Nothing
library(testthat)
context("Extract")
path_1 <- base::file.path(devtools::inst(name="IalsaSynthesis"), "test_data/2015-portland/b1_female_ae_muscle_fluid_grip_trailsb.out")
path_2 <- base::file.path(devtools::inst(name="IalsaSynthesis"), "test_data/2015-portland/b1_male_aehplus_muscle_memory_grip_logicalmemory.out")
path_3 <- base::file.path(devtools::inst(name="IalsaSynthesis"), "test_data/2015-portland/u1_male_aehplus_muscle_noCog_hand_noCogSpec.out")
output_1 <- readr::read_file(path_1)
output_2 <- readr::read_file(path_2)
output_3 <- readr::read_file(path_3)
snippet_fit_1 <- "
MODEL FIT INFORMATION
Number of Free Parameters 25
Loglikelihood
H0 Value -11183.730
Information Criteria
Akaike (AIC) 22417.460
Bayesian (BIC) 22526.536
Sample-Size Adjusted BIC 22447.171
(n* = (n + 2) / 24)
MODEL RESULTS
Two-Tailed"
test_that("Path Data File", {
expected_1 <- "C:\\Users\\Dragon Hat\\Desktop\\CbaMaster.csv"
expected_2 <- "C:\\Users\\Andrea Zammit\\Desktop\\EASMaster.csv"
expected_3 <- "\"C:\\Users\\wuche\\Dropbox\\IALSA\\Data\\HABC-9999.dta.dat\"" #Notice this one has a fishy extension and enclosing quotes.
snippet_1 <- " TITLE: m5, b1,trails, peak flow, LGM,ae Conditional,female
DATA: File = C:\\Users\\Dragon Hat\\Desktop\\CbaMaster.csv;
VARIABLE: Names are
! demographics
SubjectID Sex Ethnic Caus DemEver Bagesq deathage DEMO23 Educyrs Status "
observed_from_snippet_1 <- IalsaSynthesis::extract_output_filename(snippet_1)
observed_from_file_1 <- IalsaSynthesis::extract_output_filename(output_1)
observed_from_file_2 <- IalsaSynthesis::extract_output_filename(output_2)
observed_from_file_3 <- IalsaSynthesis::extract_output_filename(output_3)
expect_equal(observed_from_snippet_1, expected_1, "The data file path extracted from the snippet should be correct.")
expect_equal(observed_from_file_1, expected_1, "The data file path extracted from the first output file should be correct.")
expect_equal(observed_from_file_2, expected_2, "The data file path extracted from the second output file should be correct.")
expect_equal(observed_from_file_3, expected_3, "The data file path extracted from the third output file should be correct.")
})
test_that("Free Parameter Count", {
tolerance <- 0
expected_1 <- 25
expected_2 <- 41
expected_3 <- 18
observed_from_snippet_1 <- IalsaSynthesis::extract_free_parameter_count(snippet_fit_1)
observed_from_file_1 <- IalsaSynthesis::extract_free_parameter_count(output_1)
observed_from_file_2 <- IalsaSynthesis::extract_free_parameter_count(output_2)
observed_from_file_3 <- IalsaSynthesis::extract_free_parameter_count(output_3)
expect_equal(observed_from_snippet_1, expected_1, info="The free parameter count extracted from the snippet should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_1, expected_1, info="The free parameter count extracted from the first output file should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_2, expected_2, info="The free parameter count extracted from the second output file should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_3, expected_3, info="The free parameter count extracted from the third output file should be correct.", tolerance=tolerance)
})
test_that("Loglikelihood", {
tolerance <- 0.001
expected_1 <- -11183.730
expected_2 <- -1767.351
expected_3 <- -20217.511
observed_from_snippet_1 <- IalsaSynthesis::extract_loglikelihood(snippet_fit_1)
observed_from_file_1 <- IalsaSynthesis::extract_loglikelihood(output_1)
observed_from_file_2 <- IalsaSynthesis::extract_loglikelihood(output_2)
observed_from_file_3 <- IalsaSynthesis::extract_loglikelihood(output_3)
expect_equal(observed_from_snippet_1, expected_1, info="The free parameter count extracted from the snippet should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_1, expected_1, info="The loglikelihood extracted from the first output file should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_2, expected_2, info="The loglikelihood extracted from the second output file should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_3, expected_3, info="The loglikelihood extracted from the third output file should be correct.", tolerance=tolerance)
