CA: Correspondence analysis
In easyCODA: Compositional Data Analysis in Practice

Description Usage Arguments Details Value Author(s) References See Also Examples

Computation of correspondence analysis on a table of nonnegative data.

1	CA(data, nd = 2, suprow = NA, supcol = NA)

`data`	A data frame or matrix of nonnegative data (no negative values)
`nd`	Number of dimensions for summary solution if not 2 (default)
`suprow`	Indices of rows that are supplementary points
`supcol`	Indices of columns that are supplementary points

The function CA is a simple wrapper for the ca function in the ca package (Nenadic and Greenacre, 2007), for compatibility within the easyCODA package.

Supplementary rows and columns can be declared (also known as passive points) – these do not contribute to the solution but are positioned on the solution axes.

The function borrows the structure and functions of the ca package, which is required, and produces a ca object, and the same print, summary and plot methods can be used, as for a ca object. It additionally exports the principal coordinates of both the rows and columns, not presently found in the ca package.

`sv`	Singular values
`nd`	Number of dimensions in solution results
`rownames`	Row names
`rowmass`	Row weights
`rowdist`	Row logratio distances to centroid
`rowinertia`	Row inertias
`rowcoord`	Row standard coordinates
`rowpcoord`	Row principal coordinates
`rowsup`	Indices of row supplementary points
`colnames`	Column names
`colmass`	Column weights
`coldist`	Column logratio distances to centroid
`colinertia`	Column inertias
`colcoord`	Column standard coordinates
`colpcoord`	Column principal coordinates
`N`	The compositional data table

Michael Greenacre

Nenadic, O. and Greenacre, M. (2007). Correspondence analysis in R, with two- and three-dimensional graphics: The ca package. Journal of Statistical Software, 20 (3), https://www.jstatsoft.org/v20/i03/

PLOT.CA, plot.ca, summary.ca, print.ca

# (weighted) LRA of the RomanCups data set, showing default symmetric map
data(cups)
PLOT.CA(CA(cups))

data(author)
ca(author)
plot(CA(author))      # ca plot function
PLOT.CA(CA(author))   # easyCODA plot function

Loading required package: ca
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-7
Loading required package: ellipse

Attaching package: ‘ellipse’

The following object is masked from ‘package:graphics’:

    pairs


 Principal inertias (eigenvalues):
           1        2        3        4        5        6        7       
Value      0.007664 0.003688 0.002411 0.001383 0.001002 0.000723 0.000659
Percentage 40.91%   19.69%   12.87%   7.38%    5.35%    3.86%    3.52%   
           8        9        10       11      
Value      0.000455 0.000374 0.000263 0.000113
Percentage 2.43%    2%       1.4%     0.6%    


 Rows:
        three daughters (buck) drifters (michener) lost world (clark)
Mass                  0.085407            0.079728           0.084881
ChiDist               0.097831            0.094815           0.128432
Inertia               0.000817            0.000717           0.001400
Dim. 1               -0.095388            0.405697           1.157803
Dim. 2               -0.794999           -0.405560          -0.023114
        east wind (buck) farewell to arms (hemingway)
Mass            0.089411                     0.082215
ChiDist         0.118655                     0.122889
Inertia         0.001259                     0.001242
Dim. 1         -0.173901                    -0.831886
Dim. 2          0.434443                    -0.136485
        sound and fury 7 (faulkner) sound and fury 6 (faulkner)
Mass                       0.082310                    0.083338
ChiDist                    0.172918                    0.141937
Inertia                    0.002461                    0.001679
Dim. 1                     0.302025                   -0.925572
Dim. 2                     2.707599                    0.966944
        profiles of future (clark) islands (hemingway) pendorric 3 (holt)
Mass                      0.089722            0.082776           0.079501
ChiDist                   0.187358            0.165529           0.113174
Inertia                   0.003150            0.002268           0.001018
Dim. 1                    1.924060           -1.566481          -0.724758
Dim. 2                   -0.249310           -1.185338          -0.106349
        asia (michener) pendorric 2 (holt)
Mass           0.077827           0.082884
ChiDist        0.155115           0.101369
Inertia        0.001873           0.000852
Dim. 1         1.179548          -0.764937
Dim. 2        -1.186934          -0.091188


 Columns:
                a         b         c         d         e         f         g
Mass     0.079847  0.015685  0.022798  0.045967  0.127070  0.019439  0.020025
ChiDist  0.048441  0.148142  0.222783  0.189938  0.070788  0.165442  0.156640
Inertia  0.000187  0.000344  0.001132  0.001658  0.000637  0.000532  0.000491
Dim. 1   0.017623  0.984463  2.115029 -1.925632  0.086722  1.276526 -1.020713
Dim. 2  -0.320271 -0.398032 -1.373448 -1.135362 -0.684785 -0.732952  0.353017
                h        i        j         k         l        m         n
Mass     0.064928 0.070092 0.000789  0.009181  0.042667 0.025500  0.068968
ChiDist  0.154745 0.086328 0.412075  0.296727  0.120397 0.159747  0.075706
Inertia  0.001555 0.000522 0.000134  0.000808  0.000618 0.000651  0.000395
Dim. 1  -1.501277 0.267473 0.453341 -2.755177  1.018257 0.712695 -0.200364
Dim. 2  -0.302413 0.889546 0.916032  1.231557 -0.165020 1.400966 -0.417258
                o         p         q         r        s         t        u
Mass     0.076572  0.015159  0.000669  0.051897 0.060660  0.093010 0.029756
ChiDist  0.088101  0.250617  0.582298  0.111725 0.123217  0.050630 0.119215
Inertia  0.000594  0.000952  0.000227  0.000648 0.000921  0.000238 0.000423
Dim. 1  -0.108491  1.610807  4.079786  0.591372 0.860202 -0.100464 0.163295
Dim. 2   0.637987 -1.837948 -1.914791 -0.734216 0.405610  0.203141 1.017140
               v         w        x        y         z
Mass    0.009612  0.025847 0.001160 0.021902  0.000801
ChiDist 0.269770  0.232868 0.600831 0.301376  0.833700
Inertia 0.000700  0.001402 0.000419 0.001989  0.000557
Dim. 1  2.281333 -2.499232 3.340505 0.001519  6.808100
Dim. 2  0.177022 -0.284722 4.215355 4.706083 -3.509223