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I am working on the Forest type mapping dataset which is available in the UCI machine learning repository.

I have 27 features to predict the 4 types of forest. I am performing a Linear Discriminant Analysis (LDA) to reduce the number of features using lda() function available in the MASS library.

The results of my LDA are as follows -

forest.lda <- lda(class ~.,data=forest)
forest.lda
Call:
lda(class ~ ., data = forest)

Prior probabilities of groups:
   d         h         o         s  
0.2727273 0.2424242 0.1868687 0.2979798 

Group means:
     b1       b2       b3        b4       b5        b6       b7       b8       b9
  d  53.31481 48.31481 68.40741  97.66667 63.18519 103.31481 98.74074  26.07407 56.46296
  h  78.27083 29.39583 55.14583 113.66667 50.22917  95.25000 98.00000 25.10417 60.06250
  o  65.08108 66.54054 87.97297 103.62162 77.70270 118.10811 91.56757 44.18919 77.94595
  s  57.96610 27.79661 51.05085  93.47458 49.67797  91.66102 76.52542 24.28814 55.67797
     pred_minus_obs_H_b1 pred_minus_obs_H_b2 pred_minus_obs_H_b3 pred_minus_obs_H_b4
  d             60.76204            2.723704            28.25963           0.7018519
  h             35.17708           21.101250            40.25167         -15.9608333
  o             48.90054          -15.450270             8.99027          -7.0445946
  s             55.64695           22.945254            44.95712           3.6745763
     pred_minus_obs_H_b5 pred_minus_obs_H_b6 pred_minus_obs_H_b7 pred_minus_obs_H_b8
  d            -37.75296           -42.72981        -21.66481481            3.772407
  h            -25.02354           -35.37042        -21.25583333            4.638958
  o            -52.34162           -57.74297        -15.35891892          -14.684324
  s            -24.41831           -31.63898          0.06610169            5.355085
    pred_minus_obs_H_b9 pred_minus_obs_S_b1 pred_minus_obs_S_b2 pred_minus_obs_S_b3
  d           -0.6970370           -20.12778          -1.1394444           -4.508519
  h           -4.5602083           -19.90458          -0.8512500           -4.302500
  o          -22.5089189           -19.82000          -0.9532432           -4.145946
  s           -0.3098305           -20.19966          -1.0466102           -4.390508
    pred_minus_obs_S_b4 pred_minus_obs_S_b5 pred_minus_obs_S_b6 pred_minus_obs_S_b7
  d            -21.34370          -0.9635185           -4.722407           -19.31796
  h            -21.09187          -1.0172917           -4.687083           -18.68271
  o            -20.55324          -0.8581081           -4.273514           -18.23081
  s            -20.88051          -1.0201695           -4.613898           -18.91254
    pred_minus_obs_S_b8 pred_minus_obs_S_b9
  d            -1.860926           -4.510000
  h            -1.345000           -3.968542
  o            -1.442432           -4.048108
  s            -1.569492           -4.051695

 Coefficients of linear discriminants:
                        LD1          LD2         LD3
 b1                   0.15410941  0.083191904 -0.05574989
 b2                  -0.09033693 -0.098788690 -0.05294103
 b3                   0.01730795  0.034581992  0.17366457
 b4                   0.03142488  0.086065613  0.15504752
 b5                   1.01223928  0.520003333  0.41695043
 b6                  -0.40178858 -0.526621626 -0.48149395
 b7                  -0.23331487 -0.185079579 -0.05010620
 b8                  -0.32959040 -0.218615144 -0.10788013
 b9                   0.13938043  0.179366235  0.15483732
 pred_minus_obs_H_b1 -0.02732135  0.013629388 -0.02773200
 pred_minus_obs_H_b2  0.16743148 -0.086326071 -0.27561332
 pred_minus_obs_H_b3 -0.11530638  0.044265889  0.35503689
 pred_minus_obs_H_b4  0.05370740  0.068117979  0.13440809
 pred_minus_obs_H_b5  1.03718236  0.462674531  0.38562055
 pred_minus_obs_H_b6 -0.40022794 -0.541066832 -0.32075713
 pred_minus_obs_H_b7 -0.19480130 -0.138378132  0.06374322
 pred_minus_obs_H_b8 -0.13609236 -0.003440928  0.09291261
 pred_minus_obs_H_b9  0.01171503 -0.160364856 -0.11694535
 pred_minus_obs_S_b1 -0.05050788  0.019637786 -0.03832580
 pred_minus_obs_S_b2  0.05946038  0.023019484 -0.06508984
 pred_minus_obs_S_b3 -0.05777119 -0.138126136  0.07659433
 pred_minus_obs_S_b4  0.03461031  0.008094415  0.06487418
 pred_minus_obs_S_b5  0.63346845  0.105556436 -0.01382360
 pred_minus_obs_S_b6 -0.30309468 -0.109369091  0.07915327
 pred_minus_obs_S_b7 -0.07614580 -0.053089078  0.01138394
 pred_minus_obs_S_b8 -0.13416272  0.328494630 -0.44248108
 pred_minus_obs_S_b9  0.06414547 -0.347941228  0.43430498

