context("jsmurf") # a simple way to filter data, not very precise, but enough for test purposes .convolve <- function(data, filter) { stats::filter(data, filter$kern, sides = 1)[-c(1:filter$len)] / sqrt(sum(filter$kern^2)) } testOutput <- function(fit, startTime = 0) { stepR::stepblock(value = fit$value, leftEnd = c(startTime, fit$rightEnd[-length(fit$rightEnd)]), rightEnd = fit$rightEnd, x0 = startTime) } test_that("testOutput works", { test <- stepR::stepblock(value = c(1), leftEnd = c(0.01), rightEnd = c(1), x0 = NA) compare <- stepR::stepblock(value = c(1), leftEnd = c(0), rightEnd = c(1), x0 = 0) expect_identical(testOutput(test), compare) test <- stepR::stepblock(value = c(0, 1), leftEnd = c(1, 101), rightEnd = c(100, 200), x0 = NA) compare <- stepR::stepblock(value = c(0, 1), leftEnd = c(0, 100), rightEnd = c(100, 200), x0 = 0) expect_identical(testOutput(test), compare) test <- stepR::stepblock(value = c(0, 1, -4, 3), leftEnd = c(0.01, 1, 5, 10), rightEnd = c(1, 5, 10, 200), x0 = NA) compare <- stepR::stepblock(value = c(0, 1, -4, 3), leftEnd = c(0, 1, 5, 10), rightEnd = c(1, 5, 10, 200), x0 = 0) expect_identical(testOutput(test), compare) # startTime test <- stepR::stepblock(value = c(1), leftEnd = c(0.01), rightEnd = c(1), x0 = NA) compare <- stepR::stepblock(value = c(1), leftEnd = c(-1), rightEnd = c(1), x0 = -1) expect_identical(testOutput(test, startTime = -1), compare) test <- stepR::stepblock(value = c(0, 1), leftEnd = c(1, 101), rightEnd = c(100, 200), x0 = NA) compare <- stepR::stepblock(value = c(0, 1), leftEnd = c(1, 100), rightEnd = c(100, 200), x0 = 1) expect_identical(testOutput(test, startTime = 1), compare) test <- stepR::stepblock(value = c(0, 1, -4, 3), leftEnd = c(0.01, 1, 5, 10), rightEnd = c(1, 5, 10, 200), x0 = NA) compare <- stepR::stepblock(value = c(0, 1, -4, 3), leftEnd = c(0.2, 1, 5, 10), rightEnd = c(1, 5, 10, 200), x0 = 0.2) expect_identical(testOutput(test, startTime = 0.2), compare) }) test_that("it works if sd and q are given and that data and filter have to be given", { testdata <- rnorm(100) testfilter <- lowpassFilter(param = list(pole = 4L, cutoff = 0.1)) testsd <- 1 testq <- 1.44 expect_error(jsmurf(family = "jsmurfPS")) expect_error(jsmurf(family = "jsmurfPS", data = testdata)) expect_error(jsmurf(family = "jsmurfPS", filter = testfilter)) compare <- stepR::stepFit(y = testdata, x = seq(along = testdata) / testfilter$sr, x0 = 0, family = "jsmurfPS", intervalSystem = "dyaLen", q = testq, sd = testsd, filter = testfilter) compare <- testOutput(compare) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, locationCorrection = "none"), compare) expect_identical(jsmurf(data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE), jsmurf(data = testdata, filter = testfilter, family = "jsmurf", q = testq, sd = testsd, startTime = 0, locationCorrection = "deconvolution", output = "onlyIdealization", suppressWarningNoDeconvolution = TRUE)) }) test_that("locationCorrection is tested and works", { set.seed(1) testdata <- c(rnorm(50), rnorm(50, 5)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testsd <- 1 testq <- getCritVal(n = length(testdata), filter = testfilter, family = "jsmurfPS") expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, locationCorrection = 1)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, locationCorrection = c("deconvolution", "none"))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, locationCorrection = "aha")) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, locationCorrection = "de", suppressWarningNoDeconvolution = TRUE)) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE), deconvolveLocally(fit = compare, data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE)) compare$leftEnd[2] <- compare$leftEnd[2] - testfilter$jump compare$rightEnd[1] <- compare$rightEnd[1] - testfilter$jump expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE, locationCorrection = "constant"), compare) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 6L, cutoff = 0.2), sr = 1e4, len = 11L, shift = 0.5) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE), deconvolveLocally(fit = compare, data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE)) compare$leftEnd[2] <- compare$leftEnd[2] - testfilter$jump / testfilter$sr compare$rightEnd[1] <- compare$rightEnd[1] - testfilter$jump / testfilter$sr expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE, locationCorrection = "constant"), compare) }) test_that("output is tested and works", { set.seed(1) testdata <- c(rnorm(50), rnorm(50, 5)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testsd <- 1 testq <- getCritVal(n = length(testdata), filter = testfilter, family = "jsmurfPS") expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = 1)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = c("only", "every"))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "aha")) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "only", suppressWarningNoDeconvolution = TRUE)) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "each", suppressWarningNoDeconvolution = TRUE)$idealization) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none") compare <- list(idealization = compare, fit = compare, q = testq, filter = testfilter, sd = testsd) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, output = "each", locationCorrection = "none"), compare) compare <- list(idealization = list(fit = compare$fit, q = compare$q, filter = compare$filter, sd = compare$sd), fit = compare$fit, q = testq, filter = testfilter, sd = testsd) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, output = "every", locationCorrection = "none"), compare) compare <- list(idealization = deconvolveLocally(fit = compare$fit, data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE), fit = compare$fit, q = testq, filter= testfilter, sd = testsd) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "each", suppressWarningNoDeconvolution = TRUE), compare) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "every", suppressWarningNoDeconvolution = TRUE)$idealization compare2 <- compare[[3]] attr(compare2, "noDeconvolution") <- attr(compare, "noDeconvolution") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE), compare2) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, output = "every", locationCorrection = "none") compare <- list(idealization = deconvolveLocally(fit = compare$fit, data = testdata, filter = testfilter, output = "every", suppressWarningNoDeconvolution = TRUE), fit = compare$fit, q = testq, filter = testfilter, sd = testsd) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "every", suppressWarningNoDeconvolution = TRUE), compare) compare <- list(idealization = compare$fit, fit = compare$fit, q = compare$q, filter = compare$filter, sd = compare$sd) compare$idealization$leftEnd[2] <- compare$idealization$leftEnd[2] - testfilter$jump compare$idealization$rightEnd[1] <- compare$idealization$rightEnd[1] - testfilter$jump expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "each", locationCorrection = "constant", suppressWarningNoDeconvolution = TRUE), compare) compare$idealization = list(fit = compare$idealization, q = compare$q, filter = compare$filter, sd = compare$sd) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "every", locationCorrection = "constant", suppressWarningNoDeconvolution = TRUE), compare) }) test_that("more difficult scenarios work", { set.seed(NULL) testdata <- c(rnorm(108, 0), rnorm(100, 10), rnorm(100, 0), rnorm(100, 10)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) testsd <- 1 testq <- getCritVal(n = length(testdata), filter = testfilter, family = "jsmurfPS") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE), deconvolveLocally(fit = jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE)) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "each", suppressWarningNoDeconvolution = TRUE)$idealization) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none") compare <- list(idealization = deconvolveLocally(fit = compare, data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE), fit = compare, q = testq, filter= testfilter, sd = testsd) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "each", suppressWarningNoDeconvolution = TRUE), compare) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "every", suppressWarningNoDeconvolution = TRUE)$idealization compare2 <- compare[[3]] attr(compare2, "noDeconvolution") <- attr(compare, "noDeconvolution") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE), compare2) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, output = "every", locationCorrection = "none") compare <- list(idealization = deconvolveLocally(fit = compare$fit, data = testdata, filter = testfilter, output = "every", suppressWarningNoDeconvolution = TRUE), fit = compare$fit, q = testq, filter= testfilter, sd = testsd) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "every", suppressWarningNoDeconvolution = TRUE), compare) testdata <- c(rnorm(100, 0), rnorm(5, 10), rnorm(100, 0)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testsd <- 1 testq <- getCritVal(n = length(testdata), filter = testfilter, family = "jsmurfPS") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE), deconvolveLocally(fit = jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE)) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "each", suppressWarningNoDeconvolution = TRUE)$idealization) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none") compare <- list(idealization = deconvolveLocally(fit = compare, data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE), fit = compare, q = testq, filter= testfilter, sd = testsd) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "each", suppressWarningNoDeconvolution = TRUE), compare) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "every", suppressWarningNoDeconvolution = TRUE)$idealization compare2 <- compare[[3]] attr(compare2, "noDeconvolution") <- attr(compare, "noDeconvolution") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE), compare2) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, output = "every", locationCorrection = "none") compare <- list(idealization = deconvolveLocally(fit = compare$fit, data = testdata, filter = testfilter, output = "every", suppressWarningNoDeconvolution = TRUE), fit = compare$fit, q = testq, filter= testfilter, sd = testsd) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "every", suppressWarningNoDeconvolution = TRUE), compare) testdata <- c(rnorm(100, 0), rnorm(5, 15), rnorm(5, 30), rnorm(5, 45), rnorm(100, 60)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testsd <- 0.5 testq <- getCritVal(n = length(testdata), filter = testfilter, family = "jsmurfPS") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE), deconvolveLocally(fit = jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE)) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "each", suppressWarningNoDeconvolution = TRUE)$idealization) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none") compare <- list(idealization = deconvolveLocally(fit = compare, data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE), fit = compare, q = testq, filter= testfilter, sd = testsd) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "each", suppressWarningNoDeconvolution = TRUE), compare) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "every", suppressWarningNoDeconvolution = TRUE)$idealization compare2 <- compare[[3]] attr(compare2, "noDeconvolution") <- attr(compare, "noDeconvolution") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE), compare2) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, output = "every", locationCorrection = "none") compare <- list(idealization = deconvolveLocally(fit = compare$fit, data = testdata, filter = testfilter, output = "every", suppressWarningNoDeconvolution = TRUE), fit = compare$fit, q = testq, filter= testfilter, sd = testsd) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, output = "every", suppressWarningNoDeconvolution = TRUE), compare) }) test_that("argument data works and is tested", { testdata <- c(rnorm(108, 0), rnorm(5, 10), rnorm(5, 20), rnorm(5, 30), rnorm(100, 40)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) testsd <- 1 testq <- getCritVal(n = length(testdata), filter = testfilter, family = "jsmurfPS") expect_error(jsmurf(family = "jsmurfPS", data = c(testdata, "s"), filter = testfilter, sd = testsd, q = testq)) expect_error(jsmurf(family = "jsmurfPS", data = c(testdata, Inf), filter = testfilter, sd = testsd, q = testq)) expect_error(jsmurf(family = "jsmurfPS", data = c(testdata, as.numeric(NA)), filter = testfilter, sd = testsd, q = testq)) }) test_that("argument startTime works and is tested", { testdata <- c(rnorm(108, 0), rnorm(5, 20), rnorm(5, 40), rnorm(5, 60), rnorm(100, 80)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) testsd <- 0.5 testq <- getCritVal(n = length(testdata), filter = testfilter, family = "jsmurfPS") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, startTime = 0, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, startTime = "0", filter = testfilter, sd = testsd, q = testq)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, startTime = Inf, filter = testfilter, sd = testsd, q = testq)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, startTime = as.numeric(NA), filter = testfilter, sd = testsd, q = testq)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, startTime = c(0, 0.5), filter = testfilter, sd = testsd, q = testq)) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE, startTime = -1), deconvolveLocally(fit = jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, startTime = -1, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE, startTime = -1)) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE, startTime = 10), deconvolveLocally(fit = jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, startTime = 10, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE, startTime = 10)) }) test_that("argument filter works and is tested", { testdata <- c(rnorm(108, 0), rnorm(5, 20), rnorm(5, 40), rnorm(5, 60), rnorm(100, 80)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1e4, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) testsd <- 0.5 testq <- getCritVal(n = length(testdata), filter = testfilter, family = "jsmurfPS") expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = list(test = 1), sd = testsd, q = testq)) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE, startTime = 0), deconvolveLocally(fit = jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, startTime = 0, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE, startTime = 0)) testfilter <- suppressWarnings(lowpassFilter(type = "bessel", param = list(pole = 3L, cutoff = 0.05), sr = 2143, len = 3L, shift = 0.2)) testq <- getCritVal(n = length(testdata), filter = testfilter, family = "jsmurfPS") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE, startTime = 0), deconvolveLocally(fit = jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, startTime = 0, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE, startTime = 0)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 5e4, len = 8L, shift = 0.5) testq <- getCritVal(n = length(testdata), filter = testfilter, family = "jsmurfPS") teststartTime <- 10 / 5e4 expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE, startTime = teststartTime), deconvolveLocally(fit = jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, startTime = teststartTime, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE, startTime = teststartTime)) }) test_that("argument sd works and is tested", { testdata <- c(rnorm(108, 0), rnorm(5, 10), rnorm(5, 20), rnorm(5, 30), rnorm(100, 40)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) testsd <- 0.5 testq <- getCritVal(n = length(testdata), filter = testfilter, family = "jsmurfPS") expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = "s", q = testq)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = Inf, q = testq)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = c(1, 0.5), q = testq)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = -1, q = testq)) estsd <- stepR::sdrobnorm(testdata, lag = 9L) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = estsd, q = testq)) }) test_that("argument q works and is tested", { testdata <- c(rnorm(108, 0), rnorm(5, 10), rnorm(5, 20), rnorm(5, 30), rnorm(100, 40)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) testq <- getCritVal(n = length(testdata), filter = testfilter, family = "jsmurfPS") testsd <- 0.5 expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = "s")) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = as.numeric(NA))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = Inf)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = c(1, 2))) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE), deconvolveLocally(fit = jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE)) }) test_that("argument alpha works and is tested", { testdata <- c(rnorm(108, 0), rnorm(5, 10), rnorm(5, 20), rnorm(5, 30), rnorm(100, 40)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) teststat <- stepR::monteCarloSimulation(n = 215, r = 100, family = "jsmurfPS", filter = testfilter) testsd <- 0.5 expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, alpha = "s", stat = teststat)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, alpha = NULL, stat = teststat)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, alpha = as.numeric(NA), stat = teststat)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, alpha = Inf, stat = teststat)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, alpha = c(0.1, 0.05), stat = teststat)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, alpha = 0, stat = teststat)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, alpha = 1, stat = teststat)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, alpha = -0.05, stat = teststat)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, alpha = 1.01, stat = teststat)) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, alpha = 0.05)) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, output = "each"), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, alpha = 0.05, output = "each")) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, output = "every"), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, alpha = 0.05, output = "every")) testq <- getCritVal(family = "jsmurfPS", n = length(testdata), stat = teststat, filter = testfilter) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, sd = testsd, suppressWarningNoDeconvolution = TRUE), deconvolveLocally(fit = jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE)) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, stat = teststat, suppressWarningNoDeconvolution = TRUE), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, stat = teststat, output = "each", suppressWarningNoDeconvolution = TRUE)$idealization) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none") compare <- list(idealization = deconvolveLocally(fit = compare, data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE), fit = compare, q = testq, filter = testfilter, sd = testsd) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, stat = teststat, output = "each", suppressWarningNoDeconvolution = TRUE), compare) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, stat = teststat, output = "every", suppressWarningNoDeconvolution = TRUE)$idealization compare2 <- compare[[3]] attr(compare2, "noDeconvolution") <- attr(compare, "noDeconvolution") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, stat = teststat, suppressWarningNoDeconvolution = TRUE), compare2) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, output = "every", locationCorrection = "none") compare <- list(idealization = deconvolveLocally(fit = compare$fit, data = testdata, filter = testfilter, output = "every", suppressWarningNoDeconvolution = TRUE), fit = compare$fit, q = testq, filter= testfilter, sd = testsd) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, stat = teststat, output = "every", suppressWarningNoDeconvolution = TRUE), compare) testq <- getCritVal(family = "jsmurfPS", n = length(testdata), stat = teststat, alpha = 0.09, filter = testfilter) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, alpha = 0.09, sd = testsd, suppressWarningNoDeconvolution = TRUE), deconvolveLocally(fit = jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE)) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, stat = teststat, alpha = 0.09, suppressWarningNoDeconvolution = TRUE), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, stat = teststat, alpha = 0.09, output = "each", suppressWarningNoDeconvolution = TRUE)$idealization) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none") compare <- list(idealization = deconvolveLocally(fit = compare, data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE), fit = compare, q = testq, filter = testfilter, sd = testsd) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, stat = teststat, alpha = 0.09, output = "each", suppressWarningNoDeconvolution = TRUE), compare) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, stat = teststat, alpha = 0.09, output = "every", suppressWarningNoDeconvolution = TRUE)$idealization compare2 <- compare[[3]] attr(compare2, "noDeconvolution") <- attr(compare, "noDeconvolution") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, stat = teststat, alpha = 0.09, suppressWarningNoDeconvolution = TRUE), compare2) compare <- jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, output = "every", locationCorrection = "none") compare <- list(idealization = deconvolveLocally(fit = compare$fit, data = testdata, filter = testfilter, output = "every", suppressWarningNoDeconvolution = TRUE), fit = compare$fit, q = testq, filter= testfilter, sd = testsd) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, stat = teststat, alpha = 0.09, output = "every", suppressWarningNoDeconvolution = TRUE), compare) }) test_that("argument ... works and is tested", { testdata <- c(rnorm(108, 0), rnorm(5, 10), rnorm(5, 20), rnorm(5, 30), rnorm(100, 40)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) teststat <- stepR::monteCarloSimulation(n = 215, r = 100, family = "mDependentPS", filter = testfilter) expect_error(suppressWarnings(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, family = "gauss"))) expect_error(suppressWarnings(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, intervalSystem = "all"))) expect_error(suppressWarnings(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, neuv = "1"))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, n = 215)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = rnorm(100))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, stat = teststat, filter = lowpassFilter(param = list(pole = 4L, cutoff = 0.1), len = 10))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, stat = teststat, filter = lowpassFilter(param = list(pole = 4L, cutoff = 0.2), len = 11))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, r = "s", options = list(load = list()))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, r = 0, options = list(load = list()))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, r = c(100L, 200L), options = list(load = list()))) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, r = 100.5, options = list(load = list()), output = "every"), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, r = 100L, options = list(load = list()), output = "every")) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, nq = "215")) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, nq = c(1L, 2L))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, nq = as.integer(NA))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, nq = Inf)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, nq = NULL)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, stat = teststat, nq = 214L)) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, r = 100, output = "every", options = list(load = list())), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, r = 100, output = "every", options = list(load = list()), nq = 215L)) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, r = 100, output = "every", options = list(load = list()), nq = 300), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, r = 100, output = "every", options = list(load = list()), nq = 300L)) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, r = 100, output = "every", options = list(load = list()), nq = 300.5), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, r = 100, output = "every", options = list(load = list()), nq = 300L)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, options = "vector")) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, options = list(a = "vector"))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, options = list(simulation = c("vector", "matrix"), save = list(), load = list()))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, options = list(save = list(workspace = "vecto")))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, messages = "s", options = list(load = list()))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, messages = -1, options = list(load = list()))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, messages = c(1, 2), options = list(load = list()))) expect_identical(suppressMessages(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, r = 100L, messages = 10L, options = list(load = list()), output = "every")), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, r = 100L, options = list(load = list()), output = "every")) expect_identical(suppressMessages(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, r = 100L, messages = 10.5, options = list(load = list()), output = "every")), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, r = 100L, options = list(load = list()), output = "every")) testfile <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".RDS") testvariable <- "test" testStepR <- new.env() testfilter1 <- lowpassFilter(param = list(pole = 4L, cutoff = 0.1), len = 8) teststat1 <- stepR::monteCarloSimulation(n = 215, r = 100, family = "jsmurfPS", filter = testfilter1, output = "maximum") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter1, r = 100L, output = "every", options = list(save = list(RDSfile = testfile, variable = testvariable, workspace = c("vector", "vectorIncreased")), load = list(), envir = testStepR, dirs = "testStepR")), jsmurf(family = "jsmurfPS", data = testdata, stat = teststat1, filter = testfilter1, output = "every", options = list(save = list()))) expect_identical(readRDS(testfile), teststat1) expect_identical(get("test", envir = testStepR), teststat1) remove(test, envir = testStepR) testfilter2 <- lowpassFilter(param = list(pole = 4L, cutoff = 0.2), len = 8) teststat2 <- stepR::monteCarloSimulation(n = 215, r = 100, family = "jsmurfPS", filter = testfilter2, output = "maximum") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter2, r = 100L, output = "every", options = list(envir = testStepR, dirs = "testStepR", save = list(fileSystem = "vector", workspace = "vector"))), jsmurf(family = "jsmurfPS", data = testdata, stat = teststat2, filter = testfilter2, output = "every", options = list(save = list()))) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter1, r = 200L, options = list(load = list(RDSfile = testfile), save = list(fileSystem = "vector"), envir = testStepR, dirs = "testStepR")), jsmurf(family = "jsmurfPS", data = testdata, stat = teststat1, filter = testfilter1, options = list(save = list()))) unlink(testfile) testfilter3 <- lowpassFilter(param = list(pole = 4L, cutoff = 0.1), len = 11) teststat3 <- stepR::monteCarloSimulation(n = 215, r = 100, family = "jsmurfPS", filter = testfilter3, output = "maximum") expect_identical(getCritVal(family = "jsmurfPS", n = 200L, filter = testfilter3, r = 100L, nq = 215L, options = list(save = list(workspace = "vector", fileSystem = "vectorIncreased"), envir = testStepR, dirs = "testStepR")), getCritVal(family = "jsmurfPS", n = 200L, stat = teststat3, filter = testfilter3, options = list(save = list()))) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter3, r = 50L, nq = 320L, output = "every", options = list(save = list(workspace = "vector", fileSystem = "vectorIncreased"), envir = testStepR, dirs = "testStepR")), jsmurf(family = "jsmurfPS", data = testdata, stat = teststat3, filter = testfilter3, output = "every", options = list(save = list()))) teststat4 <- stepR::monteCarloSimulation(n = 320, r = 100, family = "jsmurfPS", lengths = 2^(4:7), filter = testfilter3, output = "maximum") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter3, r = 100L, nq = 320L, output = "every", options = list(save = list(workspace = "vector", fileSystem = "vectorIncreased"), load = list(workspace = "vectorIncreased"), envir = testStepR, dirs = "testStepR")), jsmurf(family = "jsmurfPS", data = testdata, stat = teststat4, filter = testfilter3, output = "every", options = list(save = list()))) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter3, r = 100L, nq = 320L, output = "every", options = list(simulation = "vector", save = list(workspace = "vector", fileSystem = "vectorIncreased"), load = list(workspace = "vectorIncreased"), envir = testStepR, dirs = "testStepR")), jsmurf(family = "jsmurfPS", data = testdata, stat = teststat3, filter = testfilter3, output = "every", options = list(save = list()))) teststat5 <- stepR::monteCarloSimulation(n = 320, r = 200, family = "jsmurfPS", lengths = 2^(4:7), filter = testfilter3, output = "maximum") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter3, r = 200L, nq = 320L, output = "every", options = list(save = list(workspace = "vectorIncreased", fileSystem = "vector"), load = list(workspace = "vectorIncreased", fileSystem = "vectorIncreased"), envir = testStepR, dirs = "testStepR")), jsmurf(family = "jsmurfPS", data = testdata, stat = teststat5, filter = testfilter3, output = "every", options = list(save = list()))) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter3, r = 100L, nq = 320L, output = "every", options = list(save = list(workspace = "vectorIncreased", fileSystem = "vector"), load = list(workspace = "vectorIncreased", fileSystem = "vectorIncreased"), envir = testStepR, dirs = "testStepR")), jsmurf(family = "jsmurfPS", data = testdata, stat = teststat5, filter = testfilter3, output = "every", options = list(save = list()))) expect_identical(length(get("critValStepRTab", envir = testStepR, inherits = FALSE)$stat), 4L) expect_identical(get("critValStepRTab", envir = testStepR, inherits = FALSE)$stat[[1]], teststat1) expect_identical(get("critValStepRTab", envir = testStepR, inherits = FALSE)$stat[[2]], teststat2) expect_identical(get("critValStepRTab", envir = testStepR, inherits = FALSE)$stat[[3]], teststat3) expect_identical(get("critValStepRTab", envir = testStepR, inherits = FALSE)$stat[[4]], teststat5) expect_identical(length(list.files(file.path(R.cache::getCacheRootPath(), "testStepR"))), 4L) expect_identical(R.cache::loadCache(attr(teststat2, "keyList"), dirs = "testStepR"), teststat2) expect_identical(R.cache::loadCache(attr(teststat1, "keyList"), dirs = "testStepR"), teststat1) expect_identical(R.cache::loadCache(attr(teststat3, "keyList"), dirs = "testStepR"), teststat3) expect_identical(R.cache::loadCache(attr(teststat4, "keyList"), dirs = "testStepR"), teststat4) remove(critValStepRTab, envir = testStepR) unlink(file.path(R.cache::getCacheRootPath(), "testStepR"), recursive = TRUE) }) test_that("additional arguments for deconvolveLocally", { testdata <- c(rnorm(108, 0), rnorm(5, 10), rnorm(5, 20), rnorm(5, 30), rnorm(100, 40)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) testsd <- 0.5 testq <- getCritVal(n = length(testdata), filter = testfilter, family = "jsmurfPS") expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE, regularization = 1, thresholdLongSegment = 10L, localEstimate = stats::median, gridSize = c(1, 1 / 10, 1 / 100), windowFactorRefinement = 1, report = FALSE), jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE, regularization = NA)) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE, regularization = c(2, 1)), deconvolveLocally(fit = jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE, regularization = c(2, 1))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE, regularisation = 1)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE, regularization = list(c(1, 0.6, 0.1), c(1, 0.5)))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE, thresholdLongSegment = 0L)) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE, localEstimate = function(x) {c(1, 2)})) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE, gridSize = c(1, "s", 0.01))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE, windowFactorRefinement = c(1, 1, 1))) expect_error(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, sd = testsd, q = testq, suppressWarningNoDeconvolution = TRUE, report = 1)) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE, regularization = 0.5, thresholdLongSegment = 8.5, localEstimate = mean, gridSize = c(1, 0.5, 0.1), windowFactorRefinement = c(0.1, 1), report = FALSE), deconvolveLocally(fit = jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE, regularization = 0.5, thresholdLongSegment = 8.5, localEstimate = mean, gridSize = c(1, 0.5, 0.1), windowFactorRefinement = c(0.1, 1), report = FALSE)) expect_identical(suppressMessages(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE, regularization = c(3, 1.1, 1.01), thresholdLongSegment = 5L, localEstimate = function(x) {1}, gridSize = c(2, 0.5, 1), windowFactorRefinement = c(0.1, 1), report = TRUE)), deconvolveLocally(fit = jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE, regularization = c(3, 1.1, 1.01), thresholdLongSegment = 5L, localEstimate = function(x) {1}, gridSize = c(2, 0.5, 1), windowFactorRefinement = c(0.1, 1))) expect_identical(jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE, regularization = list(c(1), c(2, 0.25)), thresholdLongSegment = 12, localEstimate = median, gridSize = c(1, 0.5), windowFactorRefinement = c(0.1)), deconvolveLocally(fit = jsmurf(family = "jsmurfPS", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE, regularization = list(c(1), c(2, 0.25)), thresholdLongSegment = 12, localEstimate = median, gridSize = c(1, 0.5), windowFactorRefinement = c(0.1))) }) test_that("hjsmurf works if q is given and that data and filter have to be given", { testdata <- rnorm(100) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testq <- rep(10, 3) compare <- stepR::stepFit(y = testdata, x = seq(along = testdata) / testfilter$sr, x0 = 0, family = "hjsmurf", intervalSystem = "dyaLen", q = testq, filter = testfilter) compare <- testOutput(compare) expect_error(jsmurf(family = "hjsmurf")) expect_error(jsmurf(data = testdata, family = "hjsmurf")) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, locationCorrection = "none"), compare) expect_identical(jsmurf(data = testdata, filter = testfilter, family = "hjsmurf", q = testq, suppressWarningNoDeconvolution = TRUE), jsmurf(data = testdata, filter = testfilter, family = "hjsmurf", q = testq, startTime = 0, locationCorrection = "deconvolution", output = "onlyIdealization", suppressWarningNoDeconvolution = TRUE)) }) test_that("locationCorrection is tested and works for family hjsmurf", { set.seed(1) testdata <- c(rnorm(50), rnorm(50, 5)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testq <- getCritVal(n = length(testdata), filter = testfilter, family = "hjsmurf") expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, locationCorrection = 1)) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, suppressWarningNoDeconvolution = TRUE), jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, locationCorrection = "de", suppressWarningNoDeconvolution = TRUE)) compare <- jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, locationCorrection = "none") expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, suppressWarningNoDeconvolution = TRUE), deconvolveLocally(fit = compare, data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE)) compare$leftEnd[2] <- compare$leftEnd[2] - testfilter$jump compare$rightEnd[1] <- compare$rightEnd[1] - testfilter$jump expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, suppressWarningNoDeconvolution = TRUE, locationCorrection = "constant"), compare) }) test_that("output is tested and works", { testdata <- rnorm(100) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testq <- rep(10, 3) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, output = 1)) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, output = c("only", "every"))) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, output = "aha")) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, suppressWarningNoDeconvolution = TRUE), jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, output = "only", suppressWarningNoDeconvolution = TRUE)) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, suppressWarningNoDeconvolution = TRUE), jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, output = "each", suppressWarningNoDeconvolution = TRUE)$idealization) compare <- jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, locationCorrection = "none") compare <- list(idealization = compare, fit = compare, q = testq, filter = testfilter) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, output = "each", locationCorrection = "none"), compare) compare <- list(idealization = list(fit = compare$fit, q = compare$q, filter = compare$filter), fit = compare$fit, q = testq, filter = testfilter) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, output = "every", locationCorrection = "none"), compare) compare <- list(idealization = deconvolveLocally(fit = compare$fit, data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE), fit = compare$fit, q = testq, filter= testfilter) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, output = "each", suppressWarningNoDeconvolution = TRUE), compare) compare <- jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, output = "every", suppressWarningNoDeconvolution = TRUE)$idealization compare2 <- compare[[3]] attr(compare2, "noDeconvolution") <- attr(compare, "noDeconvolution") expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, suppressWarningNoDeconvolution = TRUE), compare2) compare <- jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, output = "every", locationCorrection = "none") compare <- list(idealization = deconvolveLocally(fit = compare$fit, data = testdata, filter = testfilter, output = "every", suppressWarningNoDeconvolution = TRUE), fit = compare$fit, q = testq, filter = testfilter) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, output = "every", suppressWarningNoDeconvolution = TRUE), compare) }) test_that("more difficult scenarios work", { set.seed(NULL) testdata <- c(rnorm(108, 0), rnorm(100, 10), rnorm(100, 0), rnorm(100, 10)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) testq <- getCritVal(n = length(testdata), filter = testfilter, family = "hjsmurf") expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, suppressWarningNoDeconvolution = TRUE), deconvolveLocally(fit = jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE)) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, suppressWarningNoDeconvolution = TRUE), jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, output = "each", suppressWarningNoDeconvolution = TRUE)$idealization) compare <- jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, locationCorrection = "none") compare <- list(idealization = deconvolveLocally(fit = compare, data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE), fit = compare, q = testq, filter= testfilter) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, output = "each", suppressWarningNoDeconvolution = TRUE), compare) compare <- jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, output = "every", suppressWarningNoDeconvolution = TRUE)$idealization compare2 <- compare[[3]] attr(compare2, "noDeconvolution") <- attr(compare, "noDeconvolution") expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, suppressWarningNoDeconvolution = TRUE), compare2) compare <- jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, output = "every", locationCorrection = "none") compare <- list(idealization = deconvolveLocally(fit = compare$fit, data = testdata, filter = testfilter, output = "every", suppressWarningNoDeconvolution = TRUE), fit = compare$fit, q = testq, filter= testfilter) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = testq, output = "every", suppressWarningNoDeconvolution = TRUE), compare) }) test_that("argument data works and is tested", { testdata <- c(rnorm(108, 0), rnorm(5, 10), rnorm(5, 20), rnorm(5, 30), rnorm(100, 40)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) testq <- getCritVal(n = 215, r = 100, filter = testfilter, family = "hjsmurf") expect_error(jsmurf(family = "hjsmurf", data = c(testdata, "s"), filter = testfilter , q = testq)) expect_error(jsmurf(family = "hjsmurf", data = c(testdata, Inf), filter = testfilter , q = testq)) expect_error(jsmurf(family = "hjsmurf", data = c(testdata, as.numeric(NA)), filter = testfilter , q = testq)) }) test_that("argument startTime works and is tested", { testdata <- c(rnorm(108, 0), rnorm(5, 10), rnorm(5, 20), rnorm(5, 30), rnorm(100, 40)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) testq <- getCritVal(n = 215, r = 100, filter = testfilter, family = "hjsmurf") compare <- stepR::stepFit(y = testdata, x = seq(along = testdata) / testfilter$sr, x0 = 0, family = "hjsmurf", intervalSystem = "dyaLen", q = testq, filter = testfilter) compare <- testOutput(compare) expect_identical(jsmurf(family = "hjsmurf", data = testdata, startTime = 0, filter = testfilter , q = testq, locationCorrection = "none"), compare) expect_error(jsmurf(family = "hjsmurf", data = testdata, startTime = "0", filter = testfilter , q = testq)) expect_error(jsmurf(family = "hjsmurf", data = testdata, startTime = Inf, filter = testfilter , q = testq)) expect_error(jsmurf(family = "hjsmurf", data = testdata, startTime = as.numeric(NA), filter = testfilter , q = testq)) expect_error(jsmurf(family = "hjsmurf", data = testdata, startTime = c(0, 0.5), filter = testfilter , q = testq)) testdata <- c(rnorm(108, 0), rnorm(5, 10), rnorm(5, 20), rnorm(5, 30), rnorm(100, 40)) testdata <- .convolve(testdata, testfilter) compare <- stepR::stepFit(y = testdata, x = -1 + seq(along = testdata) / testfilter$sr, x0 = -1, family = "hjsmurf", intervalSystem = "dyaLen", q = testq, filter = testfilter) compare <- testOutput(compare, startTime = -1) expect_identical(jsmurf(family = "hjsmurf", data = testdata, startTime = -1, filter = testfilter, q = testq, locationCorrection = "none"), compare) }) test_that("argument q works and is tested", { testdata <- c(rnorm(108, 0), rnorm(5, 10), rnorm(5, 20), rnorm(5, 30), rnorm(100, 40)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = "s")) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = as.numeric(NA))) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = Inf)) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, q = c(1, 2))) }) test_that("argument alpha works and is tested", { testdata <- c(rnorm(108, 0), rnorm(5, 