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# SVN revision:
# Date of last change: 2017-08-24
# Last changed by: csweetland
#
# Original author: ccampbell
# Copyright Activinsights, Cambridge UK 2013-2017
###############################################################################
context("remove short segments")
###############################################################################
test_that("removeShortSegments", {
set.seed(45265)
tm0 <- 1001:1060
d0 <- round(c(cumsum(runif(n = 20) * 2),
20:1 + rnorm(n = 20),
runif(n = 20) * 10))
#c0 <- cpt.var(d0, penalty = "SIC",
# pen.value = 1e-3, method = "PELT")
#cp0 <- cpts(c0)
cp0 <- c(5L, 7L, 13L, 26L)
#v0 <- param.est(c0)$variance
v0 <- c(4.3, 0, 0.966666666666667, 4.1025641025641, 15.0133689839572)
t0 <- c(tm0[1], tm0[sort(cp0)], tm0[60])
sdur0 <- which(diff(t0) < 10)
expect_equal(
object = GENEAclassify:::removeShortSegments(
shortduration = sdur0,
changes = cp0,
variance = v0,
time = tm0),
expected = list(cpts = c(5, 13, 26),
times = c(1001, 1005, 1013, 1026, 1060),
duration = c(4, 8, 13, 34)))
d1 <- c(54, 30, 27, 53, 100, 204, 197)
c1 <- cpt.var(d1, penalty = "SIC", pen.value = 1e-3, method = "PELT")
expect_equal(
object = GENEAclassify:::removeShortSegments(shortduration = 1,
changes = integer(0),
variance = param.est(c1)$variance,
time = 0:10),
expected = list(cpts = integer(0), times = c(0, 10), duration = 10))
})
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