diff --git a/tests/README.md b/tests/README.md index 294b69e89..f074e1753 100644 --- a/tests/README.md +++ b/tests/README.md @@ -1,6 +1,6 @@ Tests and Coverage ================ -23 December, 2022 17:35:56 +23 December, 2022 18:09:56 - Coverage - Unit Tests @@ -48,19 +48,19 @@ Unit Test summary is created using the | file | n | time | error | failed | skipped | warning | icon | |:--------------------------------------------------------|----:|------:|------:|-------:|--------:|--------:|:-----| -| [test-component.R](testthat/test-component.R) | 20 | 0.199 | 0 | 0 | 0 | 0 | | -| [test-cpp-covariance.R](testthat/test-cpp-covariance.R) | 11 | 0.073 | 0 | 0 | 0 | 0 | | -| [test-cpp-utils.R](testthat/test-cpp-utils.R) | 1 | 0.006 | 0 | 0 | 0 | 0 | | -| [test-cpp.R](testthat/test-cpp.R) | 395 | 0.141 | 0 | 0 | 0 | 0 | | -| [test-emmeans.R](testthat/test-emmeans.R) | 30 | 0.951 | 0 | 0 | 0 | 0 | | -| [test-fit.R](testthat/test-fit.R) | 78 | 2.267 | 0 | 0 | 1 | 0 | 🔶 | -| [test-krcomp.R](testthat/test-krcomp.R) | 43 | 1.604 | 0 | 0 | 0 | 0 | | -| [test-mmrm-methods.R](testthat/test-mmrm-methods.R) | 20 | 0.402 | 0 | 0 | 0 | 0 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R) | 57 | 0.433 | 0 | 0 | 0 | 0 | | -| [test-testings.R](testthat/test-testings.R) | 5 | 0.034 | 0 | 0 | 0 | 0 | | -| [test-tmb-methods.R](testthat/test-tmb-methods.R) | 49 | 0.211 | 0 | 0 | 0 | 0 | | -| [test-tmb.R](testthat/test-tmb.R) | 405 | 3.199 | 0 | 0 | 0 | 0 | | -| [test-utils.R](testthat/test-utils.R) | 39 | 0.266 | 0 | 0 | 0 | 0 | | +| [test-component.R](testthat/test-component.R) | 20 | 0.224 | 0 | 0 | 0 | 0 | | +| [test-cpp-covariance.R](testthat/test-cpp-covariance.R) | 11 | 0.092 | 0 | 0 | 0 | 0 | | +| [test-cpp-utils.R](testthat/test-cpp-utils.R) | 1 | 0.008 | 0 | 0 | 0 | 0 | | +| [test-cpp.R](testthat/test-cpp.R) | 395 | 0.177 | 0 | 0 | 0 | 0 | | +| [test-emmeans.R](testthat/test-emmeans.R) | 30 | 1.100 | 0 | 0 | 0 | 0 | | +| [test-fit.R](testthat/test-fit.R) | 78 | 2.272 | 0 | 0 | 1 | 0 | 🔶 | +| [test-krcomp.R](testthat/test-krcomp.R) | 43 | 1.886 | 0 | 0 | 0 | 0 | | +| [test-mmrm-methods.R](testthat/test-mmrm-methods.R) | 20 | 0.519 | 0 | 0 | 0 | 0 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R) | 57 | 0.536 | 0 | 0 | 0 | 0 | | +| [test-testings.R](testthat/test-testings.R) | 5 | 0.044 | 0 | 0 | 0 | 0 | | +| [test-tmb-methods.R](testthat/test-tmb-methods.R) | 49 | 0.252 | 0 | 0 | 0 | 0 | | +| [test-tmb.R](testthat/test-tmb.R) | 405 | 3.915 | 0 | 0 | 0 | 0 | | +| [test-utils.R](testthat/test-utils.R) | 39 | 0.338 | 0 | 0 | 0 | 0 | |
@@ -69,259 +69,259 @@ Show Detailed Test Results | file | context | test | status | n | time | icon | |:-------------------------------------------------------------|:-------------------------------|:--------------------------------------------------------------------------------------------------|:--------|----:|------:|:-----| -| [test-component.R](testthat/test-component.R#L8_L19) | component | component works as expected for mmrm_tmb objects | PASS | 8 | 0.088 | | -| [test-component.R](testthat/test-component.R#L38) | component | component returns adjusted beta cov matrix for Kenward-Roger adjusted mmrm | PASS | 1 | 0.005 | | -| [test-component.R](testthat/test-component.R#L48) | component | component produces complete coefficient vector as expected in full rank model | PASS | 1 | 0.005 | | -| [test-component.R](testthat/test-component.R#L58) | component | component returns coefficient vectors as expected in rank deficient model | PASS | 4 | 0.042 | | -| [test-component.R](testthat/test-component.R#L74) | component | component produces complete variance-covariance matrix as expected in full rank model | PASS | 1 | 0.005 | | -| [test-component.R](testthat/test-component.R#L84) | component | component returns complete variance-covariance matrix as expected in rank deficient model | PASS | 5 | 0.054 | | -| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L26) | cpp-covariance | prepare numbers for homogeneous ante_dependence tests | PASS | 1 | 0.012 | | -| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L52) | cpp-covariance | prepare numbers for heterogeneous ante_dependence tests | PASS | 1 | 0.007 | | -| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L80) | cpp-covariance | prepare numbers for homogeneous toeplitz tests | PASS | 1 | 0.006 | | -| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L106) | cpp-covariance | prepare numbers for heterogeneous toeplitz tests | PASS | 1 | 0.007 | | -| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L115) | cpp-covariance | prepare numbers for autoregressive correlation function test | PASS | 2 | 0.010 | | -| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L135) | cpp-covariance | prepare numbers for homogeneous autoregressive tests | PASS | 1 | 0.006 | | -| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L154) | cpp-covariance | prepare numbers for heterogeneous autoregressive tests | PASS | 1 | 0.006 | | +| [test-component.R](testthat/test-component.R#L8_L19) | component | component works as expected for mmrm_tmb objects | PASS | 8 | 0.103 | | +| [test-component.R](testthat/test-component.R#L38) | component | component returns adjusted beta cov matrix for Kenward-Roger adjusted mmrm | PASS | 1 | 0.006 | | +| [test-component.R](testthat/test-component.R#L48) | component | component produces complete coefficient vector as expected in full rank model | PASS | 1 | 0.006 | | +| [test-component.R](testthat/test-component.R#L58) | component | component returns coefficient vectors as expected in rank deficient model | PASS | 4 | 0.044 | | +| [test-component.R](testthat/test-component.R#L74) | component | component produces complete variance-covariance matrix as expected in full rank model | PASS | 1 | 0.006 | | +| [test-component.R](testthat/test-component.R#L84) | component | component returns complete variance-covariance matrix as expected in rank deficient model | PASS | 5 | 0.059 | | +| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L26) | cpp-covariance | prepare numbers for homogeneous ante_dependence tests | PASS | 1 | 0.011 | | +| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L52) | cpp-covariance | prepare numbers for heterogeneous ante_dependence tests | PASS | 1 | 0.008 | | +| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L80) | cpp-covariance | prepare numbers for homogeneous toeplitz tests | PASS | 1 | 0.008 | | +| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L106) | cpp-covariance | prepare numbers for heterogeneous toeplitz tests | PASS | 1 | 0.008 | | +| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L115) | cpp-covariance | prepare numbers for autoregressive correlation function test | PASS | 2 | 0.013 | | +| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L135) | cpp-covariance | prepare numbers for homogeneous autoregressive tests | PASS | 1 | 0.008 | | +| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L154) | cpp-covariance | prepare numbers for heterogeneous autoregressive tests | PASS | 1 | 0.008 | | | [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L162) | cpp-covariance | prepare numbers for compound symmetry correlation function test | PASS | 1 | 0.007 | | -| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L181) | cpp-covariance | prepare numbers for homogeneous compound symmetry tests | PASS | 1 | 0.006 | | -| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L200) | cpp-covariance | prepare numbers for heterogeneous compound symmetry tests | PASS | 1 | 0.006 | | -| [test-cpp-utils.R](testthat/test-cpp-utils.R#L12) | cpp-utils | prepare numbers for get_corr_mat_chol tests | PASS | 1 | 0.006 | | -| [test-cpp.R](testthat/test-cpp.R#) | unstructured | get_unstructured produces expected result | PASS | 6 | 0.002 | | -| [test-cpp.R](testthat/test-cpp.R#) | ante_dependence | corr_fun_ante_dependence works as expected | PASS | 3 | 0.001 | | -| [test-cpp.R](testthat/test-cpp.R#) | ante_dependence | get_ante_dependence produces expected result | PASS | 11 | 0.004 | | -| [test-cpp.R](testthat/test-cpp.R#) | ante_dependence | get_ante_dependence_heterogeneous produces expected result | PASS | 11 | 0.004 | | +| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L181) | cpp-covariance | prepare numbers for homogeneous compound symmetry tests | PASS | 1 | 0.008 | | +| [test-cpp-covariance.R](testthat/test-cpp-covariance.R#L200) | cpp-covariance | prepare numbers for heterogeneous compound symmetry tests | PASS | 1 | 0.013 | | +| [test-cpp-utils.R](testthat/test-cpp-utils.R#L12) | cpp-utils | prepare numbers for get_corr_mat_chol tests | PASS | 1 | 0.008 | | +| [test-cpp.R](testthat/test-cpp.R#) | unstructured | get_unstructured produces expected result | PASS | 6 | 0.003 | | +| [test-cpp.R](testthat/test-cpp.R#) | ante_dependence | corr_fun_ante_dependence works as expected | PASS | 3 | 0.002 | | +| [test-cpp.R](testthat/test-cpp.R#) | ante_dependence | get_ante_dependence produces expected result | PASS | 11 | 0.005 | | +| [test-cpp.R](testthat/test-cpp.R#) | ante_dependence | get_ante_dependence_heterogeneous produces expected result | PASS | 11 | 0.005 | | | [test-cpp.R](testthat/test-cpp.R#) | toeplitz | corr_fun_toeplitz works as expected | PASS | 3 | 0.002 | | -| [test-cpp.R](testthat/test-cpp.R#) | toeplitz | get_toeplitz produces expected result | PASS | 11 | 0.004 | | -| [test-cpp.R](testthat/test-cpp.R#) | toeplitz | get_toeplitz_heterogeneous produces expected result | PASS | 11 | 0.004 | | -| [test-cpp.R](testthat/test-cpp.R#) | autoregressive | corr_fun_autoregressive works as expected | PASS | 2 | 0.000 | | -| [test-cpp.R](testthat/test-cpp.R#) | autoregressive | get_auto_regressive produces expected result | PASS | 11 | 0.003 | | -| [test-cpp.R](testthat/test-cpp.R#) | autoregressive | get_auto_regressive_heterogeneous produces expected result | PASS | 11 | 0.003 | | -| [test-cpp.R](testthat/test-cpp.R#) | compound symmetry | corr_fun_compound_symmetry works as expected | PASS | 3 | 0.001 | | +| [test-cpp.R](testthat/test-cpp.R#) | toeplitz | get_toeplitz produces expected result | PASS | 11 | 0.005 | | +| [test-cpp.R](testthat/test-cpp.R#) | toeplitz | get_toeplitz_heterogeneous produces expected result | PASS | 11 | 0.005 | | +| [test-cpp.R](testthat/test-cpp.R#) | autoregressive | corr_fun_autoregressive works as expected | PASS | 2 | 0.001 | | +| [test-cpp.R](testthat/test-cpp.R#) | autoregressive | get_auto_regressive produces expected result | PASS | 11 | 0.004 | | +| [test-cpp.R](testthat/test-cpp.R#) | autoregressive | get_auto_regressive_heterogeneous produces expected result | PASS | 11 | 0.005 | | +| [test-cpp.R](testthat/test-cpp.R#) | compound symmetry | corr_fun_compound_symmetry works as expected | PASS | 3 | 0.002 | | | [test-cpp.R](testthat/test-cpp.R#) | compound symmetry | get_compound_symmetry produces expected result | PASS | 11 | 0.004 | | -| [test-cpp.R](testthat/test-cpp.R#) | compound symmetry | get_compound_symmetry_heterogeneous produces expected result | PASS | 11 | 0.004 | | -| [test-cpp.R](testthat/test-cpp.R#) | get_covariance_lower_chol | get_covariance_lower_chol gives expected unstructured result | PASS | 6 | 0.002 | | +| [test-cpp.R](testthat/test-cpp.R#) | compound symmetry | get_compound_symmetry_heterogeneous produces expected result | PASS | 11 | 0.005 | | +| [test-cpp.R](testthat/test-cpp.R#) | get_covariance_lower_chol | get_covariance_lower_chol gives expected unstructured result | PASS | 6 | 0.003 | | | [test-cpp.R](testthat/test-cpp.R#) | get_cov_lower_chol_grouped | get_cov_lower_chol_grouped gives expected unstructured result | PASS | 10 | 0.004 | | -| [test-cpp.R](testthat/test-cpp.R#) | cho_jacobian | cho_jacobian works as expected | PASS | 9 | 0.003 | | -| [test-cpp.R](testthat/test-cpp.R#) | cho_jacobian | cho_jacobian’s jacabian using autodiff works as expected | PASS | 17 | 0.005 | | -| [test-cpp.R](testthat/test-cpp.R#) | chols struct works as expected | chols struct correct sigma, inverse and derivatives | PASS | 87 | 0.030 | | -| [test-cpp.R](testthat/test-cpp.R#) | Rcpp and eigen conversion | conversions does not change values | PASS | 24 | 0.008 | | -| [test-cpp.R](testthat/test-cpp.R#) | get_select_matrix | get_select_matrix works as expected | PASS | 46 | 0.020 | | -| [test-cpp.R](testthat/test-cpp.R#) | tcrossprod | tcrossprod works as expected with complete | PASS | 6 | 0.002 | | -| [test-cpp.R](testthat/test-cpp.R#) | tcrossprod | tcrossprod works as expected without complete (default) | PASS | 6 | 0.002 | | -| [test-cpp.R](testthat/test-cpp.R#) | crossprod | crossprod works as expected | PASS | 11 | 0.004 | | -| [test-cpp.R](testthat/test-cpp.R#) | map_to_cor | map_to_cor works as expected | PASS | 5 | 0.002 | | +| [test-cpp.R](testthat/test-cpp.R#) | cho_jacobian | cho_jacobian works as expected | PASS | 9 | 0.004 | | +| [test-cpp.R](testthat/test-cpp.R#) | cho_jacobian | cho_jacobian’s jacabian using autodiff works as expected | PASS | 17 | 0.007 | | +| [test-cpp.R](testthat/test-cpp.R#) | chols struct works as expected | chols struct correct sigma, inverse and derivatives | PASS | 87 | 0.035 | | +| [test-cpp.R](testthat/test-cpp.R#) | Rcpp and eigen conversion | conversions does not change values | PASS | 24 | 0.010 | | +| [test-cpp.R](testthat/test-cpp.R#) | get_select_matrix | get_select_matrix works as expected | PASS | 46 | 0.024 | | +| [test-cpp.R](testthat/test-cpp.R#) | tcrossprod | tcrossprod works as expected with complete | PASS | 6 | 0.003 | | +| [test-cpp.R](testthat/test-cpp.R#) | tcrossprod | tcrossprod works as expected without complete (default) | PASS | 6 | 0.003 | | +| [test-cpp.R](testthat/test-cpp.R#) | crossprod | crossprod works as expected | PASS | 11 | 0.005 | | +| [test-cpp.R](testthat/test-cpp.R#) | map_to_cor | map_to_cor works as expected | PASS | 5 | 0.003 | | | [test-cpp.R](testthat/test-cpp.R#) | generic_corr_fun | generic_corr_fun is initialized as expected | PASS | 5 | 0.003 | | -| [test-cpp.R](testthat/test-cpp.R#) | get_corr_mat_chol | get_corr_mat_chol works as expected | PASS | 11 | 0.003 | | +| [test-cpp.R](testthat/test-cpp.R#) | get_corr_mat_chol | get_corr_mat_chol works as expected | PASS | 11 | 0.005 | | | [test-cpp.R](testthat/test-cpp.R#) | get_heterogeneous_cov | get_heterogeneous_cov works as expected | PASS | 11 | 0.005 | | -| [test-cpp.R](testthat/test-cpp.R#) | euclidean distance | euclidean works as expected | PASS | 18 | 0.006 | | -| [test-cpp.R](testthat/test-cpp.R#) | euclidean distance | euclidean works as expected for matrix | PASS | 18 | 0.006 | | -| [test-emmeans.R](testthat/test-emmeans.R#L8) | emmeans | recover_data method works as expected | PASS | 2 | 0.020 | | -| [test-emmeans.R](testthat/test-emmeans.R#L20) | emmeans | recover_data method works as expected for rank deficient model | PASS | 2 | 0.015 | | +| [test-cpp.R](testthat/test-cpp.R#) | euclidean distance | euclidean works as expected | PASS | 18 | 0.008 | | +| [test-cpp.R](testthat/test-cpp.R#) | euclidean distance | euclidean works as expected for matrix | PASS | 18 | 0.007 | | +| [test-emmeans.R](testthat/test-emmeans.R#L8) | emmeans | recover_data method works as expected | PASS | 2 | 0.017 | | +| [test-emmeans.R](testthat/test-emmeans.R#L20) | emmeans | recover_data method works as expected for rank deficient model | PASS | 2 | 0.013 | | | [test-emmeans.R](testthat/test-emmeans.R#L43) | emmeans | emm_basis method works as expected | PASS | 2 | 0.053 | | -| [test-emmeans.R](testthat/test-emmeans.R#L65) | emmeans | emm_basis method works also for rank deficient fit | PASS | 2 | 0.113 | | -| [test-emmeans.R](testthat/test-emmeans.R#L75) | emmeans | emmeans works as expected | PASS | 3 | 0.055 | | -| [test-emmeans.R](testthat/test-emmeans.R#L86) | emmeans | emmeans gives values close to what is expected | PASS | 5 | 0.067 | | -| [test-emmeans.R](testthat/test-emmeans.R#L107_L110) | emmeans | emmeans works as expected also for rank deficient fit when singular coefficients are not involved | PASS | 3 | 0.134 | | -| [test-emmeans.R](testthat/test-emmeans.R#L122_L125) | emmeans | emmeans works as expected also for rank deficient fit when singular coefficients are involved | PASS | 4 | 0.118 | | -| [test-emmeans.R](testthat/test-emmeans.R#L138) | emmeans | emmeans works as expected also for weighted model | PASS | 3 | 0.164 | | -| [test-emmeans.R](testthat/test-emmeans.R#L158) | emmeans | emmeans gives d.f. close to what is expected for weighted model | PASS | 4 | 0.212 | | -| [test-fit.R](testthat/test-fit.R#L11) | fit | fit_single_optimizer works as expected with defaults | PASS | 5 | 0.057 | | -| [test-fit.R](testthat/test-fit.R#L27) | fit | fit_single_optimizer works as expected with nlminb optimizer but no starting values | PASS | 5 | 0.057 | | -| [test-fit.R](testthat/test-fit.R#L43) | fit | fit_single_optimizer works as expected with optimizer inputted but no starting values | PASS | 5 | 0.068 | | -| [test-fit.R](testthat/test-fit.R#L60) | fit | fit_single_optimizer works as expected with starting values and optimizer inputted | PASS | 5 | 0.068 | | -| [test-fit.R](testthat/test-fit.R#L69_L76) | fit | fit_single_optimizer gives error messages | PASS | 2 | 0.018 | | -| [test-fit.R](testthat/test-fit.R#L110) | fit | fit_single_optimizer is stable to extreme scaling with defaults | PASS | 2 | 0.031 | | -| [test-fit.R](testthat/test-fit.R#L125_L130) | fit | fit_single_optimizer catches convergence warning as expected | PASS | 4 | 0.020 | | -| [test-fit.R](testthat/test-fit.R#L138_L142) | fit | fit_single_optimizer deals correctly with unobserved visits message | PASS | 3 | 0.034 | | -| [test-fit.R](testthat/test-fit.R#L163) | fit | h_summarize_all_fits works as expected | PASS | 2 | 0.122 | | -| [test-fit.R](testthat/test-fit.R#L200) | fit | h_summarize_all_fits works when some list elements are try-error objects | PASS | 2 | 0.128 | | -| [test-fit.R](testthat/test-fit.R#L224) | fit | refit_multiple_optimizers works as expected with default arguments | PASS | 5 | 0.279 | | -| [test-fit.R](testthat/test-fit.R#L250_L254) | fit | refit_multiple_optimizers works with parallel computations and selected optimizers | PASS | 5 | 0.511 | | -| [test-fit.R](testthat/test-fit.R#L268) | fit | mmrm works as expected for unstructured | PASS | 6 | 0.103 | | -| [test-fit.R](testthat/test-fit.R#L278) | fit | mmrm works as expected for antedependence | PASS | 6 | 0.078 | | -| [test-fit.R](testthat/test-fit.R#L288) | fit | mmrm works as expected for toeplitz | PASS | 6 | 0.083 | | -| [test-fit.R](testthat/test-fit.R#L304_L307) | fit | mmrm falls back to other optimizers if default does not work | PASS | 4 | 0.204 | | -| [test-fit.R](testthat/test-fit.R#L316) | fit | mmrm fails if no optimizer works | SKIPPED | 1 | 0.002 | 🔶 | -| [test-fit.R](testthat/test-fit.R#L333) | fit | mmrm works for rank deficient original design matrix by default | PASS | 2 | 0.097 | | -| [test-fit.R](testthat/test-fit.R#L348_L351) | fit | mmrm works for specific small data example | PASS | 2 | 0.018 | | -| [test-fit.R](testthat/test-fit.R#L365) | fit | mmrm works for custom optimizer | PASS | 1 | 0.043 | | -| [test-fit.R](testthat/test-fit.R#L369_L374) | fit | mmrm works for constructed control | PASS | 1 | 0.054 | | -| [test-fit.R](testthat/test-fit.R#L378_L387) | fit | mmrm still works for deprecated ‘automatic’ optimizer | PASS | 1 | 0.102 | | -| [test-fit.R](testthat/test-fit.R#L392_L398) | fit | mmrm works and gives message for data with unobserved visit levels | PASS | 2 | 0.081 | | -| [test-fit.R](testthat/test-fit.R#L408_L417) | fit | mmrm fails when using … and control at the same time | PASS | 1 | 0.009 | | -| [test-krcomp.R](testthat/test-krcomp.R#L4) | krcomp | h_get_kr_comp works as expected on ungrouped mmrm | PASS | 1 | 0.098 | | -| [test-krcomp.R](testthat/test-krcomp.R#L10) | krcomp | h_get_kr_comp works as expected on grouped mmrm | PASS | 1 | 0.080 | | -| [test-krcomp.R](testthat/test-krcomp.R#L24) | krcomp | kr give similar results as SAS for ar1 | PASS | 2 | 0.052 | | -| [test-krcomp.R](testthat/test-krcomp.R#L34) | krcomp | kr linear give similar results as SAS for ar1 | PASS | 2 | 0.233 | | -| [test-krcomp.R](testthat/test-krcomp.R#L46) | krcomp | kr give similar results as SAS for ar1h | PASS | 2 | 0.055 | | -| [test-krcomp.R](testthat/test-krcomp.R#L56) | krcomp | kr linear give similar results as SAS for ar1h | PASS | 2 | 0.055 | | -| [test-krcomp.R](testthat/test-krcomp.R#L68) | krcomp | kr give similar results as SAS for cs | PASS | 2 | 0.049 | | -| [test-krcomp.R](testthat/test-krcomp.R#L78) | krcomp | kr linear give similar results as SAS for cs | PASS | 2 | 0.051 | | -| [test-krcomp.R](testthat/test-krcomp.R#L90) | krcomp | kr give similar results as SAS for csh | PASS | 2 | 0.056 | | -| [test-krcomp.R](testthat/test-krcomp.R#L100) | krcomp | kr linear give similar results as SAS for csh | PASS | 2 | 0.061 | | -| [test-krcomp.R](testthat/test-krcomp.R#L112) | krcomp | kr give similar results as SAS for adh | PASS | 2 | 0.068 | | -| [test-krcomp.R](testthat/test-krcomp.R#L122) | krcomp | kr linear give similar results as SAS for adh | PASS | 2 | 0.068 | | -| [test-krcomp.R](testthat/test-krcomp.R#L134) | krcomp | kr give similar results as SAS for toep | PASS | 2 | 0.060 | | -| [test-krcomp.R](testthat/test-krcomp.R#L144) | krcomp | kr linear give similar results as SAS for toep | PASS | 2 | 0.060 | | -| [test-krcomp.R](testthat/test-krcomp.R#L156) | krcomp | kr give similar results as SAS for toeph | PASS | 2 | 0.067 | | -| [test-krcomp.R](testthat/test-krcomp.R#L166) | krcomp | kr linear give similar results as SAS for toeph | PASS | 2 | 0.068 | | -| [test-krcomp.R](testthat/test-krcomp.R#L182) | krcomp | kr give similar results as SAS for unstructured | PASS | 2 | 0.079 | | -| [test-krcomp.R](testthat/test-krcomp.R#L192) | krcomp | kr linear give similar results as SAS for unstructured | PASS | 2 | 0.085 | | -| [test-krcomp.R](testthat/test-krcomp.R#L201) | krcomp | h_df_1d_kr works as expected in the standard case | PASS | 2 | 0.074 | | -| [test-krcomp.R](testthat/test-krcomp.R#L209) | krcomp | h_df_md_kr works as expected in the standard case | PASS | 2 | 0.073 | | -| [test-krcomp.R](testthat/test-krcomp.R#L220_L223) | krcomp | h_kr_df works as expected in the standard case | PASS | 1 | 0.035 | | -| [test-krcomp.R](testthat/test-krcomp.R#L230_L237) | krcomp | h_var_adj works as expected in the standard case for Kenward-Roger | PASS | 1 | 0.032 | | -| [test-krcomp.R](testthat/test-krcomp.R#L242_L249) | krcomp | h_var_adj works as expected in the standard case for Kenward-Roger-Linear | PASS | 1 | 0.032 | | -| [test-krcomp.R](testthat/test-krcomp.R#L257) | krcomp | df_md works as expected for Kenward-Roger | PASS | 2 | 0.013 | | -| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L5) | mmrm-methods | h_coef_table works as expected | PASS | 4 | 0.012 | | -| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L19) | mmrm-methods | h_coef_table works as expected | PASS | 3 | 0.015 | | -| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L32) | mmrm-methods | summary works as expected | PASS | 3 | 0.012 | | -| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L47) | mmrm-methods | h_print_call works as expected | PASS | 1 | 0.032 | | -| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L52) | mmrm-methods | h_print_call works as expected for weighted fits | PASS | 1 | 0.038 | | -| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L59) | mmrm-methods | h_print_cov works as expected | PASS | 2 | 0.062 | | -| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L66_L71) | mmrm-methods | h_print_aic_list works as expected | PASS | 1 | 0.033 | | -| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L79) | mmrm-methods | print.summary.mmrm works as expected | PASS | 1 | 0.044 | | -| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L85) | mmrm-methods | print.summary.mmrm works as expected for weighted models | PASS | 1 | 0.041 | | -| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L91) | mmrm-methods | print.summary.mmrm works as expected for rank deficient fits | PASS | 1 | 0.042 | | -| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L97) | mmrm-methods | print.summary.mmrm works as expected for grouped fits | PASS | 1 | 0.036 | | -| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L104) | mmrm-methods | print.summary.mmrm works as expected for spatial fits | PASS | 1 | 0.035 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L5) | satterthwaite | h_covbeta_fun works as expected | PASS | 4 | 0.013 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L18) | satterthwaite | h_jac_col_as_matrix works as expected | PASS | 2 | 0.007 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L31) | satterthwaite | h_jac_list works as expected | PASS | 6 | 0.028 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L44) | satterthwaite | h_quad_form_vec works as expected | PASS | 2 | 0.013 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L54) | satterthwaite | h_quad_form_mat works as expected for a true row vector as mat | PASS | 2 | 0.006 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L62) | satterthwaite | h_quad_form_mat works as expected for a larger mat | PASS | 2 | 0.007 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L75) | satterthwaite | h_gradient works as expected | PASS | 2 | 0.007 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L86) | satterthwaite | h_df_1d_list works as expected | PASS | 2 | 0.006 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L105) | satterthwaite | h_df_1d_sat works as expected | PASS | 7 | 0.081 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L125) | satterthwaite | h_df_1d_sat works as expected for singular fits | PASS | 3 | 0.117 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L134) | satterthwaite | h_md_denom_df works as expected in the standard case | PASS | 2 | 0.007 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L143) | satterthwaite | h_md_denom_df works as expected for a single t-statistic | PASS | 2 | 0.007 | | +| [test-emmeans.R](testthat/test-emmeans.R#L65) | emmeans | emm_basis method works also for rank deficient fit | PASS | 2 | 0.130 | | +| [test-emmeans.R](testthat/test-emmeans.R#L75) | emmeans | emmeans works as expected | PASS | 3 | 0.067 | | +| [test-emmeans.R](testthat/test-emmeans.R#L86) | emmeans | emmeans gives values close to what