673269 0.0000000 1.8273535 1.4873385
6 0.4242205 0.6765640 1.0539550 1.4750979 1.8273535 0.0000000 0.3420686
7 0.2704839 0.3694890 0.7145318 1.1335358 1.4873385 0.3420686 0.0000000
8 0.5694140 0.3115716 0.2962500 0.6786450 1.0298408 0.7984145 0.4577351
9 1.0335849 0.7289397 0.3318952 0.2241131 0.5448079 1.2840738 0.9449666
10 1.4308620 1.1205963 0.7028318 0.2747054 0.1693646 1.6836295 1.3459022
11 1.0348050 1.2591381 1.5837690 1.9594793 2.2823774 0.6110457 0.8924930
12 0.7578400 0.9369763 1.2376949 1.6078411 1.9314759 0.3694616 0.5677968
13 0.5971279 0.5923354 0.7778170 1.1147570 1.4322971 0.5125970 0.3277878
14 0.8660063 0.6286171 0.4404700 0.5973509 0.8831257 1.0088492 0.6943626
15 1.2589775 0.9673679 0.5901318 0.3271829 0.4486932 1.4632733 1.1347884
16 1.6408078 1.8534736 2.1486381 2.4903603 2.7871109 1.2173883 1.4842460
17 1.3755262 1.5681803 1.8490598 2.1855254 2.4818605 0.9584404 1.1992039
18 1.0340019 1.1585036 1.3881543 1.7019917 1.9917703 0.6777154 0.8048885
19 0.8791876 0.8215290 0.8852633 1.1225141 1.3897981 0.7751266 0.6129033
20 1.0814771 0.8567636 0.6390679 0.6586858 0.8605283 1.1772881 0.8866896
21 2.0544193 2.2609021 2.5412032 2.8642276 3.1453950 1.6313879 1.8916124
22 1.8606525 2.0561706 2.3273826 2.6460001 2.9259879 1.4403025 1.6874070
23 1.5406395 1.7032690 1.9462413 2.2496035 2.5238369 1.1366351 1.3396851
24 1.1838512 1.2604531 1.4294616 1.6941465 1.9544154 0.8675581 0.9329772
25 1.0367296 0.9561532 0.9633482 1.1401936 1.3723707 0.9349396 0.7728872
8 9 10 11 12 13 14
1 0.5694140 1.0335849 1.4308620 1.0348050 0.7578400 0.5971279 0.8660063
2 0.3115716 0.7289397 1.1205963 1.2591381 0.9369763 0.5923354 0.6286171
3 0.2962500 0.3318952 0.7028318 1.5837690 1.2376949 0.7778170 0.4404700
4 0.6786450 0.2241131 0.2747054 1.9594793 1.6078411 1.1147570 0.5973509
5 1.0298408 0.5448079 0.1693646 2.2823774 1.9314759 1.4322971 0.8831257
6 0.7984145 1.2840738 1.6836295 0.6110457 0.3694616 0.5125970 1.0088492
7 0.4577351 0.9449666 1.3459022 0.8924930 0.5677968 0.3277878 0.6943626
8 0.0000000 0.4877645 0.8894063 1.2963087 0.9473204 0.4818723 0.3170686
9 0.4877645 0.0000000 0.4019441 1.7461652 1.3943448 0.8977335 0.3735323
10 0.8894063 0.4019441 0.0000000 2.1234045 1.7731703 1.2734218 0.7204601
11 1.2963087 1.7461652 2.1234045 0.0000000 0.3520920 0.8507098 1.4045566
12 0.9473204 1.3943448 1.7731703 0.3520920 0.0000000 0.4999031 1.0554554
13 0.4818723 0.8977335 1.2734218 0.8507098 0.4999031 0.0000000 0.5562842
14 0.3170686 0.3735323 0.7204601 1.4045566 1.0554554 0.5562842 0.0000000
15 0.6930269 0.2605406 0.2795068 1.8675400 1.5199832 1.0217625 0.4658817
16 1.8543146 2.2697204 2.6219613 0.6064133 0.9191366 1.3806551 1.9067395
17 1.5538600 1.9645613 2.3167698 0.3685392 0.6314393 1.0775414 1.6012172
18 1.0924176 1.4796176 1.8261178 0.4265197 0.3142711 0.6105852 1.1127605
19 0.6157947 0.8989165 1.2224726 0.9640214 0.6460432 0.2879389 0.5254610
20 0.5454165 0.4585732 0.6915596 1.5004032 1.1630602 0.6842219 0.2290312
21 2.2455574 2.6416398 2.9783114 1.0206097 1.3242334 1.7663328 2.2726587
22 2.0315129 2.4232193 2.7588385 0.8338946 1.1197287 1.5511985 2.0537610
23 1.6506389 2.0263130 2.3563541 0.5826310 0.7832137 1.1688552 1.6551531
