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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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22
inst/tinytest/test-resistance_predict.R
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@ -30,7 +30,7 @@
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_stdout(AMX_R <- example_isolates %>%
filter(mo == "B_ESCHR_COLI") %>%
rsi_predict(
sir_predict(
col_ab = "AMX",
col_date = "date",
model = "binomial",
@ -51,25 +51,25 @@ expect_stdout(x <- suppressMessages(resistance_predict(example_isolates,
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(plot(x))
if (AMR:::pkg_is_available("ggplot2")) {
expect_silent(ggplot_rsi_predict(x))
expect_silent(ggplot_sir_predict(x))
expect_silent(autoplot(x))
expect_error(ggplot_rsi_predict(example_isolates))
expect_error(ggplot_sir_predict(example_isolates))
}
expect_stdout(rsi_predict(
expect_stdout(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "AMX",
col_date = "date",
info = TRUE
))
expect_stdout(rsi_predict(
expect_stdout(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "loglin",
col_ab = "AMX",
col_date = "date",
info = TRUE
))
expect_stdout(rsi_predict(
expect_stdout(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "lin",
col_ab = "AMX",
@ -77,34 +77,34 @@ expect_stdout(rsi_predict(
info = TRUE
))
expect_error(rsi_predict(
expect_error(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "INVALID MODEL",
col_ab = "AMX",
col_date = "date",
info = TRUE
))
expect_error(rsi_predict(
expect_error(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "NOT EXISTING COLUMN",
col_date = "date",
info = TRUE
))
expect_error(rsi_predict(
expect_error(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE
))
expect_error(rsi_predict(
expect_error(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE
))
expect_error(rsi_predict(
expect_error(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
col_ab = "AMX",
col_date = "date",