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

## Description

Computation of correspondence analysis on a table of nonnegative data.

## Usage

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

## Arguments

 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

## Details

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.

## Value

 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

## Author(s)

Michael Greenacre

## References

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/

## Examples

 1 2 3 4 5 6 7 8 # (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

### Example output

This is vegan 2.5-7

Attaching package:ellipseThe following object is masked frompackage: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

easyCODA documentation built on Sept. 20, 2020, 1:07 a.m.