Major Documentation Update

[gowerc]

Closes #177 #217

Despite the huge number of files changed the changes can easily be summarised as:

• Converted all methods that don't rely on multiple dispatch to S3
• Tried to standardise the documentation format as much as possible (use of @family to link methods and object pages and combining the object page with the constructor page)

To clarify other than the S4 -> S3 conversion there should be no actual code changes within the functions themselves here.

[github-actions]

Unit Tests Summary

    1 files    25 suites   2m 28s ⏱️
  57 tests   56 ✔️ 1 💤 0 ❌
228 runs  227 ✔️ 1 💤 0 ❌

Results for commit a2fd135.

♻️ This comment has been updated with latest results.

[github-actions]

Code Coverage Summary

Filename                       Stmts    Miss  Cover    Missing
---------------------------  -------  ------  -------  ----------------------
R/DataJoint.R                     27       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                      11       1  90.91%   69
R/JointModel.R                    46       5  89.13%   95-107
R/JointModelSamples.R             54       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/LongitudinalRandomSlope.R       17       1  94.12%   43
R/LongitudinalSamples.R           15       0  100.00%
R/Parameter.R                     11       0  100.00%
R/ParameterList.R                 27       0  100.00%
R/Prior.R                         63      15  76.19%   50-55, 156-164
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           156      23  85.26%   174-197
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                           1194      98  91.79%

Diff against main

Filename             Stmts    Miss  Cover
-----------------  -------  ------  --------
R/DataSurvival.R        -1       0  +100.00%
R/defaults.R            +2      +1  +0.70%
R/Parameter.R           -1       0  +100.00%
R/ParameterList.R       -1       0  +100.00%
R/Prior.R               +5      +6  -8.29%
R/StanModel.R           -1       0  +100.00%
TOTAL                   +3      +7  -0.57%

Results for commit: cc73c45

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results