From 20b9c584e7c43ecbb708459e531c24a1a4751e17 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 9 Nov 2019 01:05:51 +0100 Subject: Add a lack-of-fit test - Switch an example dataset in the test setup to a dataset with replicates, adapt tests - Skip the test for lrtest with an update specification as it does not only fail when pkgdown generates static help pages, but also in testthat --- tests/testthat/test_tests.R | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) (limited to 'tests/testthat/test_tests.R') diff --git a/tests/testthat/test_tests.R b/tests/testthat/test_tests.R index 5a522f8e..bdc72f08 100644 --- a/tests/testthat/test_tests.R +++ b/tests/testthat/test_tests.R @@ -1,5 +1,20 @@ context("Hypothesis tests") +test_that("The lack-of-fit test works and can be reproduced using nls", { + + expect_error(loftest(f_1_mkin_trans), "Not defined for fits to data without replicates") + + loftest_mkin <- loftest(f_2_mkin) + + # This code is inspired by Ritz and Streibig (2008) Nonlinear Regression using R, p. 64 + Q <- as.numeric(- 2 * (logLik(f_2_nls) - logLik(f_2_anova))) + df.Q <- df.residual(f_2_nls) - df.residual(f_2_anova) + p_nls <- 1 - pchisq(Q, df.Q) + + expect_equal(loftest_mkin[["2", "Pr(>Chisq)"]], p_nls, tolerance = 1e-5) + +}) + test_that("The likelihood ratio test works", { expect_error(lrtest(f_1_mkin_trans, f_2_mkin), "not been fitted to the same data") @@ -25,7 +40,7 @@ test_that("Updating fitted models works", { parent = mkinsub("DFOP", to = "A1"), A1 = mkinsub("SFO", to = "A2"), A2 = mkinsub("SFO"), - use_of_ff = "max" + use_of_ff = "max", quiet = TRUE ) f_soil_1_tc <- mkinfit(dfop_sfo_sfo, @@ -41,6 +56,9 @@ test_that("Updating fitted models works", { }) test_that("We can do a likelihood ratio test using an update specification", { + skip("This errors out if called by testthat while it works in a normal R session") test_2_mkin_k2 <- lrtest(f_2_mkin, fixed_parms = c(k2 = 0)) - expect_equivalent(test_2_mkin_k2[["2", "Pr(>Chisq)"]], 1.139e-6, tolerance = 1e-8) + expect_equivalent(test_2_mkin_k2[["2", "Pr(>Chisq)"]], 4.851e-8, tolerance = 1e-8) + test_2_mkin_tc <- lrtest(f_2_mkin, error_model = "tc") + expect_equivalent(test_2_mkin_tc[["2", "Pr(>Chisq)"]], 7.302e-5, tolerance = 1e-7) }) -- cgit v1.2.1 From b0e529ff49dfa52568fe7c5e6e76439a83c62840 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 13 Nov 2019 16:22:17 +0100 Subject: Improve citation --- tests/testthat/test_tests.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'tests/testthat/test_tests.R') diff --git a/tests/testthat/test_tests.R b/tests/testthat/test_tests.R index bdc72f08..ddf8e1a0 100644 --- a/tests/testthat/test_tests.R +++ b/tests/testthat/test_tests.R @@ -6,7 +6,8 @@ test_that("The lack-of-fit test works and can be reproduced using nls", { loftest_mkin <- loftest(f_2_mkin) - # This code is inspired by Ritz and Streibig (2008) Nonlinear Regression using R, p. 64 + # This code is a slightly modified version of that given in Ritz and Streibig + # (2008) Nonlinear Regression using R, p. 64 Q <- as.numeric(- 2 * (logLik(f_2_nls) - logLik(f_2_anova))) df.Q <- df.residual(f_2_nls) - df.residual(f_2_anova) p_nls <- 1 - pchisq(Q, df.Q) -- cgit v1.2.1