Basically a wrapper around predict.lda from the package MASS. Uses a LDA model to classify new data.
Usage
reLDA(newdata, LDA)
# S3 method for default
reLDA(newdata, LDA)
# S3 method for PCA
reLDA(newdata, LDA)
# S3 method for Coe
reLDA(newdata, LDA)Value
a list with components (from ?predict.lda ).
class factor of classification
posterior posterior probabilities for the classes
x the scores of test cases
res data.frame of the results
CV.tab a confusion matrix of the results
CV.correct proportion of the diagonal of CV.tab
newdata the data used to calculate passed to predict.lda
Note
Uses the same number of PC axis as the LDA object provided. You should probably use rePCA in conjunction with reLDA to get 'homologous' scores.
Examples
# We select the first 10 individuals in bot,
# for whisky and beer bottles. It will be our referential.
bot1 <- slice(bot, c(1:10, 21:30))
# Same thing for the other 10 individuals.
# It will be our unknown dataset on which we want
# to calculate classes.
bot2 <- slice(bot, c(11:20, 31:40))
# We calculate efourier on these two datasets
bot1.f <- efourier(bot1, 8)
#> 'norm=TRUE' is used and this may be troublesome. See ?efourier #Details
bot2.f <- efourier(bot2, 8)
#> 'norm=TRUE' is used and this may be troublesome. See ?efourier #Details
# Here we obtain our LDA model: first, a PCA, then a LDA
bot1.p <- PCA(bot1.f)
bot1.l <- LDA(bot1.p, "type")
#> 6 PC retained
# we redo the same PCA since we worked with scores
bot2.p <- rePCA(bot1.p, bot2.f)
# we finally "predict" with the model obtained before
bot2.l <- reLDA(bot2.p, bot1.l)
bot2.l
#> $class
#> [1] whisky whisky whisky whisky beer whisky whisky beer whisky whisky
#> [11] beer beer beer whisky beer whisky beer beer beer beer
#> Levels: beer whisky
#>
#> $posterior
#> beer whisky
#> jupiler 1.588583e-05 9.999841e-01
#> kingfisher 9.172746e-02 9.082725e-01
#> latrappe 2.276644e-02 9.772336e-01
#> lindemanskriek 5.840887e-03 9.941591e-01
#> nicechouffe 7.031244e-01 2.968756e-01
#> pecheresse 1.773492e-06 9.999982e-01
#> sierranevada 2.144720e-04 9.997855e-01
#> tanglefoot 9.372426e-01 6.275742e-02
#> tauro 1.183763e-05 9.999882e-01
#> westmalle 1.157018e-04 9.998843e-01
#> jb 9.975581e-01 2.441892e-03
#> johnniewalker 8.473188e-01 1.526812e-01
#> magallan 1.000000e+00 3.192177e-09
#> makersmark 1.093923e-01 8.906077e-01
#> oban 9.999880e-01 1.199656e-05
#> oldpotrero 2.425202e-02 9.757480e-01
#> redbreast 9.999820e-01 1.795276e-05
#> tamdhu 8.589367e-01 1.410633e-01
#> wildturkey 9.999905e-01 9.478960e-06
#> yoichi 9.744921e-01 2.550790e-02
#>
#> $x
#> LD1
#> jupiler 2.9341875
#> kingfisher 0.6087998
#> latrappe 0.9982650
#> lindemanskriek 1.3640608
#> nicechouffe -0.2289504
#> pecheresse 3.5163722
#> sierranevada 2.2430113
#> tanglefoot -0.7179197
#> tauro 3.0122943
#> westmalle 2.4069164
#> jb -1.5965434
#> johnniewalker -0.4550552
#> magallan -5.1945591
#> makersmark 0.5568188
#> oban -3.0087530
#> oldpotrero 0.9810760
#> redbreast -2.9017076
#> tamdhu -0.4796867
#> wildturkey -3.0712994
#> yoichi -0.9673275
#>
#> $newdata
#> PC1 PC2 PC3 PC4
#> jupiler 0.047558323 -0.0009556964 -1.132936e-02 -0.0038135827
#> kingfisher 0.031019804 0.0092893037 -5.639726e-03 0.0006984167
#> latrappe -0.140467542 0.0368452619 8.204030e-03 -0.0074130929
#> lindemanskriek 0.028727335 -0.0093711139 -6.350860e-03 0.0040530566
#> nicechouffe 0.014137615 -0.0087352325 -1.464619e-03 0.0102437348
#> pecheresse 0.046019149 -0.0022071144 -1.263256e-02 -0.0019483303
#> sierranevada -0.045574138 0.0101119946 -4.587309e-03 -0.0139742083
#> tanglefoot -0.083848693 0.0019607973 1.265634e-02 -0.0086813906
#> tauro 0.047804962 -0.0010302173 -1.166643e-02 -0.0038315686
#> westmalle 0.043104213 -0.0006618641 -9.661507e-03 0.0013659528
#> jb 0.033826795 -0.0043832070 8.789680e-03 -0.0012973929
#> johnniewalker 0.027546559 0.0433572509 -5.503569e-07 0.0080407513
#> magallan 0.062757370 0.0344623824 1.994348e-02 0.0054305457
#> makersmark -0.066073754 -0.0410683917 -2.500513e-02 -0.0028195062
#> oban 0.056001340 -0.0017415641 1.469954e-02 0.0024240694
#> oldpotrero -0.039446859 -0.0560097481 -1.838963e-02 0.0143275711
#> redbreast -0.070467008 -0.0453726482 1.443590e-03 0.0008230393
#> tamdhu 0.040245919 0.0099990120 8.849077e-03 -0.0054926858
#> wildturkey 0.009047941 -0.0118958979 1.825586e-02 -0.0002205672
#> yoichi -0.041919333 0.0374066929 1.388610e-02 0.0020851880
#> PC5 PC6
#> jupiler 0.0005273680 -0.003411272
#> kingfisher -0.0025505108 -0.000645225
#> latrappe 0.0014020218 -0.011164248
#> lindemanskriek -0.0005455535 -0.004342575
#> nicechouffe -0.0031229185 -0.005062708
#> pecheresse 0.0030349867 -0.005659553
#> sierranevada -0.0050825894 -0.003254912
#> tanglefoot -0.0051466484 -0.003608419
#> tauro 0.0011495431 -0.003297832
#> westmalle 0.0015195495 -0.004960376
#> jb -0.0020355558 0.003538980
#> johnniewalker -0.0046821155 -0.006875580
#> magallan 0.0055312084 0.011826574
#> makersmark 0.0039534995 0.017991125
#> oban 0.0001554770 0.005786238
#> oldpotrero 0.0023407200 0.001001825
#> redbreast -0.0038050474 0.012566253
#> tamdhu -0.0011719141 0.000222802
#> wildturkey -0.0020315441 0.003880876
#> yoichi 0.0105600234 -0.004531973
#>