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Replace RSI with SIR

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This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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18
inst/tinytest/test-proportion.R
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@ -32,8 +32,8 @@ expect_equal(proportion_SI(example_isolates$AMX), susceptibility(example_isolate
# AMX resistance in `example_isolates`
expect_equal(proportion_R(example_isolates$AMX), 0.5955556, tolerance = 0.0001)
expect_equal(proportion_I(example_isolates$AMX), 0.002222222, tolerance = 0.0001)
expect_equal(rsi_confidence_interval(example_isolates$AMX)[1], 0.5688204, tolerance = 0.0001)
expect_equal(rsi_confidence_interval(example_isolates$AMX)[2], 0.6218738, tolerance = 0.0001)
expect_equal(sir_confidence_interval(example_isolates$AMX)[1], 0.5688204, tolerance = 0.0001)
expect_equal(sir_confidence_interval(example_isolates$AMX)[2], 0.6218738, tolerance = 0.0001)
expect_equal(
1 - proportion_R(example_isolates$AMX) - proportion_I(example_isolates$AMX),
proportion_S(example_isolates$AMX)
@ -69,7 +69,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
R = proportion_R(CIP, as_percent = TRUE),
I = proportion_I(CIP, as_percent = TRUE),
S = proportion_S(CIP, as_percent = TRUE),
n = n_rsi(CIP),
n = n_sir(CIP),
total = n()
) %>%
pull(n) %>%
@ -83,11 +83,11 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
group_by(ward) %>%
summarise(
cipro_p = proportion_SI(CIP, as_percent = TRUE),
cipro_n = n_rsi(CIP),
cipro_n = n_sir(CIP),
genta_p = proportion_SI(GEN, as_percent = TRUE),
genta_n = n_rsi(GEN),
genta_n = n_sir(GEN),
combination_p = proportion_SI(CIP, GEN, as_percent = TRUE),
combination_n = n_rsi(CIP, GEN)
combination_n = n_sir(CIP, GEN)
) %>%
pull(combination_n),
c(1181, 577, 116)
@ -110,7 +110,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
)
)
expect_warning(example_isolates %>% group_by(ward) %>% summarise(across(KAN, rsi_confidence_interval)))
expect_warning(example_isolates %>% group_by(ward) %>% summarise(across(KAN, sir_confidence_interval)))
}
expect_warning(proportion_R(as.character(example_isolates$AMC)))
@ -120,12 +120,12 @@ expect_warning(proportion_S(as.character(
example_isolates$GEN
)))
expect_warning(n_rsi(as.character(
expect_warning(n_sir(as.character(
example_isolates$AMC,
example_isolates$GEN
)))
expect_equal(
suppressWarnings(n_rsi(as.character(
suppressWarnings(n_sir(as.character(
example_isolates$AMC,
example_isolates$GEN
))),