context("Argument validation")
test_that("Invalid arguments are picked up", {
expect_error(Adjusted_inv_sinh_CI_OR_2x2(-ritland_2007), "counts")
expect_error(Adjusted_inv_sinh_CI_OR_2x2(ritland_2007, -3), "positive")
expect_error(Adjusted_inv_sinh_CI_OR_2x2(ritland_2007, alpha = 1.1), "prob")
expect_error(Adjusted_inv_sinh_CI_ratio_2x2(perondi_2004, alpha = 1.1), "pro")
expect_error(Adjusted_log_CI_2x2(perondi_2004, alpha = 1.1), "pr")
expect_error(AgrestiCaffo_CI_2x2(perondi_2004, alpha = 1.1), "pr")
expect_error(AgrestiCoull_CI_1x2(perondi_2004, alpha = 1.1), "pr")
expect_error(Arcsine_CI_1x2(perondi_2004, alpha = 1.1), "pr")
expect_error(
BaptistaPike_exact_conditional_CI_2x2(perondi_2004, alpha = 1.1), "pr"
)
expect_error(BaptistaPike_midP_CI_2x2(perondi_2004, alpha = 1.1), "pr")
expect_error(Bhapkar_test_paired_cxc(-perondi_2004), "counts")
expect_error(
Blaker_exact_CI_1x2(ligarden_2010["X"], ligarden_2010["n"], alpha = 1.1),
"pr"
)
expect_error(
Blaker_exact_test_1x2(ligarden_2010["X"], ligarden_2010["n"], pi0 = 1.1),
"pr"
)
expect_error(
Blaker_midP_CI_1x2(ligarden_2010["X"], ligarden_2010["n"], alpha = 1.1),
"pr"
)
expect_error(
Blaker_midP_test_1x2(ligarden_2010["X"], ligarden_2010["n"], pi0 = 1.1),
"pr"
)
expect_error(
BonettPrice_hybrid_Wilson_score_CI_CC_paired_2x2(cavo_2012, -0.1), "prob"
)
expect_error(
BonettPrice_hybrid_Wilson_score_CI_paired_2x2(cavo_2012, -0.1), "prob"
)
expect_error(Bonferroni_type_CIs_paired_cxc(cavo_2012, -0.1), "prob")
expect_error(Bonferroni_type_CIs_rxc(cavo_2012, -0.1), "prob")
expect_error(Brant_test_2xc(-fontanella_2008), "counts")
expect_error(
BreslowDay_homogeneity_test_stratified_2x2(-fontanella_2008), "counts"
)
expect_error(Chacko_test_1xc(-fontanella_2008), "counts")
expect_error(
ClopperPearson_exact_CI_1x2_beta_version(
ligarden_2010["X"], ligarden_2010["n"], 1.1
),
"pr"
)
expect_error(
ClopperPearson_exact_CI_1x2(ligarden_2010["X"], ligarden_2010["n"], 1.1),
"pr"
)
expect_error(
ClopperPearson_midP_CI_1x2(ligarden_2010["X"], ligarden_2010["n"], 1.1),
"pr"
)
expect_error(Cochran_Q_test_stratified_2x2(hine_1989, "probit"), "logit")
expect_error(Cochran_Q_test_stratified_2x2(hine_1989, "log", "AA"), "MH")
expect_error(CochranArmitage_CI_rx2(indredavik_2008, 1:5, 2), "prob")
expect_error(
CochranArmitage_exact_cond_midP_tests_rx2(-indredavik_2008, 1:5),
"Should be counts"
)
expect_error(
CochranArmitage_MH_tests_rx2(-indredavik_2008, 1:5),
"Should be counts"
)
expect_error(
CochranMantelHaenszel_test_stratified_2x2(-hine_1989), "Should be counts"
)
expect_error(
Cornfield_exact_conditional_CI_2x2(-hine_1989), "Should be counts"
)
expect_error(
Cornfield_midP_CI_2x2(tea, 1.1), "Should be probability"
)
expect_error(
Cumulative_models_for_2xc(lydersen_2012a, alpha = 1.1), "probability"
)
expect_error(
Cumulative_models_for_2xc(lydersen_2012a, "log"),
"linkfunction contains invalid values. Should be logit, probit or identity"
)
expect_error(
Cumulative_models_for_rxc(lydersen_2012a, "logit", alpha = 1.1), "probability"
)
expect_error(
Cumulative_models_for_rxc(lydersen_2012a, "log"),
"linkfunction contains invalid values. Should be logit, probit or identity"
)
expect_error(
Exact_binomial_test_1x2(ligarden_2010["X"], ligarden_2010["n"], pi0 = -0.5),
"Should be probability"
)
expect_error(
Exact_cond_midP_linear_rank_tests_2xc(-lydersen_2012a), "Should be counts"
)
expect_error(
Exact_cond_midP_tests_rxc(-table_7.3), "Should be counts"
)
expect_error(
Exact_cond_midP_unspecific_ordering_rx2(t(lydersen_2012a), "dec"),
"Should be increasing or decreasing"
)
expect_error(
Exact_cond_midP_unspecific_ordering_rx2(t(lydersen_2012a)),
"direction cannot be empty"
)
expect_error(
Exact_multinomial_test_1xc(snp6498169$subset$n, -snp6498169$subset$pi0),
"Should be probability"
)
expect_error(
Exact_unconditional_test_2x2(tea, "LER"),
"Should be Pearson, LR, unpooled, Fisher."
