update anova type II and III

[clarkliming]

close #392

[danielinteractive]

Thanks @clarkliming , can you add a new issue for this production work? (ideally also with checkboxes for the objectives of that issue) The other issue was only for the design I think

[github-actions]

Code Coverage Summary

Filename                    Stmts    Miss  Cover    Missing
------------------------  -------  ------  -------  -------------------------------
R/between-within.R             59       0  100.00%
R/component.R                  67       0  100.00%
R/cov_struct.R                 97       1  98.97%   407
R/empirical.R                   7       0  100.00%
R/fit.R                       223      11  95.07%   186-189, 407, 450-453, 468, 498
R/interop-car.R                70       2  97.14%   9, 48
R/interop-emmeans.R            39       0  100.00%
R/interop-parsnip.R            59       1  98.31%   12
R/kenwardroger.R               92       2  97.83%   41, 63
R/mmrm-methods.R              120       0  100.00%
R/residual.R                    8       8  0.00%    10-31
R/satterthwaite.R             116      12  89.66%   238-249
R/testing.R                    64       4  93.75%   29, 31, 80, 82
R/tidiers.R                    72       2  97.22%   46-47
R/tmb-methods.R               287       3  98.95%   277-278, 338
R/tmb.R                       287       0  100.00%
R/utils-formula.R              27       0  100.00%
R/utils-nse.R                  16       0  100.00%
R/utils.R                     134      11  91.79%   276-286, 372
R/zzz.R                        70      24  65.71%   7-22, 55-60, 90, 118, 138
src/chol_cache.h               63       0  100.00%
src/covariance.h              101       1  99.01%   177
src/derivatives.h             126       0  100.00%
src/empirical.cpp              72       0  100.00%
src/exports.cpp                47       0  100.00%
src/jacobian.cpp               47       1  97.87%   54
src/kr_comp.cpp                56       0  100.00%
src/mmrm.cpp                   76       0  100.00%
src/predict.cpp                93       0  100.00%
src/test-chol_cache.cpp        58       5  91.38%   9, 18, 26, 55, 62
src/test-covariance.cpp       123       5  95.93%   9, 29, 40, 61, 72
src/test-derivatives.cpp      108       7  93.52%   44, 53, 62, 85, 94, 106, 124
src/test-utils.cpp            195       7  96.41%   9, 16, 24, 34, 44, 57, 119
src/testthat-helpers.h         15       5  66.67%   36-37, 41, 50, 53
src/utils.h                    84       0  100.00%
TOTAL                        3178     112  96.48%

Diff against main

Filename           Stmts    Miss  Cover
---------------  -------  ------  -------
R/interop-car.R      +70      +2  +97.14%
R/testing.R           +9       0  +1.02%
R/utils.R            +10      +1  -0.14%
R/zzz.R               +5      +5  -5.05%
TOTAL                +94      +8  -0.15%

Results for commit: af1155e

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

       1 files       44 suites   23s ⏱️
   467 tests    429 ✔️ 38 💤 0 ❌
1 837 runs  1 794 ✔️ 43 💤 0 ❌

Results for commit af1155e.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
car	👶		$+0.28$	$+17$	$+1$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
car	👶		$+0.20$	Anova_give_similar_results_to_SAS
car	👶		$+0.02$	Anova_works_as_expected
car	👶		$+0.04$	car_emits_a_message_about_mmrm_registration_on_load
car	👶		$+0.02$	h_get_contrast_works_as_expected
testing	👶		$+0.01$	df_md_return_df_0_and_other_stat_all_NA_if_empty_matrix_provided

Results for commit c4d26f2

♻️ This comment has been updated with latest results.

[danielinteractive]

Thanks @clarkliming , looks great!
Few suggestions:

• Could we use a similar mechanism as for emmeans so that we don't need to import car but just suggest it?
• could we add a NEWS item
• For the vignette I remember we somewhere have something on hypothesis testing already, would it make sense to integrate those together somehow?
• please add an example in introduction vignette

[clarkliming]

Thanks @clarkliming , looks great! Few suggestions:

• Could we use a similar mechanism as for emmeans so that we don't need to import car but just suggest it?

Updated. However added a new function (copy from emmeans) but it is difficult to do any testing on it

• could we add a NEWS item

Already had an entry under "new features". do we need more?

• For the vignette I remember we somewhere have something on hypothesis testing already, would it make sense to integrate those together somehow?

Is it the section in introduction? Maybe it is clearer to be separated here because it involves a lot of details?

• please add an example in introduction vignette

Added now

[danielinteractive]

Thank you @clarkliming ! Great stuff. I gave it a thorough last round of review.

[danielinteractive]

Congrats @clarkliming , good to merge after last few suggestions are in!

[danielinteractive]

maybe set in backticks to avoid the need for this?

[clarkliming]

it is in the matrix part so adding backtick is ugly and really not necessary

$$\begin{bmatrix} \mu & ARMCD & RACE & RACE & ARMCD:RACE & ARMCD:RACE\\\ 0 & 0 & 1 & 0 & 0 & 0\\ 0 & 0 & 0 & 1 & 0 & 0\\ \end{bmatrix}$$ $$\begin{bmatrix} \mu & `ARMCD` & `RACE` & `RACE` & `ARMCD`:`RACE` & `ARMCD`:`RACE`\\\ 0 & 0 & 1 & 0 & 0 & 0\\ 0 & 0 & 0 & 1 & 0 & 0\\ \end{bmatrix}$$