tests/testthat/test-extract.R
In IALSA/IalsaSynthesis: Synthesizing Information Across Collaborating Research
library(testthat)
path_1 <- system.file(package="IalsaSynthesis", "test-data/2015-portland/b1_female_a_grip_categories_4.out")
path_2 <- system.file(package="IalsaSynthesis", "test-data/2015-portland/b1_female_aehplus_gait_grip.out")
path_3 <- system.file(package="IalsaSynthesis", "test-data/2015-portland/b1_female_aehplus_grip_gait.out")
output_1 <- readr::read_file(path_1)
output_2 <- readr::read_file(path_2)
output_3 <- readr::read_file(path_3)
# MplusAutomation::extractModelSummaries(path_1)
# MplusAutomation::extractModelParameters(path_1)
error_path <- system.file(package="IalsaSynthesis", "test-data/2015-portland/has-errors/b1_female_a_fev_mmse_5.out")
# m <- MplusAutomation::readModels(error_path)
# b1_female_a_fev_mmse_5.out
# . THIS MAY BE DUE TO THE STARTING\r\n
# VALUES BUT MAY ALSO BE AN INDICATION OF MODEL NONIDENTIFICATION. THE\r\n
# CONDITION NUMBER IS 0.787D-10. PROBLEM INVOLVING THE FOLLOWING PARAMETER:\r\n
# Parameter 24, R_RES_PC\r\n\r\n\r\nTHE MODEL ESTIMATION TERMINATED NORMALLY\r\n\r\n\r\n\r\nMODEL FIT INFORMATION\r\n\r\nNumber of Free Parameters
snippet <- readr::read_file(error_path)
# snippet <- "TRUSTWORTHY FOR SOME PARAMETERS DUE TO A NON-POSITIVE DEFINITE\r\n FIRST-ORDER DERIVATIVE PRODUCT MATRIX. THIS MAY BE DUE TO THE STARTING\r\n VALUES BUT MAY ALSO BE AN INDICATION OF MODEL NONIDENTIFICATION. THE\r\n CONDITION NUMBER IS 0.787D-10. PROBLEM INVOLVING THE FOLLOWING PARAMETER:\r\n Parameter 24, R_RES_PC\r\n\r\n\r\nTHE "
# snippet <- " Parameter 24, R_RES_PC"
# gsub(".+THE STANDARD ERRORS OF THE MODEL PARAMETER ESTIMATES MAY NOT BE\r\n TRUSTWORTHY FOR SOME PARAMETERS DUE TO A NON-POSITIVE DEFINITE\r\n FIRST-ORDER DERIVATIVE PRODUCT MATRIX\\. THIS MAY BE DUE TO THE STARTING\r\n VALUES BUT MAY ALSO BE AN INDICATION OF MODEL NONIDENTIFICATION\\. THE\r\n CONDITION NUMBER IS\\s+(.+?)\\. PROBLEM INVOLVING THE FOLLOWING PARAMETER:\r\n Parameter (\\d+), ([\\w_]+).+",
# gsub("(?s).+Parameter (\\d{2}), ([\\w_]+).*", "\\2", snippet, perl=TRUE)
gsub("(?s).+THE STANDARD ERRORS OF THE MODEL PARAMETER ESTIMATES MAY NOT BE\r\n TRUSTWORTHY FOR SOME PARAMETERS DUE TO A NON-POSITIVE DEFINITE\r\n FIRST-ORDER DERIVATIVE PRODUCT MATRIX\\. THIS MAY BE DUE TO THE STARTING\r\n VALUES BUT MAY ALSO BE AN INDICATION OF MODEL NONIDENTIFICATION\\. THE\r\n CONDITION NUMBER IS\\s+(.+?)\\. PROBLEM INVOLVING THE FOLLOWING PARAMETER:\r\n Parameter (\\d+), ([\\w_]+).+", "\\3: \\2 & \\1", snippet, perl=TRUE);
snippet <- "1998-2014 Muthen & Muthen"
gsub("19(\\d{2})-.+", "\\1", snippet, perl=TRUE)
txt <- "a test of capitalizing"
gsub("(\\w)(\\w*)", "\\1", txt, perl=TRUE)
# m$warnings
snippet_fit_1 <-
"THE MODEL ESTIMATION TERMINATED NORMALLY
MODEL FIT INFORMATION
Number of Free Parameters 23
Loglikelihood
H0 Value -21788.910
H0 Scaling Correction Factor 1.1594
for MLR
Information Criteria
Akaike (AIC) 43623.820
Bayesian (BIC) 43736.928
Sample-Size Adjusted BIC 43663.878
(n* = (n + 2) / 24)
MODEL RESULTS
Two-Tailed
Estimate S.E. Est./S.E. P-Value"
snippet_new_parameters <-
"New/Additional Parameters
R_IPIC 0.146 0.040 3.608 0.000
R_SPSC 0.038 0.235 0.161 0.872
R_RES_PC 0.051 0.033 1.566 0.117
QUALITY OF NUMERICAL RESULTS"
test_that("parameter_estimate", {
tolerance <- 0.001
expected_R_IPIC <- c(0.146, 0.040, 3.608, 0.000)
expected_R_SPSC <- c(0.038, 0.235, 0.161, 0.872)