)
expect_error(
Fisher_exact_test_2x2(tea, "Fisher"),
"Should be Pearson, hypergeometric, LR."
)
expect_error(
Fisher_midP_test_2x2(tea, "Fisher"),
"Should be Pearson, hypergeometric, LR."
)
expect_error(
FisherFreemanHalton_asymptotic_test_rxc(-table_7.3),
"Should be counts."
)
expect_error(
FleissEveritt_test_paired_cxc(-fleiss_2003),
"Should be counts."
)
expect_error(
FleissLevinPaik_test_paired_cxc(-peterson_2007[-4, -4]),
"Should be counts."
)
expect_error(
gamma_coefficient_rxc_bca(table_7.7, -80),
"nboot contains invalid values. Should be counts."
)
expect_error(
gamma_coefficient_rxc(-table_7.7),
"n contains invalid values. Should be counts."
)
expect_error(
Gart_adjusted_logit_CI_2x2(-lampasona_2013),
"n contains invalid values. Should be counts."
)
expect_error(
Gold_Wald_CIs_1xc(snp6498169$complete$n, 1.1),
"alpha contains invalid values. Should be probability."
)
expect_error(
Goodman_Wald_CIs_1xc(n = -snp6498169$complete$n),
"n contains invalid values. Should be counts."
)
expect_error(
Goodman_Wald_CIs_for_diffs_1xc(n = snp6498169$complete$n, .1, "Scheffield"),
"adjustment contains invalid values. Should be Bonferroni, Scheffe."
)
expect_error(
Goodman_Wilson_score_CIs_1xc(-snp6498169$complete$n),
"n contains invalid values. Should be counts."
)
expect_error(
Independence_smoothed_logit_CI_2x2(-ritland_2007),
"n contains invalid values. Should be counts."
)
expect_error(
Inv_sinh_CI_OR_2x2(-ritland_2007),
"n contains invalid values. Should be counts."
)
expect_error(
Inv_sinh_CI_ratio_2x2(-ritland_2007),
"n contains invalid values. Should be counts."
)
expect_error(
InverseVariance_estimate_stratified_2x2(hine_1989, "probit"),
"link contains invalid values. Should be linear, log or logit."
)
expect_error(
Jeffreys_CI_1x2(-ligarden_2010["X"], ligarden_2010["n"]),
"X contains invalid values. Should be counts."
)
expect_error(
JonckheereTerpstra_test_rxc(-table_7.7),
"n contains invalid values. Should be counts."
)
expect_error(
Katz_log_CI_2x2(-ritland_2007),
"n contains invalid values. Should be counts."
)
expect_error(
Kendalls_tau_b_rxc_bca(table_7.9, -1),
"nboot contains invalid values. Should be counts."
)
expect_error(
Kendalls_tau_b_rxc(-table_7.8),
"n contains invalid values. Should be counts."
)
expect_error(
Koopman_asymptotic_score_CI_2x2(-ritland_2007),
"n contains invalid values. Should be counts."
)
expect_error(
KruskalWallis_asymptotic_test_rxc(-table_7.6),
"n contains invalid values. Should be counts."
)
expect_error(
linear_by_linear_test_rxc(-table_7.7),
"n contains invalid values. Should be counts."
)
expect_error(
LR_CI_1x2(ligarden_2010["X"], -ligarden_2010["n"]),
"n contains invalid values. Should be counts."