is expected | PASS | 5 | 0.073 | | +| [test-emmeans.R](testthat/test-emmeans.R#L107_L110) | emmeans | emmeans works as expected also for rank deficient fit when singular coefficients are not involved | PASS | 3 | 0.164 | | +| [test-emmeans.R](testthat/test-emmeans.R#L122_L125) | emmeans | emmeans works as expected also for rank deficient fit when singular coefficients are involved | PASS | 4 | 0.144 | | +| [test-emmeans.R](testthat/test-emmeans.R#L138) | emmeans | emmeans works as expected also for weighted model | PASS | 3 | 0.189 | | +| [test-emmeans.R](testthat/test-emmeans.R#L158) | emmeans | emmeans gives d.f. close to what is expected for weighted model | PASS | 4 | 0.250 | | +| [test-fit.R](testthat/test-fit.R#L11) | fit | fit_single_optimizer works as expected with defaults | PASS | 5 | 0.073 | | +| [test-fit.R](testthat/test-fit.R#L27) | fit | fit_single_optimizer works as expected with nlminb optimizer but no starting values | PASS | 5 | 0.066 | | +| [test-fit.R](testthat/test-fit.R#L43) | fit | fit_single_optimizer works as expected with optimizer inputted but no starting values | PASS | 5 | 0.072 | | +| [test-fit.R](testthat/test-fit.R#L60) | fit | fit_single_optimizer works as expected with starting values and optimizer inputted | PASS | 5 | 0.078 | | +| [test-fit.R](testthat/test-fit.R#L69_L76) | fit | fit_single_optimizer gives error messages | PASS | 2 | 0.024 | | +| [test-fit.R](testthat/test-fit.R#L110) | fit | fit_single_optimizer is stable to extreme scaling with defaults | PASS | 2 | 0.030 | | +| [test-fit.R](testthat/test-fit.R#L125_L130) | fit | fit_single_optimizer catches convergence warning as expected | PASS | 4 | 0.023 | | +| [test-fit.R](testthat/test-fit.R#L138_L142) | fit | fit_single_optimizer deals correctly with unobserved visits message | PASS | 3 | 0.038 | | +| [test-fit.R](testthat/test-fit.R#L163) | fit | h_summarize_all_fits works as expected | PASS | 2 | 0.128 | | +| [test-fit.R](testthat/test-fit.R#L200) | fit | h_summarize_all_fits works when some list elements are try-error objects | PASS | 2 | 0.141 | | +| [test-fit.R](testthat/test-fit.R#L224) | fit | refit_multiple_optimizers works as expected with default arguments | PASS | 5 | 0.306 | | +| [test-fit.R](testthat/test-fit.R#L250_L254) | fit | refit_multiple_optimizers works with parallel computations and selected optimizers | PASS | 5 | 0.240 | | +| [test-fit.R](testthat/test-fit.R#L268) | fit | mmrm works as expected for unstructured | PASS | 6 | 0.121 | | +| [test-fit.R](testthat/test-fit.R#L278) | fit | mmrm works as expected for antedependence | PASS | 6 | 0.105 | | +| [test-fit.R](testthat/test-fit.R#L288) | fit | mmrm works as expected for toeplitz | PASS | 6 | 0.093 | | +| [test-fit.R](testthat/test-fit.R#L304_L307) | fit | mmrm falls back to other optimizers if default does not work | PASS | 4 | 0.243 | | +| [test-fit.R](testthat/test-fit.R#L316) | fit | mmrm fails if no optimizer works | SKIPPED | 1 | 0.003 | 🔶 | +| [test-fit.R](testthat/test-fit.R#L333) | fit | mmrm works for rank deficient original design matrix by default | PASS | 2 | 0.115 | | +| [test-fit.R](testthat/test-fit.R#L348_L351) | fit | mmrm works for specific small data example | PASS | 2 | 0.024 | | +| [test-fit.R](testthat/test-fit.R#L365) | fit | mmrm works for custom optimizer | PASS | 1 | 0.055 | | +| [test-fit.R](testthat/test-fit.R#L369_L374) | fit | mmrm works for constructed control | PASS | 1 | 0.058 | | +| [test-fit.R](testthat/test-fit.R#L378_L387) | fit | mmrm still works for deprecated ‘automatic’ optimizer | PASS | 1 | 0.133 | | +| [test-fit.R](testthat/test-fit.R#L392_L398) | fit | mmrm works and gives message for data with unobserved visit levels | PASS | 2 | 0.090 | | +| [test-fit.R](testthat/test-fit.R#L408_L417) | fit | mmrm fails when using … and control at the same time | PASS | 1 | 0.013 | | +| [test-krcomp.R](testthat/test-krcomp.R#L4) | krcomp | h_get_kr_comp works as expected on ungrouped mmrm | PASS | 1 | 0.112 | | +| [test-krcomp.R](testthat/test-krcomp.R#L10) | krcomp | h_get_kr_comp works as expected on grouped mmrm | PASS | 1 | 0.089 | | +| [test-krcomp.R](testthat/test-krcomp.R#L24) | krcomp | kr give similar results as SAS for ar1 | PASS | 2 | 0.299 | | +| [test-krcomp.R](testthat/test-krcomp.R#L34) | krcomp | kr linear give similar results as SAS for ar1 | PASS | 2 | 0.057 | | +| [test-krcomp.R](testthat/test-krcomp.R#L46) | krcomp | kr give similar results as SAS for ar1h | PASS | 2 | 0.061 | | +| [test-krcomp.R](testthat/test-krcomp.R#L56) | krcomp | kr linear give similar results as SAS for ar1h | PASS | 2 | 0.063 | | +| [test-krcomp.R](testthat/test-krcomp.R#L68) | krcomp | kr give similar results as SAS for cs | PASS | 2 | 0.056 | | +| [test-krcomp.R](testthat/test-krcomp.R#L78) | krcomp | kr linear give similar results as SAS for cs | PASS | 2 | 0.059 | | +| [test-krcomp.R](testthat/test-krcomp.R#L90) | krcomp | kr give similar results as SAS for csh | PASS | 2 | 0.066 | | +| [test-krcomp.R](testthat/test-krcomp.R#L100) | krcomp | kr linear give similar results as SAS for csh | PASS | 2 | 0.068 | | +| [test-krcomp.R](testthat/test-krcomp.R#L112) | krcomp | kr give similar results as SAS for adh | PASS | 2 | 0.076 | | +| [test-krcomp.R](testthat/test-krcomp.R#L122) | krcomp | kr linear give similar results as SAS for adh | PASS | 2 | 0.078 | | +| [test-krcomp.R](testthat/test-krcomp.R#L134) | krcomp | kr give similar results as SAS for toep | PASS | 2 | 0.069 | | +| [test-krcomp.R](testthat/test-krcomp.R#L144) | krcomp | kr linear give similar results as SAS for toep | PASS | 2 | 0.065 | | +| [test-krcomp.R](testthat/test-krcomp.R#L156) | krcomp | kr give similar results as SAS for toeph | PASS | 2 | 0.078 | | +| [test-krcomp.R](testthat/test-krcomp.R#L166) | krcomp | kr linear give similar results as SAS for toeph | PASS | 2 | 0.076 | | +| [test-krcomp.R](testthat/test-krcomp.R#L182) | krcomp | kr give similar results as SAS for unstructured | PASS | 2 | 0.090 | | +| [test-krcomp.R](testthat/test-krcomp.R#L192) | krcomp | kr linear give similar results as SAS for unstructured | PASS | 2 | 0.092 | | +| [test-krcomp.R](testthat/test-krcomp.R#L201) | krcomp | h_df_1d_kr works as expected in the standard case | PASS | 2 | 0.089 | | +| [test-krcomp.R](testthat/test-krcomp.R#L209) | krcomp | h_df_md_kr works as expected in the standard case | PASS | 2 | 0.093 | | +| [test-krcomp.R](testthat/test-krcomp.R#L220_L223) | krcomp | h_kr_df works as expected in the standard case | PASS | 1 | 0.044 | | +| [test-krcomp.R](testthat/test-krcomp.R#L230_L237) | krcomp | h_var_adj works as expected in the standard case for Kenward-Roger | PASS | 1 | 0.045 | | +| [test-krcomp.R](testthat/test-krcomp.R#L242_L249) | krcomp | h_var_adj works as expected in the standard case for Kenward-Roger-Linear | PASS | 1 | 0.044 | | +| [test-krcomp.R](testthat/test-krcomp.R#L257) | krcomp | df_md works as expected for Kenward-Roger | PASS | 2 | 0.017 | | +| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L5) | mmrm-methods | h_coef_table works as expected | PASS | 4 | 0.018 | | +| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L19) | mmrm-methods | h_coef_table works as expected | PASS | 3 | 0.023 | | +| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L32) | mmrm-methods | summary works as expected | PASS | 3 | 0.020 | | +| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L47) | mmrm-methods | h_print_call works as expected | PASS | 1 | 0.050 | | +| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L52) | mmrm-methods | h_print_call works as expected for weighted fits | PASS | 1 | 0.039 | | +| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L59) | mmrm-methods | h_print_cov works as expected | PASS | 2 | 0.075 | | +| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L66_L71) | mmrm-methods | h_print_aic_list works as expected | PASS | 1 | 0.040 | | +| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L79) | mmrm-methods | print.summary.mmrm works as expected | PASS | 1 | 0.057 | | +| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L85) | mmrm-methods | print.summary.mmrm works as expected for weighted models | PASS | 1 | 0.054 | | +| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L91) | mmrm-methods | print.summary.mmrm works as expected for rank deficient fits | PASS | 1 | 0.054 | | +| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L97) | mmrm-methods | print.summary.mmrm works as expected for grouped fits | PASS | 1 | 0.045 | | +| [test-mmrm-methods.R](testthat/test-mmrm-methods.R#L104) | mmrm-methods | print.summary.mmrm works as expected for spatial fits | PASS | 1 | 0.044 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L5) | satterthwaite | h_covbeta_fun works as expected | PASS | 4 | 0.016 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L18) | satterthwaite | h_jac_col_as_matrix works as expected | PASS | 2 | 0.008 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L31) | satterthwaite | h_jac_list works as expected | PASS | 6 | 0.043 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L44) | satterthwaite | h_quad_form_vec works as expected | PASS | 2 | 0.009 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L54) | satterthwaite | h_quad_form_mat works as expected for a true row vector as mat | PASS | 2 | 0.010 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L62) | satterthwaite | h_quad_form_mat works as expected for a larger mat | PASS | 2 | 0.013 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L75) | satterthwaite | h_gradient works as expected | PASS | 2 | 0.008 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L86) | satterthwaite | h_df_1d_list works as expected | PASS | 2 | 0.008 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L105) | satterthwaite | h_df_1d_sat works as expected | PASS | 7 | 0.103 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L125) | satterthwaite | h_df_1d_sat works as expected for singular fits | PASS | 3 | 0.137 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L134) | satterthwaite | h_md_denom_df works as expected in the standard case | PASS | 2 | 0.009 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L143) | satterthwaite | h_md_denom_df works as expected for a single t-statistic | PASS | 2 | 0.009 | | | [test-satterthwaite.R](testthat/test-satterthwaite.R#L150) | satterthwaite | h_md_denom_df works as expected when the t-statistics are almost identical | PASS | 2 | 0.007 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L156) | satterthwaite | h_md_denom_df works as expected when one t-statistic is 2 or smaller | PASS | 3 | 0.014 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L164) | satterthwaite | h_df_md_list works as expected | PASS | 2 | 0.010 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L181) | satterthwaite | h_df_md_from_1d works as expected | PASS | 3 | 0.059 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L193) | satterthwaite | h_df_md_sat works as expected | PASS | 6 | 0.024 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L205) | satterthwaite | h_df_md_sat works as expected with a non-full rank contrast matrix | PASS | 2 | 0.009 | | -| [test-satterthwaite.R](testthat/test-satterthwaite.R#L214) | satterthwaite | h_df_md_sat works as expected for rank deficient model | PASS | 3 | 0.011 | | -| [test-testings.R](testthat/test-testings.R#L7) | testings | df_1d use correct function on Satterthewaite method fit | PASS | 1 | 0.006 | | -| [test-testings.R](testthat/test-testings.R#L14) | testings | df_1d use correct function on Kenward-Roger method fit | PASS | 1 | 0.006 | | -| [test-testings.R](testthat/test-testings.R#L24) | testings | df_md use correct function on Satterthewaite method fit | PASS | 1 | 0.008 | | -| [test-testings.R](testthat/test-testings.R#L32) | testings | df_md use correct function on Kenward-Roger method fit | PASS | 1 | 0.007 | | -| [test-testings.R](testthat/test-testings.R#L40) | testings | df_md use correct function on Kenward-Roger-Linear method fit | PASS | 1 | 0.007 | | -| [test-tmb-methods.R](testthat/test-tmb-methods.R#L5) | tmb-methods | coef works as expected | PASS | 2 | 0.008 | | -| [test-tmb-methods.R](testthat/test-tmb-methods.R#L16) | tmb-methods | coef works as expected for rank deficient model | PASS | 4 | 0.016 | | -| [test-tmb-methods.R](testthat/test-tmb-methods.R#L33) | tmb-methods | fitted works as expected | PASS | 2 | 0.003 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L156) | satterthwaite | h_md_denom_df works as expected when one t-statistic is 2 or smaller | PASS | 3 | 0.018 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L164) | satterthwaite | h_df_md_list works as expected | PASS | 2 | 0.013 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L181) | satterthwaite | h_df_md_from_1d works as expected | PASS | 3 | 0.068 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L193) | satterthwaite | h_df_md_sat works as expected | PASS | 6 | 0.030 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L205) | satterthwaite | h_df_md_sat works as expected with a non-full rank contrast matrix | PASS | 2 | 0.012 | | +| [test-satterthwaite.R](testthat/test-satterthwaite.R#L214) | satterthwaite | h_df_md_sat works as expected for rank deficient model | PASS | 3 | 0.015 | | +| [test-testings.R](testthat/test-testings.R#L7) | testings | df_1d use correct function on Satterthewaite method fit | PASS | 1 | 0.008 | | +| [test-testings.R](testthat/test-testings.R#L14) | testings | df_1d use correct function on Kenward-Roger method fit | PASS | 1 | 0.008 | | +| [test-testings.R](testthat/test-testings.R#L24) | testings | df_md use correct function on Satterthewaite method fit | PASS | 1 | 0.010 | | +| [test-testings.R](testthat/test-testings.R#L32) | testings | df_md use correct function on Kenward-Roger method fit | PASS | 1 | 0.009 | | +| [test-testings.R](testthat/test-testings.R#L40) | testings | df_md use correct function on Kenward-Roger-Linear method fit | PASS | 1 | 0.009 | | +| [test-tmb-methods.R](testthat/test-tmb-methods.R#L5) | tmb-methods | coef works as expected | PASS | 2 | 0.011 | | +| [test-tmb-methods.R](testthat/test-tmb-methods.R#L16) | tmb-methods | coef works as expected for rank deficient model | PASS | 4 | 0.020 | | +| [test-tmb-methods.R](testthat/test-tmb-methods.R#L33) | tmb-methods | fitted works as expected | PASS | 2 | 0.004 | | | [test-tmb-methods.R](testthat/test-tmb-methods.R#L41) | tmb-methods | model.frame works as expected with defaults | PASS | 4 | 0.005 | | -| [test-tmb-methods.R](testthat/test-tmb-methods.R#L49) | tmb-methods | model.frame returns full model frame if requested | PASS | 4 | 0.004 | | -| [test-tmb-methods.R](testthat/test-tmb-methods.R#L59) | tmb-methods | logLik works as expected | PASS | 2 | 0.007 | | -| [test-tmb-methods.R](testthat/test-tmb-methods.R#L68) | tmb-methods | formula works as expected | PASS | 3 | 0.012 | | +| [test-tmb-methods.R](testthat/test-tmb-methods.R#L49) | tmb-methods | model.frame returns full model frame if requested | PASS | 4 | 0.006 | | +| [test-tmb-methods.R](testthat/test-tmb-methods.R#L59) | tmb-methods | logLik works as expected | PASS | 2 | 0.008 | | +| [test-tmb-methods.R](testthat/test-tmb-methods.R#L68) | tmb-methods | formula works as expected | PASS | 3 | 0.015 | | | [test-tmb-methods.R](testthat/test-tmb-methods.R#L78) | tmb-methods | vcov works as expected | PASS | 4 | 0.005 | | -| [test-tmb-methods.R](testthat/test-tmb-methods.R#L87) | tmb-methods | vcov works as expected for rank deficient model | PASS | 7 | 0.008 | | -| [test-tmb-methods.R](testthat/test-tmb-methods.R#L103) | tmb-methods | VarCorr works as expected | PASS | 4 | 0.004 | | -| [test-tmb-methods.R](testthat/test-tmb-methods.R#L114) | tmb-methods | deviance works as expected | PASS | 2 | 0.007 | | -| [test-tmb-methods.R](testthat/test-tmb-methods.R#L123) | tmb-methods | AIC works as expected with defaults | PASS | 2 | 0.014 | | -| [test-tmb-methods.R](testthat/test-tmb-methods.R#L130) | tmb-methods | AIC works as expected with different k | PASS | 2 | 0.007 | | -| [test-tmb-methods.R](testthat/test-tmb-methods.R#L137) | tmb-methods | corrected AIC works as expected | PASS | 2 | 0.007 | | -| [test-tmb-methods.R](testthat/test-tmb-methods.R#L149) | tmb-methods | BIC works as expected | PASS | 2 | 0.007 | | -| [test-tmb-methods.R](testthat/test-tmb-methods.R#L158) | tmb-methods | print.mmrm_tmb works as expected | PASS | 2 | 0.065 | | -| [test-tmb-methods.R](testthat/test-tmb-methods.R#L165) | tmb-methods | print.mmrm_tmb works as expected for rank deficient fits | PASS | 1 | 0.032 | | -| [test-tmb.R](testthat/test-tmb.R#L19) | tmb | mmrm_control works as expected | PASS | 1 | 0.006 | | -| [test-tmb.R](testthat/test-tmb.R#L24_L27) | tmb | h_mmrm_tmb_extract_terms works for covariance terms as expected | PASS | 6 | 0.041 | | -| [test-tmb.R](testthat/test-tmb.R#L52_L55) | tmb | h_mmrm_tmb_extract_vars works for non-grouped formula as expected | PASS | 3 | 0.018 | | -| [test-tmb.R](testthat/test-tmb.R#L67_L70) | tmb | h_mmrm_tmb_extract_vars works for grouped formula as expected | PASS | 4 | 0.029 | | -| [test-tmb.R](testthat/test-tmb.R#L87_L90) | tmb | h_mmrm_tmb_extract_vars works for multiple coordinates as expected | PASS | 3 | 0.020 | | -| [test-tmb.R](testthat/test-tmb.R#L104_L106) | tmb | h_mmrm_tmb_formula_parts works as expected | PASS | 10 | 0.062 | | -| [test-tmb.R](testthat/test-tmb.R#L173_L175) | tmb | h_mmrm_tmb_formula_parts works without covariates | PASS | 2 | 0.007 | | -| [test-tmb.R](testthat/test-tmb.R#L193_L195) | tmb | h_mmrm_tmb_formula_parts works as expected