guides/boot.md
In Albluca/ElPiGraph.R: Elastic principal graph construction
- Setup
- Effect of noisy points
- Density dependent inizialisation and trimming
radius
- Density dependent inizialisation and trimming radius and
bootstrapping
- Visualizing the effect of the trimming
radius
In real word examples, the data distributions to be approximated can be
contaminated by the presence of outliers or points belonging to a
different distribution. To address this aspect, the ElPiGraph.R package
implement two functionalities that can be used to minimize the impact of
these points: density-dependent initialization and trimming radius.
Setup
To show the effect of these features, we will start by generating noisy
datasets from the tree example present in the package, with an increased
intensity of noise. Similar ideas and concepts apply to the construction
of curves as well.
library(ElPiGraph.R)
library(igraph)
##
## Attaching package: 'igraph'
## The following objects are masked from 'package:stats':
##
## decompose, spectrum
## The following object is masked from 'package:base':
##
## union
nPoints <- round(nrow(tree_data)*.5)
NewPoints <- apply(apply(tree_data, 2, range), 2, function(x){
runif(n = nPoints, x[1], x[2])
})
TD_LowNoise <- rbind(tree_data, NewPoints)
TD_LowNoise_Cat <- c(rep("Real", nrow(tree_data)), rep("Noise", nrow(NewPoints)))
nPoints <- nrow(tree_data)*2
NewPoints <- apply(apply(tree_data, 2, range), 2, function(x){
runif(n = nPoints, x[1], x[2])
})
TD_MedNoise <- rbind(tree_data, NewPoints)
TD_MedNoise_Cat <- c(rep("Real", nrow(tree_data)), rep("Noise", nrow(NewPoints)))
nPoints <- nrow(tree_data)*8
NewPoints <- apply(apply(tree_data, 2, range), 2, function(x){
runif(n = nPoints, x[1], x[2])
})
TD_HighNoise <- rbind(tree_data, NewPoints)
TD_HighNoise_Cat <- c(rep("Real", nrow(tree_data)), rep("Noise", nrow(NewPoints)))
Effect of noisy points
By default the ElPiGraph algorithm uses all the points and generate the
initial points on the 1st PC of the data. Therefore, noise can affect
significantly the reconstructed tree.
TreeEPG <- computeElasticPrincipalTree(X = TD_LowNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE, drawPCAView = FALSE, n.cores = 4)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a chain in the 1st PC with 2 nodes"
## [1] "Constructing tree 1 of 1 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 738 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 7||50 0.04324 50 49 34 7 0 0 0.02181 0.02058 0.9679 0.9697 0.02094 0.0004823 0.02411 1.206 0
## 11.875 sec elapsed
PlotPG(X = TD_LowNoise, TargetPG = TreeEPG[[1]], GroupsLab = TD_LowNoise_Cat, DimToPlot = 1:2)
## [[1]]
TreeEPG <- computeElasticPrincipalTree(X = TD_MedNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE, drawPCAView = FALSE, n.cores = 4)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a chain in the 1st PC with 2 nodes"
## [1] "Constructing tree 1 of 1 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 1476 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|5||50 0.06049 50 49 35 5 0 0 0.03383 0.03204 0.9582 0.9604 0.02644 0.0002185 0.01092 0.5462 0
## 23.924 sec elapsed
PlotPG(X = TD_MedNoise, TargetPG = TreeEPG[[1]], GroupsLab = TD_MedNoise_Cat, DimToPlot = 1:2)
## [[1]]
TreeEPG <- computeElasticPrincipalTree(X = TD_HighNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE, drawPCAView = FALSE, n.cores = 4)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a chain in the 1st PC with 2 nodes"
## [1] "Constructing tree 1 of 1 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4428 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|0|4||50 0.06942 50 49 36 4 0 0 0.03442 0.03204 0.9619 0.9646 0.0347 0.0002977 0.01489 0.7443 0
## 29.285 sec elapsed
PlotPG(X = TD_HighNoise, TargetPG = TreeEPG[[1]], GroupsLab = TD_HighNoise_Cat, DimToPlot = 1:2)
## [[1]]
Density dependent inizialisation and trimming radius
To limit the effect of noise, we can specify a trimming radius (which
informs the algorithm to use only points with a distance lower than this
radius when computing the position of the nodes), and use a density
dependent initialization ICOver = "Density". Note that when using
ICOver = "Density", the parameter DensityRadius, which is used to
determine the area of the space with the highest density of points, need
to be specified as well.
When a trimming radius is used, tree construction becomes local, hence
it may be necessary to increase the number of points in order to better
cover all areas of the space containing the points under consideration.
Moreover certain feature of the topology may be lost due to corruption
due by the noise.
TreeEPG <- computeElasticPrincipalTree(X = TD_LowNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE, drawPCAView = FALSE,
n.cores = 4,
TrimmingRadius = .15,
ICOver = "Density", DensityRadius = .15)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 1 of 1 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 738 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.1019 50 49 39 3 0 0 0.09409 Inf 0.8615 -Inf 0.007783 5.928e-05 0.002964 0.1482 0
## 22.125 sec elapsed
PlotPG(X = TD_LowNoise, TargetPG = TreeEPG[[1]], GroupsLab = TD_LowNoise_Cat, DimToPlot = 1:2)
## [[1]]
TreeEPG <- computeElasticPrincipalTree(X = TD_MedNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE, drawPCAView = FALSE,
n.cores = 4,
TrimmingRadius = .15,
ICOver = "Density", DensityRadius = .15)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 1 of 1 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 1476 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.1601 50 49 40 4 0 0 0.1536 Inf 0.8101 -Inf 0.006474 2.614e-05 0.001307 0.06534 0
## 21.406 sec elapsed
PlotPG(X = TD_MedNoise, TargetPG = TreeEPG[[1]], GroupsLab = TD_MedNoise_Cat, DimToPlot = 1:2)
## [[1]]
TreeEPG <- computeElasticPrincipalTree(X = TD_HighNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE, drawPCAView = FALSE,
n.cores = 4,
TrimmingRadius = .15,
ICOver = "Density", DensityRadius = .15)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 1 of 1 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4428 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1||50 0.3318 50 49 46 1 0 0 0.3298 Inf 0.6352 -Inf 0.001968 3.924e-06 0.0001962 0.00981 0
## 25.035 sec elapsed
PlotPG(X = TD_HighNoise, TargetPG = TreeEPG[[1]], GroupsLab = TD_HighNoise_Cat, DimToPlot = 1:2)
## [[1]]
Density dependent inizialisation and trimming radius and bootstrapping
To further address the problem of noise in the data it advisable to use
bootstrapping. To enable bootstrapping it is sufficient to use the
parameter nReps, which defines the number of repetitions, and
ProbPoint, which defines the probability of selecting a point in each
iteration. Bootstrapping can be also helpfull to mitigate the effect of
outliers in the data, when the trimming radius is unspecified.
Note that when bootstrapped is enabled (i.e. when nRep is larger than
1), an average graph is generated by using the nodes of the graph
generated during the single execution of the algorithm. Hence if nRep
is equalt to n, the returned lists will contain n+1 ElPiGraph
structures: the n repetitions, and the final average graph.
Visualization of bootstrapped data can be easilty perfomred via the
PlorPG function. To this end, it is sufficient to pass the
bootstrapped structures via the BootPG parameter. Currently a primary
ElPiGraph structure is required (the TargetPG parameter).