)
expect_error(
LR_test_1x2(ligarden_2010["X"], ligarden_2010["n"], pi0 = -.5),
"pi0 contains invalid values. Should be probability."
)
expect_error(
LR_test_1xc(n = snp6498169$subset$n, pi0 = -snp6498169$subset$pi0),
"pi0 contains invalid values. Should be probability."
)
expect_error(
LR_test_2x2(-ritland_2007),
"n contains invalid values. Should be counts."
)
expect_error(
MantelHaenszel_estimate_stratified_2x2(hine_1989, 1),
"link contains invalid values. Should be linear, log or logit."
)
expect_error(
MantelHaenszel_test_2xc(-lydersen_2012a),
"n contains invalid values. Should be counts."
)
expect_error(
McNemar_asymptotic_test_CC_paired_2x2(-ezra_2010),
"n contains invalid values. Should be counts."
)
expect_error(
McNemar_asymptotic_test_paired_2x2(-ezra_2010),
"n contains invalid values. Should be counts."
)
expect_error(
McNemar_exact_cond_test_paired_2x2(-ezra_2010),
"n contains invalid values. Should be counts."
)
expect_error(
McNemar_exact_unconditional_test_paired_2x2(-bentur_2009),
"n contains invalid values. Should be counts."
)
expect_error(
McNemar_midP_test_paired_2x2(-ezra_2010),
"n contains invalid values. Should be counts."
)
expect_error(
McNemarBowker_test_paired_cxc(-peterson_2007),
"n contains invalid values. Should be counts."
)
expect_error(
Mee_asymptotic_score_CI_2x2(ritland_2007, 9),
"alpha contains invalid values. Should be probability."
)
expect_error(
MidP_binomial_test_1x2(ligarden_2010["X"], ligarden_2010["n"], pi0 = -.5),
"pi0 contains invalid values. Should be probability."
)
expect_error(
MidP_multinomial_test_1xc(-snp6498169$subset$n, snp6498169$subset$pi0),
"n contains invalid values. Should be counts."
)
expect_error(
MiettinenNurminen_asymptotic_score_CI_difference_2x2(-perondi_2004),
"n contains invalid values. Should be counts."
)
expect_error(
MiettinenNurminen_asymptotic_score_CI_OR_2x2(-ritland_2007),
"n contains invalid values. Should be counts."
)
expect_error(
MiettinenNurminen_asymptotic_score_CI_ratio_2x2(-ritland_2007),
"n contains invalid values. Should be counts."
)
expect_error(
ML_estimates_and_CIs_stratified_2x2(hine_1989, "probit"),
"link contains invalid values. Should be linear, log or logit."
)
expect_error(
MOVER_R_Wilson_CI_OR_2x2(-ritland_2007),
"n contains invalid values. Should be counts."
)
expect_error(
MOVER_R_Wilson_CI_ratio_2x2(-ritland_2007),
"n contains invalid values. Should be counts."
)
expect_error(
MOVER_Wilson_score_CI_paired_2x2(cavo_2012, 5),
"alpha contains invalid values. Should be probability."
)
expect_error(
Newcombe_hybrid_score_CI_2x2(ritland_2007, 1.1),
"alpha contains invalid values. Should be probability."
)
expect_error(
Newcombe_square_and_add_CI_paired_2x2(cavo_2012, 3),
"alpha contains invalid values. Should be probability."
)
expect_error(
Pearson_chi_squared_test_1xc(snp6498169$subset$n, -snp6498169$subset$pi0),
"pi0 contains invalid values. Should be probability."
)
expect_error(
Pearson_chi_squared_test_2x2(-ritland_2007),
"n contains invalid values. Should be counts."
)
expect_error(
Pearson_chi_squared_test_CC_2x2(-tea),
"n contains invalid values. Should be counts."
)
expect_error(
Pearson_correlation_coefficient_rxc_bca(table_7.7, -1),
"nboot contains invalid values. Should be counts."
)
expect_error(
Pearson_correlation_coefficient_rxc(table_7.7, alpha = 1.1),
"alpha contains invalid values. Should be probability."
)
expect_error(
Pearson_LR_homogeneity_test_stratified_2x2(doll_hill_1950, "probit"),
"link contains invalid values. Should be linear, log or logit."
)
expect_error(
Pearson_LR_test_common_effect_stratified_2x2(doll_hill_1950, "probit"),
"link contains invalid values. Should be linear, log or logit."