24 1.1405811 1.4706616 1.7862895 0.6350482 0.5219592 0.6752231 1.0973415
25 0.7190423 0.9209502 1.2036693 1.0723852 0.7767204 0.4503646 0.5572813
15 16 17 18 19 20 21
1 1.2589775 1.6408078 1.3755262 1.0340019 0.8791876 1.0814771 2.0544193
2 0.9673679 1.8534736 1.5681803 1.1585036 0.8215290 0.8567636 2.2609021
3 0.5901318 2.1486381 1.8490598 1.3881543 0.8852633 0.6390679 2.5412032
4 0.3271829 2.4903603 2.1855254 1.7019917 1.1225141 0.6586858 2.8642276
5 0.4486932 2.7871109 2.4818605 1.9917703 1.3897981 0.8605283 3.1453950
6 1.4632733 1.2173883 0.9584404 0.6777154 0.7751266 1.1772881 1.6313879
7 1.1347884 1.4842460 1.1992039 0.8048885 0.6129033 0.8866896 1.8916124
8 0.6930269 1.8543146 1.5538600 1.0924176 0.6157947 0.5454165 2.2455574
9 0.2605406 2.2697204 1.9645613 1.4796176 0.8989165 0.4585732 2.6416398
10 0.2795068 2.6219613 2.3167698 1.8261178 1.2224726 0.6915596 2.9783114
11 1.8675400 0.6064133 0.3685392 0.4265197 0.9640214 1.5004032 1.0206097
12 1.5199832 0.9191366 0.6314393 0.3142711 0.6460432 1.1630602 1.3242334
13 1.0217625 1.3806551 1.0775414 0.6105852 0.2879389 0.6842219 1.7663328
14 0.4658817 1.9067395 1.6012172 1.1127605 0.5254610 0.2290312 2.2726587
15 0.0000000 2.3516788 2.0469230 1.5555180 0.9485152 0.4122360 2.7033532
16 2.3516788 0.0000000 0.3056046 0.7963138 1.4048423 1.9543409 0.4143859
17 2.0469230 0.3056046 0.0000000 0.4915611 1.1010452 1.6512356 0.6947122
18 1.5555180 0.7963138 0.4915611 0.0000000 0.6098425 1.1603892 1.1629165
19 0.9485152 1.4048423 1.1010452 0.6098425 0.0000000 0.5506592 1.7562793
20 0.4122360 1.9543409 1.6512356 1.1603892 0.5506592 0.0000000 2.2972550
21 2.7033532 0.4143859 0.6947122 1.1629165 1.7562793 2.2972550 0.0000000
22 2.4838161 0.2485315 0.4883687 0.9454023 1.5367972 2.0777898 0.2195744
23 2.0806484 0.3519411 0.2318452 0.5582924 1.1350659 1.6737731 0.6237036
24 1.5091223 0.8823263 0.5978739 0.2235936 0.5720155 1.1001523 1.1989014
25 0.9247886 1.4621966 1.1644495 0.6838115 0.1632056 0.5129428 1.7904188
22 23 24 25
1 1.8606525 1.5406395 1.1838512 1.0367296
2 2.0561706 1.7032690 1.2604531 0.9561532
3 2.3273826 1.9462413 1.4294616 0.9633482
4 2.6460001 2.2496035 1.6941465 1.1401936
5 2.9259879 2.5238369 1.9544154 1.3723707
6 1.4403025 1.1366351 0.8675581 0.9349396
7 1.6874070 1.3396851 0.9329772 0.7728872
8 2.0315129 1.6506389 1.1405811 0.7190423
9 2.4232193 2.0263130 1.4706616 0.9209502
10 2.7588385 2.3563541 1.7862895 1.2036693
11 0.8338946 0.5826310 0.6350482 1.0723852
12 1.1197287 0.7832137 0.5219592 0.7767204
13 1.5511985 1.1688552 0.6752231 0.4503646
14 2.0537610 1.6551531 1.0973415 0.5572813
15 2.4838161 2.0806484 1.5091223 0.9247886
16 0.2485315 0.3519411 0.8823263 1.4621966
17 0.4883687 0.2318452 0.5978739 1.1644495
18 0.9454023 0.5582924 0.2235936 0.6838115
19 1.5367972 1.1350659 0.5720155 0.1632056
20 2.0777898 1.6737731 1.1001523 0.5129428
21 0.2195744 0.6237036 1.1989014 1.7904188
22 0.0000000 0.4045136 0.9798912 1.5714013
23 0.4045136 0.0000000 0.5754035 1.1669217
24 0.9798912 0.5754035 0.0000000 0.5915595
25 1.5714013 1.1669217 0.5915595 0.0000000
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