It is further possible to control if the bootstrapped and target graphs
shoudl be plotted via the VizMode parameter.
nRep <- 20
TreeEPG <- computeElasticPrincipalTree(X = tree_data, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE,
drawPCAView = FALSE,
n.cores = 4,
nReps = nRep, ProbPoint = .8,
TrimmingRadius = Inf,
ICOver = "DensityProb", DensityRadius = .3)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 1 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 407 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01549 50 49 39 3 0 0 0.004223 0.003548 0.992 0.9933 0.01109 0.0001693 0.008463 0.4232 0
## 17.74 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 2 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 385 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01561 50 49 39 3 0 0 0.004097 0.0034 0.992 0.9934 0.01137 0.0001429 0.007144 0.3572 0
## 16.751 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 3 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 396 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.0158 50 49 39 3 0 0 0.004186 0.00353 0.9922 0.9934 0.01142 0.0002006 0.01003 0.5016 0
## 16.631 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Graphical output will be suppressed for the remaining replicas"
## [1] "Constructing tree 4 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 392 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01587 50 49 39 3 0 0 0.004284 0.003527 0.9922 0.9936 0.0114 0.0001878 0.009391 0.4695 0
## 15.975 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 5 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 399 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 6||50 0.01581 50 49 36 6 0 0 0.00445 0.003786 0.9916 0.9928 0.01112 0.0002393 0.01196 0.5982 0
## 17.31 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 6 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 391 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01586 50 49 39 3 0 0 0.004037 0.003327 0.9925 0.9939 0.01156 0.0002679 0.0134 0.6698 0
## 16.828 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 7 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 391 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01596 50 49 39 3 0 0 0.004905 0.004219 0.9905 0.9918 0.01078 0.0002805 0.01402 0.7012 0
## 15.969 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 8 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 397 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|2||50 0.01551 50 49 41 2 0 0 0.004026 0.003382 0.9927 0.9939 0.01109 0.0003891 0.01945 0.9727 0
## 16.789 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 9 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 404 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|2||50 0.01549 50 49 41 2 0 0 0.004039 0.003318 0.9926 0.9939 0.01101 0.0004419 0.0221 1.105 0
## 17.321 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 10 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 383 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01573 50 49 39 3 0 0 0.004033 0.003324 0.993 0.9942 0.01146 0.0002345 0.01172 0.5861 0
## 17.805 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 11 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 410 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|2||50 0.01588 50 49 41 2 0 0 0.004394 0.003693 0.9921 0.9934 0.01105 0.0004412 0.02206 1.103 0
## 16.468 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 12 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 380 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|2||50 0.0156 50 49 41 2 0 0 0.004058 0.003407 0.9925 0.9937 0.01112 0.0004255 0.02128 1.064 0
## 16.974 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 13 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 387 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01562 50 49 39 3 0 0 0.00428 0.003535 0.992 0.9934 0.0111 0.0002363 0.01182 0.5908 0
## 16.798 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 14 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 394 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01546 50 49 39 3 0 0 0.003882 0.003217 0.9927 0.994 0.01136 0.0002175 0.01088 0.5439 0
## 16.515 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 15 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 394 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01589 50 49 39 3 0 0 0.004135 0.00345 0.9922 0.9935 0.01151 0.0002429 0.01215 0.6073 0
## 16.503 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 16 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 413 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01546 50 49 39 3 0 0 0.003906 0.003229 0.9927 0.9939 0.01138 0.0001809 0.009047 0.4523 0
## 17.021 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 17 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 382 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|2||50 0.01611 50 49 41 2 0 0 0.004269 0.003526 0.9922 0.9935 0.01135 0.0004919 0.02459 1.23 0
## 16.871 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 18 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 396 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|2||50 0.01505 50 49 41 2 0 0 0.004223 0.003507 0.9922 0.9935 0.01046 0.0003645 0.01823 0.9113 0
## 17.664 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 19 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 386 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01593 50 49 39 3 0 0 0.004296 0.003628 0.9921 0.9933 0.01145 0.0001855 0.009277 0.4639 0
## 17.404 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 20 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 408 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01551 50 49 39 3 0 0 0.003897 0.003213 0.9928 0.994 0.01145 0.0001653 0.008265 0.4133 0
## 17.83 sec elapsed
## [1] "Constructing average tree"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Computing EPG with 50 nodes on 1000 points and 3 dimensions"
## [1] "Using a single core"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01088 50 49 39 3 0 0 0.001641 0.001193 0.9968 0.9977 0.009133 0.0001072 0.005359 0.268 0
## 9.252 sec elapsed
PlotPG(X = tree_data, BootPG = TreeEPG[1:nRep], TargetPG = TreeEPG[[nRep+1]], DimToPlot = 1:2, VizMode = c("Target", "Boot"))
## [[1]]
PlotPG(X = tree_data, BootPG = TreeEPG[1:nRep], TargetPG = TreeEPG[[nRep+1]], DimToPlot = 1:2, VizMode = "Boot")
## [[1]]
PlotPG(X = tree_data, TargetPG = TreeEPG[[nRep+1]], DimToPlot = 1:2)
## [[1]]
nRep <- 20
TreeEPG <- computeElasticPrincipalTree(X = TD_LowNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE,
drawPCAView = FALSE,
n.cores = 4,
nReps = nRep, ProbPoint = .9,
TrimmingRadius = .155,
ICOver = "DensityProb", DensityRadius = .155)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 1 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 674 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||50 0.09967 50 49 38 5 0 0 0.09076 Inf 0.8649 -Inf 0.008838 6.769e-05 0.003385 0.1692 0
## 18.581 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 2 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 664 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 6||50 0.09261 50 49 36 6 0 0 0.08366 Inf 0.8756 -Inf 0.008901 4.391e-05 0.002196 0.1098 0
## 16.208 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 3 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 672 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 6||50 0.09199 50 49 36 6 0 0 0.08288 Inf 0.8766 -Inf 0.009058 5.442e-05 0.002721 0.136 0
## 16.095 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Graphical output will be suppressed for the remaining replicas"
## [1] "Constructing tree 4 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 665 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1||50 1.877 50 49 46 1 0 0 1.877 Inf -1.773 -Inf 3.362e-05 9.731e-07 4.865e-05 0.002433 0
## 15.574 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 5 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 664 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.09072 50 49 40 4 0 0 0.08211 Inf 0.8788 -Inf 0.008568 3.683e-05 0.001842 0.09208 0
## 16.231 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 6 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 671 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||50 0.1 50 49 38 5 0 0 0.09144 Inf 0.8673 -Inf 0.008532 2.527e-05 0.001264 0.06318 0
## 16.653 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 7 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 655 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.09426 50 49 39 3 0 0 0.08579 Inf 0.8696 -Inf 0.008432 3.175e-05 0.001588 0.07939 0
## 17.353 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 8 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 662 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 7||50 0.09301 50 49 34 7 0 0 0.08444 Inf 0.8757 -Inf 0.008527 3.976e-05 0.001988 0.0994 0
## 17.627 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 9 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 661 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 6||50 0.09687 50 49 36 6 0 0 0.08941 Inf 0.87 -Inf 0.007397 7.048e-05 0.003524 0.1762 0
## 17.474 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 10 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 667 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|5||50 0.104 50 49 35 5 0 0 0.09538 Inf 0.8613 -Inf 0.008527 7.651e-05 0.003826 0.1913 0
## 16.967 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 11 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 673 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.09588 50 49 39 3 0 0 0.08747 Inf 0.8723 -Inf 0.008373 3.283e-05 0.001642 0.08208 0
## 18.435 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 12 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 661 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2|2||50 0.1 50 49 38 2 0 0 0.09121 Inf 0.8649 -Inf 0.008775 5.056e-05 0.002528 0.1264 0
## 16.923 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 13 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 660 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.1079 50 49 40 4 0 0 0.09971 Inf 0.8543 -Inf 0.008121 