mcoa {ade4}R Documentation

Multiple CO-inertia Analysis

Description

performs a multiple CO-inertia analysis, using an object of class ktab.

Usage

mcoa(X, option = c("inertia", "lambda1", "uniform", "internal"), 
    scannf = TRUE, nf = 3, tol = 1e-07)
## S3 method for class 'mcoa':
print(x, ...)
## S3 method for class 'mcoa':
summary(object, ...)
## S3 method for class 'mcoa':
plot(x, xax = 1, yax = 2, eig.bottom = TRUE, ...)

Arguments

X an object of class ktab
option a string of characters for the weightings of the arrays options :
"inertia"
weighting of group k by the inverse of the total inertia of the array k
"lambda1"
weighting of group k by the inverse of the first eigenvalue of the k analysis
"uniform"
uniform weighting of groups
"internal"
weighting included in X$tabw
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
tol a tolerance threshold, an eigenvalue is considered positive if it is larger than -tol*lambda1 where lambda1 is the largest eigenvalue.
x, object an object of class 'mcoa'
... further arguments passed to or from other methods
xax, yax the numbers of the x-axis and the y-axis
eig.bottom a logical value indicating whether the eigenvalues bar plot should be added

Value

mcoa returns a list of class 'mcoa' containing :
pseudoeig a numeric vector with the all pseudo eigenvalues
call the call-up order
nf a numeric value indicating the number of kept axes
SynVar a data frame with the synthetic scores
axis a data frame with the co-inertia axes
Tli a data frame with the co-inertia coordinates
Tl1 a data frame with the co-inertia normed scores
Tax a data frame with the inertia axes onto co-inertia axis
Tco a data frame with the column coordinates onto synthetic scores
TL a data frame with the factors for Tli Tl1
TC a data frame with the factors for Tco
T4 a data frame with the factors for Tax
lambda a data frame with the all eigenvalues (computed on the separate analyses)
cov2 a numeric vector with the all pseudo eigenvalues (synthetic analysis)

Author(s)

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

References

Chessel, D. and Hanafi, M. (1996) Analyses de la co-inertie de K nuages de points, Revue de Statistique Appliquée, 44, 35–60.

Examples

data(friday87)
w1 <- data.frame(scale(friday87$fau, scal = FALSE))
w2 <- ktab.data.frame(w1, friday87$fau.blo, tabnames = friday87$tab.names)
mcoa1 <- mcoa(w2, "lambda1", scan = FALSE)
mcoa1
summary(mcoa1)
plot(mcoa1)

Worked out examples


> library(ade4)
> ### Name: mcoa
> ### Title: Multiple CO-inertia Analysis
> ### Aliases: mcoa print.mcoa summary.mcoa plot.mcoa
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(friday87)
> w1 <- data.frame(scale(friday87$fau, scal = FALSE))
> w2 <- ktab.data.frame(w1, friday87$fau.blo, tabnames = friday87$tab.names)
> mcoa1 <- mcoa(w2, "lambda1", scan = FALSE)
> mcoa1
Multiple Co-inertia Analysis
list of class mcoa

$pseudoeig: 16 pseudo eigen values
6.459 4.07 1.914 1.644 0.98 ...

$call: mcoa(X = w2, option = "lambda1", scannf = FALSE)

$nf: 3 axis saved

   data.frame nrow ncol content                                 
1  $SynVar    16   3    synthetic scores                        
2  $axis      91   3    co-inertia axis                         
3  $Tli       160  3    co-inertia coordinates                  
4  $Tl1       160  3    co-inertia normed scores                
5  $Tax       40   3    inertia axes onto co-inertia axis       
6  $Tco       91   3    columns onto synthetic scores           
7  $TL        160  2    factors for Tli Tl1                     
8  $TC        91   2    factors for Tco                         
9  $T4        40   2    factors for Tax                         
10 $lambda    10   3    eigen values (separate analysis)        
11 $cov2      10   3    pseudo eigen values (synthetic analysis)
other elements: NULL
> summary(mcoa1)
Multiple Co-inertia Analysis
Array number 1 Hemiptera Rows 16 Cols 11 
  Iner  Iner+ Var   Var+  cos2  cov2 
1 1     1     0.688 0.688 0.68  0.468
2 0.748 1.748 0.979 1.667 0.82  0.803
3 0.384 2.132 0.356 2.023 0.668 0.238

Array number 2 Odonata Rows 16 Cols 7 
  Iner  Iner+ Var   Var+  cos2  cov2 
1 1     1     0.839 0.839 0.853 0.715
2 0.856 1.856 0.873 1.712 0.681 0.594
3 0.573 2.43  0.268 1.979 0.444 0.119

Array number 3 Trichoptera Rows 16 Cols 13 
  Iner  Iner+ Var   Var+  cos2  cov2 
1 1     1     0.941 0.941 0.76  0.715
2 0.395 1.395 0.361 1.302 0.715 0.258
3 0.238 1.634 0.176 1.478 0.726 0.128

Array number 4 Ephemeroptera Rows 16 Cols 4 
  Iner  Iner+ Var   Var+  cos2  cov2 
1 1     1     0.942 0.942 0.915 0.861
2 0.697 1.697 0.752 1.694 0.53  0.399
3 0.079 1.777 0.035 1.728 0.134 0.005

Array number 5 Coleoptera Rows 16 Cols 13 
  Iner  Iner+ Var   Var+  cos2  cov2 
1 1     1     0.691 0.691 0.695 0.481
2 0.683 1.683 0.659 1.351 0.663 0.437
3 0.527 2.21  0.579 1.93  0.804 0.466

Array number 6 Diptera Rows 16 Cols 22 
  Iner  Iner+ Var   Var+  cos2  cov2 
1 1     1     0.951 0.951 0.854 0.812
2 0.478 1.478 0.393 1.343 0.584 0.23 
3 0.369 1.847 0.239 1.582 0.665 0.159

Array number 7 Hydracarina Rows 16 Cols 4 
  Iner  Iner+ Var   Var+  cos2  cov2 
1 1     1     0.915 0.915 0.693 0.634
2 0.87  1.87  0.851 1.766 0.548 0.466
3 0.591 2.461 0.667 2.434 0.86  0.574

Array number 8 Malacostraca Rows 16 Cols 3 
  Iner  Iner+ Var   Var+  cos2  cov2 
1 1     1     0.876 0.876 0.751 0.657
2 0.529 1.529 0.653 1.528 0.672 0.438
3 0.154 1.683 0.155 1.683 0.075 0.012

Array number 9 Mollusca Rows 16 Cols 8 
  Iner  Iner+ Var   Var+  cos2  cov2 
1 1     1     0.974 0.974 0.773 0.753
2 0.286 1.286 0.261 1.235 0.805 0.21 
3 0.207 1.493 0.173 1.408 0.481 0.083

Array number 10 Oligochaeta Rows 16 Cols 6 
  Iner  Iner+ Var   Var+  cos2  cov2 
1 1     1     0.755 0.755 0.482 0.364
2 0.799 1.799 0.443 1.198 0.53  0.234
3 0.383 2.183 0.244 1.442 0.539 0.132

> plot(mcoa1)

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[Package ade4 Index]