tests/testthat/test.brownian.bridge.dyn.R

In move: Visualizing and Analyzing Animal Track Data

context("Brownian bridge dyn")
test_that("dbbmm error handling", {
  skip_on_os("solaris")
  skip_on_cran()

  data(leroy)
  expect_error(
    brownian.bridge.dyn(
      object = leroy2, location.error = 23.5, dimSize = 150, ext = .3, time.step =
        600
    ), "object 'leroy2' not found"
  )
  data2 <- spTransform(leroy[1:50, ], center = T)
  expect_error(
    brownian.bridge.dyn(data2, dimSize = 150, location.error = "2346"), "column indicated for location error probably does not exist"
  ) # character loc
  expect_error(
    brownian.bridge.dyn(data2, location.error = 1:5), "The location error vector has not the same length as the move object"
  )
})
test_that("dbbmm error handling in relation to projections", {
  skip_on_cran()
  skip_on_os("solaris")
  data(leroy)
  data <- leroy
  expect_error(
    brownian.bridge.dyn(
      object = data, location.error = 23.5, dimSize = 150, ext = .3, time.step =
        600
    ),
    "You can not use longitude latitude projection for this function. To transform your coordinates use the spTransform function."
  )
  r <- raster(
    nrows = 100, ncols = 100, xmn = 0, xmx = 10
  )
  expect_error(
    brownian.bridge.dyn(
      data2 <-
        spTransform(data[1:50, ], center = T),
      raster = r, location.error = 20
    ), "The projection of the raster and the Move object are not equal"
  ) # equal projection
})
test_that("brownian bridge dyn for bursted", {
  skip_on_cran()
  skip_on_os("solaris")
  data(leroy)
  data <- leroy
  dataP <- spTransform(data[1:100, ], center = T)
  dataPB <- move::burst(dataP, round((1:(n.locs(
    dataP
  ) - 1) / 50)))
  expect_error(brownian.bridge.dyn(
    dataPB,
    dimSize = 150, location.error = 23, ext = .3, time.step = 4, window.size = 29, burstType = "l"
  ), "none of the burstTypes is in the data")
  expect_equivalent(class(brownian.bridge.dyn(
    dataPB,
    dimSize = 150, location.error = 23, ext = 1.3, time.step = 4, window.size = 29, burstType = c("l", "X1")
  )), "DBBMMBurstStack")

  expect_message(
    udS <-
      brownian.bridge.dyn(
        dataPB,
        dimSize = 150, location.error = 23, ext = 1.3, time.step = 4, window.size =
          29
      ), "Computational size"
  )
  expect_is(udS, "DBBMMBurstStack")
  expect_true(validObject(udS))
  expect_message(
    ud <-
      brownian.bridge.dyn(
        dataP,
        dimSize = 150,
        location.error = 23,
        ext = 1.3,
        time.step = 4,
        window.size =
          29
      ),
    "Computational size"
  )
  expect_equal(
    udS@DBMvar@means,
    ud@DBMvar@means
  )
  expect_true(validObject(ud))
  b <- as.numeric(getZ(udS))
  expect_equal(colSums(values(udS)),
    b / sum(b),
    check.attributes = F
  )
  expect_equal(
    UDStack(udS),
    UDStack(udS / cellStats(udS, sum))
  )
})
test_that("verbosity brownian bridge works", {
  skip_on_cran()
  skip_on_os("solaris")
  skip("will only work with testthat .11")
  p <- seq(0, 2 * pi, length.out = 49)
  tmp <-
    move(sin(p), cos(p), as.POSIXct(1:length(p), origin = "1970-1-1"),
      proj =
        "+proj=aeqd +ellps=WGS84"
    )
  t <- .05
  expect_message(
    u <-
      brownian.bridge.dyn(
        tmp,
        dimSize = 200, location.error = .1, time.step = t,
        verbose = T
      ), "Computational size"
  )
  expect_silent(brownian.bridge.dyn(
    tmp,
    dimSize = 200, location.error = .1, time.step = t, verbose = F
  ))
})
test_that("brownian bridge dyn value comparison bursted", {
  skip_on_cran()
  skip_on_os("solaris")
  p <- seq(0, 2 * pi, length.out = 49)
  tmp <-
    move(sin(p), cos(p), as.POSIXct(1:length(p), origin = "1970-1-1"),
      proj =
        "+proj=aeqd +ellps=WGS84"
    )
  t <- .05
  expect_message(
    u <-
      brownian.bridge.dyn(
        tmp,
        dimSize = 200, location.error = .1, time.step = t
      ), "Computational size"
  )

