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Style code and document #647

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merged 1 commit into from
Jul 9, 2024
Merged

Style code and document #647

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5 changes: 3 additions & 2 deletions tests/testthat/fixtures/simulate-integration-test-data.R
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Original file line number Diff line number Diff line change
Expand Up @@ -36,12 +36,13 @@ on.exit(setwd(working_dir), add = TRUE)
# .RData files and save them into one file
om_input_list <- om_output_list <- em_input_list <-
vector(mode = "list", length = sim_num)
for (i in 1:sim_num){
for (i in 1:sim_num) {
load(file.path(maindir, "FIMS_100iter", "output", "OM", paste0("OM", i, ".RData")))
om_input_list[[i]] <- om_input
om_output_list[[i]] <- om_output
em_input_list[[i]] <- em_input
}

save(om_input_list, om_output_list, em_input_list,
file = test_path("fixtures", "integration_test_data.RData"))
file = test_path("fixtures", "integration_test_data.RData")
)
9 changes: 4 additions & 5 deletions tests/testthat/helper-integration-tests-setup.R
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Expand Up @@ -156,13 +156,12 @@ setup_and_run_FIMS <- function(iter_id,
CreateTMBModel()
# Create parameter list from Rcpp modules
parameters <- list(p = get_fixed())
obj <- TMB::MakeADFun(data = list(), parameters, DLL = "FIMS", silent=TRUE)

if (estimation_mode == TRUE){
obj <- TMB::MakeADFun(data = list(), parameters, DLL = "FIMS", silent = TRUE)

if (estimation_mode == TRUE) {
opt <- with(obj, optim(par, fn, gr,
method = "BFGS",
control = list(maxit = 1000000, reltol = 1e-15)
method = "BFGS",
control = list(maxit = 1000000, reltol = 1e-15)
))
}
# Call report using MLE parameter values, or
Expand Down
26 changes: 16 additions & 10 deletions tests/testthat/test-parallel-with-snowfall.R
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Expand Up @@ -22,13 +22,13 @@ for (i in 1:length(om_input_list)) {
om_input_list = om_input_list,
om_output_list = om_output_list,
em_input_list = em_input_list,
estimation_mode = TRUE)
estimation_mode = TRUE
)
}
end_time_serial <- Sys.time()
estimation_time_serial <- end_time_serial - start_time_serial

test_that("Run FIMS in parallel using {snowfall}", {

core_num <- parallel::detectCores() - 1
snowfall::sfInit(parallel = TRUE, cpus = core_num)
start_time_parallel <- Sys.time()
Expand All @@ -39,7 +39,8 @@ test_that("Run FIMS in parallel using {snowfall}", {
om_input_list,
om_output_list,
em_input_list,
TRUE)
TRUE
)

end_time_parallel <- Sys.time()

Expand All @@ -53,17 +54,22 @@ test_that("Run FIMS in parallel using {snowfall}", {

# Compare parameters in results:
# Verify that the results from both runs are equivalent.
expect_setequal(unname(unlist(lapply(results_parallel, `[[`, "parameters"))),
unname(unlist(lapply(estimation_results_serial, `[[`, "parameters"))))
expect_setequal(
unname(unlist(lapply(results_parallel, `[[`, "parameters"))),
unname(unlist(lapply(estimation_results_serial, `[[`, "parameters")))
)

# Compare sdr_fixed values in results:
# Verify that the results from both runs are equivalent.
expect_setequal(unlist(lapply(results_parallel, `[[`, "sdr_fixed")),
unlist(lapply(estimation_results_serial, `[[`, "sdr_fixed")))
expect_setequal(
unlist(lapply(results_parallel, `[[`, "sdr_fixed")),
unlist(lapply(estimation_results_serial, `[[`, "sdr_fixed"))
)

# Compare sdr_report values in results:
# Verify that the results from both runs are equivalent.
expect_setequal(unlist(lapply(results_parallel, `[[`, "sdr_report")),
unlist(lapply(estimation_results_serial, `[[`, "sdr_report")))

expect_setequal(
unlist(lapply(results_parallel, `[[`, "sdr_report")),
unlist(lapply(estimation_results_serial, `[[`, "sdr_report"))
)
})
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