withinpca {ade4}R Documentation

Normed within Principal Component Analysis

Description

performs a normed within Principal Component Analysis.

Usage

withinpca(df, fac, scaling = c("partial", "total"), 
    scannf = TRUE, nf = 2)

Arguments

df a data frame with quantitative variables
fac a factor distributing the rows of df in classes
scaling a string of characters as a scaling option :
if "partial", for each factor level, the sub-array is centred and normed.
If "total", for each factor level, the sub-array is centred and the total array is then normed.
scannf a logical value indicating whether the eigenvalues bar plot should be displayed
nf if scannf FALSE, an integer indicating the number of kept axes

Value

returns a list of the sub-class within of class dudi. See within

Author(s)

Daniel Chessel
Anne B Dufour dufour@biomserv.univ-lyon1.fr

References

Bouroche, J. M. (1975) Analyse des données ternaires: la double analyse en composantes principales. Thèse de 3ème cycle, Université de Paris VI.

Examples

data(meaudret)
wit1 <- withinpca(meaudret$mil, meaudret$plan$dat, 
    scan = FALSE, scal = "partial")
kta1 <- ktab.within(wit1, colnames = rep(c("S1","S2","S3","S4","S5"), 4))
unclass(kta1)
# See pta
plot(wit1)

Worked out examples


> library(ade4)
> ### Name: withinpca
> ### Title: Normed within Principal Component Analysis
> ### Aliases: withinpca
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(meaudret)
> wit1 <- withinpca(meaudret$mil, meaudret$plan$dat, 
+     scan = FALSE, scal = "partial")
> kta1 <- ktab.within(wit1, colnames = rep(c("S1","S2","S3","S4","S5"), 4))
> unclass(kta1)
$spring
                 S1         S2          S3         S4         S5
Temp  -1.372813e+00 -0.3922323 -0.39223227  0.5883484  1.5689291
Debit -1.615156e+00 -0.4251482 -0.01830782  0.8157149  1.2428973
pH     2.041241e-01 -1.8371173  0.20412415  1.2247449  0.2041241
Condu  9.457838e-17  1.9069252 -0.47673129 -0.4767313 -0.9534626
Dbo5  -9.621078e-01  1.9351487 -0.41545565 -0.3061252 -0.2514600
Oxyd  -6.364382e-01  1.9923283 -0.49808208 -0.4980821 -0.3597259
Ammo  -7.376580e-01  1.9837018 -0.45854414 -0.4087024 -0.3787973
Nitra -5.281643e-01 -1.6155614  0.40389035  0.4038903  1.3359450
Phos  -1.047323e+00  1.6189391 -1.06650488  0.1419449  0.3529441

$summer
              S1         S2         S3          S4         S5
Temp  -1.1666667 -1.1666667  0.5000000  1.33333333  0.5000000
Debit -1.2683846 -0.7763389 -0.2296214  0.86381368  1.4105312
pH     0.9354143 -1.4031215 -0.7349684 -0.06681531  1.2694909
Condu -1.5297323  0.9448347  1.1697953  0.04499213 -0.6298898
Dbo5  -1.0875080  1.4231586  0.6175971  0.21481639 -1.1680641
Oxyd  -0.7664063  1.9508524 -0.2786932 -0.20901990 -0.6967330
Ammo  -1.1379075  1.3255250  0.8424990  0.07982640 -1.1099429
Nitra -0.8553618 -1.4868370  0.4936988  0.69462267  1.1538773
Phos  -1.6393299  0.6112322  1.1546918  0.48335936 -0.6099535

$autumn
              S1          S2          S3          S4         S5
Temp  -1.6035675  1.06904497 -0.26726124  1.06904497 -0.2672612
Debit -1.8766905 -0.08487545  0.66957300  0.95249116  0.3395018
pH     0.5619515 -1.31122014 -0.84292723  0.09365858  1.4985373
Condu -0.7012869  1.87009833  0.11688115 -0.35064344 -0.9350492
Dbo5  -0.6044785  1.97542987 -0.19199318 -0.57447961 -0.6044785
Oxyd  -0.7363901  1.97092649 -0.23102435 -0.41151212 -0.5919999
Ammo  -0.6470895  1.95761335 -0.09597377 -0.57374709 -0.6408030
Nitra -0.5674453 -1.62198962  1.13991221  0.83861383  0.2109089
Phos  -1.1374069  1.70830946  0.47677844 -0.44686983 -0.6008112

$winter
              S1         S2          S3         S4         S5
Temp   0.5000000  0.5000000 0.500000000  0.5000000 -2.0000000
Debit -1.5362076 -0.4891485 0.003125549  1.4330644  0.5891661
pH    -1.8864844  0.6859943 0.685994341  0.6859943 -0.1714986
Condu -0.9819805  0.9274260 1.472970759 -0.7092081 -0.7092081
Dbo5  -1.0927369  1.2659029 1.027053299 -0.1373385 -1.0628807
Oxyd  -0.9763927  1.2666716 1.134726600 -0.4486128 -0.9763927
Ammo  -1.1833898  1.0449484 1.310452499 -0.3584306 -0.8135805
Nitra -1.9709202  0.4077766 0.577683516  0.2378697  0.7475904
Phos  -1.0886790  0.4133145 1.744869109 -0.4175755 -0.6519291

$lw
[1] 1 1 1 1 1 1 1 1 1

$cw
 [1] 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2
[20] 0.2

$blo
spring summer autumn winter 
     5      5      5      5 

$TL
   T L
1  1 1
2  1 2
3  1 3
4  1 4
5  1 5
6  1 6
7  1 7
8  1 8
9  1 9
10 2 1
11 2 2
12 2 3
13 2 4
14 2 5
15 2 6
16 2 7
17 2 8
18 2 9
19 3 1
20 3 2
21 3 3
22 3 4
23 3 5
24 3 6
25 3 7
26 3 8
27 3 9
28 4 1
29 4 2
30 4 3
31 4 4
32 4 5
33 4 6
34 4 7
35 4 8
36 4 9

$TC
   T C
1  1 1
2  1 2
3  1 3
4  1 4
5  1 5
6  2 1
7  2 2
8  2 3
9  2 4
10 2 5
11 3 1
12 3 2
13 3 3
14 3 4
15 3 5
16 4 1
17 4 2
18 4 3
19 4 4
20 4 5

$T4
   T 4
1  1 1
2  1 2
3  1 3
4  1 4
5  2 1
6  2 2
7  2 3
8  2 4
9  3 1
10 3 2
11 3 3
12 3 4
13 4 1
14 4 2
15 4 3
16 4 4

$call
ktab.within(dudiwit = wit1, colnames = rep(c("S1", "S2", "S3", 
    "S4", "S5"), 4))

$tabw
autumn spring summer winter 
  0.25   0.25   0.25   0.25 

> # See pta
> plot(wit1)
> 
> 
> 
> 

[Package ade4 Index]