rnlm

Process Help

RNLM - compute R-mode nonlinear mapping

Process Name	Menu Path	Link to Command Table
RNLM	Sample Analysis ribbon \| Geochemical Processes \| R Mode Non Linear Mapping	Click here

Introduction
Files, Fields and Parameters
Notes
Example
Errors

Introduction

R - mode non linear mapping groups together elements using the angular distances calculated from the Pearsson correlation coefficient matrix.

Note the difference with Q mode non linear mapping which clusters samples on the basis of composition.

How to use

A two dimensional view of the element clusters, or the scores NLM-X versus NLM-Y, is calculated to represent them as they would appear in multi-dimensional space on the basis of element similarity between pairs of samples. All input data is standardized prior to the calculation of the correlation matrix and the linear mapping output scores are normalized prior to plotting.

R - mode non linear mapping, when compared with R - mode factor analysis, is more sophisticated and does not distort or sub-divide the element or parameter clusters. Non linear mapping will give more separable clusters than other hierarchical techniques such as R - mode cluster analysis.

File Handling

The input file &(IN) must have a separate identifier field (*SAMPID). The output file &(SCORES) contains three parameters, FIELD the field identifier, NLM-X and NLM-Y the output scores for plotting the multi-dimensional inter-element distances as a two dimensional flat plane. Results can be displayed using QUIG, PLOTDA or PLOTAN.

Iteration Procedure

In order to present a two dimensional view of multi-dimensional space with minimum distortion of the sample clusters, the calculated mapping error has to be minimized by an iterative method (steepest descent). This is controlled by the @CONVLIM parameter, that is the minimum difference allowed in the mapping error between iterations, @MAXIT, the maximum number of iterations permitted and the @MAGIC parameter which specifies the stepping function used for each iteration. If the stepping function @MAGIC is decreased, the number of iterations is increased with an obvious time penalty on the length of the calculation. The value used must be taken into account when there are a large number of samples. However the results can be more stable.

Files, Fields and Parameters

Input Files

Name	Description	I/O Status	Required	Type
IN	Input file.	Input	Yes	Undefined

Output Files

Name	I/O Status	Required	Type	Description
SCORES	Output	No	Undefined	Optional output file for principal component scores.

Fields

Name	Description	Source	Required	Type	Default
SAMPID	Field containing sample identification	IN	Yes	Any	Undefined
F1	First field to be used. No fields specified means all.	IN	No	Numeric	Undefined
F2	Second field to be used.	IN	No	Numeric	Undefined
F3	Third field to be used.	IN	No	Numeric	Undefined
F4	Fourth field to be used.	IN	No	Numeric	Undefined
F5	Fifth field to be used.	IN	No	Numeric	Undefined
F6	Sixth field to be used.	IN	No	Numeric	Undefined
F7	Seventh field to be used.	IN	No	Numeric	Undefined
F8	Eighth field to be used.	IN	No	Numeric	Undefined
F9	Ninth field to be used.	IN	No	Numeric	Undefined
F10	Tenth field to be used.	IN	No	Numeric	Undefined

Parameters

Name

Description

Required

Default

Range

Values

CONVLIM

Convergence limit (0.0001)

0.0001

Undefined

MAGIC

Convergence [magic] factor (0.35)

0.35

Undefined

MAXIT

Maximum number of iterations (100)

100

Undefined

Option	Description
(0)	Print configuration results to screen.

0,1

Notes

There is a restriction of 2000 samples. Note, as the process is iterative, it may take some time to calculate the results (30 minutes).

Example

!RNLM

&IN(AEG2),@SCORES(RSCORES),@SAMPID='ID',
@CONVLIM=0.0001,@MAGIC=0.35,@PRINT=1

Error and Warning Messages

Message	Description	Solution
* Error * No numeric fields on file. >>> ERROR 122 <<< ( fileno.) IN RNLM

* Error * Compulsory file, field or parameter missing. >>> ERROR 120 <<< ( fileno.) IN RNLM