3.877e-05 0.001938 0.09692 0
## 17.244 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 14 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 648 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|5||50 0.09916 50 49 35 5 0 0 0.0905 Inf 0.8657 -Inf 0.00863 2.803e-05 0.001401 0.07007 0
## 17.218 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 15 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 668 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|5||50 0.0822 50 49 35 5 0 0 0.07227 Inf 0.8942 -Inf 0.009869 6.238e-05 0.003119 0.156 0
## 18.794 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 16 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 676 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|5||50 0.09419 50 49 35 5 0 0 0.08541 Inf 0.8718 -Inf 0.008731 5.264e-05 0.002632 0.1316 0
## 19.41 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 17 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 675 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2|2||50 0.09903 50 49 38 2 0 0 0.0907 Inf 0.8664 -Inf 0.008285 4.706e-05 0.002353 0.1177 0
## 24.901 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 18 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 657 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|4||50 0.09145 50 49 37 4 0 0 0.08245 Inf 0.8794 -Inf 0.008974 2.536e-05 0.001268 0.06341 0
## 18.695 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 19 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 676 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|0|3||50 0.0879 50 49 38 3 0 0 0.07859 Inf 0.8835 -Inf 0.009268 4.764e-05 0.002382 0.1191 0
## 17.937 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 20 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 661 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.08563 50 49 40 4 0 0 0.07581 Inf 0.8876 -Inf 0.009712 0.0001098 0.005491 0.2745 0
## 17.393 sec elapsed
## [1] "Constructing average tree"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Computing EPG with 50 nodes on 1000 points and 3 dimensions"
## [1] "Using a single core"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|2||50 0.04098 50 49 41 2 0 0 0.03304 Inf 0.9357 -Inf 0.007839 0.0001005 0.005026 0.2513 0
## 8.353 sec elapsed
PlotPG(X = TD_LowNoise, BootPG = TreeEPG[1:nRep], TargetPG = TreeEPG[[nRep+1]], GroupsLab = TD_LowNoise_Cat, DimToPlot = 1:2, VizMode = "Boot")
## [[1]]
PlotPG(X = TD_LowNoise, TargetPG = TreeEPG[[nRep+1]], GroupsLab = TD_LowNoise_Cat, DimToPlot = 1:2)
## [[1]]
nRep <- 20
TreeEPG <- computeElasticPrincipalTree(X = TD_MedNoise, NumNodes = 60,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE,
drawPCAView = FALSE,
n.cores = 4,
nReps = nRep, ProbPoint = .9,
TrimmingRadius = .16,
ICOver = "DensityProb", DensityRadius = .16)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 1 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1324 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 6||60 0.1479 60 59 46 6 0 0 0.1394 Inf 0.8285 -Inf 0.008407 1.703e-05 0.001022 0.06132 0
## 29.884 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 2 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1322 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1481 60 59 48 5 0 0 0.14 Inf 0.8271 -Inf 0.008018 2.182e-05 0.001309 0.07856 0
## 28.93 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 3 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1338 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1409 60 59 48 5 0 0 0.1326 Inf 0.8334 -Inf 0.00827 1.8e-05 0.00108 0.06479 0
## 25.512 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Graphical output will be suppressed for the remaining replicas"
## [1] "Constructing tree 4 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1330 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1481 60 59 48 5 0 0 0.1406 Inf 0.8241 -Inf 0.007509 1.164e-05 0.0006985 0.04191 0
## 25.088 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 5 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1298 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||60 0.14 60 59 50 4 0 0 0.1322 Inf 0.8377 -Inf 0.00778 1.532e-05 0.0009193 0.05516 0
## 25.13 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 6 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1333 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1459 60 59 48 5 0 0 0.1372 Inf 0.8326 -Inf 0.008611 5.196e-05 0.003118 0.1871 0
## 28.057 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 7 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1321 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||60 0.1447 60 59 50 4 0 0 0.1365 Inf 0.8301 -Inf 0.008156 1.902e-05 0.001141 0.06848 0
## 31.709 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 8 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1345 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1448 60 59 48 5 0 0 0.1354 Inf 0.8325 -Inf 0.009377 5.185e-05 0.003111 0.1867 0
## 26.245 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 9 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1327 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|4||60 0.1451 60 59 47 4 0 0 0.1369 Inf 0.8312 -Inf 0.008158 3.857e-05 0.002314 0.1389 0
## 28.343 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 10 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1324 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1445 60 59 48 5 0 0 0.1361 Inf 0.8307 -Inf 0.00838 3.125e-05 0.001875 0.1125 0
## 26.801 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 11 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1312 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|4||60 0.1407 60 59 47 4 0 0 0.1323 Inf 0.8364 -Inf 0.008396 1.866e-05 0.00112 0.06718 0
## 28.802 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 12 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1329 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||60 0.1495 60 59 52 3 0 0 0.142 Inf 0.8237 -Inf 0.007382 4.076e-05 0.002445 0.1467 0
## 27.097 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 13 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1334 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1382 60 59 48 5 0 0 0.1294 Inf 0.8393 -Inf 0.008733 6.605e-05 0.003963 0.2378 0
## 29.954 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 14 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1343 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 7||60 0.1469 60 59 44 7 0 0 0.1383 Inf 0.8295 -Inf 0.008615 2.008e-05 0.001205 0.07228 0
## 28.557 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 15 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1306 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1456 60 59 48 5 0 0 0.1384 Inf 0.8291 -Inf 0.007194 3.948e-05 0.002369 0.1421 0
## 30.915 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 16 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1349 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.5179 60 59 48 5 0 0 0.5154 Inf 0.3627 -Inf 0.002451 2.115e-05 0.001269 0.07614 0
## 30.402 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 17 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1316 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1602 60 59 48 5 0 0 0.1521 Inf 0.8126 -Inf 0.008123 2.686e-05 0.001612 0.0967 0
## 28.682 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 18 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1300 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 6||60 0.1469 60 59 46 6 0 0 0.1382 Inf 0.8294 -Inf 0.008689 2.109e-05 0.001265 0.07591 0
## 30.952 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 19 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1330 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||60 0.1422 60 59 50 4 0 0 0.1342 Inf 0.8347 -Inf 0.007914 3.172e-05 0.001903 0.1142 0
## 29.241 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 20 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1316 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 6||60 0.1491 60 59 46 6 0 0 0.1414 Inf 0.8248 -Inf 0.007701 3.706e-05 0.002223 0.1334 0
## 27.885 sec elapsed
## [1] "Constructing average tree"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Computing EPG with 60 nodes on 1200 points and 3 dimensions"
## [1] "Using a single core"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 7||60 0.01886 60 59 44 7 0 0 0.01067 Inf 0.9767 -Inf 0.00805 0.0001414 0.008482 0.5089 0
## 19.716 sec elapsed
PlotPG(X = TD_MedNoise, BootPG = TreeEPG[1:nRep], TargetPG = TreeEPG[[nRep+1]], GroupsLab = TD_MedNoise_Cat, DimToPlot = 1:2, VizMode = "Boot")
## [[1]]
PlotPG(X = TD_MedNoise, TargetPG = TreeEPG[[nRep+1]], GroupsLab = TD_MedNoise_Cat, DimToPlot = 1:2)
## [[1]]
nRep <- 20
TreeEPG <- computeElasticPrincipalTree(X = TD_HighNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE,
drawPCAView = FALSE,
n.cores = 4,
nReps = nRep, ProbPoint = .9,
TrimmingRadius = .155,
ICOver = "DensityProb", DensityRadius = .155)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 1 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4003 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2||50 0.3133 50 49 44 2 0 0 0.3093 Inf 0.6597 -Inf 0.003981 8.424e-06 0.0004212 0.02106 0
