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

To inspect the structure of a large sparse matrix, it is often highly useful to reduce the matrix to a few major dimensions (cf. multidimensional scaling). This functions implements a rough approach to provide a few major dimensions. The function provides a simple wrapper around `Cholesky`

and `sparsesvd`

.

1 | ```
dimRed(sim, k = 2, method = "svd")
``` |

`sim` |
Sparse, symmetric, positive-definite matrix (typically a similarity matrix produces by |

`k` |
Number of dimensions to be returned, defaults to two. |

`method` |
Method used for the decomposition. Currently implemted are |

Based on the Cholesky decomposition, the Matrix `sim`

is decomposed into:

* L D L'*

The D Matrix is a diagonal matrix, the values of which are returned here as `$D`

. Only the first few columns of the L Matrix are returned (possibly after permutation, see the details at `Cholesky`

).

Based on the svd decomposition, the Matrix `sim`

is decomposed into:

* U D V*

The U Matrix and the values from D are returned.

A list of two elements is returned:

`L ` |
: a sparse matrix of type |

`D ` |
: the diagional values from the Cholesky decomposition, or the eigenvalues from the svd decomposition |

Michael Cysouw <[email protected]>

See Also as `Cholesky`

and `sparsesvd`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 | ```
# some random points in two dimensions
coor <- cbind(sample(1:30), sample(1:30))
# using cmdscale() to reconstruct the coordinates from a distance matrix
d <- dist(coor)
mds <- cmdscale(d)
# using dimRed() on a similarity matrix.
# Note that normL works much better than other norms in this 2-dimensional case
s <- cosSparse(t(coor), norm = normL)
red <- as.matrix(dimRed(s)$L)
# show the different point clouds
par(mfrow = c(1,3))
plot(coor, type = "n", axes = FALSE, xlab = "", ylab = "")
text(coor, labels = 1:30)
title("Original coordinates")
plot(mds, type = "n", axes = FALSE, xlab = "", ylab = "")
text(mds, labels = 1:30)
title("MDS from euclidean distances")
plot(red, type = "n", axes = FALSE, xlab = "", ylab = "")
text(red, labels = 1:30)
title("dimRed from cosSparse similarity")
par(mfrow = c(1,1))
# ======
# example, using the iris data
data(iris)
X <- t(as.matrix(iris[,1:4]))
cols <- rainbow(3)[iris$Species]
s <- cosSparse(X, norm = norm1)
d <- dist(t(X), method = "manhattan")
svd <- as.matrix(dimRed(s, method = "svd")$L)
chol <- as.matrix(dimRed(s, method = "cholesky")$L)
mds <- cmdscale(d)
par(mfrow = c(1,3))
plot(mds, col = cols, main = "cmdscale\nfrom euclidean distances")
plot(svd, col = cols, main = "dimRed with svd\nfrom cosSparse with norm1")
plot(chol, col = cols, main = "dimRed with cholesky\nfrom cosSparse with norm1")
par(mfrow = c(1,1))
``` |

cysouw/qlcMatrix documentation built on April 22, 2018, 4:59 a.m.

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