expected_R_RES_PC <- c(0.051, 0.033, 1.566, 0.117)
# Retrieve values
observed_from_snippet_R_IPIC <- IalsaSynthesis::extract_named_wald("R_IPIC", snippet_new_parameters)
observed_from_file_R_IPIC <- IalsaSynthesis::extract_named_wald("R_IPIC", output_1)
observed_from_snippet_R_SPSC <- IalsaSynthesis::extract_named_wald("R_SPSC", snippet_new_parameters)
observed_from_file_R_SPSC <- IalsaSynthesis::extract_named_wald("R_SPSC", output_1)
observed_from_snippet_R_RES_PC <- IalsaSynthesis::extract_named_wald("R_RES_PC", snippet_new_parameters)
observed_from_file_R_RES_PC <- IalsaSynthesis::extract_named_wald("R_RES_PC", output_1)
# Compare values
expect_equal(as.numeric(observed_from_snippet_R_IPIC), expected_R_IPIC, info="The R_IPIC parameter should be correct.", tolerance=tolerance)
expect_equal(as.numeric(observed_from_file_R_IPIC), expected_R_IPIC, info="The R_IPIC parameter should be correct.", tolerance=tolerance)
expect_equal(as.numeric(observed_from_snippet_R_SPSC), expected_R_SPSC, info="The R_SPSC parameter should be correct.", tolerance=tolerance)
expect_equal(as.numeric(observed_from_file_R_SPSC), expected_R_SPSC, info="The R_SPSC parameter should be correct.", tolerance=tolerance)
expect_equal(as.numeric(observed_from_snippet_R_RES_PC), expected_R_RES_PC, info="The R_RES_PC parameter should be correct.", tolerance=tolerance)
expect_equal(as.numeric(observed_from_file_R_RES_PC), expected_R_RES_PC, info="The R_RES_PC parameter should be correct.", tolerance=tolerance)
})
test_that("Path Data File", {
expected_1 <- "radcMAP_wide.dat"
expected_2 <- "\"C:\\Users\\wuche\\Dropbox\\IALSA\\Data\\HABC-9999.dta.dat\"" #Notice this one has a fishy extension and enclosing quotes.
expected_3 <- "C:\\Users\\Andrea Zammit\\Desktop\\EASMaster.csv"
snippet_1 <- "INPUT INSTRUCTIONS
TITLE: M6 Pulmonary Function, Grip, Fully Conditional, Male
DATA: File = radcMAP_wide.dat;
VARIABLE: Names are
projid study_x scaled_to_x agreeableness conscientiousness extraversion"
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 <- 23
expected_2 <- 61
expected_3 <- 41
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 <- -21788.910
expected_2 <- -23971.552
expected_3 <- -2700.358
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 <- 1.1594
expected_2 <- 1.0763
expected_3 <- NA_real_
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_equal(observed_from_snippet_1, expected_1, info="The Scaling Correction Factor extracted from the snippet should be NA")
expect_equal(observed_from_file_1, expected_1, info="The Scaling Correction Factor extracted from the first output file should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_2, expected_2, info="The Scaling Correction Factor extracted from the second output file should be correct.", tolerance=tolerance)
expect_true(is.na(observed_from_file_3), info="The Scaling Correction Factor extracted from the third output file should be NA")
})
test_that("AIC", {
tolerance <- 0.001
expected_1 <- 43623.820
expected_2 <- 48065.105
expected_3 <- 5482.716
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 <- 43736.928
expected_2 <- 48447.544
expected_3 <- 5605.324
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 <- 43663.878
expected_2 <- 48253.714
expected_3 <- 5475.578
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)
})
IALSA/IalsaSynthesis documentation built on April 20, 2021, 3:06 p.m.
