mirror of
https://github.com/msberends/AMR.git
synced 2025-07-12 08:21:51 +02:00
(v2.1.1.9186) replace antibiotics with antimicrobials!
This commit is contained in:
@ -27,152 +27,154 @@
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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# used in multiple functions, also in plotting
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expect_true(all(as.mic(AMR:::COMMON_MIC_VALUES) %in% AMR:::VALID_MIC_LEVELS))
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expect_true(all(paste0("<=", as.mic(AMR:::COMMON_MIC_VALUES)) %in% AMR:::VALID_MIC_LEVELS))
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expect_true(all(paste0(">=", as.mic(AMR:::COMMON_MIC_VALUES)) %in% AMR:::VALID_MIC_LEVELS))
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test_that("mic works", {
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# used in multiple functions, also in plotting
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expect_true(all(as.mic(AMR:::COMMON_MIC_VALUES) %in% AMR:::VALID_MIC_LEVELS))
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expect_true(all(paste0("<=", as.mic(AMR:::COMMON_MIC_VALUES)) %in% AMR:::VALID_MIC_LEVELS))
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expect_true(all(paste0(">=", as.mic(AMR:::COMMON_MIC_VALUES)) %in% AMR:::VALID_MIC_LEVELS))
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expect_true(as.mic(8) == as.mic("8"))
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expect_true(as.mic("1") > as.mic("<=0.0625"))
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expect_true(as.mic("1") < as.mic(">=32"))
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expect_true(is.mic(as.mic(8)))
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expect_true(as.mic(8) == as.mic("8"))
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expect_true(as.mic("1") > as.mic("<=0.0625"))
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expect_true(as.mic("1") < as.mic(">=32"))
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expect_true(is.mic(as.mic(8)))
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expect_equal(as.double(as.mic(">=32")), 32)
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expect_equal(as.numeric(as.mic(">=32")), 32)
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expect_equal(
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as.integer(as.mic(">=32")), # should be factor level, not the MIC
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as.integer(factor(as.character(">=32"),
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levels = levels(as.mic(">=32"))
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))
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)
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expect_equal(suppressWarnings(as.logical(as.mic("INVALID VALUE"))), NA)
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expect_equal(as.double(as.mic(">=32")), 32)
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expect_equal(as.numeric(as.mic(">=32")), 32)
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expect_equal(
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as.integer(as.mic(">=32")), # should be factor level, not the MIC
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as.integer(factor(as.character(">=32"),
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levels = levels(as.mic(">=32"))
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))
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)
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expect_equal(suppressWarnings(as.logical(as.mic("INVALID VALUE"))), NA)
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# all levels should be valid MICs
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x <- as.mic(c(2, 4))
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expect_inherits(x[1], "mic")
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expect_inherits(x[[1]], "mic")
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expect_inherits(c(x[1], x[9]), "mic")
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expect_inherits(unique(x[1], x[9]), "mic")
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expect_inherits(droplevels(c(x[1], x[9]), as.mic = TRUE), "factor")
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expect_inherits(droplevels(c(x[1], x[9]), as.mic = TRUE), "mic")
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x[2] <- 32
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expect_inherits(x, "mic")
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# expect_warning(as.mic("INVALID VALUE"))
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# all levels should be valid MICs
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x <- as.mic(c(2, 4))
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expect_inherits(x[1], "mic")
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expect_inherits(x[[1]], "mic")
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expect_inherits(c(x[1], x[9]), "mic")
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expect_inherits(unique(x[1], x[9]), "mic")
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expect_inherits(droplevels(c(x[1], x[9]), as.mic = TRUE), "factor")
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expect_inherits(droplevels(c(x[1], x[9]), as.mic = TRUE), "mic")
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x[2] <- 32
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expect_inherits(x, "mic")
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# expect_warning(as.mic("INVALID VALUE"))
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pdf(NULL) # prevent Rplots.pdf being created
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expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
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expect_silent(plot(as.mic(c(1, 2, 4, 8))))
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expect_silent(plot(as.mic(c(1, 2, 4, 8)), expand = FALSE))
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expect_silent(plot(as.mic(c(1, 2, 4, 8)), mo = "Escherichia coli", ab = "cipr"))
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if (AMR:::pkg_is_available("ggplot2")) {
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expect_inherits(ggplot2::autoplot(as.mic(c(1, 2, 4, 8))), "gg")
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expect_inherits(ggplot2::autoplot(as.mic(c(1, 2, 4, 8)), expand = FALSE), "gg")
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expect_inherits(ggplot2::autoplot(as.mic(c(1, 2, 4, 8, 32)), mo = "Escherichia coli", ab = "cipr"), "gg")
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}
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expect_stdout(print(as.mic(c(1, 2, 4, 8))))
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pdf(NULL) # prevent Rplots.pdf being created
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expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
