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(v1.6.0.9023) new unit test flow

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dr. M.S. (Matthijs) Berends
2021-05-13 19:31:47 +02:00
parent 655b813e99
commit aeea00881e
34 changed files with 408 additions and 355 deletions
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50
tests/testthat/test-resistance_predict.R
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@ -28,65 +28,71 @@ context("resistance_predict.R")
test_that("prediction of rsi works", {
skip_on_cran()
library(dplyr)
expect_output(AMX_R <- example_isolates %>%
filter(mo == "B_ESCHR_COLI") %>%
rsi_predict(col_ab = "AMX",
col_date = "date",
model = "binomial",
minimum = 10,
info = TRUE) %>%
pull("value"))
# AMX resistance will increase according to data set `example_isolates`
expect_true(AMX_R[3] < AMX_R[20])
expect_output(x <- suppressMessages(resistance_predict(example_isolates, col_ab = "AMX", year_min = 2010, model = "binomial", info = TRUE)))
if (require("dplyr")) {
expect_output(AMX_R <- example_isolates %>%
filter(mo == "B_ESCHR_COLI") %>%
rsi_predict(col_ab = "AMX",
col_date = "date",
model = "binomial",
minimum = 10,
info = TRUE) %>%
pull("value"))
# AMX resistance will increase according to data set `example_isolates`
expect_true(AMX_R[3] < AMX_R[20])
}
expect_output(x <- suppressMessages(resistance_predict(example_isolates,
col_ab = "AMX",
year_min = 2010,
model = "binomial",
info = TRUE)))
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(plot(x))
expect_silent(ggplot_rsi_predict(x))
expect_silent(ggplot(x))
expect_error(ggplot_rsi_predict(example_isolates))
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
expect_output(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
expect_output(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "loglin",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
expect_output(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "lin",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "INVALID MODEL",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
expect_error(rsi_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(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
expect_error(rsi_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(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE))
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
col_ab = "AMX",
col_date = "date",
info = TRUE))
# almost all E. coli are MEM S in the Netherlands :)
expect_error(resistance_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
expect_error(resistance_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "MEM",
col_date = "date",