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documentation, unit tests

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dr. M.S. (Matthijs) Berends
2023-01-24 10:20:27 +01:00
parent eef00069fd
commit 830c67f1bf
60 changed files with 45 additions and 7 deletions
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36
inst/tinytest/test-_deprecated.R
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@ -26,3 +26,39 @@
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
sir <- random_sir(100)
rsi <- sir
class(rsi) <- gsub("sir", "rsi", class(rsi))
mic <- random_mic(100)
disk <- random_disk(100)
expect_identical(summary(sir), summary(rsi))
expect_identical(c(sir), c(rsi))
expect_identical(suppressWarnings(suppressMessages(as.rsi(as.character(rsi)))),
suppressWarnings(suppressMessages(as.sir(as.character(sir)))))
expect_identical(suppressWarnings(suppressMessages(as.rsi(mic, mo = "Escherichia coli", ab = "CIP"))),
suppressWarnings(suppressMessages(as.sir(mic, mo = "Escherichia coli", ab = "CIP"))))
expect_identical(suppressWarnings(suppressMessages(as.rsi(disk, mo = "Escherichia coli", ab = "CIP"))),
suppressWarnings(suppressMessages(as.sir(disk, mo = "Escherichia coli", ab = "CIP"))))
expect_identical(suppressWarnings(suppressMessages(as.rsi(data.frame(CIP = mic, mo = "Escherichia coli")))),
suppressWarnings(suppressMessages(as.sir(data.frame(CIP = mic, mo = "Escherichia coli")))))
expect_identical(suppressWarnings(n_rsi(example_isolates$CIP)),
suppressWarnings(n_sir(example_isolates$CIP)))
expect_identical(suppressWarnings(rsi_df(example_isolates$CIP)),
suppressWarnings(sir_df(example_isolates$CIP)))
expect_identical(suppressWarnings(is.rsi.eligible(example_isolates)),
suppressWarnings(is_sir_eligible(example_isolates)))
if (pkg_is_available("ggplot2", also_load = FALSE)) {
expect_identical(suppressWarnings(ggplot_rsi(example_isolates[, c("CIP", "GEN", "TOB")])),
suppressWarnings(ggplot_sir(example_isolates[, c("CIP", "GEN", "TOB")])))
p <- ggplot2::ggplot(example_isolates[, c("CIP", "GEN", "TOB")])
expect_equal(suppressWarnings(p + geom_rsi() + scale_rsi_colours() + labels_rsi_count() + facet_rsi() + theme_rsi()),
suppressWarnings(p + geom_sir() + scale_sir_colours() + labels_sir_count() + facet_sir() + theme_sir()))
}