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replaced bactid by mo

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dr. M.S. (Matthijs) Berends
2018-08-31 13:36:19 +02:00
parent 98ff131680
commit 5965d3c794
41 changed files with 786 additions and 411 deletions
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16
tests/testthat/test-portion.R
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@@ -122,7 +122,7 @@ test_that("old rsi works", {
test_that("prediction of rsi works", {
amox_R <- septic_patients %>%
filter(bactid == "ESCCOL") %>%
filter(mo == "ESCCOL") %>%
rsi_predict(col_ab = "amox",
col_date = "date",
minimum = 10,
@@ -131,37 +131,37 @@ test_that("prediction of rsi works", {
# amox resistance will increase according to data set `septic_patients`
expect_true(amox_R[3] < amox_R[20])
expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
model = "binomial",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
model = "loglin",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
model = "lin",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
model = "INVALID MODEL",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
col_ab = "NOT EXISTING COLUMN",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
col_ab = "amox",
col_date = "NOT EXISTING COLUMN",
info = TRUE))
# almost all E. coli are mero S in the Netherlands :)
expect_error(resistance_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
expect_error(resistance_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
col_ab = "mero",
col_date = "date",
info = TRUE))