| MVA.scores {RVAideMemoire} | R Documentation |
Scores of multivariate analyses
Description
Returns scores of a multivariate analysis.
Usage
MVA.scores(x, xax = 1, yax = 2, scaling = 2, set = c(12, 1, 2), space = 1, ...)
Arguments
x |
a multivariate analysis (see Details). |
xax |
axis or axes for which to extract scores. |
yax |
axis for which to extract scores (ignored if |
scaling |
type of scaling. Only available with some analyses performed with the |
set |
scores to be displayed, when several sets are available (see Details). |
space |
scores to be displayed, when several spaces are available (see Details). |
... |
not used. |
Details
Many multivariate analyses are supported, from various packages:
- PCA: prcomp, princomp (if scores=TRUE), dudi.pca, rda, pca, pca. scaling can be defined for rda (see scores.rda).
- sPCA: spca.
- IPCA: ipca.
- sIPCA: sipca.
- PCoA: cmdscale (with at least on non-default argument), dudi.pco, wcmdscale (with at least one non-default argument), capscale, pco, pcoa.
- nMDS: monoMDS, metaMDS, nmds, isoMDS.
- PLS-DA (PLS2 on a dummy-coded factor): plsda. X space only.
- sPLS-DA (sPLS2 on a dummy-coded factor): splsda. X space only.
- CPPLS: mvr. X space only.
- PLSR: mvr, pls, plsR (plsRglm package). X space only.
- sPLSR: pls. X space only.
- PLS-GLR: plsRglm (plsRglm package).
- PCR: mvr.
- CDA: discrimin, discrimin.coa.
- NSCOA: dudi.nsc.
- MCA: dudi.acm.
- Mix analysis: dudi.mix, dudi.hillsmith.
- COA: dudi.coa, cca. Set 1 is rows, set 2 is columns. If set=12 (default), fac is not available and pch,cex, col can be defined differently for each set. scaling can be defined for cca (see scores.cca).
- DCOA: dudi.dec. Set 1 is rows, set 2 is columns. If set=12 (default), fac is not available and pch,cex, col can be defined differently for each set.
- PCIA: procuste. Set 1 is X, set 2 is Y. If set=12 (default), fac is not available and pch,cex, col can be defined differently for each set.
- Procrustean superimposition: procrustes. Set 1 is X, set 2 is Y. If set=12 (default), fac is not available and pch,cex, col can be defined differently for each set.
- GPA: GPA. Only the consensus ordination can be displayed.
- DPCoA: dpcoa. Set 1 is categories, set 2 is collections. If set=12 (default), fac is not available and pch,cex, col can be defined differently for each set.
- RDA (or PCAIV): pcaiv, pcaivortho, rda. With rda, space 1 is constrained space, space 2 is unconstrained space. Only constrained space is available with pcaiv, the opposite for pcaivortho. scaling can be defined for rda (see scores.rda).
- db-RDA (or CAP): capscale, dbrda. Space 1 is constrained space, space 2 is unconstrained space.
- CCA: pcaiv, cca. With rda, space 1 is constrained space, space 2 is unconstrained space. Only constrained space is available with pcaiv. Set 1 is rows, set 2 is columns. scaling can be defined for cca (see scores.cca).
- CCorA: CCorA, rcc. Space 1 is X, space 2 is Y. With rcc a third space is available, in which coordinates are means of X and Y coordinates.
- rCCorA: rcc. Space 1 is X, space 2 is Y, space 3 is a "common" space in which coordinates are means of X and Y coordinates.
- CIA: coinertia. Space 1 is X, space 2 is Y, space 3 is a "common" space where X and Y scores are normed. In space 3, set 1 is X and set 2 is Y. If set=12 in space 3 (default), fac is not available and pch,cex, col can be defined differently for each set.
- 2B-PLS: pls. Space 1 is X, space 2 is Y, space 3 is a "common" space in which coordinates are means of X and Y coordinates.
- 2B-sPLS: pls. Space 1 is X, space 2 is Y, space 3 is a "common" space in which coordinates are means of X and Y coordinates.
- rGCCA: rgcca, wrapper.rgcca. Space can be 1 to n, the number of blocks (i.e. datasets).
- sGCCA: rgcca, wrapper.sgcca. Space can be 1 to n, the number of blocks (i.e. datasets).
- DIABLO: block.plsda, block.splsda. Space can be 1 to n, the number of blocks (i.e. datasets).
Author(s)
Maxime HERVE <maxime.herve@univ-rennes1.fr>