## 23.567 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 2 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4016 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||50 0.3042 50 49 42 3 0 0 0.3006 Inf 0.6675 -Inf 0.003525 1.108e-05 0.0005539 0.02769 0
## 21.78 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 3 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3992 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2||50 0.2626 50 49 44 2 0 0 0.259 Inf 0.7135 -Inf 0.00356 1.1e-05 0.0005498 0.02749 0
## 20.498 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Graphical output will be suppressed for the remaining replicas"
## [1] "Constructing tree 4 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4010 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.2329 50 49 40 4 0 0 0.2285 Inf 0.7469 -Inf 0.004375 8.558e-06 0.0004279 0.02139 0
## 20.768 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 5 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4003 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1||50 0.4109 50 49 46 1 0 0 0.4082 Inf 0.55 -Inf 0.002713 1.475e-05 0.0007374 0.03687 0
## 20.372 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 6 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3954 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||50 0.3061 50 49 42 3 0 0 0.3033 Inf 0.6659 -Inf 0.002758 4.551e-07 2.276e-05 0.001138 0
## 21.11 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 7 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3953 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2||50 0.2905 50 49 44 2 0 0 0.2875 Inf 0.6803 -Inf 0.002941 2.199e-05 0.0011 0.05498 0
## 20.956 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 8 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3970 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||50 0.2501 50 49 42 3 0 0 0.246 Inf 0.7286 -Inf 0.004085 7.068e-06 0.0003534 0.01767 0
## 21.797 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 9 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4041 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1||50 0.344 50 49 46 1 0 0 0.3417 Inf 0.6231 -Inf 0.002275 1.783e-05 0.0008917 0.04459 0
## 21.292 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 10 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3988 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2||50 0.2644 50 49 44 2 0 0 0.2609 Inf 0.7115 -Inf 0.003429 5.115e-05 0.002558 0.1279 0
## 21.304 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 11 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4021 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2||50 0.2398 50 49 44 2 0 0 0.2353 Inf 0.74 -Inf 0.004491 1.46e-05 0.0007302 0.03651 0
## 22.474 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 12 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3989 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.2487 50 49 40 4 0 0 0.244 Inf 0.7308 -Inf 0.004682 1.767e-06 8.834e-05 0.004417 0
## 21.956 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 13 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3961 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2||50 0.2539 50 49 44 2 0 0 0.2506 Inf 0.7229 -Inf 0.003332 5.566e-06 0.0002783 0.01391 0
## 21.634 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 14 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3980 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2||50 0.2888 50 49 44 2 0 0 0.2862 Inf 0.6854 -Inf 0.002592 1.061e-05 0.0005307 0.02653 0
## 21.377 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 15 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3994 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2||50 0.262 50 49 44 2 0 0 0.2587 Inf 0.7136 -Inf 0.003236 1.878e-05 0.0009392 0.04696 0
## 22.31 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 16 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3972 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|1||50 0.2378 50 49 43 1 0 0 0.233 Inf 0.7427 -Inf 0.004756 8.053e-06 0.0004026 0.02013 0
## 24.227 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 17 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3964 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1||50 0.2791 50 49 46 1 0 0 0.276 Inf 0.6943 -Inf 0.003024 1.428e-05 0.0007142 0.03571 0
## 21.998 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 18 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4007 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||50 0.2375 50 49 42 3 0 0 0.2332 Inf 0.7421 -Inf 0.004353 3.543e-05 0.001771 0.08857 0
## 22.621 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 19 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3960 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||50 0.2453 50 49 42 3 0 0 0.2408 Inf 0.7347 -Inf 0.004524 3.03e-05 0.001515 0.07574 0
## 23.446 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 20 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3947 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.4812 50 49 40 4 0 0 0.4791 Inf 0.4712 -Inf 0.002107 1.059e-06 5.295e-05 0.002648 0
## 22.182 sec elapsed
## [1] "Constructing average tree"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Computing EPG with 50 nodes on 1000 points and 3 dimensions"
## [1] "Using a single core"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||50 0.01968 50 49 38 5 0 0 0.0113 Inf 0.9639 -Inf 0.008161 0.0002176 0.01088 0.544 0
## 9.197 sec elapsed
PlotPG(X = TD_HighNoise, BootPG = TreeEPG[1:nRep], TargetPG = TreeEPG[[nRep+1]], GroupsLab = TD_HighNoise_Cat, DimToPlot = 1:2, VizMode = "Boot")
## [[1]]
PlotPG(X = TD_HighNoise, TargetPG = TreeEPG[[nRep+1]], GroupsLab = TD_HighNoise_Cat, DimToPlot = 1:2)
## [[1]]
Visualizing the effect of the trimming radius
ElPiGrph.R also provides functions to derive (and visualize) which
points are within the a distance from the the nodes of the graph. An
obvious application of this functionality is to explore which points are
being captured by ElPiGraph when a trimming radius is being used.
The central function to perfom this analysis is FindAssocited. The
function takes 3 parameters: a dataset (X), a list of ElPiGraph
stuctures (BootPG), and an optional parameter describing the distance
to be used (TrimmingRadius). If the TrimmingRadius parameter is not
specified, the distance is equal to the trimming radius used for the
construction of the graphs.
This function returns a vector that describe, for each point, the number
of graphs of the list with nodes within the specified distance.
nRep <- 10
TreeEPG <- computeElasticPrincipalTree(X = TD_MedNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE,
drawPCAView = FALSE,
n.cores = 4,
nReps = nRep, ProbPoint = .6,
TrimmingRadius = .155,
ICOver = "DensityProb", DensityRadius = .155)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 1 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 882 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.1697 50 49 39 3 0 0 0.1626 Inf 0.8 -Inf 0.007085 4.74e-05 0.00237 0.1185 0
## 17.464 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 2 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 878 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||50 0.1975 50 49 42 3 0 0 0.1904 Inf 0.7723 -Inf 0.007013 5.271e-05 0.002635 0.1318 0
## 15.986 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 3 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 915 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.1611 50 49 40 4 0 0 0.1535 Inf 0.8105 -Inf 0.007561 2.315e-05 0.001157 0.05787 0
## 16.108 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Graphical output will be suppressed for the remaining replicas"
## [1] "Constructing tree 4 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 904 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.1529 50 49 39 3 0 0 0.1453 Inf 0.8214 -Inf 0.007578 3.193e-05 0.001597 0.07983 0
## 16.417 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 5 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 862 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.1587 50 49 39 3 0 0 0.1515 Inf 0.8171 -Inf 0.007266 1.17e-05 0.0005851 0.02925 0
## 16.558 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 6 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 884 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.1721 50 49 40 4 0 0 0.1638 Inf 0.8001 -Inf 0.008349 1.838e-05 0.000919 0.04595 0
## 16.614 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 7 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 842 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.1529 50 49 39 3 0 0 0.1459 Inf 0.8147 -Inf 0.006931 3.418e-05 0.001709 0.08544 0
## 16.612 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 8 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 882 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||50 0.1633 50 49 42 3 0 0 0.1564 Inf 0.8089 -Inf 0.006902 3.676e-05 0.001838 0.09189 0
## 16.565 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 9 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 922 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.1654 50 49 40 4 0 0 0.1577 Inf 0.8092 -Inf 0.007696 4.219e-05 0.002109 0.1055 0
## 17.425 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 10 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 891 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|4||50 0.1657 50 49 37 4 0 0 0.1586 Inf 0.8028 -Inf 0.007135 4.874e-05 0.002437 0.1219 0
## 18.17 sec elapsed
## [1] "Constructing average tree"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Computing EPG with 50 nodes on 500 points and 3 dimensions"
## [1] "Using a single core"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||50 0.01335 50 49 42 3 0 0 0.007506 Inf 0.9813 -Inf 0.005746 9.566e-05 0.004783 0.2392 0
## 8.652 sec elapsed
BootAssociation_Multi <- FindAssocited(X = TD_MedNoise, BootPG = TreeEPG[1:nRep])
PlotPG(X = TD_MedNoise, TargetPG = TreeEPG[[nRep+1]], BootPG = TreeEPG[1:nRep],
GroupsLab = BootAssociation_Multi, DimToPlot = 1:2, VizMode = "Boot")
## [[1]]
TB <- table(BootAssociation_Multi, TD_MedNoise_Cat)
pheatmap::pheatmap(t(TB)/colSums(TB), cluster_cols = FALSE)
BootAssociation_Single <- FindAssocited(X = TD_MedNoise, BootPG = TreeEPG[nRep+1])
PlotPG(X = TD_MedNoise, TargetPG = TreeEPG[[nRep+1]],
GroupsLab = factor(BootAssociation_Single), DimToPlot = 1:2, VizMode = "Target")
## [[1]]
TB <- table(BootAssociation_Single, TD_MedNoise_Cat)
pheatmap::pheatmap(t(TB)/colSums(TB), cluster_cols = FALSE)
Albluca/ElPiGraph.R documentation built on May 28, 2019, 11:02 a.m.
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- Setup
- Effect of noisy points
- Density dependent inizialisation and trimming radius
- Density dependent inizialisation and trimming radius and bootstrapping
- Visualizing the effect of the trimming radius
In real word examples, the data distributions to be approximated can be contaminated by the presence of outliers or points belonging to a different distribution. To address this aspect, the ElPiGraph.R package implement two functionalities that can be used to minimize the impact of these points: density-dependent initialization and trimming radius.
