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update to septic_patients, speed improvements

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-07-25 14:17:04 +02:00
parent 03a3cb397b
commit d9e204031d
26 changed files with 273 additions and 233 deletions
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16
tests/testthat/test-first_isolate.R
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@ -8,9 +8,9 @@ test_that("first isolates work", {
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
info = FALSE),
info = TRUE),
na.rm = TRUE),
1959)
1326)
# septic_patients contains 1962 out of 2000 first *weighted* isolates
expect_equal(
@ -24,8 +24,8 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1962)
# and 1997 when using points
1421)
# and 1961 when using points
expect_equal(
suppressWarnings(
sum(
@ -37,7 +37,7 @@ test_that("first isolates work", {
type = "points",
info = TRUE),
na.rm = TRUE)),
1997)
1425)
# septic_patients contains 1732 out of 2000 first non-ICU isolates
expect_equal(
@ -50,7 +50,7 @@ test_that("first isolates work", {
info = TRUE,
icu_exclude = TRUE),
na.rm = TRUE),
1732)
1171)
# set 1500 random observations to be of specimen type 'Urine'
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
@ -59,7 +59,7 @@ test_that("first isolates work", {
first_isolate(tbl = mutate(septic_patients,
specimen = if_else(row_number() %in% random_rows,
"Urine",
"Unknown")),
"Other")),
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
@ -74,7 +74,7 @@ test_that("first isolates work", {
first_isolate(tbl = mutate(septic_patients,
specimen = if_else(row_number() %in% random_rows,
"Urine",
"Unknown")),
"Other")),
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",