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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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6
inst/tinytest/test-count.R
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@ -29,7 +29,7 @@
expect_equal(count_resistant(example_isolates$AMX), count_R(example_isolates$AMX))
expect_equal(count_susceptible(example_isolates$AMX), count_SI(example_isolates$AMX))
expect_equal(count_all(example_isolates$AMX), n_rsi(example_isolates$AMX))
expect_equal(count_all(example_isolates$AMX), n_sir(example_isolates$AMX))
# AMX resistance in `example_isolates`
expect_equal(count_R(example_isolates$AMX), 804)
@ -103,10 +103,10 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
)
)
# grouping in rsi_calc_df() (= backbone of rsi_df())
# grouping in sir_calc_df() (= backbone of sir_df())
expect_true("ward" %in% (example_isolates %>%
group_by(ward) %>%
select(ward, AMX, CIP, gender) %>%
rsi_df() %>%
sir_df() %>%
colnames()))
}