Setup
To show the effect of these features, we will start by generating noisy datasets from the tree example present in the package, with an increased intensity of noise. Similar ideas and concepts apply to the construction of curves as well.
library(ElPiGraph.R)
library(igraph)
##
## Attaching package: 'igraph'
## The following objects are masked from 'package:stats':
##
## decompose, spectrum
## The following object is masked from 'package:base':
##
## union
nPoints <- round(nrow(tree_data)*.5)
NewPoints <- apply(apply(tree_data, 2, range), 2, function(x){
runif(n = nPoints, x[1], x[2])
})
TD_LowNoise <- rbind(tree_data, NewPoints)
TD_LowNoise_Cat <- c(rep("Real", nrow(tree_data)), rep("Noise", nrow(NewPoints)))
nPoints <- nrow(tree_data)*2
NewPoints <- apply(apply(tree_data, 2, range), 2, function(x){
runif(n = nPoints, x[1], x[2])
})
TD_MedNoise <- rbind(tree_data, NewPoints)
TD_MedNoise_Cat <- c(rep("Real", nrow(tree_data)), rep("Noise", nrow(NewPoints)))
nPoints <- nrow(tree_data)*8
NewPoints <- apply(apply(tree_data, 2, range), 2, function(x){
runif(n = nPoints, x[1], x[2])
})
TD_HighNoise <- rbind(tree_data, NewPoints)
TD_HighNoise_Cat <- c(rep("Real", nrow(tree_data)), rep("Noise", nrow(NewPoints)))
Effect of noisy points
By default the ElPiGraph algorithm uses all the points and generate the initial points on the 1st PC of the data. Therefore, noise can affect significantly the reconstructed tree.
TreeEPG <- computeElasticPrincipalTree(X = TD_LowNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE, drawPCAView = FALSE, n.cores = 4)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a chain in the 1st PC with 2 nodes"
## [1] "Constructing tree 1 of 1 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 738 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 7||50 0.04324 50 49 34 7 0 0 0.02181 0.02058 0.9679 0.9697 0.02094 0.0004823 0.02411 1.206 0
## 11.875 sec elapsed
PlotPG(X = TD_LowNoise, TargetPG = TreeEPG[[1]], GroupsLab = TD_LowNoise_Cat, DimToPlot = 1:2)
## [[1]]
TreeEPG <- computeElasticPrincipalTree(X = TD_MedNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE, drawPCAView = FALSE, n.cores = 4)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a chain in the 1st PC with 2 nodes"
## [1] "Constructing tree 1 of 1 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 1476 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|5||50 0.06049 50 49 35 5 0 0 0.03383 0.03204 0.9582 0.9604 0.02644 0.0002185 0.01092 0.5462 0
## 23.924 sec elapsed
PlotPG(X = TD_MedNoise, TargetPG = TreeEPG[[1]], GroupsLab = TD_MedNoise_Cat, DimToPlot = 1:2)
## [[1]]
TreeEPG <- computeElasticPrincipalTree(X = TD_HighNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE, drawPCAView = FALSE, n.cores = 4)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a chain in the 1st PC with 2 nodes"
## [1] "Constructing tree 1 of 1 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4428 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|0|4||50 0.06942 50 49 36 4 0 0 0.03442 0.03204 0.9619 0.9646 0.0347 0.0002977 0.01489 0.7443 0
## 29.285 sec elapsed
PlotPG(X = TD_HighNoise, TargetPG = TreeEPG[[1]], GroupsLab = TD_HighNoise_Cat, DimToPlot = 1:2)
## [[1]]
Density dependent inizialisation and trimming radius
To limit the effect of noise, we can specify a trimming radius (which
informs the algorithm to use only points with a distance lower than this
radius when computing the position of the nodes), and use a density
dependent initialization ICOver = "Density". Note that when using
ICOver = "Density", the parameter DensityRadius, which is used to
determine the area of the space with the highest density of points, need
to be specified as well.
When a trimming radius is used, tree construction becomes local, hence it may be necessary to increase the number of points in order to better cover all areas of the space containing the points under consideration. Moreover certain feature of the topology may be lost due to corruption due by the noise.
TreeEPG <- computeElasticPrincipalTree(X = TD_LowNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE, drawPCAView = FALSE,
n.cores = 4,
TrimmingRadius = .15,
ICOver = "Density", DensityRadius = .15)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 1 of 1 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 738 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.1019 50 49 39 3 0 0 0.09409 Inf 0.8615 -Inf 0.007783 5.928e-05 0.002964 0.1482 0
## 22.125 sec elapsed
PlotPG(X = TD_LowNoise, TargetPG = TreeEPG[[1]], GroupsLab = TD_LowNoise_Cat, DimToPlot = 1:2)
## [[1]]
TreeEPG <- computeElasticPrincipalTree(X = TD_MedNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE, drawPCAView = FALSE,
n.cores = 4,
TrimmingRadius = .15,
ICOver = "Density", DensityRadius = .15)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 1 of 1 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 1476 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.1601 50 49 40 4 0 0 0.1536 Inf 0.8101 -Inf 0.006474 2.614e-05 0.001307 0.06534 0
## 21.406 sec elapsed
PlotPG(X = TD_MedNoise, TargetPG = TreeEPG[[1]], GroupsLab = TD_MedNoise_Cat, DimToPlot = 1:2)
## [[1]]
TreeEPG <- computeElasticPrincipalTree(X = TD_HighNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE, drawPCAView = FALSE,
n.cores = 4,
TrimmingRadius = .15,
ICOver = "Density", DensityRadius = .15)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 1 of 1 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4428 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1||50 0.3318 50 49 46 1 0 0 0.3298 Inf 0.6352 -Inf 0.001968 3.924e-06 0.0001962 0.00981 0
## 25.035 sec elapsed
PlotPG(X = TD_HighNoise, TargetPG = TreeEPG[[1]], GroupsLab = TD_HighNoise_Cat, DimToPlot = 1:2)
## [[1]]
Density dependent inizialisation and trimming radius and bootstrapping
To further address the problem of noise in the data it advisable to use
bootstrapping. To enable bootstrapping it is sufficient to use the
parameter nReps, which defines the number of repetitions, and
ProbPoint, which defines the probability of selecting a point in each
iteration. Bootstrapping can be also helpfull to mitigate the effect of
outliers in the data, when the trimming radius is unspecified.
Note that when bootstrapped is enabled (i.e. when nRep is larger than
1), an average graph is generated by using the nodes of the graph
generated during the single execution of the algorithm. Hence if nRep
is equalt to n, the returned lists will contain n+1 ElPiGraph
structures: the n repetitions, and the final average graph.
Visualization of bootstrapped data can be easilty perfomred via the
PlorPG function. To this end, it is sufficient to pass the
bootstrapped structures via the BootPG parameter. Currently a primary
ElPiGraph structure is required (the TargetPG parameter).
