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#! /usr/bin/env Rscript
# jvcoords - implement various coordinate transforms (e.g. PCA, whitening).
# https://github.com/seehuhn/jvcoords
#
# Copyright (C) 2018 Jochen Voss <voss@seehuhn.de>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
library(jvcoords)
set.seed(1)
X1 <- matrix(rnorm(99), nrow = 33, ncol = 3)
colnames(X1) <- c("first", "second", "third")
X2 <- matrix(rnorm(99), nrow = 3, ncol = 33)
X3 <- matrix(rnorm(99), nrow = 99, ncol = 1)
X4 <- matrix(1:6, 3, 2)
for (x in list(X1, X2, X3, X4)) {
for (scale in c(TRUE, FALSE)) {
pc <- PCA(x, scale = scale)
# check that the dimensions match
stopifnot(pc$p == ncol(x))
stopifnot(pc$q == ncol(pc$y))
# check that transformed data in centred
stopifnot(max(abs(colMeans(pc$y))) < 1e-14)
# check that the variances are computed correctly
stopifnot(ncol(pc$loadings) == length(pc$var))
stopifnot(isTRUE(all.equal(pc$var, apply(pc$y, 2, var))))
# check that the variances are in decreasing order
stopifnot(!is.unsorted(-pc$var))
# check that the coordinate transforms work
stopifnot(isTRUE(all.equal(toCoords(pc, x), pc$y)))
stopifnot(isTRUE(all.equal(x, fromCoords(pc, pc$y))))
# check some aspects of the printed representation
lines <- capture.output(pc)
stopifnot(startsWith(lines[1], "PCA"))
stopifnot(grepl(paste0("p = ", pc$p), lines[1]))
stopifnot(grepl(paste0("q = ", pc$q), lines[1]))
}
}
# check that n.comp works
pc <- PCA(X1, n.comp = 2)
stopifnot(pc$q == 2)
stopifnot(ncol(pc$loadings) == 2)
stopifnot(isTRUE(all.equal(rownames(pc$loadings), colnames(X1))))
# check that invalid n.comp is detected
err <- NULL
tryCatch(PCA(X1, n.comp = 4), error=function(e) err <<- e)
stopifnot(is(err, "simpleError"))
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