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112 lines
4.5 KiB
112 lines
4.5 KiB
# ==================================================================== # |
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# TITLE # |
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# Antimicrobial Resistance (AMR) Data Analysis for R # |
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# # |
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# SOURCE # |
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# https://github.com/msberends/AMR # |
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# # |
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# LICENCE # |
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# (c) 2018-2021 Berends MS, Luz CF et al. # |
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# Developed at the University of Groningen, the Netherlands, in # |
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# collaboration with non-profit organisations Certe Medical # |
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# Diagnostics & Advice, and University Medical Center Groningen. # |
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# # |
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# This R package is free software; you can freely use and distribute # |
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# it for both personal and commercial purposes under the terms of the # |
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# GNU General Public License version 2.0 (GNU GPL-2), as published by # |
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# the Free Software Foundation. # |
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# We created this package for both routine data analysis and academic # |
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# research and it was publicly released in the hope that it will be # |
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # |
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# # |
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# Visit our website for the full manual and a complete tutorial about # |
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # |
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# ==================================================================== # |
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0") & AMR:::pkg_is_available("ggplot2")) { |
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pdf(NULL) # prevent Rplots.pdf being created |
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# data should be equal |
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expect_equal( |
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(example_isolates %>% |
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select(AMC, CIP) %>% |
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ggplot_rsi())$data %>% |
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summarise_all(resistance) %>% |
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as.double(), |
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example_isolates %>% |
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select(AMC, CIP) %>% |
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summarise_all(resistance) %>% |
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as.double() |
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) |
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expect_stdout(print(example_isolates %>% |
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select(AMC, CIP) %>% |
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ggplot_rsi(x = "interpretation", facet = "antibiotic"))) |
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expect_stdout(print(example_isolates %>% |
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select(AMC, CIP) %>% |
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ggplot_rsi(x = "antibiotic", facet = "interpretation"))) |
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expect_equal( |
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(example_isolates %>% |
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select(AMC, CIP) %>% |
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ggplot_rsi(x = "interpretation", facet = "antibiotic"))$data %>% |
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summarise_all(resistance) %>% |
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as.double(), |
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example_isolates %>% |
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select(AMC, CIP) %>% |
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summarise_all(resistance) %>% |
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as.double() |
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) |
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expect_equal( |
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(example_isolates %>% |
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select(AMC, CIP) %>% |
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ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>% |
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summarise_all(resistance) %>% |
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as.double(), |
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example_isolates %>% |
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select(AMC, CIP) %>% |
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summarise_all(resistance) %>% |
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as.double() |
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) |
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expect_equal( |
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(example_isolates %>% |
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select(AMC, CIP) %>% |
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ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>% |
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summarise_all(count_resistant) %>% |
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as.double(), |
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example_isolates %>% |
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select(AMC, CIP) %>% |
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summarise_all(count_resistant) %>% |
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as.double() |
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) |
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# support for scale_type ab and mo |
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expect_inherits((data.frame(mo = as.mo(c("e. coli", "s aureus")), |
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n = c(40, 100)) %>% |
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ggplot(aes(x = mo, y = n)) + |
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geom_col())$data, |
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"data.frame") |
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expect_inherits((data.frame(ab = as.ab(c("amx", "amc")), |
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n = c(40, 100)) %>% |
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ggplot(aes(x = ab, y = n)) + |
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geom_col())$data, |
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"data.frame") |
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expect_inherits((data.frame(ab = as.ab(c("amx", "amc")), |
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n = c(40, 100)) %>% |
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ggplot(aes(x = ab, y = n)) + |
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geom_col())$data, |
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"data.frame") |
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# support for manual colours |
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expect_inherits((ggplot(data.frame(x = c("Value1", "Value2", "Value3"), |
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y = c(1, 2, 3), |
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z = c("Value4", "Value5", "Value6"))) + |
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geom_col(aes(x = x, y = y, fill = z)) + |
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scale_rsi_colours(Value4 = "S", Value5 = "I", Value6 = "R"))$data, |
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"data.frame") |
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}
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