Nothing
context("Testing pca()")
test_that("pca functions works", {
"mysign" <- function(a,b) {
if(all(sign(a)==sign(b)))
return(1)
else
return(-1)
}
attach(transducin)
inds <- unlist(lapply(c("1TND_A", "1TAG", "1AS0", "1AS2"), grep, pdbs$id))
pdbs <- trim.pdbs(pdbs, row.inds=inds)
gaps <- gap.inspect(pdbs$xyz)
## Calc modes
invisible(capture.output(pc <- pca(pdbs)))
## check dimensions
expect_that(dim(pc$U), equals(c(939, 939)))
expect_that(length(pc$L), equals(939))
## check eigenvalues
Lexpected <- c(1.964689e+02, 1.715903e+02, 7.091482e+01)
expect_that(head(pc$L, n=3), equals(Lexpected, tolerance=1e-6))
## check atom-wise loadings
AUexpected <- c(0.013422274, 0.023879443, 0.022779307, 0.023490288, 0.006308588, 0.010057694)
expect_that(head(pc$au[,1], n=6), equals(AUexpected, tolerance=1e-6))
Z1expected <- c(-3.555218, -12.081135, -4.602888, 20.239240)
Z1now <- as.numeric(head(pc$z[,1], n=4))
expect_that(Z1now * mysign(Z1expected, Z1now), equals(Z1expected, tolerance=1e-6))
Mexpected <- c(30.12193, 67.76449, 43.36594, 27.01919, 69.66411, 44.47434)
expect_that(head(pc$mean, n=6), equals(Mexpected, tolerance=1e-6))
detach(transducin)
})
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