Align Longitudinal Plots API

[gowerc]

Closes #227

Main part of this feature was to bring the longitudinal plotting code in line with the survival plotting code. The longitudinal API is now:

long_quantities <- LongitudinalQuantities(
    mcmc_results,
    groups = selected_patients
)
as.data.frame(long_quantities)   # raw samples
summary(long_quantities)         # Summary statistics of raw samples
autoplot(long_quantities)        # Plots 

Behind the scenes I extract out the common elements of the LongitudinalQuantities and the SurvivalQuantites into a dedicated Quantities object that dos the heavy lifting.

[github-actions]

Unit Tests Summary

    1 files    26 suites   3m 26s ⏱️
  58 tests   56 ✔️ 2 💤 0 ❌
226 runs  224 ✔️ 2 💤 0 ❌

Results for commit 1539f90.

♻️ This comment has been updated with latest results.

[github-actions]

Code Coverage Summary

Filename                       Stmts    Miss  Cover    Missing
---------------------------  -------  ------  -------  ----------------------
R/DataJoint.R                     36       0  100.00%
R/DataLongitudinal.R              71       0  100.00%
R/DataSurvival.R                  45       0  100.00%
R/defaults.R                      13       7  46.15%   27, 45-84, 111
R/generics.R                      10       1  90.00%   69
R/JointModel.R                    46       5  89.13%   93-105
R/JointModelSamples.R             20       0  100.00%
R/Link.R                           6       0  100.00%
R/LinkGSF.R                       63      12  80.95%   109-120
R/LinkNone.R                       3       1  66.67%   36
R/LinkRandomSlope.R               10       0  100.00%
R/LongitudinalGSF.R               23       0  100.00%
R/LongitudinalModel.R             10       0  100.00%
R/LongitudinalQuantities.R        71       8  88.73%   89-96
R/LongitudinalRandomSlope.R       17       1  94.12%   43
R/Parameter.R                     11       0  100.00%
R/ParameterList.R                 27       0  100.00%
R/Prior.R                         63      15  76.19%   49-54, 155-163
R/Quantities.R                    89       0  100.00%
R/simulations_gsf.R               43       0  100.00%
R/simulations_os.R                11       5  54.55%   35-39
R/simulations_rs.R                21       0  100.00%
R/simulations.R                   99       1  98.99%   122
R/StanModel.R                      6       0  100.00%
R/StanModule.R                   145       5  96.55%   188-189, 205, 241, 252
R/SurvivalExponential.R            9       0  100.00%
R/SurvivalLoglogistic.R           10      10  0.00%    31-40
R/SurvivalModel.R                 12       0  100.00%
R/SurvivalQuantities.R           103       6  94.17%   161-166
R/SurvivalWeibullPH.R             10       0  100.00%
R/utilities.R                    146       1  99.32%   13
R/zzz.R                           11      11  0.00%    4-29
TOTAL                           1260      89  92.94%

Diff against main

Filename                      Stmts    Miss  Cover
--------------------------  -------  ------  --------
R/DataJoint.R                    +9       0  +100.00%
R/generics.R                     -1       0  -0.91%
R/JointModelSamples.R           -34       0  +100.00%
R/LongitudinalQuantities.R      +71      +8  +88.73%
R/Quantities.R                  +89       0  +100.00%
R/SurvivalQuantities.R          -53     -17  +8.92%
TOTAL                           +81      -9  +1.14%

Results for commit: 1539f90

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[gowerc]

@danielinteractive - Ok ready for review, finally got all the cicd checks passing

[danielinteractive]

Thanks @gowerc , it is a bit too long for me to review everything, just gave a few general suggestions

[gowerc]

@danielinteractive - Apologies, unfortunately most of the outstanding issues are quite chunky 😢 I appreciate this makes reviews quite difficult so I've tried to be a bit more comprehensive with the unit testing and assertions to compensate.