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expect_silent(plot(as.mic(c(1, 2, 4, 8))))
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expect_silent(plot(as.mic(c(1, 2, 4, 8)), expand = FALSE))
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expect_silent(plot(as.mic(c(1, 2, 4, 8)), mo = "Escherichia coli", ab = "cipr"))
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if (AMR:::pkg_is_available("ggplot2")) {
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expect_inherits(ggplot2::autoplot(as.mic(c(1, 2, 4, 8))), "gg")
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expect_inherits(ggplot2::autoplot(as.mic(c(1, 2, 4, 8)), expand = FALSE), "gg")
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expect_inherits(ggplot2::autoplot(as.mic(c(1, 2, 4, 8, 32)), mo = "Escherichia coli", ab = "cipr"), "gg")
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}
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expect_output(print(as.mic(c(1, 2, 4, 8))))
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expect_inherits(summary(as.mic(c(2, 8))), c("summaryDefault", "table"))
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expect_inherits(summary(as.mic(c(2, 8))), c("summaryDefault", "table"))
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if (AMR:::pkg_is_available("tibble")) {
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expect_stdout(print(tibble::tibble(m = as.mic(2:4))))
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}
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if (AMR:::pkg_is_available("tibble")) {
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expect_output(print(tibble::tibble(m = as.mic(2:4))))
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}
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# all mathematical operations
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x <- random_mic(50)
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x_double <- as.double(gsub("[<=>]+", "", as.character(x)))
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suppressWarnings(expect_identical(mean(x), mean(x_double)))
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suppressWarnings(expect_identical(median(x), median(x_double)))
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suppressWarnings(expect_identical(quantile(x), quantile(x_double)))
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suppressWarnings(expect_identical(abs(x), abs(x_double)))
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suppressWarnings(expect_identical(sign(x), sign(x_double)))
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suppressWarnings(expect_identical(sqrt(x), sqrt(x_double)))
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suppressWarnings(expect_identical(floor(x), floor(x_double)))
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suppressWarnings(expect_identical(ceiling(x), ceiling(x_double)))
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suppressWarnings(expect_identical(trunc(x), trunc(x_double)))
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suppressWarnings(expect_identical(round(x), round(x_double)))
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suppressWarnings(expect_identical(signif(x), signif(x_double)))
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suppressWarnings(expect_identical(exp(x), exp(x_double)))
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suppressWarnings(expect_identical(log(x), log(x_double)))
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suppressWarnings(expect_identical(log10(x), log10(x_double)))
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suppressWarnings(expect_identical(log2(x), log2(x_double)))
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suppressWarnings(expect_identical(expm1(x), expm1(x_double)))
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suppressWarnings(expect_identical(log1p(x), log1p(x_double)))
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suppressWarnings(expect_identical(cos(x), cos(x_double)))
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suppressWarnings(expect_identical(sin(x), sin(x_double)))
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suppressWarnings(expect_identical(tan(x), tan(x_double)))
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if (getRversion() >= "3.1") {
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suppressWarnings(expect_identical(cospi(x), cospi(x_double)))
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suppressWarnings(expect_identical(sinpi(x), sinpi(x_double)))
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suppressWarnings(expect_identical(tanpi(x), tanpi(x_double)))
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}
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suppressWarnings(expect_identical(acos(x), acos(x_double)))
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suppressWarnings(expect_identical(asin(x), asin(x_double)))
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suppressWarnings(expect_identical(atan(x), atan(x_double)))
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suppressWarnings(expect_identical(cosh(x), cosh(x_double)))
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suppressWarnings(expect_identical(sinh(x), sinh(x_double)))
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suppressWarnings(expect_identical(tanh(x), tanh(x_double)))
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suppressWarnings(expect_identical(acosh(x), acosh(x_double)))
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suppressWarnings(expect_identical(asinh(x), asinh(x_double)))
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suppressWarnings(expect_identical(atanh(x), atanh(x_double)))
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suppressWarnings(expect_identical(lgamma(x), lgamma(x_double)))
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suppressWarnings(expect_identical(gamma(x), gamma(x_double)))
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suppressWarnings(expect_identical(digamma(x), digamma(x_double)))
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suppressWarnings(expect_identical(trigamma(x), trigamma(x_double)))
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suppressWarnings(expect_identical(cumsum(x), cumsum(x_double)))
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suppressWarnings(expect_identical(cumprod(x), cumprod(x_double)))
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suppressWarnings(expect_identical(cummax(x), cummax(x_double)))
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suppressWarnings(expect_identical(cummin(x), cummin(x_double)))
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suppressWarnings(expect_identical(!x, !x_double))
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# all mathematical operations
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x <- random_mic(50)
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x_double <- as.double(gsub("[<=>]+", "", as.character(x)))
