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(v0.7.1.9063) septic_patients -> example_isolates

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dr. M.S. (Matthijs) Berends
2019-08-27 16:45:42 +02:00
parent 7a6fce4eb8
commit 93be16484b
92 changed files with 1143 additions and 818 deletions
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26
tests/testthat/test-resistance_predict.R
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@ -22,7 +22,7 @@
context("resistance_predict.R")
test_that("prediction of rsi works", {
AMX_R <- septic_patients %>%
AMX_R <- example_isolates %>%
filter(mo == "B_ESCHR_COL") %>%
rsi_predict(col_ab = "AMX",
col_date = "date",
@ -30,57 +30,57 @@ test_that("prediction of rsi works", {
minimum = 10,
info = TRUE) %>%
pull("value")
# AMX resistance will increase according to data set `septic_patients`
# AMX resistance will increase according to data set `example_isolates`
expect_true(AMX_R[3] < AMX_R[20])
x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010, model = "binomial")
x <- resistance_predict(example_isolates, col_ab = "AMX", year_min = 2010, model = "binomial")
plot(x)
ggplot_rsi_predict(x)
expect_error(ggplot_rsi_predict(septic_patients))
expect_error(ggplot_rsi_predict(example_isolates))
library(dplyr)
expect_output(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
model = "binomial",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
model = "loglin",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
model = "lin",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
model = "INVALID MODEL",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
model = "binomial",
col_ab = "NOT EXISTING COLUMN",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
model = "binomial",
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE))
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE))
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
col_ab = "AMX",
col_date = "date",
info = TRUE))
# almost all E. coli are MEM S in the Netherlands :)
expect_error(resistance_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_error(resistance_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
model = "binomial",
col_ab = "MEM",
col_date = "date",