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Selecting predictors for discriminant analysis of species performance: an example from an amphibious softwater plant

Floris Vanderhaeghe, Alfons JP Smolders, Jan GM Roelofs and Maurice Hoffmann UGent (2012) PLANT BIOLOGY. 14(2). p.271-277
abstract
Selecting an appropriate variable subset in linear multivariate methods is an important methodological issue for ecologists. Interest often exists in obtaining general predictive capacity or in finding causal inferences from predictor variables. Because of a lack of solid knowledge on a studied phenomenon, scientists explore predictor variables in order to find the most meaningful (i.e. discriminating) ones. As an example, we modelled the response of the amphibious softwater plant Eleocharis multicaulis using canonical discriminant function analysis. We asked how variables can be selected through comparison of several methods: univariate Pearson chisquare screening, principal components analysis (PCA) and step-wise analysis, as well as combinations of some methods. We expected PCA to perform best. The selected methods were evaluated through fit and stability of the resulting discriminant functions and through correlations between these functions and the predictor variables. The chi-square subset, at P < 0.05, followed by a step-wise sub-selection, gave the best results. In contrast to expectations, PCA performed poorly, as so did step-wise analysis. The different chi-square subset methods all yielded ecologically meaningful variables, while probable noise variables were also selected by PCA and step-wise analysis. We advise against the simple use of PCA or step-wise discriminant analysis to obtain an ecologically meaningful variable subset; the former because it does not take into account the response variable, the latter because noise variables are likely to be selected. We suggest that univariate screening techniques are a worthwhile alternative for variable selection in ecology.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
model evaluation, Data mining, overfitting, principal components analysis, goodness-of-fit test, Pearson chi-square test, step-wise analysis, DISTRIBUTION MODELS, PRINCIPAL-COMPONENTS, ECOLOGICAL THEORY, DISTRIBUTIONS, REGRESSION, VARIABLES, NICHE
journal title
PLANT BIOLOGY
Plant Biol.
volume
14
issue
2
pages
271 - 277
Web of Science type
Article
Web of Science id
000299928900003
JCR category
PLANT SCIENCES
JCR impact factor
2.32 (2012)
JCR rank
56/193 (2012)
JCR quartile
2 (2012)
ISSN
1435-8603
DOI
10.1111/j.1438-8677.2011.00497.x
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1989459
handle
http://hdl.handle.net/1854/LU-1989459
date created
2012-01-17 12:28:23
date last changed
2016-12-19 15:42:53
@article{1989459,
  abstract     = {Selecting an appropriate variable subset in linear multivariate methods is an important methodological issue for ecologists. Interest often exists in obtaining general predictive capacity or in finding causal inferences from predictor variables. Because of a lack of solid knowledge on a studied phenomenon, scientists explore predictor variables in order to find the most meaningful (i.e. discriminating) ones. As an example, we modelled the response of the amphibious softwater plant Eleocharis multicaulis using canonical discriminant function analysis. We asked how variables can be selected through comparison of several methods: univariate Pearson chisquare screening, principal components analysis (PCA) and step-wise analysis, as well as combinations of some methods. We expected PCA to perform best. The selected methods were evaluated through fit and stability of the resulting discriminant functions and through correlations between these functions and the predictor variables. The chi-square subset, at P {\textlangle} 0.05, followed by a step-wise sub-selection, gave the best results. In contrast to expectations, PCA performed poorly, as so did step-wise analysis. The different chi-square subset methods all yielded ecologically meaningful variables, while probable noise variables were also selected by PCA and step-wise analysis. We advise against the simple use of PCA or step-wise discriminant analysis to obtain an ecologically meaningful variable subset; the former because it does not take into account the response variable, the latter because noise variables are likely to be selected. We suggest that univariate screening techniques are a worthwhile alternative for variable selection in ecology.},
  author       = {Vanderhaeghe, Floris and Smolders, Alfons JP and Roelofs, Jan GM and Hoffmann, Maurice},
  issn         = {1435-8603},
  journal      = {PLANT BIOLOGY},
  keyword      = {model evaluation,Data mining,overfitting,principal components analysis,goodness-of-fit test,Pearson chi-square test,step-wise analysis,DISTRIBUTION MODELS,PRINCIPAL-COMPONENTS,ECOLOGICAL THEORY,DISTRIBUTIONS,REGRESSION,VARIABLES,NICHE},
  language     = {eng},
  number       = {2},
  pages        = {271--277},
  title        = {Selecting predictors for discriminant analysis of species performance: an example from an amphibious softwater plant},
  url          = {http://dx.doi.org/10.1111/j.1438-8677.2011.00497.x},
  volume       = {14},
  year         = {2012},
}

Chicago
Vanderhaeghe, Floris, Alfons JP Smolders, Jan GM Roelofs, and Maurice Hoffmann. 2012. “Selecting Predictors for Discriminant Analysis of Species Performance: An Example from an Amphibious Softwater Plant.” Plant Biology 14 (2): 271–277.
APA
Vanderhaeghe, F., Smolders, A. J., Roelofs, J. G., & Hoffmann, M. (2012). Selecting predictors for discriminant analysis of species performance: an example from an amphibious softwater plant. PLANT BIOLOGY, 14(2), 271–277.
Vancouver
1.
Vanderhaeghe F, Smolders AJ, Roelofs JG, Hoffmann M. Selecting predictors for discriminant analysis of species performance: an example from an amphibious softwater plant. PLANT BIOLOGY. 2012;14(2):271–7.
MLA
Vanderhaeghe, Floris, Alfons JP Smolders, Jan GM Roelofs, et al. “Selecting Predictors for Discriminant Analysis of Species Performance: An Example from an Amphibious Softwater Plant.” PLANT BIOLOGY 14.2 (2012): 271–277. Print.