Description Details Overview 1. Data preparation 2. Building "optimal" clustering 3. Exporting results 4. Visualizing and exporting 3D object How to get help? Examples

`KmL3D`

is a new implementation of k-means for longitudinal data (or trajectories).
Here is an overview of the package.

Package: | KmL3D |

Type: | Package |

Version: | 2.4.2 |

Date: | 2017-08-01 |

License: | GPL (>= 2) |

LazyData: | yes |

Depends: | methods,graphics,rgl,misc3d,longitudinalData(>=2.2),KmL(>=2.2) |

URL: | http://www.r-project.org |

URL: | http://christophe.genolini.free.fr/kml |

To cluster data, `KmL3D`

go through three steps, each of which
is associated to some functions:

Data preparation

Building "optimal" clusterization.

Exporting results

Visualizing and exporting 3D object

`kml3d`

works on object of class `ClusterLongData3d`

.
Data preparation therefore simply consists in transforming data into an object `ClusterLongData3d`

.
This can be done via function
`clusterLongData3d`

(`cld3d`

in short) that
converts a `data.frame`

or an `array`

into a `ClusterLongData3d`

.

Working on several variables mesured on different scales can give to
much weight to one of the dimension. So the function `scale`

normalizes data.

Instead of working on real data, one can also work on artificial
data. Such data can be created with `generateArtificialLongData3d`

(`gald3d`

in short).

Once an object of class `ClusterLongData3d`

has been created, the algorithm
`kml3d`

can be run.

Starting with a `ClusterLongData3d`

, `kml3d`

built several `Partition`

.
A object of class `Partition`

is a partition of trajectories
into subgroups. It also contains some information like the
percentage of trajectories contained in each group or some quality critetion (like the Calinski &
Harabasz).

`k-means`

is a "hill-climbing" algorithm. The specificity of this
kind of algorithm is that it always converges towards a maximum, but
one cannot know whether it is a local or a global maximum. It offers
no guarantee of optimality.

To maximize one's chances of getting a quality `Partition`

,
it is better to execute the hill climbing algorithm several times,
then to choose the best solution. By default, `kml3d`

executes the hill climbing algorithm 20 times.

To date, it is not possible to know the optimum number of clusters
even if the calculatous of some qualities criterion can gives some
clues. `kml3d`

computes various of them.

In the end, `kml3d`

tests by default 2, 3, 4, 5 et 6 clusters, 20 times each.

When `kml3d`

has constructed some
`Partition`

, the user can examine them one by one and choose
to export some. This can be done via function
`choice`

. `choice`

opens a graphic windows showing
various information including the trajectories cluterized by a specific
`Partition`

.

When some `Partition`

has been selected (the user can select
more than 1), it is possible to
save them. The clusters are therefore exported towards the file
`name-cluster.csv`

. Criteria are exported towards
`name-criteres.csv`

. The graphs are exported according to their
extension.

`KmL3D`

also propose tools to visualize the trajectories in
3D. `plot3d`

using the library `rgl`

to plot two
variables according to time (either the all set of joint-trajectories, or
just the mean joint-trajectories). Then the user can make the
graphical representation turn using the mouse. `plot3dPdf`

build an
`Triangles`

object. These kind of
object can be include in a `pdf`

file using
`saveTrianglesAsASY`

and the software
`asymptote`

. Once again, it is possible to make the image in the
pdf file move using the mouse -so the reader gets real 3D-.

For those who are not familiar with S4 programming: In S4 programming, each function can be adapted for some specific arguments.

To get help on a function (for example

`plot`

), use:`?(plot)`

.To get help on a function adapted to its argument (for example

`plot`

on argument`ClusterLongData`

), used:`?"plot,ClusterLongData"`

.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ```
### 1. Data Preparation
data(pregnandiol)
names(pregnandiol)
cld3dPregTemp <- cld3d(pregnandiol,timeInData=list(temp=1:30*2,preg=1:30*2+1))
### 2. Building "optimal" clusteration (with only 2 redrawings)
### Real analysis needs at least 20 redrawings
kml3d(cld3dPregTemp,3:5,nbRedrawing=2,toPlot="both")
### 3. Exporting results
try(choice(cld3dPregTemp))
### 4. Visualizing in 3D
plotMeans3d(cld3dPregTemp,4)
``` |

kml3d documentation built on Aug. 8, 2017, 9:09 a.m.

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