)
expect_error(
Pearson_LR_tests_cum_OR_2xc(lydersen_2012a, "blah"),
"direction contains invalid values. Should be increasing or decreasing."
)
expect_error(
Pearson_LR_tests_rxc(-table_7.5),
"n contains invalid values. Should be counts."
)
expect_error(
Pearson_LR_tests_unspecific_ordering_rx2(indredavik_2008, "decrease"),
"direction contains invalid values. Should be increasing or decreasing."
)
expect_error(
Pearson_residuals_rxc(-table_7.5),
"n contains invalid values. Should be counts."
)
expect_error(
Peto_homogeneity_test_stratified_2x2(hine_1989 / 3),
"n contains invalid values. Should be counts."
)
expect_error(
Peto_OR_estimate_stratified_2x2(hine_1989 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
PriceBonett_approximate_Bayes_CI_2x2(ritland_2007 / 8),
"n contains invalid values. Should be counts."
)
expect_error(
QuesenberryHurst_Wilson_score_CIs_1xc(snp6498169$complete$n, 5),
"alpha contains invalid values. Should be probability."
)
expect_error(
RBG_test_and_CI_stratified_2x2(doll_hill_1950, 54),
"alpha contains invalid values. Should be probability."
)
expect_error(
Scheffe_type_CIs_paired_cxc(peterson_2007 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
Scheffe_type_CIs_rxc(table_7.3, "A"),
"alpha contains invalid values. Should be probability."
)
expect_error(
Score_test_1x2(ligarden_2010["X"], ligarden_2010["n"], pi0 = 5),
"pi0 contains invalid values. Should be probability."
)
expect_error(
Score_test_and_CI_marginal_mean_scores_paired_cxc(
fischer_1999, c(8, 3.5, 0, -3.5, -8), pi
),
"alpha contains invalid values. Should be probability."
)
expect_error(
Score_test_CC_1x2(ligarden_2010["X"], ligarden_2010["n"], pi0 = 5),
"pi0 contains invalid values. Should be probability."
)
expect_error(
Score_test_for_effect_in_the_probit_model_2xc(
-fontanella_2008, c(-1.246452, -0.5097363, 0.2087471)
),
"n contains invalid values. Should be counts."
)
expect_error(
Spearman_correlation_coefficient_rxc_bca(-table_7.7),
"n contains invalid values. Should be counts."
)
expect_error(
Spearman_correlation_coefficient_rxc(table_7.7, 3),
"alpha contains invalid values. Should be probability."
)
expect_error(
stratified_2x2_tables(hine_1989 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
Stuart_test_paired_cxc(peterson_2007 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
Tang_asymptotic_score_CI_paired_2x2(cavo_2012 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
Tango_asymptotic_score_CI_paired_2x2(cavo_2012 / 6),
"n contains invalid values. Should be counts."
)
expect_error(
the_1x2_table_CIs(ligarden_2010["X"], -ligarden_2010["n"]),
"n contains invalid values. Should be counts."
)
expect_error(
the_1x2_table_tests(ligarden_2010["X"], ligarden_2010["n"], pi0 = -0.5),
"pi0 contains invalid values. Should be probability."
)
expect_error(
the_1xc_table_CIs(-snp6498169$complete$n),
"n contains invalid values. Should be counts."
)
expect_error(
the_1xc_table_tests(-snp6498169$complete$n, snp6498169$complete$pi0),
"n contains invalid values. Should be counts."
)
expect_error(
the_2x2_table_CIs_difference(perondi_2004, 7),
"alpha contains invalid values. Should be probability."
)
expect_error(
the_2x2_table_CIs_OR(ritland_2007, 7),
"alpha contains invalid values. Should be probability."
)
expect_error(
the_2x2_table_CIs_ratio(ritland_2007 / 6),
"n contains invalid values. Should be counts."
)
expect_error(
the_2x2_table_tests(lampasona_2013 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
the_2xc_table(lydersen_2012a, direction = "decrease"),
"direction contains invalid values. Should be increasing or decreasing."
)
expect_error(
the_paired_2x2_table_CIs_difference(cavo_2012 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
the_paired_2x2_table_CIs_OR(ezra_2010 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
the_paired_2x2_table_CIs_ratio(cavo_2012 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
the_paired_2x2_table_tests(bentur_2009 / 8),
"n contains invalid values. Should be counts."