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suppressWarnings(expect_identical(mean(x), mean(x_double)))
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suppressWarnings(expect_identical(median(x), median(x_double)))
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suppressWarnings(expect_identical(quantile(x), quantile(x_double)))
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suppressWarnings(expect_identical(abs(x), abs(x_double)))
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suppressWarnings(expect_identical(sign(x), sign(x_double)))
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suppressWarnings(expect_identical(sqrt(x), sqrt(x_double)))
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suppressWarnings(expect_identical(floor(x), floor(x_double)))
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suppressWarnings(expect_identical(ceiling(x), ceiling(x_double)))
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suppressWarnings(expect_identical(trunc(x), trunc(x_double)))
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suppressWarnings(expect_identical(round(x), round(x_double)))
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suppressWarnings(expect_identical(signif(x), signif(x_double)))
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suppressWarnings(expect_identical(exp(x), exp(x_double)))
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suppressWarnings(expect_identical(log(x), log(x_double)))
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suppressWarnings(expect_identical(log10(x), log10(x_double)))
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suppressWarnings(expect_identical(log2(x), log2(x_double)))
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suppressWarnings(expect_identical(expm1(x), expm1(x_double)))
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suppressWarnings(expect_identical(log1p(x), log1p(x_double)))
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suppressWarnings(expect_identical(cos(x), cos(x_double)))
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suppressWarnings(expect_identical(sin(x), sin(x_double)))
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suppressWarnings(expect_identical(tan(x), tan(x_double)))
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if (getRversion() >= "3.1") {
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suppressWarnings(expect_identical(cospi(x), cospi(x_double)))
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suppressWarnings(expect_identical(sinpi(x), sinpi(x_double)))
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suppressWarnings(expect_identical(tanpi(x), tanpi(x_double)))
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}
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suppressWarnings(expect_identical(acos(x), acos(x_double)))
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suppressWarnings(expect_identical(asin(x), asin(x_double)))
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suppressWarnings(expect_identical(atan(x), atan(x_double)))
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suppressWarnings(expect_identical(cosh(x), cosh(x_double)))
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suppressWarnings(expect_identical(sinh(x), sinh(x_double)))
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suppressWarnings(expect_identical(tanh(x), tanh(x_double)))
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suppressWarnings(expect_identical(acosh(x), acosh(x_double)))
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suppressWarnings(expect_identical(asinh(x), asinh(x_double)))
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suppressWarnings(expect_identical(atanh(x), atanh(x_double)))
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suppressWarnings(expect_identical(lgamma(x), lgamma(x_double)))
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suppressWarnings(expect_identical(gamma(x), gamma(x_double)))
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suppressWarnings(expect_identical(digamma(x), digamma(x_double)))
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suppressWarnings(expect_identical(trigamma(x), trigamma(x_double)))
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suppressWarnings(expect_identical(cumsum(x), cumsum(x_double)))
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suppressWarnings(expect_identical(cumprod(x), cumprod(x_double)))
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suppressWarnings(expect_identical(cummax(x), cummax(x_double)))
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suppressWarnings(expect_identical(cummin(x), cummin(x_double)))
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suppressWarnings(expect_identical(!x, !x_double))
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suppressWarnings(expect_identical(all(x), all(x_double)))
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suppressWarnings(expect_identical(any(x), any(x_double)))
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suppressWarnings(expect_identical(sum(x), sum(x_double)))
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suppressWarnings(expect_identical(prod(x), prod(x_double)))
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suppressWarnings(expect_identical(min(x), min(x_double)))
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suppressWarnings(expect_identical(max(x), max(x_double)))
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suppressWarnings(expect_identical(range(x), range(x_double)))
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suppressWarnings(expect_identical(all(x), all(x_double)))
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suppressWarnings(expect_identical(any(x), any(x_double)))
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suppressWarnings(expect_identical(sum(x), sum(x_double)))
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suppressWarnings(expect_identical(prod(x), prod(x_double)))
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suppressWarnings(expect_identical(min(x), min(x_double)))
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suppressWarnings(expect_identical(max(x), max(x_double)))
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suppressWarnings(expect_identical(range(x), range(x_double)))
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el1 <- random_mic(50)
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el1_double <- as.double(gsub("[<=>]+", "", as.character(el1)))
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el2 <- random_mic(50)
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el2_double <- as.double(gsub("[<=>]+", "", as.character(el2)))
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suppressWarnings(expect_identical(el1 + el2, el1_double + el2_double))
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suppressWarnings(expect_identical(el1 - el2, el1_double - el2_double))
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suppressWarnings(expect_identical(el1 * el2, el1_double * el2_double))
