library(recurse) context("recurse") # support functions #------------------------------------------------------------------------------------------------ getRevisits = function(data, radius) { return(getRecursions(data, radius)$revisits) } createTimeVector = function(n, tz = "") { return(as.POSIXct("2009-5-1 1:00:00", tz = tz) + (1:n) * 60 * 60) # every hour } createMoveObj = function(df) { if (requireNamespace("move", quietly = TRUE)) { # remove projection in order to remove sp dependency (was proj = sp::CRS("+proj=aeqd")) moveObj = move::move(x = df$x, y = df$y, time = df$t, animal = df$id) move::idData(moveObj) = df$id[1] # move ignores id, so set it directly } else { moveObj = NULL } return(moveObj) } testTz = function(df) { output = getRecursions(df, 1) expect_equal(attr(output$revisitStats$entranceTime, "tzone"), attr(df$t, "tzone")) expect_equal(attr(output$revisitStats$exitTime, "tzone"), attr(df$t, "tzone")) } # data #------------------------------------------------------------------------------------------------ # expected revisits for data "track" included in pacakge and calculated using an alternate method # as.double(.Call("nvisits", df = track, radius = 1, maxt = 0, PACKAGE = "adehabitatHR")) expectedRevisistsRadius1 = c(2, 2, 3, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 1, 1, 1, 2, 2, 2, 2, 1, 1, 2) # points on a line so distances between are unit lengths simplePts = data.frame(x = 1, y = 1:5, t = createTimeVector(5), id = "A1") simplePtsDist = matrix(0, nrow = 5, ncol = 5) simplePtsDist = abs(row(simplePtsDist) - col(simplePtsDist)) # different locations than simplePts, but still x = 1 so with easy distances simpleLocs = data.frame(x = c(1, 1, 1), y = c(1, 0, 10)) simpleLocsDist = matrix(0, nrow = 5, ncol = 3) simpleLocsDist = cbind(0:4, 1:5, 9:5) # two tracks, one vertical x = 1, one horizontal y = 3 horzTrack = data.frame(x = -1:3, y = 3, t = createTimeVector(5), id = "B2") twoTracks = rbind(simplePts, horzTrack) # one track that revisits one location oneTrack = twoTracks oneTrack$t[5:10] = oneTrack$t[5:10] + 1 * 24 * 60 * 60 # make second part of track a day later oneTrack$id = 1 # track with data points on radius boundries so time in/out is easy to caluculate gridTrack = data.frame( x = c(0, 1, 2, 1, 0, 1, 2, 2, 3, 5, 6, 3, 1, 3, 4), y = rep(0, 15), t = createTimeVector(15), id = rep(1, 15) ) #plot(gridTrack$x, gridTrack$t/10, type = "b") # tests #------------------------------------------------------------------------------------------------ test_that("correct number of revisits", { expect_equal(length(getRevisits(track, 1)), 100) expect_equal(getRevisits(track, 1), expectedRevisistsRadius1) expect_equal(getRevisits(twoTracks, 0.5), rep(c(1, 1, 2, 1, 1), 2)) # middle pt overlaps }) test_that("distance matrix", { expect_equal(getRecursions(simplePts, 1, verbose = TRUE)$dists, simplePtsDist) expect_equal(getRecursionsAtLocations(simplePts, simpleLocs, 1, verbose = TRUE)$dists, simpleLocsDist) }) test_that("time in radius", { # examine visits to point at x=2 (use first time at t=3) stats = getRecursions(gridTrack, 1)$revisitStats expect_equal(as.numeric(stats[stats$coordIdx==3, "timeInside"]), c(2, 3, 2)) expect_equal(as.numeric(stats[stats$coordIdx==3, "timeSinceLastVisit"]), c(NA, 2, 3)) }) test_that("verbose", { verbose = getRecursions(simplePts, 1, verbose = TRUE) nonVerbose = getRecursions(simplePts, 1, verbose = FALSE) }) test_that("revisit