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first inclusion of ITIS data

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dr. M.S. (Matthijs) Berends
2018-09-24 23:33:29 +02:00
parent df5d82fff3
commit 9c566585b0
29 changed files with 734 additions and 466 deletions
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40
tests/testthat/test-portion.R
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@@ -2,8 +2,8 @@ context("portion.R")
test_that("portions works", {
# amox resistance in `septic_patients`
expect_equal(portion_R(septic_patients$amox), 0.6603, tolerance = 0.0001)
expect_equal(portion_I(septic_patients$amox), 0.0030, tolerance = 0.0001)
expect_equal(portion_R(septic_patients$amox), 0.662, tolerance = 0.0001)
expect_equal(portion_I(septic_patients$amox), 0.003, tolerance = 0.0001)
expect_equal(1 - portion_R(septic_patients$amox) - portion_I(septic_patients$amox),
portion_S(septic_patients$amox))
expect_equal(portion_R(septic_patients$amox) + portion_I(septic_patients$amox),
@@ -12,17 +12,17 @@ test_that("portions works", {
portion_SI(septic_patients$amox))
expect_equal(septic_patients %>% portion_S(amcl),
0.673,
0.6706853,
tolerance = 0.001)
expect_equal(septic_patients %>% portion_S(amcl, gent),
0.921,
0.9202373,
tolerance = 0.001)
# amcl+genta susceptibility around 92.1%
expect_equal(suppressWarnings(rsi(septic_patients$amcl,
septic_patients$gent,
interpretation = "S")),
0.9208777,
0.9202373,
tolerance = 0.000001)
# percentages
@@ -35,7 +35,7 @@ test_that("portions works", {
total = n()) %>%
pull(n) %>%
sum(),
1404)
1409)
# count of cases
expect_equal(septic_patients %>%
@@ -47,7 +47,7 @@ test_that("portions works", {
combination_p = portion_S(cipr, gent, as_percent = TRUE),
combination_n = n_rsi(cipr, gent)) %>%
pull(combination_n),
c(202, 482, 201, 499))
c(202, 488, 201, 499))
expect_warning(portion_R(as.character(septic_patients$amcl)))
expect_warning(portion_S(as.character(septic_patients$amcl)))
@@ -57,7 +57,7 @@ test_that("portions works", {
septic_patients$gent)))
expect_equal(suppressWarnings(n_rsi(as.character(septic_patients$amcl,
septic_patients$gent))),
1570)
1576)
# check for errors
expect_error(portion_IR("test", minimum = "test"))
@@ -84,15 +84,15 @@ test_that("portions works", {
test_that("old rsi works", {
# amox resistance in `septic_patients` should be around 66.33%
expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.6633, tolerance = 0.0001)
expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.6633, tolerance = 0.0001)
expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.665, tolerance = 0.0001)
expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.665, tolerance = 0.0001)
# pita+genta susceptibility around 98.09%
expect_equal(suppressWarnings(rsi(septic_patients$pita,
septic_patients$gent,
interpretation = "S",
info = TRUE)),
0.9535,
0.9540412,
tolerance = 0.0001)
# count of cases
@@ -108,7 +108,7 @@ test_that("old rsi works", {
as_percent = TRUE, warning = FALSE)),
combination_n = n_rsi(cipr, gent)) %>%
pull(combination_n),
c(202, 482, 201, 499))
c(202, 488, 201, 499))
# portion_df
expect_equal(
@@ -122,7 +122,7 @@ test_that("old rsi works", {
test_that("prediction of rsi works", {
amox_R <- septic_patients %>%
filter(mo == "ESCCOL") %>%
filter(mo == "B_ESCHR_COL") %>%
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, mo == "ESCCOL"),
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
model = "binomial",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
model = "loglin",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
model = "lin",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
model = "INVALID MODEL",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
col_ab = "NOT EXISTING COLUMN",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
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, mo == "ESCCOL"),
expect_error(resistance_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
col_ab = "mero",
col_date = "date",
info = TRUE))