  expect_message(
    us <-
      brownian.bridge.dyn(
        move::burst(tmp, round(1:length(p[-1]) / 50)),
        dimSize = 200, location.error =
          .1, time.step = t
      ), "Computational size"
  )
  expect_equal(
    values(u),
    c(values(u))
  )
  p <- seq(0, 2 * pi, length.out = 199)
  set.seed(3245)
  tmp <- move(
    sin(p) + rnorm(length(p)) * round(sin(p)) * .03,
    cos(p),
    as.POSIXct(1:length(p),
      origin = "1970-1-1"
    ),
    proj = "+proj=aeqd +ellps=WGS84"
  )
  t <- .000025213
  expect_message(
    u <- brownian.bridge.dyn(
      tmp,
      dimSize = 400,
      location.error = .01, time.step = t,
      ext = .3, margin = 15
    ), "Computational size"
  )
  expect_message(
    us <- brownian.bridge.dyn(
      b <- move::burst(
        tmp,
        round(1:length(p[-1]) / 80)
      ),
      dimSize = 400, location.error = .01,
      time.step = t, ext = .3, margin = 15
    ), "Computational size"
  )
  expect_equal(values(u), values(sum(us)), tolerance = 5e-5)
})
test_that("Brownian bridge, running with character and vector input to location error", {
  skip_on_cran()
  skip_on_os("solaris")
  data(leroy)
  data <- spTransform(leroy[1:51, ], center = T)
  data2 <- data
  lc <- 6.54
  data2$asdf <- lc
  expect_message(
    a <-
      brownian.bridge.dyn(
        data,
        location.error = lc, ext = 2, dimSize = 50
      ), "Computational size"
  )
  a@DBMvar$asdf <- lc
  expect_equal(
    a,
    suppressMessages(
      brownian.bridge.dyn(
        data2,
        location.error = "asdf",
        ext = 2, dimSize = 50
      )
    )
  )
  set.seed(3245)
  lc <- rweibull(n.locs(data), 2, 3)
  data2$asdf <- lc
  expect_message(
    a <-
      brownian.bridge.dyn(
        data,
        location.error = lc, ext = 2, dimSize = 50
      ), "Computational size"
  )
  a@DBMvar$asdf <- lc
  expect_message(
    xx <- brownian.bridge.dyn(
      data2,
      location.error = "asdf",
      ext = 2, dimSize =
        50
    ), "Computational size"
  )

  expect_equal(a, xx)
})

test_that("Brownian bridge, running with character and vector input to location error for stacks", {
  skip_on_cran()
  skip_on_os("solaris")
  data(leroy)
  ricky <- move(system.file("extdata", "ricky.csv.gz", package = "move"))
  leroy <- spTransform(leroy, crs(ricky))
  data <-
    spTransform(moveStack(list(leroy[1:75, ], ricky[1:73, ])), center = T)
  data2 <- data
  lc <- 6.54
  data2$asdf <- lc
  expect_message(
    a <-
      brownian.bridge.dyn(
        data,
        location.error = lc, ext = 2, dimSize = 50
      ), "Computational size"
  )
  expect_true(validObject(a))

  a@DBMvar$asdf <- lc
  expect_equal(a, suppressMessages(
    brownian.bridge.dyn(
      data2,
      location.error = "asdf",
      ext = 2, dimSize = 50
    )
  ))
  set.seed(3245)
  lc <- rweibull(sum(n.locs(data)), 2, 3)
  data2$asdf <- lc
  expect_message(
    a <-
      brownian.bridge.dyn(
        data,
        location.error = lc, ext = 2, dimSize = 50
      ), "Computational size"
  )
  a@DBMvar$asdf <- lc
  expect_equal(
    a,
    suppressMessages(
      brownian.bridge.dyn(
        data2,
        location.error = "asdf",
        ext = 2, dimSize = 50
      )
    )
  )
  expect_error(
    suppressMessages(
      brownian.bridge.dyn(
        data,
        location.error = lc[-1], ext = 2, dimSize = 50
      )
    ),
    "Location error needs to be the same length as the number of locations"
  )
})
test_that("split stack", {
  skip_on_cran()
  data("dbbmmstack")
  l <- split(dbbmmstack)
  expect_s4_class(l[[1]], "DBBMM")
})