10), rnorm(5, 20), rnorm(5, 30), rnorm(100, 40)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) teststat <- stepR::monteCarloSimulation(n = 215, r = 100, family = "hjsmurf", filter = testfilter) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, alpha = "s", stat = teststat)) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, alpha = NULL, stat = teststat)) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, alpha = as.numeric(NA), stat = teststat)) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, alpha = Inf, stat = teststat)) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, alpha = c(0.1, 0.05), stat = teststat)) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, alpha = 0, stat = teststat)) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, alpha = 1, stat = teststat)) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, alpha = -0.05, stat = teststat)) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, alpha = 1.01, stat = teststat)) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = teststat), jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = teststat, alpha = 0.05)) compareq <- getCritVal(family = "hjsmurf", n = length(testdata), stat = teststat, filter = testfilter) compare <- stepR::stepFit(y = testdata, x = seq(along = testdata) / testfilter$sr, x0 = 0, family = "hjsmurf", intervalSystem = "dyaLen", q = compareq, filter = testfilter) compare <- testOutput(compare) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = teststat, locationCorrection = "none"), compare) compare <- list(fit = compare, q = compareq, filter = testfilter) compare <- list(idealization = compare, fit = compare$fit, q = compare$q, filter = compare$filter) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = teststat, output = "every", locationCorrection = "none"), compare) compareq <- getCritVal(family = "hjsmurf", n = length(testdata), stat = teststat, alpha = 0.135, filter = testfilter) compare <- stepR::stepFit(y = testdata, x = seq(along = testdata) / testfilter$sr, x0 = 0, family = "hjsmurf", intervalSystem = "dyaLen", q = compareq, filter = testfilter) compare <- testOutput(compare) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = teststat, alpha = 0.135, locationCorrection = "none"), compare) }) test_that("argument ... works and is tested", { testdata <- c(rnorm(108, 0), rnorm(5, 10), rnorm(5, 20), rnorm(5, 30), rnorm(100, 40)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) teststat <- stepR::monteCarloSimulation(n = 215, r = 100, family = "hjsmurf", filter = testfilter) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = teststat, family = "gauss")) expect_error(suppressWarnings(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = teststat, intervalSystem = "all"))) expect_error(suppressWarnings(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = teststat, neuv = "1"))) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = teststat, n = 215)) expect_warning(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = teststat, sd = 1)) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = rnorm(100))) expect_error(jsmurf(family = "hjsmurf", data = testdata, stat = teststat, filter = lowpassFilter(param = list(pole = 4L, cutoff = 0.1), len = 10))) expect_error(jsmurf(family = "hjsmurf", data = testdata, stat = teststat, filter = lowpassFilter(param = list(pole = 4L, cutoff = 0.2), len = 11))) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, r = "s", options = list(load = list()))) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, r = 0, options = list(load = list()))) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, r = c(100L, 200L), options = list(load = list()))) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, r = 100.5, options = list(load = list()), output = "every"), jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, r = 100L, options = list(load = list()), output = "every")) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = teststat, nq = "215")) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = teststat, nq = c(1L, 2L))) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = teststat, nq = as.integer(NA))) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = teststat, nq = Inf)) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = teststat, nq = NULL)) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, stat = teststat, nq = 214L)) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, r = 100, output = "every", options = list(load = list())), jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, r = 100, output = "every", options = list(load = list()), nq = 215L)) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, r = 100, output = "every", options = list(load = list()), nq = 300), jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, r = 100, output = "every", options = list(load = list()), nq = 300L)) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, r = 100, output = "every", options = list(load = list()), nq = 300.5), jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, r = 100, output = "every", options = list(load = list()), nq = 300L)) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, options = "vector")) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, options = list(a = "vector"))) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, options = list(simulation = c("vector", "matrix"), save = list(), load = list()))) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, options = list(save = list(workspace = "vecto")))) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, messages = "s")) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, messages = "s")) expect_error(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, messages = "s")) expect_identical(suppressMessages(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, r = 100L, messages = 10L, options = list(load = list()), output = "every")), jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, r = 100L, options = list(load = list()), output = "every")) expect_identical(suppressMessages(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, r = 100L, messages = 10.5, options = list(load = list()), output = "every")), jsmurf(family = "hjsmurf", data = testdata, filter = testfilter, r = 100L, options = list(load = list()), output = "every")) testfile <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".RDS") testvariable <- "test" testStepR <- new.env() testfilter1 <- lowpassFilter(param = list(pole = 4L, cutoff = 0.1), len = 8) teststat1 <- stepR::monteCarloSimulation(n = 215, r = 100, family = "hjsmurf", filter = testfilter1) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter1, r = 100L, output = "every", options = list(save = list(RDSfile = testfile, variable = testvariable, workspace = c("vector", "vectorIncreased")), load = list(), envir = testStepR, dirs = "testStepR")), jsmurf(family = "hjsmurf", data = testdata, stat = teststat1, filter = testfilter1, output = "every", options = list(save = list()))) expect_identical(readRDS(testfile), teststat1) expect_identical(get("test", envir = testStepR), teststat1) remove(test, envir = testStepR) testfilter2 <- lowpassFilter(param = list(pole = 4L, cutoff = 0.2), len = 8) teststat2 <- stepR::monteCarloSimulation(n = 215, r = 100, family = "hjsmurf", filter = testfilter2) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter2, r = 100L, output = "every", options = list(envir = testStepR, dirs = "testStepR", save = list(fileSystem = "vector", workspace = "vector"))), jsmurf(family = "hjsmurf", data = testdata, stat = teststat2, filter = testfilter2, output = "every", options = list(save = list()))) expect_identical(jsmurf(family = "hjsmurf", data = testdata, filter = testfilter1, r = 200L, options = list(load = list(RDSfile = testfile), save = list(fileSystem = "vector"), envir = testStepR, dirs = "testStepR")), jsmurf(family = "hjsmurf", data = testdata, stat = teststat1, filter = testfilter1, options = list(save = list()))) unlink(testfile) unlink(file.path(R.cache::getCacheRootPath(), "testStepR"), recursive = TRUE) }) test_that("other families work", { testdata <- rnorm(100) testfilter <- lowpassFilter(param = list(pole = 4L, cutoff = 0.1)) testsd <- 1 testq <- 1.44 expect_error(jsmurf(family = "jsmurf")) expect_error(jsmurf(family = "jsmurf", data = testdata)) expect_error(jsmurf(family = "jsmurf", filter = testfilter)) expect_error(jsmurf(family = "jsmurfLR")) expect_error(jsmurf(family = "jsmurfLR", data = testdata)) expect_error(jsmurf(family = "jsmurfLR", filter = testfilter)) expect_error(jsmurf(family = "hjsmurfSPS")) expect_error(jsmurf(family = "hjsmurfSPS", data = testdata)) expect_error(jsmurf(family = "hjsmurfSPS", filter = testfilter)) expect_error(jsmurf(family = "hjsmurfLR")) expect_error(jsmurf(family = "hjsmurfLR", data = testdata)) expect_error(jsmurf(family = "hjsmurfLR", filter = testfilter)) compare <- stepR::stepFit(y = testdata, x = seq(along = testdata) / testfilter$sr, x0 = 0, family = "jsmurf", intervalSystem = "dyaLen", q = testq, sd = testsd, filter = testfilter) expect_identical(jsmurf(family = "jsmurf", data = testdata, filter = testfilter, sd = testsd, q = testq, locationCorrection = "none"), testOutput(compare)) compare <- stepR::stepFit(y = testdata, x = seq(along = testdata) / testfilter$sr, x0 = 0, family = "jsmurfLR", intervalSystem = "dyaLen", q = testq, sd = testsd, filter = testfilter) expect_identical(jsmurf(family = "jsmurfLR", data = testdata, filter = testfilter, sd = testsd, q = testq, locationCorrection = "none"), testOutput(compare)) compare <- stepR::stepFit(y = testdata, x = seq(along = testdata) / testfilter$sr, x0 = 0, family = "hjsmurfSPS", intervalSystem = "dyaLen", q = rep(10, 3), filter = testfilter) expect_identical(jsmurf(family = "hjsmurfSPS", data = testdata, filter = testfilter, q = rep(10, 3), locationCorrection = "none"), testOutput(compare)) compare <- stepR::stepFit(y = testdata, x = seq(along = testdata) / testfilter$sr, x0 = 0, family = "hjsmurfLR", intervalSystem = "dyaLen", q = rep(10, 3), filter = testfilter) expect_identical(jsmurf(family = "hjsmurfLR", data = testdata, filter = testfilter, q = rep(10, 3), locationCorrection = "none"), testOutput(compare)) set.seed(1) testdata <- c(rnorm(50), rnorm(50, 5)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testsd <- 1 testq <- getCritVal(n = length(testdata), filter = testfilter, family = "jsmurf") compare <- jsmurf(family = "jsmurf", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none") expect_identical(jsmurf(family = "jsmurf", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE), deconvolveLocally(fit = compare, data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE)) testq <- getCritVal(n = length(testdata), filter = testfilter, family = "jsmurfLR") compare <- jsmurf(family = "jsmurfLR", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none") expect_identical(jsmurf(family = "jsmurfLR", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE), deconvolveLocally(fit = compare, data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE)) testq <- getCritVal(n = length(testdata), filter = testfilter, family = "hjsmurfLR") compare <- jsmurf(family = "hjsmurfLR", data = testdata, filter = testfilter, q = testq, locationCorrection = "none") expect_identical(jsmurf(family = "hjsmurfLR", data = testdata, filter = testfilter, q = testq, suppressWarningNoDeconvolution = TRUE), deconvolveLocally(fit = compare, data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE)) testdata <- c(rnorm(108, 0), rnorm(5, 10), rnorm(5, 20), rnorm(5, 30), rnorm(100, 40)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) testq <- getCritVal(n = length(testdata), filter = testfilter, family = "jsmurf") testsd <- 0.5 expect_identical(jsmurf(family = "jsmurf", data = testdata, filter = testfilter, q = testq, sd = testsd, suppressWarningNoDeconvolution = TRUE), deconvolveLocally(fit = jsmurf(family = "jsmurf", data = testdata, filter = testfilter, q = testq, sd = testsd, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE)) testq <- getCritVal(n = length(testdata), filter = testfilter, family = "hjsmurfSPS") expect_identical(jsmurf(family = "hjsmurfSPS", data = testdata, filter = testfilter, q = testq, suppressWarningNoDeconvolution = TRUE), deconvolveLocally(fit = jsmurf(family = "hjsmurfSPS", data = testdata, filter = testfilter, q = testq, locationCorrection = "none"), data = testdata, filter = testfilter, suppressWarningNoDeconvolution = TRUE)) testdata <- c(rnorm(108, 0), rnorm(5, 10), rnorm(5, 20), rnorm(5, 30), rnorm(100, 40)) testfilter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 0.1), sr = 1, len = 8L, shift = 0.5) testdata <- .convolve(testdata, testfilter) teststat <- stepR::monteCarloSimulation(n = 215, r = 100, family = "jsmurf", filter = testfilter) expect_error(jsmurf(family = "jsmurf", data = testdata, filter = testfilter, stat = teststat, family = "gauss")) expect_error(suppressWarnings(jsmurf(family = "jsmurf", data = testdata, filter = testfilter, stat = teststat, intervalSystem = "all"))) expect_error(suppressWarnings(jsmurf(family = "jsmurf", data = testdata, filter = testfilter, stat = teststat, neuv = "1"))) expect_error(jsmurf(family = "jsmurf", data = testdata, filter = testfilter, stat = teststat, n = 215)) expect_identical(suppressMessages(jsmurf(family = "jsmurf", data = testdata, filter = testfilter, r = 100L, messages = 10L, options = list(load = list()), output = "every")), jsmurf(family = "jsmurf", data = testdata, filter = testfilter, r = 100L, options = list(load = list()), output = "every")) testfile <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".RDS") testvariable <- "test" testStepR <- new.env() testfilter1 <- lowpassFilter(param = list(pole = 4L, cutoff = 0.1), len = 8) teststat1 <- stepR::monteCarloSimulation(n = 215, r = 100, family = "jsmurf", filter = testfilter1, output = "maximum") expect_identical(jsmurf(family = "jsmurf", data = testdata, filter = testfilter1, r = 100L, output = "every", options = list(save = list(RDSfile = testfile, variable = testvariable, workspace = c("vector", "vectorIncreased")), load = list(), envir = testStepR, dirs = "testStepR")), jsmurf(family = "jsmurf", data = testdata, stat = teststat1, filter = testfilter1, output = "every", options = list(save = list()))) expect_identical(readRDS(testfile), teststat1) expect_identical(get("test", envir = testStepR), teststat1) remove(test, envir = testStepR) })