for antedependence | PASS | 2 | 0.007 | | -| [test-tmb.R](testthat/test-tmb.R#L217_L224) | tmb | h_mmrm_tmb_data works as expected | PASS | 12 | 0.042 | | -| [test-tmb.R](testthat/test-tmb.R#L249_L256) | tmb | h_mmrm_tmb_data works as expected for grouped covariance | PASS | 12 | 0.031 | | -| [test-tmb.R](testthat/test-tmb.R#L280_L287) | tmb | h_mmrm_tmb_data works as expected for mutli-dimensional spatial exponential covariance | PASS | 12 | 0.029 | | -| [test-tmb.R](testthat/test-tmb.R#L313_L320) | tmb | h_mmrm_tmb_data works also for character ID variable | PASS | 3 | 0.020 | | -| [test-tmb.R](testthat/test-tmb.R#L336_L343) | tmb | h_mmrm_tmb_data correctly processes design matrix below full rank correctly | PASS | 1 | 0.007 | | -| [test-tmb.R](testthat/test-tmb.R#L353_L367) | tmb | h_mmrm_tmb_data gives error for rank deficient design matrix when not accepted | PASS | 1 | 0.012 | | -| [test-tmb.R](testthat/test-tmb.R#L393_L406) | tmb | h_mmrm_tmb_data catches case with multiple time points per subject early | PASS | 1 | 0.011 | | -| [test-tmb.R](testthat/test-tmb.R#L422) | tmb | h_mmrm_tmb_data has no side effect of overwrite the weights in global env | PASS | 1 | 0.011 | | -| [test-tmb.R](testthat/test-tmb.R#L438) | tmb | h_mmrm_tmb_data will not be affecte by `weights` in data | PASS | 2 | 0.016 | | -| [test-tmb.R](testthat/test-tmb.R#L455) | tmb | h_mmrm_tmb_parameters works as expected without start values | PASS | 2 | 0.012 | | -| [test-tmb.R](testthat/test-tmb.R#L472) | tmb | h_mmrm_tmb_parameters works as expected with start values | PASS | 2 | 0.012 | | -| [test-tmb.R](testthat/test-tmb.R#L488) | tmb | h_mmrm_tmb_parameters works as expected with antedependence | PASS | 2 | 0.011 | | -| [test-tmb.R](testthat/test-tmb.R#L504) | tmb | h_mmrm_tmb_parameters works as expected with heterogeneous antedependence | PASS | 2 | 0.011 | | -| [test-tmb.R](testthat/test-tmb.R#L520) | tmb | h_mmrm_tmb_parameters works as expected with Toeplitz | PASS | 2 | 0.012 | | -| [test-tmb.R](testthat/test-tmb.R#L536) | tmb | h_mmrm_tmb_parameters works as expected with heterogeneous Toeplitz | PASS | 2 | 0.012 | | -| [test-tmb.R](testthat/test-tmb.R#L552) | tmb | h_mmrm_tmb_parameters works as expected with autoregressive | PASS | 2 | 0.011 | | -| [test-tmb.R](testthat/test-tmb.R#L568) | tmb | h_mmrm_tmb_parameters works as expected with heterogeneous autoregressive | PASS | 2 | 0.011 | | -| [test-tmb.R](testthat/test-tmb.R#L584) | tmb | h_mmrm_tmb_parameters works as expected with compound symmetry | PASS | 2 | 0.011 | | -| [test-tmb.R](testthat/test-tmb.R#L600) | tmb | h_mmrm_tmb_parameters works as expected with heterogeneous compound symmetry | PASS | 2 | 0.011 | | -| [test-tmb.R](testthat/test-tmb.R#L616) | tmb | h_mmrm_tmb_parameters works as expected with spatial exponential | PASS | 2 | 0.010 | | -| [test-tmb.R](testthat/test-tmb.R#L629) | tmb | h_mmrm_tmb_assert_start passes as expected for sane start values | PASS | 2 | 0.006 | | -| [test-tmb.R](testthat/test-tmb.R#L639_L642) | tmb | h_mmrm_tmb_assert_start fails as expected for NaN objective function at start | PASS | 1 | 0.008 | | -| [test-tmb.R](testthat/test-tmb.R#L651_L654) | tmb | h_mmrm_tmb_assert_start fails as expected for NaN gradient function at start | PASS | 1 | 0.009 | | -| [test-tmb.R](testthat/test-tmb.R#L670) | tmb | h_mmrm_tmb_check_conv passes as expected for sane optimization result | PASS | 2 | 0.007 | | -| [test-tmb.R](testthat/test-tmb.R#L685_L688) | tmb | h_mmrm_tmb_check_conv raises singular hessian warning as expected | PASS | 1 | 0.008 | | -| [test-tmb.R](testthat/test-tmb.R#L702_L705) | tmb | h_mmrm_tmb_check_conv warns if convergence code signals non-convergence | PASS | 1 | 0.008 | | +| [test-tmb-methods.R](testthat/test-tmb-methods.R#L87) | tmb-methods | vcov works as expected for rank deficient model | PASS | 7 | 0.010 | | +| [test-tmb-methods.R](testthat/test-tmb-methods.R#L103) | tmb-methods | VarCorr works as expected | PASS | 4 | 0.005 | | +| [test-tmb-methods.R](testthat/test-tmb-methods.R#L114) | tmb-methods | deviance works as expected | PASS | 2 | 0.009 | | +| [test-tmb-methods.R](testthat/test-tmb-methods.R#L123) | tmb-methods | AIC works as expected with defaults | PASS | 2 | 0.008 | | +| [test-tmb-methods.R](testthat/test-tmb-methods.R#L130) | tmb-methods | AIC works as expected with different k | PASS | 2 | 0.009 | | +| [test-tmb-methods.R](testthat/test-tmb-methods.R#L137) | tmb-methods | corrected AIC works as expected | PASS | 2 | 0.010 | | +| [test-tmb-methods.R](testthat/test-tmb-methods.R#L149) | tmb-methods | BIC works as expected | PASS | 2 | 0.009 | | +| [test-tmb-methods.R](testthat/test-tmb-methods.R#L158) | tmb-methods | print.mmrm_tmb works as expected | PASS | 2 | 0.078 | | +| [test-tmb-methods.R](testthat/test-tmb-methods.R#L165) | tmb-methods | print.mmrm_tmb works as expected for rank deficient fits | PASS | 1 | 0.040 | | +| [test-tmb.R](testthat/test-tmb.R#L19) | tmb | mmrm_control works as expected | PASS | 1 | 0.007 | | +| [test-tmb.R](testthat/test-tmb.R#L24_L27) | tmb | h_mmrm_tmb_extract_terms works for covariance terms as expected | PASS | 6 | 0.058 | | +| [test-tmb.R](testthat/test-tmb.R#L52_L55) | tmb | h_mmrm_tmb_extract_vars works for non-grouped formula as expected | PASS | 3 | 0.024 | | +| [test-tmb.R](testthat/test-tmb.R#L67_L70) | tmb | h_mmrm_tmb_extract_vars works for grouped formula as expected | PASS | 4 | 0.040 | | +| [test-tmb.R](testthat/test-tmb.R#L87_L90) | tmb | h_mmrm_tmb_extract_vars works for multiple coordinates as expected | PASS | 3 | 0.027 | | +| [test-tmb.R](testthat/test-tmb.R#L104_L106) | tmb | h_mmrm_tmb_formula_parts works as expected | PASS | 10 | 0.084 | | +| [test-tmb.R](testthat/test-tmb.R#L173_L175) | tmb | h_mmrm_tmb_formula_parts works without covariates | PASS | 2 | 0.011 | | +| [test-tmb.R](testthat/test-tmb.R#L193_L195) | tmb | h_mmrm_tmb_formula_parts works as expected for antedependence | PASS | 2 | 0.010 | | +| [test-tmb.R](testthat/test-tmb.R#L217_L224) | tmb | h_mmrm_tmb_data works as expected | PASS | 12 | 0.053 | | +| [test-tmb.R](testthat/test-tmb.R#L249_L256) | tmb | h_mmrm_tmb_data works as expected for grouped covariance | PASS | 12 | 0.038 | | +| [test-tmb.R](testthat/test-tmb.R#L280_L287) | tmb | h_mmrm_tmb_data works as expected for mutli-dimensional spatial exponential covariance | PASS | 12 | 0.037 | | +| [test-tmb.R](testthat/test-tmb.R#L313_L320) | tmb | h_mmrm_tmb_data works also for character ID variable | PASS | 3 | 0.024 | | +| [test-tmb.R](testthat/test-tmb.R#L336_L343) | tmb | h_mmrm_tmb_data correctly processes design matrix below full rank correctly | PASS | 1 | 0.009 | | +| [test-tmb.R](testthat/test-tmb.R#L353_L367) | tmb | h_mmrm_tmb_data gives error for rank deficient design matrix when not accepted | PASS | 1 | 0.017 | | +| [test-tmb.R](testthat/test-tmb.R#L393_L406) | tmb | h_mmrm_tmb_data catches case with multiple time points per subject early | PASS | 1 | 0.015 | | +| [test-tmb.R](testthat/test-tmb.R#L422) | tmb | h_mmrm_tmb_data has no side effect of overwrite the weights in global env | PASS | 1 | 0.014 | | +| [test-tmb.R](testthat/test-tmb.R#L438) | tmb | h_mmrm_tmb_data will not be affecte by `weights` in data | PASS | 2 | 0.021 | | +| [test-tmb.R](testthat/test-tmb.R#L455) | tmb | h_mmrm_tmb_parameters works as expected without start values | PASS | 2 | 0.017 | | +| [test-tmb.R](testthat/test-tmb.R#L472) | tmb | h_mmrm_tmb_parameters works as expected with start values | PASS | 2 | 0.016 | | +| [test-tmb.R](testthat/test-tmb.R#L488) | tmb | h_mmrm_tmb_parameters works as expected with antedependence | PASS | 2 | 0.016 | | +| [test-tmb.R](testthat/test-tmb.R#L504) | tmb | h_mmrm_tmb_parameters works as expected with heterogeneous antedependence | PASS | 2 | 0.015 | | +| [test-tmb.R](testthat/test-tmb.R#L520) | tmb | h_mmrm_tmb_parameters works as expected with Toeplitz | PASS | 2 | 0.016 | | +| [test-tmb.R](testthat/test-tmb.R#L536) | tmb | h_mmrm_tmb_parameters works as expected with heterogeneous Toeplitz | PASS | 2 | 0.019 | | +| [test-tmb.R](testthat/test-tmb.R#L552) | tmb | h_mmrm_tmb_parameters works as expected with autoregressive | PASS | 2 | 0.016 | | +| [test-tmb.R](testthat/test-tmb.R#L568) | tmb | h_mmrm_tmb_parameters works as expected with heterogeneous autoregressive | PASS | 2 | 0.016 | | +| [test-tmb.R](testthat/test-tmb.R#L584) | tmb | h_mmrm_tmb_parameters works as expected with compound symmetry | PASS | 2 | 0.018 | | +| [test-tmb.R](testthat/test-tmb.R#L600) | tmb | h_mmrm_tmb_parameters works as expected with heterogeneous compound symmetry | PASS | 2 | 0.015 | | +| [test-tmb.R](testthat/test-tmb.R#L616) | tmb | h_mmrm_tmb_parameters works as expected with spatial exponential | PASS | 2 | 0.015 | | +| [test-tmb.R](testthat/test-tmb.R#L629) | tmb | h_mmrm_tmb_assert_start passes as expected for sane start values | PASS | 2 | 0.008 | | +| [test-tmb.R](testthat/test-tmb.R#L639_L642) | tmb | h_mmrm_tmb_assert_start fails as expected for NaN objective function at start | PASS | 1 | 0.011 | | +| [test-tmb.R](testthat/test-tmb.R#L651_L654) | tmb | h_mmrm_tmb_assert_start fails as expected for NaN gradient function at start | PASS | 1 | 0.012 | | +| [test-tmb.R](testthat/test-tmb.R#L670) | tmb | h_mmrm_tmb_check_conv passes as expected for sane optimization result | PASS | 2 | 0.009 | | +| [test-tmb.R](testthat/test-tmb.R#L685_L688) | tmb | h_mmrm_tmb_check_conv raises singular hessian warning as expected | PASS | 1 | 0.012 | | +| [test-tmb.R](testthat/test-tmb.R#L702_L705) | tmb | h_mmrm_tmb_check_conv warns if convergence code signals non-convergence | PASS | 1 | 0.019 | | | [test-tmb.R](testthat/test-tmb.R#L738_L741) | tmb | h_mmrm_tmb_extract_cov works as expected | PASS | 2 | 0.050 | | -| [test-tmb.R](testthat/test-tmb.R#L776_L779) | tmb | h_mmrm_tmb_extract_cov works as expected for group covariance | PASS | 3 | 0.042 | | -| [test-tmb.R](testthat/test-tmb.R#L819_L826) | tmb | h_mmrm_tmb_fit works as expected | PASS | 16 | 0.065 | | -| [test-tmb.R](testthat/test-tmb.R#L875_L877) | tmb | h_mmrm_tmb_fit works as expected for grouped covariance | PASS | 18 | 0.071 | | -| [test-tmb.R](testthat/test-tmb.R#L916_L925) | tmb | h_mmrm_tmb_fit errors when an invalid covariance type is used | PASS | 2 | 0.026 | | -| [test-tmb.R](testthat/test-tmb.R#L946) | tmb | h_mmrm_tmb works as expected in a simple model without covariates and ML | PASS | 8 | 0.050 | | -| [test-tmb.R](testthat/test-tmb.R#L969) | tmb | h_mmrm_tmb works as expected in a simple model without covariates and REML | PASS | 8 | 0.051 | | -| [test-tmb.R](testthat/test-tmb.R#L996) | tmb | h_mmrm_tmb works with ad covariance structure and ML | PASS | 6 | 0.048 | | -| [test-tmb.R](testthat/test-tmb.R#L1010) | tmb | h_mmrm_tmb works with ad covariance structure and REML | PASS | 6 | 0.048 | | -| [test-tmb.R](testthat/test-tmb.R#L1026) | tmb | h_mmrm_tmb works with adh covariance structure and ML | PASS | 6 | 0.048 | | -| [test-tmb.R](testthat/test-tmb.R#L1043) | tmb | h_mmrm_tmb works with adh covariance structure and REML | PASS | 6 | 0.048 | | -| [test-tmb.R](testthat/test-tmb.R#L1062) | tmb | h_mmrm_tmb works with grouped adh covariance structure and ML | PASS | 5 | 0.057 | | -| [test-tmb.R](testthat/test-tmb.R#L1080) | tmb | h_mmrm_tmb works with grouped adh covariance structure and REML | PASS | 5 | 0.049 | | -| [test-tmb.R](testthat/test-tmb.R#L1104) | tmb | h_mmrm_tmb works with toep covariance structure and ML | PASS | 6 | 0.051 | | -| [test-tmb.R](testthat/test-tmb.R#L1123) | tmb | h_mmrm_tmb works with toep covariance structure and REML | PASS | 6 | 0.050 | | -| [test-tmb.R](testthat/test-tmb.R#L1144) | tmb | h_mmrm_tmb works with toeph covariance structure and ML | PASS | 6 | 0.050 | | -| [test-tmb.R](testthat/test-tmb.R#L1163) | tmb | h_mmrm_tmb works with toeph covariance structure and REML | PASS | 6 | 0.050 | | -| [test-tmb.R](testthat/test-tmb.R#L1184) | tmb | h_mmrm_tmb works with grouped toeph covariance structure and ML | PASS | 8 | 0.063 | | -| [test-tmb.R](testthat/test-tmb.R#L1212) | tmb | h_mmrm_tmb works with grouped toeph covariance structure and REML | PASS | 8 | 0.064 | | -| [test-tmb.R](testthat/test-tmb.R#L1241) | tmb | h_mmrm_tmb works with ar1 covariance structure and ML | PASS | 6 | 0.051 | | -| [test-tmb.R](testthat/test-tmb.R#L1257) | tmb | h_mmrm_tmb works with ar1 covariance structure and REML | PASS | 6 | 0.050 | | -| [test-tmb.R](testthat/test-tmb.R#L1275) | tmb | h_mmrm_tmb works with ar1h covariance structure and ML | PASS | 6 | 0.051 | | -| [test-tmb.R](testthat/test-tmb.R#L1291) | tmb | h_mmrm_tmb works with ar1h covariance structure and REML | PASS | 6 | 0.051 | | -| [test-tmb.R](testthat/test-tmb.R#L1308) | tmb | h_mmrm_tmb works with grouped ar1 covariance structure and ML | PASS | 6 | 0.052 | | -| [test-tmb.R](testthat/test-tmb.R#L1324) | tmb | h_mmrm_tmb works with grouped ar1 covariance structure and REML | PASS | 6 | 0.053 | | -| [test-tmb.R](testthat/test-tmb.R#L1341) | tmb | h_mmrm_tmb works with grouped ar1h covariance structure and ML | PASS | 6 | 0.052 | | -| [test-tmb.R](testthat/test-tmb.R#L1357) | tmb | h_mmrm_tmb works with grouped ar1h covariance structure and REML | PASS | 6 | 0.052 | | -| [test-tmb.R](testthat/test-tmb.R#L1383) | tmb | h_mmrm_tmb works with cs covariance structure and ML | PASS | 6 | 0.049 | | -| [test-tmb.R](testthat/test-tmb.R#L1400) | tmb | h_mmrm_tmb works with cs covariance structure and REML | PASS | 6 | 0.050 | | -| [test-tmb.R](testthat/test-tmb.R#L1418) | tmb | h_mmrm_tmb works with csh covariance structure and ML | PASS | 6 | 0.050 | | -| [test-tmb.R](testthat/test-tmb.R#L1434) | tmb | h_mmrm_tmb works with csh covariance structure and REML | PASS | 6 | 0.051 | | -| [test-tmb.R](testthat/test-tmb.R#L1453) | tmb | h_mmrm_tmb works with weights and ML | PASS | 6 | 0.055 | | -| [test-tmb.R](testthat/test-tmb.R#L1471) | tmb | h_mmrm_tmb works with weights and REML | PASS | 6 | 0.083 | | -| [test-tmb.R](testthat/test-tmb.R#L1491) | tmb | h_mmrm_tmb works with group cs covariance structure and ML | PASS | 6 | 0.051 | | -| [test-tmb.R](testthat/test-tmb.R#L1508) | tmb | h_mmrm_tmb works with cs covariance structure and REML | PASS | 6 | 0.050 | | -| [test-tmb.R](testthat/test-tmb.R#L1526) | tmb | h_mmrm_tmb works with grouped csh covariance structure and ML | PASS | 6 | 0.053 | | -| [test-tmb.R](testthat/test-tmb.R#L1542) | tmb | h_mmrm_tmb works with grouped csh covariance structure and REML | PASS | 6 | 0.053 | | -| [test-tmb.R](testthat/test-tmb.R#L1562) | tmb | h_mmrm_tmb works with group cs covariance structure and ML | PASS | 6 | 0.053 | | -| [test-tmb.R](testthat/test-tmb.R#L1579) | tmb | h_mmrm_tmb works with cs covariance structure and REML | PASS | 6 | 0.053 | | -| [test-tmb.R](testthat/test-tmb.R#L1597) | tmb | h_mmrm_tmb works with grouped csh covariance structure and ML | PASS | 6 | 0.054 | | -| [test-tmb.R](testthat/test-tmb.R#L1613) | tmb | h_mmrm_tmb works with grouped csh covariance structure and REML | PASS | 6 | 0.052 | | -| [test-tmb.R](testthat/test-tmb.R#L1631) | tmb | h_mmrm_tmb works with sp_exp covariance structure and ML | PASS | 5 | 0.045 | | -| [test-tmb.R](testthat/test-tmb.R#L1642) | tmb | h_mmrm_tmb works with sp_exp covariance structure and ML(2-dimension) | PASS | 5 | 0.054 | | -| [test-tmb.R](testthat/test-tmb.R#L1653) | tmb | h_mmrm_tmb works with sp_exp covariance structure and REML | PASS | 5 | 0.053 | | -| [test-tmb.R](testthat/test-tmb.R#L1664) | tmb | h_mmrm_tmb works with sp_exp covariance structure and REML(2-dimension) | PASS | 5 | 0.055 | | -| [test-tmb.R](testthat/test-tmb.R#L1678) | tmb | fit_mmrm also works with character ID variable | PASS | 3 | 0.058 | | -| [test-tmb.R](testthat/test-tmb.R#L1687) | tmb | fit_mmrm saves data name in call element as expected | PASS | 2 | 0.030 | | -| [test-tmb.R](testthat/test-tmb.R#L1694_L1701) | tmb | fit_mmrm works even when time point variable has unused factor levels | PASS | 3 | 0.058 | | -| [test-tmb.R](testthat/test-tmb.R#L1713_L1718) | tmb | fit_mmrm works if we keep the unused factor levels for specific covariance structure | PASS | 3 | 0.047 | | -| [test-tmb.R](testthat/test-tmb.R#L1730_L1738) | tmb | fit_mmrm warns if we keep the unused factor levels for unstructured covariance | PASS | 3 | 0.059 | | -| [test-tmb.R](testthat/test-tmb.R#L1750) | tmb | fit_mmrm works with below full rank original design matrix by default | PASS | 2 | 0.051 | | +| [test-tmb.R](testthat/test-tmb.R#L776_L779) | tmb | h_mmrm_tmb_extract_cov works as expected for group covariance | PASS | 3 | 0.051 | | +| [test-tmb.R](testthat/test-tmb.R#L819_L826) | tmb | h_mmrm_tmb_fit works as expected | PASS | 16 | 0.081 | | +| [test-tmb.R](testthat/test-tmb.R#L875_L877) | tmb | h_mmrm_tmb_fit works as expected for grouped covariance | PASS | 18 | 0.088 | | +| [test-tmb.R](testthat/test-tmb.R#L916_L925) | tmb | h_mmrm_tmb_fit errors when an invalid covariance type is used | PASS | 2 | 0.035 | | +| [test-tmb.R](testthat/test-tmb.R#L946) | tmb | h_mmrm_tmb works as expected in a simple model without covariates and ML | PASS | 8 | 0.063 | | +| [test-tmb.R](testthat/test-tmb.R#L969) | tmb | h_mmrm_tmb works as expected in a simple model without covariates and REML | PASS | 8 | 0.064 | | +| [test-tmb.R](testthat/test-tmb.R#L996) | tmb | h_mmrm_tmb works with ad covariance structure and ML | PASS | 6 | 0.060 | | +| [test-tmb.R](testthat/test-tmb.R#L1010) | tmb | h_mmrm_tmb works with ad covariance structure and REML | PASS | 6 | 0.054 | | +| [test-tmb.R](testthat/test-tmb.R#L1026) | tmb | h_mmrm_tmb works with adh covariance