nmds 2.0 program description dealing with missing values (mv) basic knowledge about the interface...

NMDS 2.0 Program Description

Dealing with Missing Values (MV)

Basic Knowledge about the Interface

This is a usual Power Point Presentation.Use Mouse-Clicks or the Hyperlinks to proceed.

How to start a NMDS

Dealing with the Temperature Option

The Menu of NMDS

The menu of NMDS is very simpleEach topic directly leads to a

window of the application

The Menu of NMDS

The menu of Access calls the Access data-base that contains the

rank-matrixes. Call this option to import your own matrix.

You, for instance, can simply import any correlation matrix generated by excel using the access import filter

and visualize the relations using NMDS

The list of all matrixes that are stored in theAccess database are listed in this combo box

The NMDS Rank-Matrix

This is the examle rank-matrix of the example “Staedte” (towns)This is the classical example in psychological text-books.


This is the example rank-matrix based on reaction times (1/100-seconds) typing several letters with a QWERTY keyboard


This is the example rank-matrix based on an imported correlation matrix produced in EXCEL and imported in ACCESS

If you start NMDS, you see the following Windows.

This is the Information Line showing you the actual Progress of the NMDS

This is the Option Box where you select the

Rank Matrix you want toelaborate

Here you have to adjust whether high values in the rank-matrix mean similarity or no-similarity

Here you choose the dimensionality of the NMDS graph

(since a screen only has a 2D presentation, usually keep the default)

Here you select how to deal with missing values

The Interface - NMDS Control 1/5

This button loads thespecified rank-matrix

This button starts theNMDS calculation


Here you select the Random Algorithm you want to use for calculation

(usually you*ll keep 0 as default)

This option box determines the temperature for the

NMDS calculation

This option box determines what is affected by

the temperature

This button shows you theNMDS graph

This is the information that is generated automatically with

each start of the program

This option decides whether the information in the text-field

is presented on the NMDS graph


In this field you can specufy how long the

labels are on the NMDS graph

This option box determines the size of NMDS graph

Mirroring the NMDS graphhorizontally

Mirroring the NMDS graphvertically

Rotating the NMDS graphin steps of 45 degrees

An information field of the actual calculated

alienus

An information field of the actual iterations

calculated


This button shows you theAlienus graph

Switching into thesingle step mode

(you then have to press a key for each iteration step)


This button stopsand continues the NMDS calculation

This button terminates theNMDS program

This button exports the NMDScalculation into *.txt files

This button prints the NMDS graph on the standard printer

Click into this window to refresh the NMDS drawing

Use right button to move an item

The Interface - NMDS Graph

Moving an item manually is useful to test

certain hypotheses about relationships of variables

The Interface - Alienus Monitor

The Alienus Monitor showsthe development of the

alienus over time.

It is useful to set the appropriate temperature

for a give rank matrix

How to Start a NMDS

1. Press here

2. Press here

3. Press here4. Press here

5. Enter 10 here

6. Press here & wait

To see how NMDS is working just try the default “Städte” (towns)

How to deal with Missing Values (MV)

NMDS has various options to deal with Missing Values (MV)

by choosing several options in thiscombo-box

How to deal with Missing Values (MV)

Missing-Values can be treated with the following options

• MV set to -1All MV are set to -1

• MV set to 0All MV are set to 0

• inverse-singleOptimal Option if the Rank-Matrix contains values from 0 to 1

• positive-doubleOptimal Option if the Rank-Matrix contains values from 1 onwards

• negative-doubleOption if the Rank-Matrix contains values from 0 to 1 and the MV are to be distinguished very clearly from known values

• inverse-doubleOption if the Rank-Matrix contains values from 0 to 1 and the MV are to be distinguished clearly from known values

• all-inverseFits to all problems that cannot be treated with means above

The Temperature Option

The temperature Option is a highly efficient option to avoid local minima in a NMDS calculation.

A temperature of 0 would, for instance lead to about 1%-4% wrong representations in a simple Example with about 10 varibales and a defined optimal solution, as “Städte” (towns) in this software package.

Using a temperature of 1.0 for this example reduces this error to zero, i.e. in all times the optimal minimum is found.

Set the temperature in a way that the calculated points are “shaken” and cooled down in order to find the best fit of the NMDS graph to your rank matrix. Consider the following experience-based suggestions:

• For 10 Variables: Temperature set to 0.5 or higher • For 30 Variables: Temperature set to 1.0 or higher• For 90 Variables: Temperature set to 3.0 or higher


.

Input the value for the temperature as you like here.

The most efficient value for about 10 variables

in terms of time and result-quality for the temperature is preset.

There are two algorithms implemented how the temperature boils the points in the

NMDS graph.

“Dots+Alineation” or “Alineation”

“Dots+Alineation” is more efficient in finding local minima

“Alineation” is more efficient in terms of time until the solution is found


Without the temperature, a Rank-Matrix may fall into a local minimum.

This means, the NMDS will not find the optimal interrelation of the

variables

The temperature avoidsthat a NMDS graph falls into a local minimum and fixes 90% to 100% of all possible local mimima.

In general the Alienus-Monitor is showing a graph like

the green one if the temperature has successfully

overcome a local minima


Don’t worry, if the NMDS graph looks like this during the

NMDS calculation.The temperature cools down

with each iteration so that an optimum is found after

a certain amount of interations.The absolute number of

iterations required depends on the quality of the data as well as the

temperature set

nmds 2.0 program description dealing with missing values (mv) basic knowledge about the interface...

Documents

nmds rankmatrix

nmds calculation

menu of nmds

nmds program

interface nmds graph

rank matrix slide

interface nmds control

size of nmds graph