The validity of the {ramnog} framework is ensured on several levels:
- Unit test individual functions/modules in all packages
- Integration/end-to-end testing to ensure the interactions between individual functions/modules (that have been unit tested) are as expected
- CI/CD to ensure changes are properly tested and deployed to the users
Unit testing
Each package contains the unit tests for the functionality that package is responsible for. This means, for example, it is the responsibility of the unit-tests in {chefStats} to ensure that the statistical functions written in chefStats produce the result they are supposed to produce.
Integration testing
Integration testing verifies the framework produces the expected results
The integration testing is done via the {testthat} framework, and are essentially unit-tests that cover many different units
The goal is to compare the results of an analysis run via ramnog with the expected results done from a manual calculation of the same analysis.
For example, below is the unit test to ensure the results of an endpoint definition defined and run via chef match those calculated manually
Example of integration test using {testthat} framework
testthat::test_that("Valide stats when one strata level is not found",
{
# SETUP -------------------------------------------------------------------
testr::create_local_project()
mk_adae <- function(study_metadata) {
adsl <- pharmaverseadam::adsl |> data.table::setDT()
adae <- pharmaverseadam::adae |> data.table::setDT()
adae_out <-
merge(adsl, adae[, c(setdiff(names(adae), names(adsl)), "USUBJID"), with =
F], by = "USUBJID", all = TRUE)
adae_out[TRT01A %in% c('Placebo', 'Xanomeline High Dose'),]
}
mk_ep_def <- function() {
chef::mk_endpoint_str(
study_metadata = list(),
pop_var = "SAFFL",
pop_value = "Y",
treatment_var = "TRT01A",
treatment_refval = "Xanomeline High Dose",
stratify_by = list(c("SEX")),
data_prepare = mk_adae,
endpoint_label = "A",
custom_pop_filter = "SEX == 'F'",
group_by = list(list(AESEV = c())),
stat_by_strata_by_trt = list(
"N" = chefStats::n_subj,
"E" = chefStats::n_event,
"N subj E" = chefStats::n_subj_event
),
stat_by_strata_across_trt = list("RR" = chefStats::RR,
"OR" = chefStats::OR),
stat_across_strata_across_trt = list("P-interaction" = chefStats::p_val_interaction)
)
}
chef::use_chef(
pipeline_dir = "pipeline",
r_functions_dir = "R/",
pipeline_id = "01",
mk_endpoint_def_fn = mk_ep_def,
mk_adam_fn = list(mk_adae)
)
# ACT ---------------------------------------------------------------------
targets::tar_make()
targets::tar_load(ep_stat)
# EXPECT ------------------------------------------------------------------
# Manually calculated expected results
x <- mk_adae(study_metadata = NULL)
# Relative Risk
actual <-
ep_stat[endpoint_group_filter == "AESEV == \"SEVERE\"" &
fn_name == "RR" &
stat_filter == "SEX == \"F\"" & stat_result_label == "RR", stat_result_value]
x1 <- x[SEX == "F" & SAFFL == "Y"]
x1[, event := FALSE]
x1[AESEV == "SEVERE", event := TRUE] |> data.table::setorder(-event)
x1_unique <-
unique(x1, by = "USUBJID", fromLast = FALSE)
two_by_two <-
x1_unique[, .N, by = .(TRT01A, event)][order(TRT01A, event)]
# Outcome, exposed
a <-
two_by_two[TRT01A == "Xanomeline High Dose" &
(event), N]
# No outcome, exposed
b <-
two_by_two[TRT01A == "Xanomeline High Dose" &
!(event), N]
# Outcome, not exposed
c <-
two_by_two[TRT01A == "Placebo" &
(event), N]
# No outcome, not exposed
d <-
two_by_two[TRT01A == "Placebo" &
!(event), N]
expected <- (a / sum(a, b)) / (c / sum(c, d))
expect_identical(actual, expected)
# Number of Events
actual <-
ep_stat[endpoint_group_filter == "AESEV == \"SEVERE\"" &
fn_name == "E" &
strata_var == "SEX"]
expected <-
x1[(event), .N, by = .(TRT01A)][order(TRT01A)][, as.double(N)]
expect_identical(actual$stat_result_value, expected)
})
#> v Setting active project to '/tmp/Rtmp2Qer9r/testproj1c8318edb087'
#> v Writing 'R/packages.R'
#> v Writing 'pipeline/pipeline_01.R'
#> * Edit 'pipeline/pipeline_01.R'
#> * Edit 'R/mk_adae.R'
#> i Renaming "mk_ep_def" to "mk_endpoint_def.R"
#>
#> * Edit 'R/mk_endpoint_def.R'
#> Loading required package: targets
#> ▶ dispatched target ep
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#> ▶ dispatched target ep_rejected
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#> ▶ ended pipeline [0.839 seconds]
#> v Restoring original working directory: '/home/runner/work/ramnog/ramnog/vignettes/'
#> v Setting active project to '<no active project>'
#> v Deleting temporary project: '/tmp/Rtmp2Qer9r/testproj1c8318edb087/'
#> Test passedCI/CD
Please see the DevOps vignette for details on the CI/CD infrastructure.