structure and ML | PASS | 6 | 0.056 | | +| [test-tmb.R](testthat/test-tmb.R#L1043) | tmb | h_mmrm_tmb works with adh covariance structure and REML | PASS | 6 | 0.056 | | +| [test-tmb.R](testthat/test-tmb.R#L1062) | tmb | h_mmrm_tmb works with grouped adh covariance structure and ML | PASS | 5 | 0.064 | | +| [test-tmb.R](testthat/test-tmb.R#L1080) | tmb | h_mmrm_tmb works with grouped adh covariance structure and REML | PASS | 5 | 0.056 | | +| [test-tmb.R](testthat/test-tmb.R#L1104) | tmb | h_mmrm_tmb works with toep covariance structure and ML | PASS | 6 | 0.059 | | +| [test-tmb.R](testthat/test-tmb.R#L1123) | tmb | h_mmrm_tmb works with toep covariance structure and REML | PASS | 6 | 0.061 | | +| [test-tmb.R](testthat/test-tmb.R#L1144) | tmb | h_mmrm_tmb works with toeph covariance structure and ML | PASS | 6 | 0.064 | | +| [test-tmb.R](testthat/test-tmb.R#L1163) | tmb | h_mmrm_tmb works with toeph covariance structure and REML | PASS | 6 | 0.072 | | +| [test-tmb.R](testthat/test-tmb.R#L1184) | tmb | h_mmrm_tmb works with grouped toeph covariance structure and ML | PASS | 8 | 0.076 | | +| [test-tmb.R](testthat/test-tmb.R#L1212) | tmb | h_mmrm_tmb works with grouped toeph covariance structure and REML | PASS | 8 | 0.077 | | +| [test-tmb.R](testthat/test-tmb.R#L1241) | tmb | h_mmrm_tmb works with ar1 covariance structure and ML | PASS | 6 | 0.061 | | +| [test-tmb.R](testthat/test-tmb.R#L1257) | tmb | h_mmrm_tmb works with ar1 covariance structure and REML | PASS | 6 | 0.060 | | +| [test-tmb.R](testthat/test-tmb.R#L1275) | tmb | h_mmrm_tmb works with ar1h covariance structure and ML | PASS | 6 | 0.067 | | +| [test-tmb.R](testthat/test-tmb.R#L1291) | tmb | h_mmrm_tmb works with ar1h covariance structure and REML | PASS | 6 | 0.063 | | +| [test-tmb.R](testthat/test-tmb.R#L1308) | tmb | h_mmrm_tmb works with grouped ar1 covariance structure and ML | PASS | 6 | 0.064 | | +| [test-tmb.R](testthat/test-tmb.R#L1324) | tmb | h_mmrm_tmb works with grouped ar1 covariance structure and REML | PASS | 6 | 0.065 | | +| [test-tmb.R](testthat/test-tmb.R#L1341) | tmb | h_mmrm_tmb works with grouped ar1h covariance structure and ML | PASS | 6 | 0.064 | | +| [test-tmb.R](testthat/test-tmb.R#L1357) | tmb | h_mmrm_tmb works with grouped ar1h covariance structure and REML | PASS | 6 | 0.061 | | +| [test-tmb.R](testthat/test-tmb.R#L1383) | tmb | h_mmrm_tmb works with cs covariance structure and ML | PASS | 6 | 0.058 | | +| [test-tmb.R](testthat/test-tmb.R#L1400) | tmb | h_mmrm_tmb works with cs covariance structure and REML | PASS | 6 | 0.058 | | +| [test-tmb.R](testthat/test-tmb.R#L1418) | tmb | h_mmrm_tmb works with csh covariance structure and ML | PASS | 6 | 0.058 | | +| [test-tmb.R](testthat/test-tmb.R#L1434) | tmb | h_mmrm_tmb works with csh covariance structure and REML | PASS | 6 | 0.060 | | +| [test-tmb.R](testthat/test-tmb.R#L1453) | tmb | h_mmrm_tmb works with weights and ML | PASS | 6 | 0.096 | | +| [test-tmb.R](testthat/test-tmb.R#L1471) | tmb | h_mmrm_tmb works with weights and REML | PASS | 6 | 0.062 | | +| [test-tmb.R](testthat/test-tmb.R#L1491) | tmb | h_mmrm_tmb works with group cs covariance structure and ML | PASS | 6 | 0.059 | | +| [test-tmb.R](testthat/test-tmb.R#L1508) | tmb | h_mmrm_tmb works with cs covariance structure and REML | PASS | 6 | 0.063 | | +| [test-tmb.R](testthat/test-tmb.R#L1526) | tmb | h_mmrm_tmb works with grouped csh covariance structure and ML | PASS | 6 | 0.064 | | +| [test-tmb.R](testthat/test-tmb.R#L1542) | tmb | h_mmrm_tmb works with grouped csh covariance structure and REML | PASS | 6 | 0.074 | | +| [test-tmb.R](testthat/test-tmb.R#L1562) | tmb | h_mmrm_tmb works with group cs covariance structure and ML | PASS | 6 | 0.074 | | +| [test-tmb.R](testthat/test-tmb.R#L1579) | tmb | h_mmrm_tmb works with cs covariance structure and REML | PASS | 6 | 0.064 | | +| [test-tmb.R](testthat/test-tmb.R#L1597) | tmb | h_mmrm_tmb works with grouped csh covariance structure and ML | PASS | 6 | 0.065 | | +| [test-tmb.R](testthat/test-tmb.R#L1613) | tmb | h_mmrm_tmb works with grouped csh covariance structure and REML | PASS | 6 | 0.063 | | +| [test-tmb.R](testthat/test-tmb.R#L1631) | tmb | h_mmrm_tmb works with sp_exp covariance structure and ML | PASS | 5 | 0.053 | | +| [test-tmb.R](testthat/test-tmb.R#L1642) | tmb | h_mmrm_tmb works with sp_exp covariance structure and ML(2-dimension) | PASS | 5 | 0.070 | | +| [test-tmb.R](testthat/test-tmb.R#L1653) | tmb | h_mmrm_tmb works with sp_exp covariance structure and REML | PASS | 5 | 0.051 | | +| [test-tmb.R](testthat/test-tmb.R#L1664) | tmb | h_mmrm_tmb works with sp_exp covariance structure and REML(2-dimension) | PASS | 5 | 0.064 | | +| [test-tmb.R](testthat/test-tmb.R#L1678) | tmb | fit_mmrm also works with character ID variable | PASS | 3 | 0.065 | | +| [test-tmb.R](testthat/test-tmb.R#L1687) | tmb | fit_mmrm saves data name in call element as expected | PASS | 2 | 0.033 | | +| [test-tmb.R](testthat/test-tmb.R#L1694_L1701) | tmb | fit_mmrm works even when time point variable has unused factor levels | PASS | 3 | 0.061 | | +| [test-tmb.R](testthat/test-tmb.R#L1713_L1718) | tmb | fit_mmrm works if we keep the unused factor levels for specific covariance structure | PASS | 3 | 0.052 | | +| [test-tmb.R](testthat/test-tmb.R#L1730_L1738) | tmb | fit_mmrm warns if we keep the unused factor levels for unstructured covariance | PASS | 3 | 0.064 | | +| [test-tmb.R](testthat/test-tmb.R#L1750) | tmb | fit_mmrm works with below full rank original design matrix by default | PASS | 2 | 0.053 | | | [test-utils.R](testthat/test-utils.R#L13) | utils | h_record_all_outputs correctly removes specified messages | PASS | 1 | 0.006 | | -| [test-utils.R](testthat/test-utils.R#L27) | utils | h_record_all_outputs works as expected with no removal list given for messages | PASS | 1 | 0.005 | | -| [test-utils.R](testthat/test-utils.R#L35) | utils | trace of a matrix works as expected | PASS | 2 | 0.012 | | -| [test-utils.R](testthat/test-utils.R#L44_L48) | utils | free_cores throws deprecation warning | PASS | 1 | 0.065 | | -| [test-utils.R](testthat/test-utils.R#L56) | utils | h_split_control split the control args based on optimizers | PASS | 9 | 0.042 | | -| [test-utils.R](testthat/test-utils.R#L70) | utils | h_split_control split the control args with updated arguments | PASS | 8 | 0.037 | | -| [test-utils.R](testthat/test-utils.R#L79) | utils | h_get_optimizers works for default optimizers | PASS | 2 | 0.015 | | -| [test-utils.R](testthat/test-utils.R#L85) | utils | h_get_optimizers works added arguments | PASS | 1 | 0.005 | | -| [test-utils.R](testthat/test-utils.R#L90) | utils | h_get_optimizers works custom optimizer | PASS | 2 | 0.011 | | -| [test-utils.R](testthat/test-utils.R#L98) | utils | h_optimizer_fun return correct optimizer | PASS | 8 | 0.049 | | -| [test-utils.R](testthat/test-utils.R#L112) | utils | h_partial_fun_args works correctly to add attributes | PASS | 4 | 0.019 | | +| [test-utils.R](testthat/test-utils.R#L27) | utils | h_record_all_outputs works as expected with no removal list given for messages | PASS | 1 | 0.008 | | +| [test-utils.R](testthat/test-utils.R#L35) | utils | trace of a matrix works as expected | PASS | 2 | 0.018 | | +| [test-utils.R](testthat/test-utils.R#L44_L48) | utils | free_cores throws deprecation warning | PASS | 1 | 0.082 | | +| [test-utils.R](testthat/test-utils.R#L56) | utils | h_split_control split the control args based on optimizers | PASS | 9 | 0.058 | | +| [test-utils.R](testthat/test-utils.R#L70) | utils | h_split_control split the control args with updated arguments | PASS | 8 | 0.046 | | +| [test-utils.R](testthat/test-utils.R#L79) | utils | h_get_optimizers works for default optimizers | PASS | 2 | 0.018 | | +| [test-utils.R](testthat/test-utils.R#L85) | utils | h_get_optimizers works added arguments | PASS | 1 | 0.006 | | +| [test-utils.R](testthat/test-utils.R#L90) | utils | h_get_optimizers works custom optimizer | PASS | 2 | 0.022 | | +| [test-utils.R](testthat/test-utils.R#L98) | utils | h_optimizer_fun return correct optimizer | PASS | 8 | 0.050 | | +| [test-utils.R](testthat/test-utils.R#L112) | utils | h_partial_fun_args works correctly to add attributes | PASS | 4 | 0.024 | | | Failed | Warning | Skipped | |:-------|:--------|:--------| @@ -336,7 +336,7 @@ Session Info | Field | Value | | |:---------|:-----------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | Version | R version 4.2.2 (2022-10-31) | | -| Platform | x86_64-pc-linux-gnu (64-bit) | ![](https://github.com/metrumresearchgroup/covrpage/blob/actions/inst/logo/gh.png?raw=true) | +| Platform | x86_64-pc-linux-gnu (64-bit) | ![](https://github.com/metrumresearchgroup/covrpage/blob/actions/inst/logo/gh.png?raw=true) | | Running | Ubuntu 22.04.1 LTS | | | Language | C | | | Timezone | UTC | |