It is further possible to control if the bootstrapped and target graphs
shoudl be plotted via the VizMode parameter.
nRep <- 20
TreeEPG <- computeElasticPrincipalTree(X = tree_data, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE,
drawPCAView = FALSE,
n.cores = 4,
nReps = nRep, ProbPoint = .8,
TrimmingRadius = Inf,
ICOver = "DensityProb", DensityRadius = .3)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 1 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 407 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01549 50 49 39 3 0 0 0.004223 0.003548 0.992 0.9933 0.01109 0.0001693 0.008463 0.4232 0
## 17.74 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 2 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 385 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01561 50 49 39 3 0 0 0.004097 0.0034 0.992 0.9934 0.01137 0.0001429 0.007144 0.3572 0
## 16.751 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 3 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 396 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.0158 50 49 39 3 0 0 0.004186 0.00353 0.9922 0.9934 0.01142 0.0002006 0.01003 0.5016 0
## 16.631 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Graphical output will be suppressed for the remaining replicas"
## [1] "Constructing tree 4 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 392 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01587 50 49 39 3 0 0 0.004284 0.003527 0.9922 0.9936 0.0114 0.0001878 0.009391 0.4695 0
## 15.975 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 5 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 399 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 6||50 0.01581 50 49 36 6 0 0 0.00445 0.003786 0.9916 0.9928 0.01112 0.0002393 0.01196 0.5982 0
## 17.31 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 6 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 391 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01586 50 49 39 3 0 0 0.004037 0.003327 0.9925 0.9939 0.01156 0.0002679 0.0134 0.6698 0
## 16.828 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 7 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 391 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01596 50 49 39 3 0 0 0.004905 0.004219 0.9905 0.9918 0.01078 0.0002805 0.01402 0.7012 0
## 15.969 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 8 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 397 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|2||50 0.01551 50 49 41 2 0 0 0.004026 0.003382 0.9927 0.9939 0.01109 0.0003891 0.01945 0.9727 0
## 16.789 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 9 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 404 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|2||50 0.01549 50 49 41 2 0 0 0.004039 0.003318 0.9926 0.9939 0.01101 0.0004419 0.0221 1.105 0
## 17.321 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 10 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 383 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01573 50 49 39 3 0 0 0.004033 0.003324 0.993 0.9942 0.01146 0.0002345 0.01172 0.5861 0
## 17.805 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 11 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 410 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|2||50 0.01588 50 49 41 2 0 0 0.004394 0.003693 0.9921 0.9934 0.01105 0.0004412 0.02206 1.103 0
## 16.468 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 12 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 380 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|2||50 0.0156 50 49 41 2 0 0 0.004058 0.003407 0.9925 0.9937 0.01112 0.0004255 0.02128 1.064 0
## 16.974 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 13 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 387 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01562 50 49 39 3 0 0 0.00428 0.003535 0.992 0.9934 0.0111 0.0002363 0.01182 0.5908 0
## 16.798 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 14 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 394 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01546 50 49 39 3 0 0 0.003882 0.003217 0.9927 0.994 0.01136 0.0002175 0.01088 0.5439 0
## 16.515 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 15 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 394 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01589 50 49 39 3 0 0 0.004135 0.00345 0.9922 0.9935 0.01151 0.0002429 0.01215 0.6073 0
## 16.503 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 16 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 413 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01546 50 49 39 3 0 0 0.003906 0.003229 0.9927 0.9939 0.01138 0.0001809 0.009047 0.4523 0
## 17.021 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 17 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 382 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|2||50 0.01611 50 49 41 2 0 0 0.004269 0.003526 0.9922 0.9935 0.01135 0.0004919 0.02459 1.23 0
## 16.871 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 18 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 396 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|2||50 0.01505 50 49 41 2 0 0 0.004223 0.003507 0.9922 0.9935 0.01046 0.0003645 0.01823 0.9113 0
## 17.664 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 19 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 386 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01593 50 49 39 3 0 0 0.004296 0.003628 0.9921 0.9933 0.01145 0.0001855 0.009277 0.4639 0
## 17.404 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 20 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 408 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01551 50 49 39 3 0 0 0.003897 0.003213 0.9928 0.994 0.01145 0.0001653 0.008265 0.4133 0
## 17.83 sec elapsed
## [1] "Constructing average tree"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Computing EPG with 50 nodes on 1000 points and 3 dimensions"
## [1] "Using a single core"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.01088 50 49 39 3 0 0 0.001641 0.001193 0.9968 0.9977 0.009133 0.0001072 0.005359 0.268 0
## 9.252 sec elapsed
PlotPG(X = tree_data, BootPG = TreeEPG[1:nRep], TargetPG = TreeEPG[[nRep+1]], DimToPlot = 1:2, VizMode = c("Target", "Boot"))
## [[1]]
PlotPG(X = tree_data, BootPG = TreeEPG[1:nRep], TargetPG = TreeEPG[[nRep+1]], DimToPlot = 1:2, VizMode = "Boot")
## [[1]]
PlotPG(X = tree_data, TargetPG = TreeEPG[[nRep+1]], DimToPlot = 1:2)
## [[1]]
nRep <- 20
TreeEPG <- computeElasticPrincipalTree(X = TD_LowNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE,
drawPCAView = FALSE,
n.cores = 4,
nReps = nRep, ProbPoint = .9,
TrimmingRadius = .155,
ICOver = "DensityProb", DensityRadius = .155)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 1 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 674 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||50 0.09967 50 49 38 5 0 0 0.09076 Inf 0.8649 -Inf 0.008838 6.769e-05 0.003385 0.1692 0
## 18.581 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 2 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 664 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 6||50 0.09261 50 49 36 6 0 0 0.08366 Inf 0.8756 -Inf 0.008901 4.391e-05 0.002196 0.1098 0
## 16.208 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 3 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 672 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 6||50 0.09199 50 49 36 6 0 0 0.08288 Inf 0.8766 -Inf 0.009058 5.442e-05 0.002721 0.136 0
## 16.095 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Graphical output will be suppressed for the remaining replicas"
## [1] "Constructing tree 4 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 665 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1||50 1.877 50 49 46 1 0 0 1.877 Inf -1.773 -Inf 3.362e-05 9.731e-07 4.865e-05 0.002433 0
## 15.574 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 5 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 664 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.09072 50 49 40 4 0 0 0.08211 Inf 0.8788 -Inf 0.008568 3.683e-05 0.001842 0.09208 0
## 16.231 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 6 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 671 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||50 0.1 50 49 38 5 0 0 0.09144 Inf 0.8673 -Inf 0.008532 2.527e-05 0.001264 0.06318 0
## 16.653 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 7 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 655 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.09426 50 49 39 3 0 0 0.08579 Inf 0.8696 -Inf 0.008432 3.175e-05 0.001588 0.07939 0
## 17.353 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 8 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 662 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 7||50 0.09301 50 49 34 7 0 0 0.08444 Inf 0.8757 -Inf 0.008527 3.976e-05 0.001988 0.0994 0
## 17.627 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 9 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 661 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 6||50 0.09687 50 49 36 6 0 0 0.08941 Inf 0.87 -Inf 0.007397 7.048e-05 0.003524 0.1762 0
## 17.474 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 10 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 667 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|5||50 0.104 50 49 35 5 0 0 0.09538 Inf 0.8613 -Inf 0.008527 7.651e-05 0.003826 0.1913 0
## 16.967 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 11 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 673 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.09588 50 49 39 3 0 0 0.08747 Inf 0.8723 -Inf 0.008373 3.283e-05 0.001642 0.08208 0
## 18.435 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 12 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 661 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2|2||50 0.1 50 49 38 2 0 0 0.09121 Inf 0.8649 -Inf 0.008775 5.056e-05 0.002528 0.1264 0
## 16.923 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 13 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 660 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.1079 50 49 40 4 0 0 0.09971 Inf 0.8543 -Inf 0.008121 3.877e-05 0.001938 0.09692 