Implements growth link function

[gowerc]

Partially addresses #170

Only thing that is making me a bit nervous about this is that the confidence intervals for this link parameter in my testing seem all most excessively wide. For example with ~12 observations per subject and 800 subjects and a real value of 3 I'm getting:

# A tibble: 2 × 7
  variable       mean   q01   q99  rhat ess_bulk ess_tail
  <chr>         <dbl> <dbl> <dbl> <dbl>    <dbl>    <dbl>
1 link_growth   2.99  2.04   3.91  1.00    2035.    1249.

That might not seem so bad but then compare it to the other model parameters:

> dat
# A tibble: 5 × 7
  variable           mean    q01    q99  rhat ess_bulk ess_tail
  <chr>             <dbl>  <dbl>  <dbl> <dbl>    <dbl>    <dbl>
1 lm_sf_mu_bsld[1] 60.3   59.9   60.9    1.00    1895.     624.
2 lm_sf_mu_ks[1]    0.200  0.197  0.203  1.00    1879.    1311.
3 lm_sf_mu_ks[2]    0.251  0.248  0.254  1.00    1814.    1210.
4 lm_sf_mu_kg[1]    0.150  0.146  0.154  1.00    1691.     803.
5 lm_sf_mu_kg[2]    0.300  0.293  0.307  1.00    1770.    1302.

The confidence intervals are noticeably tighter. Admittedly this isn't really a unique problem for the growth link as it happens with all of them, but still makes me a little nervous... maybe its fine ?

Either way the full link testing code takes ages to run so I've marked it as "not for cran" meaning it will only run in our twice a month CRON job. I done a parser check though, e.g. it checks stans static parser to ensure the stan code is syntactically valid.

[github-actions]

Unit Tests Summary

  1 files   42 suites   8m 15s ⏱️
138 tests 106 ✅ 32 💤 0 ❌
929 runs  897 ✅ 32 💤 0 ❌

Results for commit 43ceccb.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
Grid	💔	$203.88$	$+4.90$	$0$	$0$	$0$	$0$
GridPrediction	💚	$130.96$	$-4.67$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
Grid	💔	$76.66$	$+3.54$	GridObservered_Constructs_correct_quantities
Grid	💔	$38.02$	$+1.42$	GridPopulation_works_as_expected_for_GSF_models
GridPrediction	💚	$106.38$	$-3.66$	GridPrediction_works_as_expected_for_Survival_models
GridPrediction	💚	$24.20$	$-1.01$	GridPrediction_works_for_survival_only_models
LongitudinalSteinFojo	👶		$+0.01$	Can_recover_known_distributional_parameters_from_a_SF_joint_model_with_growth_link

Results for commit 960c9eb

♻️ This comment has been updated with latest results.

[github-actions]

Code Coverage Summary

Filename                           Stmts    Miss  Cover    Missing
-------------------------------  -------  ------  -------  --------------------------------
R/brier_score.R                      166       0  100.00%
R/DataJoint.R                         76       2  97.37%   264, 270
R/DataLongitudinal.R                 119       1  99.16%   244
R/DataSubject.R                       85       1  98.82%   142
R/DataSurvival.R                      98       0  100.00%
R/defaults.R                          10       6  40.00%   18-57, 84
R/generics.R                          30       3  90.00%   51, 394, 444
R/Grid.R                              27       1  96.30%   170
R/GridEven.R                          32       0  100.00%
R/GridFixed.R                         30       0  100.00%
R/GridGrouped.R                       52       0  100.00%
R/GridManual.R                        23       3  86.96%   78-80
R/GridObserved.R                      20       0  100.00%
R/GridPopulation.R                    31       4  87.10%   61, 69-71
R/GridPrediction.R                    36       6  83.33%   83, 91-95
R/JointModel.R                       123       8  93.50%   141-143, 193, 197, 239, 285, 291
R/JointModelSamples.R                 59       0  100.00%
R/link_generics.R                     13       3  76.92%   59, 76, 91
R/Link.R                              62       4  93.55%   200-203
R/LinkComponent.R                     19       3  84.21%   88, 120-121
R/LongitudinalGSF.R                   82       0  100.00%
R/LongitudinalModel.R                 19       0  100.00%
R/LongitudinalQuantities.R            71       0  100.00%
R/LongitudinalRandomSlope.R           41       5  87.80%   93-97
R/LongitudinalSteinFojo.R             75       5  93.33%   143-147
R/Parameter.R                         14       0  100.00%
R/ParameterList.R                     42       1  97.62%   184
R/Prior.R                            236       8  96.61%   480, 576, 588-606
R/Promise.R                           25       0  100.00%
R/Quantities.R                        60       0  100.00%
R/QuantityGeneratorPopulation.R       22       0  100.00%
R/QuantityGeneratorPrediction.R       48       0  100.00%
R/QuantityGeneratorSubject.R          19       0  100.00%
R/settings.R                          12      12  0.00%    55-69
R/SimGroup.R                           5       0  100.00%
R/SimJointData.R                      72       1  98.61%   103
R/SimLongitudinal.R                    5       2  60.00%   22, 40
R/SimLongitudinalGSF.R                53       0  100.00%
R/SimLongitudinalRandomSlope.R        42       0  100.00%
R/SimLongitudinalSteinFojo.R          50       0  100.00%
R/SimSurvival.R                      104       0  100.00%
R/StanModel.R                         15       0  100.00%
R/StanModule.R                       176       6  96.59%   192-193, 235, 246, 383, 411
R/SurvivalExponential.R               10       0  100.00%
R/SurvivalLoglogistic.R               11       0  100.00%
R/SurvivalModel.R                     19       0  100.00%
R/SurvivalQuantities.R               170       1  99.41%   125
R/SurvivalWeibullPH.R                 11       0  100.00%
R/utilities.R                        143       1  99.30%   13
R/zzz.R                               28      25  10.71%   3, 8-12, 14-35, 47
TOTAL                               2791     112  95.99%

Diff against main

Filename                        Stmts    Miss  Cover
----------------------------  -------  ------  --------
R/link_generics.R                  +3      +1  -3.08%
R/LongitudinalGSF.R                +5       0  +100.00%
R/LongitudinalRandomSlope.R        +5      +5  -12.20%
R/LongitudinalSteinFojo.R          +5       0  +0.48%
R/SimLongitudinalGSF.R             +2       0  +100.00%
R/SimLongitudinalSteinFojo.R       +2       0  +100.00%
TOTAL                             +22      +6  -0.18%

Results for commit: 43ceccb

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[danielinteractive]

looks good, I think this just means that there is not a lot of information in the data about the link coefficient...