Proportion of trace:
 LD1    LD2    LD3 
 0.7365 0.1971 0.0664 

From wiki and other links what I understand is LD1, LD2 and LD3 are functions that I can use to classify the new data (LD1 73.7% and LD2 19.7%). I am not able to interpret how I can use this result to reduce the number of features or select only the relevant features as LD1 and LD2 functions have coefficient for each feature.

I am looking for help on interpreting the results to reduce the number of features from $27$ to some $x<27$.

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  • 1
    $\begingroup$ In my opinion, you should be leveraging canonical discriminant analysis as opposed to LDA. LDA is not, in and of itself, dimension reducing. It simply creates a model based on the inputs, generating coefficients for each variable that maximize the between class differences. CDA, on the other hand, is dimension reducing in that it finds "canonical discriminant" functions -- linear combinations in this instance -- as suggested by the input variables. $\endgroup$ – Mike Hunter Oct 27 '15 at 1:40
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    $\begingroup$ I changed the title of your Q because it is about feature selection and not dimensionality reduction. LDA (its discriminant functions) are already the reduced dimensionality. But you say you want to work with some original variables in the end, not the functions. $\endgroup$ – ttnphns Oct 27 '15 at 9:12
  • $\begingroup$ What are the individual variances of your 27 predictors? Do they differ a lot between each other? $\endgroup$ – amoeba Oct 27 '15 at 14:49
  • $\begingroup$ @amoeba - They vary slightly as below (provided for first 20 features) b1- 1.9142711 b2 - 1.4353474 b3 - 2.3370815 b4 - 0.6618505 b5 - (-0.5993427) b6 - (-0.7542855) b7 - (-2.0807758) b8 - 0.4600133 b9 - 0.7224606 pred_minus_obs_H_b1 -(-4.3475477) pred_minus_obs_H_b2 -(-2.6358098) pred_minus_obs_H_b3 - (-4.7219599) pred_minus_obs_H_b4 - (-4.6866373) pred_minus_obs_H_b5 - 0.1267812 pred_minus_obs_H_b6 - (-0.6738532) pred_minus_obs_H_b7 - (-0.7955976) pred_minus_obs_H_b8 - (-1.8085106) pred_minus_obs_H_b9 - (-2.4828457) pred_minus_obs_S_b1 - 1.1921676 pred_minus_obs_S_b2 - 2.4012840 $\endgroup$ – Arvind Oct 28 '15 at 2:52
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If it doesn't need to be vanilla LDA (which is not supposed to select from input features), there's e.g. Sparse Discriminant Analysis, which is a LASSO penalized LDA: Line Clemmensen, Trevor Hastie, Daniela Witten, Bjarne Ersbøll: Sparse Discriminant Analysis (2011)

This uses a discrete subset of the input features via the LASSO regularization.

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Lda models are used to predict a categorical variable (factor) using one or several continuous (numerical) features. So given some measurements about a forest, you will be able to predict which type of forest a given observation belongs to. Before applying a lda model, you have to determine which features are relevant to discriminate the data. To do so, you need to use and apply an ANOVA model to each numerical variable. In each of these ANOVA models, the variable to explain (Y) is the numerical feature, and the explicative variable (X) is the categorical feature you want to predict in the lda model. This will tell you for each forest type, if the mean of the numerical feature stays the same or not. If it does, it will not give you any information to discriminate the data. Therefore it'll not be relevant to the model and you will not use it. However if the mean of a numerical feature differs depending on the forest type, it will help you discriminate the data and you'll use it in the lda model.

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