0
## 17.244 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 14 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 648 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|5||50 0.09916 50 49 35 5 0 0 0.0905 Inf 0.8657 -Inf 0.00863 2.803e-05 0.001401 0.07007 0
## 17.218 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 15 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 668 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|5||50 0.0822 50 49 35 5 0 0 0.07227 Inf 0.8942 -Inf 0.009869 6.238e-05 0.003119 0.156 0
## 18.794 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 16 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 676 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|5||50 0.09419 50 49 35 5 0 0 0.08541 Inf 0.8718 -Inf 0.008731 5.264e-05 0.002632 0.1316 0
## 19.41 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 17 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 675 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2|2||50 0.09903 50 49 38 2 0 0 0.0907 Inf 0.8664 -Inf 0.008285 4.706e-05 0.002353 0.1177 0
## 24.901 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 18 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 657 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|4||50 0.09145 50 49 37 4 0 0 0.08245 Inf 0.8794 -Inf 0.008974 2.536e-05 0.001268 0.06341 0
## 18.695 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 19 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 676 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|0|3||50 0.0879 50 49 38 3 0 0 0.07859 Inf 0.8835 -Inf 0.009268 4.764e-05 0.002382 0.1191 0
## 17.937 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 20 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 661 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.08563 50 49 40 4 0 0 0.07581 Inf 0.8876 -Inf 0.009712 0.0001098 0.005491 0.2745 0
## 17.393 sec elapsed
## [1] "Constructing average tree"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Computing EPG with 50 nodes on 1000 points and 3 dimensions"
## [1] "Using a single core"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|2||50 0.04098 50 49 41 2 0 0 0.03304 Inf 0.9357 -Inf 0.007839 0.0001005 0.005026 0.2513 0
## 8.353 sec elapsed
PlotPG(X = TD_LowNoise, BootPG = TreeEPG[1:nRep], TargetPG = TreeEPG[[nRep+1]], GroupsLab = TD_LowNoise_Cat, DimToPlot = 1:2, VizMode = "Boot")
## [[1]]
PlotPG(X = TD_LowNoise, TargetPG = TreeEPG[[nRep+1]], GroupsLab = TD_LowNoise_Cat, DimToPlot = 1:2)
## [[1]]
nRep <- 20
TreeEPG <- computeElasticPrincipalTree(X = TD_MedNoise, NumNodes = 60,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE,
drawPCAView = FALSE,
n.cores = 4,
nReps = nRep, ProbPoint = .9,
TrimmingRadius = .16,
ICOver = "DensityProb", DensityRadius = .16)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 1 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1324 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 6||60 0.1479 60 59 46 6 0 0 0.1394 Inf 0.8285 -Inf 0.008407 1.703e-05 0.001022 0.06132 0
## 29.884 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 2 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1322 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1481 60 59 48 5 0 0 0.14 Inf 0.8271 -Inf 0.008018 2.182e-05 0.001309 0.07856 0
## 28.93 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 3 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1338 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1409 60 59 48 5 0 0 0.1326 Inf 0.8334 -Inf 0.00827 1.8e-05 0.00108 0.06479 0
## 25.512 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Graphical output will be suppressed for the remaining replicas"
## [1] "Constructing tree 4 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1330 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1481 60 59 48 5 0 0 0.1406 Inf 0.8241 -Inf 0.007509 1.164e-05 0.0006985 0.04191 0
## 25.088 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 5 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1298 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||60 0.14 60 59 50 4 0 0 0.1322 Inf 0.8377 -Inf 0.00778 1.532e-05 0.0009193 0.05516 0
## 25.13 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 6 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1333 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1459 60 59 48 5 0 0 0.1372 Inf 0.8326 -Inf 0.008611 5.196e-05 0.003118 0.1871 0
## 28.057 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 7 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1321 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||60 0.1447 60 59 50 4 0 0 0.1365 Inf 0.8301 -Inf 0.008156 1.902e-05 0.001141 0.06848 0
## 31.709 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 8 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1345 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1448 60 59 48 5 0 0 0.1354 Inf 0.8325 -Inf 0.009377 5.185e-05 0.003111 0.1867 0
## 26.245 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 9 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1327 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|4||60 0.1451 60 59 47 4 0 0 0.1369 Inf 0.8312 -Inf 0.008158 3.857e-05 0.002314 0.1389 0
## 28.343 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 10 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1324 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1445 60 59 48 5 0 0 0.1361 Inf 0.8307 -Inf 0.00838 3.125e-05 0.001875 0.1125 0
## 26.801 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 11 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1312 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|4||60 0.1407 60 59 47 4 0 0 0.1323 Inf 0.8364 -Inf 0.008396 1.866e-05 0.00112 0.06718 0
## 28.802 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 12 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1329 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||60 0.1495 60 59 52 3 0 0 0.142 Inf 0.8237 -Inf 0.007382 4.076e-05 0.002445 0.1467 0
## 27.097 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 13 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1334 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1382 60 59 48 5 0 0 0.1294 Inf 0.8393 -Inf 0.008733 6.605e-05 0.003963 0.2378 0
## 29.954 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 14 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1343 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 7||60 0.1469 60 59 44 7 0 0 0.1383 Inf 0.8295 -Inf 0.008615 2.008e-05 0.001205 0.07228 0
## 28.557 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 15 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1306 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1456 60 59 48 5 0 0 0.1384 Inf 0.8291 -Inf 0.007194 3.948e-05 0.002369 0.1421 0
## 30.915 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 16 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1349 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.5179 60 59 48 5 0 0 0.5154 Inf 0.3627 -Inf 0.002451 2.115e-05 0.001269 0.07614 0
## 30.402 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 17 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1316 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||60 0.1602 60 59 48 5 0 0 0.1521 Inf 0.8126 -Inf 0.008123 2.686e-05 0.001612 0.0967 0
## 28.682 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 18 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1300 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 6||60 0.1469 60 59 46 6 0 0 0.1382 Inf 0.8294 -Inf 0.008689 2.109e-05 0.001265 0.07591 0
## 30.952 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 19 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1330 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||60 0.1422 60 59 50 4 0 0 0.1342 Inf 0.8347 -Inf 0.007914 3.172e-05 0.001903 0.1142 0
## 29.241 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 20 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 60 nodes on 1316 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 6||60 0.1491 60 59 46 6 0 0 0.1414 Inf 0.8248 -Inf 0.007701 3.706e-05 0.002223 0.1334 0
## 27.885 sec elapsed
## [1] "Constructing average tree"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Computing EPG with 60 nodes on 1200 points and 3 dimensions"
## [1] "Using a single core"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 7||60 0.01886 60 59 44 7 0 0 0.01067 Inf 0.9767 -Inf 0.00805 0.0001414 0.008482 0.5089 0
## 19.716 sec elapsed
PlotPG(X = TD_MedNoise, BootPG = TreeEPG[1:nRep], TargetPG = TreeEPG[[nRep+1]], GroupsLab = TD_MedNoise_Cat, DimToPlot = 1:2, VizMode = "Boot")
## [[1]]
PlotPG(X = TD_MedNoise, TargetPG = TreeEPG[[nRep+1]], GroupsLab = TD_MedNoise_Cat, DimToPlot = 1:2)
## [[1]]
nRep <- 20
TreeEPG <- computeElasticPrincipalTree(X = TD_HighNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE,
drawPCAView = FALSE,
n.cores = 4,
nReps = nRep, ProbPoint = .9,
TrimmingRadius = .155,
ICOver = "DensityProb", DensityRadius = .155)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 1 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4003 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2||50 0.3133 50 49 44 2 0 0 0.3093 Inf 0.6597 -Inf 0.003981 8.424e-06 0.0004212 0.02106 0
