/usr/lib/R/site-library/S4Vectors/doc/RleTricks.R is in r-bioc-s4vectors 0.16.0-1.
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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 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 | ### R code from vignette source 'RleTricks.Rnw'
### Encoding: UTF-8
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### code chunk number 1: options
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options(width=60)
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### code chunk number 2: Rle-rollmean
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rollmeanRle <- function (x, k)
{
n <- length(x)
cumsum(c(Rle(sum(window(x, 1, k))), window(x, k + 1, n) - window(x, 1, n - k))) / k
}
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### code chunk number 3: Rle-rollvar
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rollvarRle <- function(x, k)
{
n <- length(x)
means <- rollmeanRle(x, k)
nextMean <- window(means, 2, n - k + 1)
cumsum(c(Rle(sum((window(x, 1, k) - means[1])^2)),
k * diff(means)^2 -
(window(x, 1, n - k) - nextMean)^2 +
(window(x, k + 1, n) - nextMean)^2)) / (k - 1)
}
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### code chunk number 4: Rle-rollcov
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rollcovRle <- function(x, y, k)
{
n <- length(x)
meanX <- rollmeanRle(x, k)
meanY <- rollmeanRle(y, k)
nextMeanX <- window(meanX, 2, n - k + 1)
nextMeanY <- window(meanY, 2, n - k + 1)
cumsum(c(Rle(sum((window(x, 1, k) - meanX[1]) * (window(y, 1, k) - meanY[1]))),
k * diff(meanX) * diff(meanY) -
(window(x, 1, n - k) - nextMeanX) * (window(y, 1, n - k) - nextMeanY) +
(window(x, k + 1, n) - nextMeanX) * (window(y, k + 1, n) - nextMeanY))) / (k - 1)
}
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### code chunk number 5: Rle-rollsd
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rollsdRle <- function(x, k)
{
sqrt(rollvarRle(x, k))
}
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### code chunk number 6: Rle-rollcor
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rollcorRle <- function(x, y, k)
{
rollcovRle(x, y, k) / (rollsdRle(x, k) * rollsdRle(y, k))
}
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