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library(testthat)
path_1 <- system.file(package="IalsaSynthesis", "test-data/2015-portland/b1_female_a_grip_categories_4.out")
path_2 <- system.file(package="IalsaSynthesis", "test-data/2015-portland/b1_female_aehplus_gait_grip.out")
path_3 <- system.file(package="IalsaSynthesis", "test-data/2015-portland/b1_female_aehplus_grip_gait.out")
output_1 <- readr::read_file(path_1)
output_2 <- readr::read_file(path_2)
output_3 <- readr::read_file(path_3)
# MplusAutomation::extractModelSummaries(path_1)
# MplusAutomation::extractModelParameters(path_1)
error_path <- system.file(package="IalsaSynthesis", "test-data/2015-portland/has-errors/b1_female_a_fev_mmse_5.out")
# m <- MplusAutomation::readModels(error_path)
# b1_female_a_fev_mmse_5.out
# . THIS MAY BE DUE TO THE STARTING\r\n
# VALUES BUT MAY ALSO BE AN INDICATION OF MODEL NONIDENTIFICATION. THE\r\n
# CONDITION NUMBER IS 0.787D-10. PROBLEM INVOLVING THE FOLLOWING PARAMETER:\r\n
# Parameter 24, R_RES_PC\r\n\r\n\r\nTHE MODEL ESTIMATION TERMINATED NORMALLY\r\n\r\n\r\n\r\nMODEL FIT INFORMATION\r\n\r\nNumber of Free Parameters
snippet <- readr::read_file(error_path)
# snippet <- "TRUSTWORTHY FOR SOME PARAMETERS DUE TO A NON-POSITIVE DEFINITE\r\n FIRST-ORDER DERIVATIVE PRODUCT MATRIX. THIS MAY BE DUE TO THE STARTING\r\n VALUES BUT MAY ALSO BE AN INDICATION OF MODEL NONIDENTIFICATION. THE\r\n CONDITION NUMBER IS 0.787D-10. PROBLEM INVOLVING THE FOLLOWING PARAMETER:\r\n Parameter 24, R_RES_PC\r\n\r\n\r\nTHE "
# snippet <- " Parameter 24, R_RES_PC"
# gsub(".+THE STANDARD ERRORS OF THE MODEL PARAMETER ESTIMATES MAY NOT BE\r\n TRUSTWORTHY FOR SOME PARAMETERS DUE TO A NON-POSITIVE DEFINITE\r\n FIRST-ORDER DERIVATIVE PRODUCT MATRIX\\. THIS MAY BE DUE TO THE STARTING\r\n VALUES BUT MAY ALSO BE AN INDICATION OF MODEL NONIDENTIFICATION\\. THE\r\n CONDITION NUMBER IS\\s+(.+?)\\. PROBLEM INVOLVING THE FOLLOWING PARAMETER:\r\n Parameter (\\d+), ([\\w_]+).+",
# gsub("(?s).+Parameter (\\d{2}), ([\\w_]+).*", "\\2", snippet, perl=TRUE)
gsub("(?s).+THE STANDARD ERRORS OF THE MODEL PARAMETER ESTIMATES MAY NOT BE\r\n TRUSTWORTHY FOR SOME PARAMETERS DUE TO A NON-POSITIVE DEFINITE\r\n FIRST-ORDER DERIVATIVE PRODUCT MATRIX\\. THIS MAY BE DUE TO THE STARTING\r\n VALUES BUT MAY ALSO BE AN INDICATION OF MODEL NONIDENTIFICATION\\. THE\r\n CONDITION NUMBER IS\\s+(.+?)\\. PROBLEM INVOLVING THE FOLLOWING PARAMETER:\r\n Parameter (\\d+), ([\\w_]+).+", "\\3: \\2 & \\1", snippet, perl=TRUE);
snippet <- "1998-2014 Muthen & Muthen"
gsub("19(\\d{2})-.+", "\\1", snippet, perl=TRUE)
txt <- "a test of capitalizing"
gsub("(\\w)(\\w*)", "\\1", txt, perl=TRUE)
# m$warnings
snippet_fit_1 <-
"THE MODEL ESTIMATION TERMINATED NORMALLY
MODEL FIT INFORMATION
Number of Free Parameters 23
Loglikelihood
H0 Value -21788.910
H0 Scaling Correction Factor 1.1594
for MLR
Information Criteria
Akaike (AIC) 43623.820
Bayesian (BIC) 43736.928
Sample-Size Adjusted BIC 43663.878
(n* = (n + 2) / 24)
MODEL RESULTS
Two-Tailed
Estimate S.E. Est./S.E. P-Value"
snippet_new_parameters <-
"New/Additional Parameters
R_IPIC 0.146 0.040 3.608 0.000
R_SPSC 0.038 0.235 0.161 0.872
R_RES_PC 0.051 0.033 1.566 0.117
QUALITY OF NUMERICAL RESULTS"
test_that("parameter_estimate", {
tolerance <- 0.001
expected_R_IPIC <- c(0.146, 0.040, 3.608, 0.000)
expected_R_SPSC <- c(0.038, 0.235, 0.161, 0.872)