## 23.567 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 2 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4016 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||50 0.3042 50 49 42 3 0 0 0.3006 Inf 0.6675 -Inf 0.003525 1.108e-05 0.0005539 0.02769 0
## 21.78 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 3 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3992 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2||50 0.2626 50 49 44 2 0 0 0.259 Inf 0.7135 -Inf 0.00356 1.1e-05 0.0005498 0.02749 0
## 20.498 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Graphical output will be suppressed for the remaining replicas"
## [1] "Constructing tree 4 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4010 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.2329 50 49 40 4 0 0 0.2285 Inf 0.7469 -Inf 0.004375 8.558e-06 0.0004279 0.02139 0
## 20.768 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 5 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4003 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1||50 0.4109 50 49 46 1 0 0 0.4082 Inf 0.55 -Inf 0.002713 1.475e-05 0.0007374 0.03687 0
## 20.372 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 6 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3954 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||50 0.3061 50 49 42 3 0 0 0.3033 Inf 0.6659 -Inf 0.002758 4.551e-07 2.276e-05 0.001138 0
## 21.11 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 7 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3953 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2||50 0.2905 50 49 44 2 0 0 0.2875 Inf 0.6803 -Inf 0.002941 2.199e-05 0.0011 0.05498 0
## 20.956 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 8 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3970 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||50 0.2501 50 49 42 3 0 0 0.246 Inf 0.7286 -Inf 0.004085 7.068e-06 0.0003534 0.01767 0
## 21.797 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 9 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4041 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1||50 0.344 50 49 46 1 0 0 0.3417 Inf 0.6231 -Inf 0.002275 1.783e-05 0.0008917 0.04459 0
## 21.292 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 10 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3988 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2||50 0.2644 50 49 44 2 0 0 0.2609 Inf 0.7115 -Inf 0.003429 5.115e-05 0.002558 0.1279 0
## 21.304 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 11 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4021 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2||50 0.2398 50 49 44 2 0 0 0.2353 Inf 0.74 -Inf 0.004491 1.46e-05 0.0007302 0.03651 0
## 22.474 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 12 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3989 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.2487 50 49 40 4 0 0 0.244 Inf 0.7308 -Inf 0.004682 1.767e-06 8.834e-05 0.004417 0
## 21.956 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 13 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3961 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2||50 0.2539 50 49 44 2 0 0 0.2506 Inf 0.7229 -Inf 0.003332 5.566e-06 0.0002783 0.01391 0
## 21.634 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 14 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3980 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2||50 0.2888 50 49 44 2 0 0 0.2862 Inf 0.6854 -Inf 0.002592 1.061e-05 0.0005307 0.02653 0
## 21.377 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 15 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3994 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 2||50 0.262 50 49 44 2 0 0 0.2587 Inf 0.7136 -Inf 0.003236 1.878e-05 0.0009392 0.04696 0
## 22.31 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 16 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3972 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|1||50 0.2378 50 49 43 1 0 0 0.233 Inf 0.7427 -Inf 0.004756 8.053e-06 0.0004026 0.02013 0
## 24.227 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 17 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3964 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1||50 0.2791 50 49 46 1 0 0 0.276 Inf 0.6943 -Inf 0.003024 1.428e-05 0.0007142 0.03571 0
## 21.998 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 18 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 4007 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||50 0.2375 50 49 42 3 0 0 0.2332 Inf 0.7421 -Inf 0.004353 3.543e-05 0.001771 0.08857 0
## 22.621 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 19 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3960 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||50 0.2453 50 49 42 3 0 0 0.2408 Inf 0.7347 -Inf 0.004524 3.03e-05 0.001515 0.07574 0
## 23.446 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 20 of 20 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 3947 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.4812 50 49 40 4 0 0 0.4791 Inf 0.4712 -Inf 0.002107 1.059e-06 5.295e-05 0.002648 0
## 22.182 sec elapsed
## [1] "Constructing average tree"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Computing EPG with 50 nodes on 1000 points and 3 dimensions"
## [1] "Using a single core"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 5||50 0.01968 50 49 38 5 0 0 0.0113 Inf 0.9639 -Inf 0.008161 0.0002176 0.01088 0.544 0
## 9.197 sec elapsed
PlotPG(X = TD_HighNoise, BootPG = TreeEPG[1:nRep], TargetPG = TreeEPG[[nRep+1]], GroupsLab = TD_HighNoise_Cat, DimToPlot = 1:2, VizMode = "Boot")
## [[1]]
PlotPG(X = TD_HighNoise, TargetPG = TreeEPG[[nRep+1]], GroupsLab = TD_HighNoise_Cat, DimToPlot = 1:2)
## [[1]]
Visualizing the effect of the trimming radius
ElPiGrph.R also provides functions to derive (and visualize) which points are within the a distance from the the nodes of the graph. An obvious application of this functionality is to explore which points are being captured by ElPiGraph when a trimming radius is being used.
The central function to perfom this analysis is FindAssocited. The
function takes 3 parameters: a dataset (X), a list of ElPiGraph
stuctures (BootPG), and an optional parameter describing the distance
to be used (TrimmingRadius). If the TrimmingRadius parameter is not
specified, the distance is equal to the trimming radius used for the
construction of the graphs.
This function returns a vector that describe, for each point, the number of graphs of the list with nodes within the specified distance.
nRep <- 10
TreeEPG <- computeElasticPrincipalTree(X = TD_MedNoise, NumNodes = 50,
drawAccuracyComplexity = FALSE, drawEnergy = FALSE,
drawPCAView = FALSE,
n.cores = 4,
nReps = nRep, ProbPoint = .6,
TrimmingRadius = .155,
ICOver = "DensityProb", DensityRadius = .155)
## [1] "Creating a sock cluster with 4 nodes"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 1 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 882 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.1697 50 49 39 3 0 0 0.1626 Inf 0.8 -Inf 0.007085 4.74e-05 0.00237 0.1185 0
## 17.464 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 2 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 878 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||50 0.1975 50 49 42 3 0 0 0.1904 Inf 0.7723 -Inf 0.007013 5.271e-05 0.002635 0.1318 0
## 15.986 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 3 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 915 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.1611 50 49 40 4 0 0 0.1535 Inf 0.8105 -Inf 0.007561 2.315e-05 0.001157 0.05787 0
## 16.108 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Graphical output will be suppressed for the remaining replicas"
## [1] "Constructing tree 4 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 904 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.1529 50 49 39 3 0 0 0.1453 Inf 0.8214 -Inf 0.007578 3.193e-05 0.001597 0.07983 0
## 16.417 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 5 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 862 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.1587 50 49 39 3 0 0 0.1515 Inf 0.8171 -Inf 0.007266 1.17e-05 0.0005851 0.02925 0
## 16.558 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 6 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 884 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.1721 50 49 40 4 0 0 0.1638 Inf 0.8001 -Inf 0.008349 1.838e-05 0.000919 0.04595 0
## 16.614 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 7 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 842 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|3||50 0.1529 50 49 39 3 0 0 0.1459 Inf 0.8147 -Inf 0.006931 3.418e-05 0.001709 0.08544 0
## 16.612 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 8 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 882 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||50 0.1633 50 49 42 3 0 0 0.1564 Inf 0.8089 -Inf 0.006902 3.676e-05 0.001838 0.09189 0
## 16.565 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 9 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 922 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 4||50 0.1654 50 49 40 4 0 0 0.1577 Inf 0.8092 -Inf 0.007696 4.219e-05 0.002109 0.1055 0
## 17.425 sec elapsed
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Constructing tree 10 of 10 / Subset 1 of 1"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Using a user supplied cluster. Updating the value of X"
## [1] "Computing EPG with 50 nodes on 891 points and 3 dimensions"
## [1] "Using a user supplied cluster. It must contains the data points in a matrix X"
## [1] "Exporting the additional variables to the cluster"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 1|4||50 0.1657 50 49 37 4 0 0 0.1586 Inf 0.8028 -Inf 0.007135 4.874e-05 0.002437 0.1219 0
## 18.17 sec elapsed
## [1] "Constructing average tree"
## [1] "Creating a line in the densest part of the graph. DensityRadius needs to be specified!"
## [1] "Performing PCA on the data"
## [1] "Using standard PCA"
## [1] "3 dimensions are being used"
## [1] "100% of the original variance has been retained"
## [1] "Computing EPG with 50 nodes on 500 points and 3 dimensions"
## [1] "Using a single core"
## Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
## BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD
## 3||50 0.01335 50 49 42 3 0 0 0.007506 Inf 0.9813 -Inf 0.005746 9.566e-05 0.004783 0.2392 0
## 8.652 sec elapsed
BootAssociation_Multi <- FindAssocited(X = TD_MedNoise, BootPG = TreeEPG[1:nRep])
PlotPG(X = TD_MedNoise, TargetPG = TreeEPG[[nRep+1]], BootPG = TreeEPG[1:nRep],
GroupsLab = BootAssociation_Multi, DimToPlot = 1:2, VizMode = "Boot")
## [[1]]
TB <- table(BootAssociation_Multi, TD_MedNoise_Cat)
pheatmap::pheatmap(t(TB)/colSums(TB), cluster_cols = FALSE)
BootAssociation_Single <- FindAssocited(X = TD_MedNoise, BootPG = TreeEPG[nRep+1])
PlotPG(X = TD_MedNoise, TargetPG = TreeEPG[[nRep+1]],
GroupsLab = factor(BootAssociation_Single), DimToPlot = 1:2, VizMode = "Target")
## [[1]]
TB <- table(BootAssociation_Single, TD_MedNoise_Cat)
pheatmap::pheatmap(t(TB)/colSums(TB), cluster_cols = FALSE)
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