stats", { stats = getRecursions(simplePts, 0.5)$revisitStats n = nrow(simplePts) expect_equal(stats$id, simplePts$id) expect_equal(stats$x, simplePts$x) expect_equal(stats$y, simplePts$y) expect_equal(stats$coordIdx, 1:n) expect_equal(stats$visitIdx, rep(1, n)) expect_equal(stats$entranceTime, c(simplePts$t[1], simplePts$t[2:n] - as.difftime(30, units = "mins"))) expect_equal(stats$exitTime, c(simplePts$t[1:(n-1)] + as.difftime(30, units = "mins"), simplePts$t[n])) expect_equal(stats$timeInside, c(0.5, 1, 1, 1, 0.5)) expect_equal(stats$timeSinceLastVisit, c(1, rep(NA, n))[-1]) stats2 = getRecursions(twoTracks, 0.5)$revisitStats expectedCoordIdx = c(1, 2, 3, 3, 4, 5, 6, 7, 8, 8, 9, 10) expectedIdIdx = c(1, 1, 1, 2, 1, 1, 2, 2, 1, 2, 2, 2) expect_equal(stats2$id, unique(twoTracks$id)[expectedIdIdx]) #unique orders A1 B2 expect_equal(stats2$x, twoTracks$x[expectedCoordIdx]) expect_equal(stats2$y, twoTracks$y[expectedCoordIdx]) expect_equal(stats2$coordIdx, expectedCoordIdx) expect_equal(stats2$visitIdx, rep(c(1, 1, 1, 2, 1, 1), 2)) expect_equal(stats2$entranceTime, twoTracks$t[expectedCoordIdx] - as.difftime(rep(c(0, rep(30, 5)), 2), units = "mins")) expect_equal(stats2$exitTime, twoTracks$t[expectedCoordIdx] + as.difftime(rep(c(rep(30, 5), 0), 2), units = "mins")) expect_equal(stats2$timeInside, rep(c(0.5, 1, 1, 1, 1, 0.5), 2)) expect_equal(stats2$timeSinceLastVisit, c(1, rep(NA, length(expectedCoordIdx)))[-1]) }) test_that("threshold", { expect_equal(sum(getRecursions(oneTrack, 0.5, threshold = 0)$revisits), 12) expect_equal(sum(getRecursions(oneTrack, 0.5, threshold = 1)$revisits), 12) expect_equal(sum(getRecursions(oneTrack, 0.5, threshold = 23)$revisits), 12) expect_equal(sum(getRecursions(oneTrack, 0.5, threshold = 24)$revisits), 10) expect_equal(sum(getRecursions(oneTrack, 0.5, threshold = 100)$revisits), 10) }) test_that("move objects", { if (requireNamespace("move", quietly = TRUE)) { movePts = createMoveObj(simplePts) expect_equal( getRecursions(movePts, 1), getRecursions(simplePts,1) ) moveStackPts = createMoveObj(twoTracks) expect_equal( getRecursions(moveStackPts, 1), getRecursions(twoTracks,1) ) } }) test_that("timezone", { defaultTz = data.frame(x = 1, y = 1:5, t = createTimeVector(5), id = "default") utcTz = data.frame(x = 1, y = 1:5, t = createTimeVector(5, tz = "UTC"), id = "UTC") sydneyTz = data.frame(x = 1, y = 1:5, t = createTimeVector(5, tz = "Australia/Sydney"), id = "Australia/Sydney") limaTz = data.frame(x = 1, y = 1:5, t = createTimeVector(5, tz = "America/Lima"), id = "America/Lima") testTz(defaultTz) testTz(utcTz) testTz(sydneyTz) testTz(limaTz) }) test_that("interval res time", { vis = getRecursions(simplePts, 0.5) expect_equal(as.vector(calculateIntervalResidenceTime(vis, breaks = simplePts$t[c(1,5)])), vis$residenceTime) expectedMatrix = matrix(c(0.5, 1, 0.5, 0, 0, 0, 0, 0.5, 1, 0.5), ncol = 2, dimnames = list(1:5, c("A", "B"))) expect_equal(calculateIntervalResidenceTime(vis, breaks = simplePts$t[c(1,3,5)], labels = c("A", "B")), expectedMatrix) }) test_that("polygon", { require(sf) poly = sf::st_polygon(list(cbind(c(4,6,6,3,4), c(1,2,4,3,1)))) polyc = sf::st_sfc(poly, crs = "EPSG:4326") recursions = getRecursionsInPolygon(track, polyc) expect_equal(recursions$revisits, 2) expect_equal(round(as.numeric(recursions$revisitStats$timeInside[1]), digits = 2), 44.99) expect_equal(round(as.numeric(recursions$revisitStats$timeInside[2]), digits = 2), 108.9) })