expected_R_RES_PC <- c(0.051, 0.033, 1.566, 0.117)
# Retrieve values
observed_from_snippet_R_IPIC <- IalsaSynthesis::extract_named_wald("R_IPIC", snippet_new_parameters)
observed_from_file_R_IPIC <- IalsaSynthesis::extract_named_wald("R_IPIC", output_1)
observed_from_snippet_R_SPSC <- IalsaSynthesis::extract_named_wald("R_SPSC", snippet_new_parameters)
observed_from_file_R_SPSC <- IalsaSynthesis::extract_named_wald("R_SPSC", output_1)
observed_from_snippet_R_RES_PC <- IalsaSynthesis::extract_named_wald("R_RES_PC", snippet_new_parameters)
observed_from_file_R_RES_PC <- IalsaSynthesis::extract_named_wald("R_RES_PC", output_1)
# Compare values
expect_equal(as.numeric(observed_from_snippet_R_IPIC), expected_R_IPIC, info="The R_IPIC parameter should be correct.", tolerance=tolerance)
expect_equal(as.numeric(observed_from_file_R_IPIC), expected_R_IPIC, info="The R_IPIC parameter should be correct.", tolerance=tolerance)
expect_equal(as.numeric(observed_from_snippet_R_SPSC), expected_R_SPSC, info="The R_SPSC parameter should be correct.", tolerance=tolerance)
expect_equal(as.numeric(observed_from_file_R_SPSC), expected_R_SPSC, info="The R_SPSC parameter should be correct.", tolerance=tolerance)
expect_equal(as.numeric(observed_from_snippet_R_RES_PC), expected_R_RES_PC, info="The R_RES_PC parameter should be correct.", tolerance=tolerance)
expect_equal(as.numeric(observed_from_file_R_RES_PC), expected_R_RES_PC, info="The R_RES_PC parameter should be correct.", tolerance=tolerance)
})
test_that("Path Data File", {
expected_1 <- "radcMAP_wide.dat"
expected_2 <- "\"C:\\Users\\wuche\\Dropbox\\IALSA\\Data\\HABC-9999.dta.dat\"" #Notice this one has a fishy extension and enclosing quotes.
expected_3 <- "C:\\Users\\Andrea Zammit\\Desktop\\EASMaster.csv"
snippet_1 <- "INPUT INSTRUCTIONS
TITLE: M6 Pulmonary Function, Grip, Fully Conditional, Male
DATA: File = radcMAP_wide.dat;
VARIABLE: Names are
projid study_x scaled_to_x agreeableness conscientiousness extraversion"
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 <- 23
expected_2 <- 61
expected_3 <- 41
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 <- -21788.910
expected_2 <- -23971.552
expected_3 <- -2700.358
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 <- 1.1594
expected_2 <- 1.0763
expected_3 <- NA_real_
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_equal(observed_from_snippet_1, expected_1, info="The Scaling Correction Factor extracted from the snippet should be NA")
expect_equal(observed_from_file_1, expected_1, info="The Scaling Correction Factor extracted from the first output file should be correct.", tolerance=tolerance)
expect_equal(observed_from_file_2, expected_2, info="The Scaling Correction Factor extracted from the second output file should be correct.", tolerance=tolerance)
expect_true(is.na(observed_from_file_3), info="The Scaling Correction Factor extracted from the third output file should be NA")
})
test_that("AIC", {
tolerance <- 0.001
expected_1 <- 43623.820
expected_2 <- 48065.105
expected_3 <- 5482.716
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 <- 43736.928
expected_2 <- 48447.544
expected_3 <- 5605.324
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 <- 43663.878
expected_2 <- 48253.714
expected_3 <- 5475.578
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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