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suppressWarnings(expect_identical(el1 / el2, el1_double / el2_double))
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suppressWarnings(expect_identical(el1^el2, el1_double^el2_double))
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suppressWarnings(expect_identical(el1 %% el2, el1_double %% el2_double))
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suppressWarnings(expect_identical(el1 %/% el2, el1_double %/% el2_double))
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suppressWarnings(expect_identical(el1 & el2, el1_double & el2_double))
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el1 <- random_mic(50)
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el1_double <- as.double(gsub("[<=>]+", "", as.character(el1)))
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el2 <- random_mic(50)
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el2_double <- as.double(gsub("[<=>]+", "", as.character(el2)))
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suppressWarnings(expect_identical(el1 + el2, el1_double + el2_double))
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suppressWarnings(expect_identical(el1 - el2, el1_double - el2_double))
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suppressWarnings(expect_identical(el1 * el2, el1_double * el2_double))
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suppressWarnings(expect_identical(el1 / el2, el1_double / el2_double))
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suppressWarnings(expect_identical(el1^el2, el1_double^el2_double))
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suppressWarnings(expect_identical(el1 %% el2, el1_double %% el2_double))
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suppressWarnings(expect_identical(el1 %/% el2, el1_double %/% el2_double))
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suppressWarnings(expect_identical(el1 & el2, el1_double & el2_double))
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# for comparison operators, be more strict:
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expect_true(as.mic(">32") > as.mic(32))
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expect_true(as.mic(">32") >= as.mic(32))
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expect_true(as.mic(">32") >= as.mic("<32"))
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expect_true(as.mic(">32") >= as.mic("<=32"))
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expect_true(as.mic(">32") > as.mic("<=32"))
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# for comparison operators, be more strict:
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expect_true(as.mic(">32") > as.mic(32))
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expect_true(as.mic(">32") >= as.mic(32))
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expect_true(as.mic(">32") >= as.mic("<32"))
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expect_true(as.mic(">32") >= as.mic("<=32"))
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expect_true(as.mic(">32") > as.mic("<=32"))
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expect_false(as.mic("32") > as.mic(32))
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expect_true(as.mic("32") >= as.mic(32))
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expect_true(as.mic("32") >= as.mic("<32"))
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expect_true(as.mic("32") >= as.mic("<=32"))
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expect_false(as.mic("32") > as.mic("<=32"))
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expect_false(as.mic("32") > as.mic(32))
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expect_true(as.mic("32") >= as.mic(32))
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expect_true(as.mic("32") >= as.mic("<32"))
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expect_true(as.mic("32") >= as.mic("<=32"))
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expect_false(as.mic("32") > as.mic("<=32"))
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expect_true(as.mic("32") == as.mic(32))
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expect_true(as.mic("32") == as.mic(32))
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expect_false(as.mic("32") == as.mic("<32"))
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expect_true(as.mic("32") == as.mic("<=32"))
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expect_true(as.mic("32") == as.mic("<=32"))
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expect_true(as.mic("32") == as.mic(32))
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expect_true(as.mic("32") == as.mic(32))
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expect_false(as.mic("32") == as.mic("<32"))
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expect_true(as.mic("32") == as.mic("<=32"))
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expect_true(as.mic("32") == as.mic("<=32"))
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expect_false(as.mic(">32") < as.mic(32))
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expect_false(as.mic(">32") <= as.mic(32))
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expect_false(as.mic(">32") <= as.mic("<32"))
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expect_false(as.mic(">32") <= as.mic("<=32"))
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expect_false(as.mic(">32") < as.mic("<=32"))
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expect_false(as.mic(">32") < as.mic(32))
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expect_false(as.mic(">32") <= as.mic(32))
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expect_false(as.mic(">32") <= as.mic("<32"))
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expect_false(as.mic(">32") <= as.mic("<=32"))
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expect_false(as.mic(">32") < as.mic("<=32"))
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expect_false(as.mic("32") < as.mic(32))
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expect_true(as.mic("32") <= as.mic(32))
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expect_false(as.mic("32") <= as.mic("<32"))
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expect_true(as.mic("32") <= as.mic("<=32"))
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expect_false(as.mic("32") < as.mic("<=32"))
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expect_false(as.mic("32") < as.mic(32))
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expect_true(as.mic("32") <= as.mic(32))
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expect_false(as.mic("32") <= as.mic("<32"))
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expect_true(as.mic("32") <= as.mic("<=32"))
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expect_false(as.mic("32") < as.mic("<=32"))
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})
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