)
expect_error(
the_paired_cxc_table_nominal(peterson_2007, 6),
"alpha contains invalid values. Should be probability."
)
expect_error(
the_paired_cxc_table_ordinal(-fischer_1999, c(8, 3.5, 0, -3.5, -8)),
"n contains invalid values. Should be counts."
)
expect_error(
the_rx2_table(-mills_graubard_1987, .4, "increasing"),
"n contains invalid values. Should be counts."
)
expect_error(
the_rx2_table(indredavik_2008, 4),
"alpha contains invalid values. Should be probability."
)
expect_error(
the_rxc_table(-table_7.9),
"n contains invalid values. Should be counts."
)
expect_error(
Transformed_Blaker_exact_CI_paired_2x2(ezra_2010 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
Transformed_Clopper_Pearson_exact_CI_paired_2x2(ezra_2010 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
Transformed_Clopper_Pearson_midP_CI_paired_2x2(ezra_2010 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
Transformed_Wilson_score_CI_paired_2x2(ezra_2010 / 6),
"n contains invalid values. Should be counts."
)
expect_error(
Trend_estimate_CI_tests_rx2(indredavik_2008, 1:5, "logit", 5),
"alpha contains invalid values. Should be probability."
)
expect_error(
Uncorrected_asymptotic_score_CI_2x2(ritland_2007 / 8),
"n contains invalid values. Should be counts."
)
expect_error(
Wald_CI_1x2(singh_2010["1st", "X"], -singh_2010["1st", "n"]),
"n contains invalid values. Should be counts."
)
expect_error(
Wald_CI_2x2(ritland_2007, 6),
"alpha contains invalid values. Should be probability."
)
expect_error(
Wald_CI_AgrestiMin_paired_2x2(cavo_2012 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
Wald_CI_BonettPrice_paired_2x2(cavo_2012, 6),
"alpha contains invalid values. Should be probability."
)
expect_error(
Wald_CI_CC_1x2(ligarden_2010["X"] / 7, ligarden_2010["n"]),
"X contains invalid values. Should be counts."
)
expect_error(
Wald_CI_CC_2x2(ritland_2007 / 8),
"n contains invalid values. Should be counts."
)
expect_error(
Wald_CI_diff_CC_paired_2x2(cavo_2012 / 6),
"n contains invalid values. Should be counts."
)
expect_error(
Wald_CI_diff_paired_2x2(cavo_2012 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
Wald_CI_OR_Laplace_paired_2x2(ezra_2010, 5),
"alpha contains invalid values. Should be probability."
)
expect_error(
Wald_CI_OR_paired_2x2(ezra_2010 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
Wald_CI_ratio_paired_2x2(cavo_2012 / 8),
"n contains invalid values. Should be counts."
)
expect_error(
Wald_test_1x2(ligarden_2010["X"], -ligarden_2010["n"], pi0 = 0.1),
"n contains invalid values. Should be counts."
)
expect_error(
Wald_test_and_CI_common_diff_stratified_2x2(hine_1989, "HH"),
"estimatetype contains invalid values. Should be MH or IV."
)
expect_error(
Wald_test_and_CI_common_ratio_stratified_2x2(-hine_1989),
"n contains invalid values. Should be counts."
)
expect_error(
Wald_test_and_CI_marginal_mean_ranks_paired_cxc(fischer_1999 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
Wald_test_and_CI_marginal_mean_scores_paired_cxc(
fischer_1999, c(8, 3.5, 0, -3.5, -8), 4
),
"alpha contains invalid values. Should be probability."
)
expect_error(
Wald_test_CC_1x2(ligarden_2010["X"], ligarden_2010["n"], pi0 = -1),
"pi0 contains invalid values. Should be probability."
)
expect_error(
Wilson_score_CI_1x2(singh_2010["1st", "X"], -singh_2010["1st", "n"]),
"n contains invalid values. Should be counts."
)
expect_error(
Wilson_score_CI_CC_1x2(ligarden_2010["X"] / 7, ligarden_2010["n"]),
"X contains invalid values. Should be counts."
)
expect_error(
Woolf_logit_CI_2x2(ritland_2007, 7),
"alpha contains invalid values. Should be probability."
)
expect_error(
Woolf_test_and_CI_stratified_2x2(hine_1989 / 7),
"n contains invalid values. Should be counts."
)
expect_error(
Z_unpooled_test_2x2(ritland_2007 / 8),
"n contains invalid values. Should be counts."
)
})
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