})
test_that("Scaling Correction Factor", {
tolerance <- 0.001
# expected_1 <- NA_real_
# expected_2 <- NA_real_
expected_3 <- 1.3467
observed_from_snippet_1 <- IalsaSynthesis::extract_scaling_correction(snippet_fit_1)
observed_from_file_1 <- IalsaSynthesis::extract_scaling_correction(output_1)
observed_from_file_2 <- IalsaSynthesis::extract_scaling_correction(output_2)
observed_from_file_3 <- IalsaSynthesis::extract_scaling_correction(output_3)
expect_true(is.na(observed_from_snippet_1), info="The Scaling Correction Factor extracted from the snippet should be NA")
expect_true(is.na(observed_from_file_1), info="The Scaling Correction Factor extracted from the first output file should be NA")
expect_true(is.na(observed_from_file_2), info="The Scaling Correction Factor extracted from the second output file should be NA")
expect_equal(observed_from_file_3, expected_3, info="The Scaling Correction Factor extracted from the third output file should be correct.", tolerance=tolerance)
})
test_that("AIC", {
tolerance <- 0.001
expected_1 <- 22417.460
expected_2 <- 3616.701
expected_3 <- 40471.022
observed_from_snippet_1 <- IalsaSynthesis::extract_aic(snippet_fit_1)
observed_from_file_1 <- IalsaSynthesis::extract_aic(output_1)
observed_from_file_2 <- IalsaSynthesis::extract_aic(output_2)
observed_from_file_3 <- IalsaSynthesis::extract_aic(output_3)
expect_equal(observed_from_snippet_1, expected_1, info="The AIC extracted from the snippet should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_1, expected_1, info="The AIC extracted from the first output file should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_2, expected_2, info="The AIC extracted from the second output file should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_3, expected_3, info="The AIC extracted from the third output file should be correct.", tolerance=tolerance)
})
test_that("BIC", {
tolerance <- 0.001
expected_1 <- 22526.536
expected_2 <- 3710.044
expected_3 <- 40566.198
observed_from_snippet_1 <- IalsaSynthesis::extract_bic(snippet_fit_1)
observed_from_file_1 <- IalsaSynthesis::extract_bic(output_1)
observed_from_file_2 <- IalsaSynthesis::extract_bic(output_2)
observed_from_file_3 <- IalsaSynthesis::extract_bic(output_3)
expect_equal(observed_from_snippet_1, expected_1, info="The BIC extracted from the snippet should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_1, expected_1, info="The BIC extracted from the first output file should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_2, expected_2, info="The BIC extracted from the second output file should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_3, expected_3, info="The BIC extracted from the third output file should be correct.", tolerance=tolerance)
})
test_that("BIC: Sample-Size Adjusted", {
tolerance <- 0.001
expected_1 <- 22447.171
expected_2 <- 3580.867
expected_3 <- 40509.018
observed_from_snippet_1 <- IalsaSynthesis::extract_bic_adjusted(snippet_fit_1)
observed_from_file_1 <- IalsaSynthesis::extract_bic_adjusted(output_1)
observed_from_file_2 <- IalsaSynthesis::extract_bic_adjusted(output_2)
observed_from_file_3 <- IalsaSynthesis::extract_bic_adjusted(output_3)
expect_equal(observed_from_snippet_1, expected_1, info="The Sample-Size Adjusted BIC extracted from the snippet should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_1, expected_1, info="The Sample-Size Adjusted BIC extracted from the first output file should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_2, expected_2, info="The Sample-Size Adjusted BIC extracted from the second output file should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_3, expected_3, info="The Sample-Size Adjusted BIC extracted from the third output file should be correct.", tolerance=tolerance)
})
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