Add ability to extract raw samples

[gowerc]

Closes #220

Fixes previous regression of not being able to return the individual quantity samples. I ended up having to re-work the functions a little bit as it was getting too nested. With this change the api has gone from:

survival_samples <- SurvivalSamples(stan_samples)
predict(
    survival_samples,
    patients = pts,
    type = "haz",
    time_grid = c(0, 100, 200)
)
autoplot(
    survival_samples,
    patients = pts,
    time_grid = c(0, 100, 200),
    type = "haz"
)

to

samps <- extractSurvivalQuantities(
    stan_samples,
    patients =  sample(dat_os$pt, 4),
    type = "haz",
    time_grid = c(0, 100, 200)
)
summary(samps)
as.data.frame(samps) |> tibble()
autoplot(samps)

To summarise

• The logic of running generated_quantities has been moved into the constructor-method rather than the individual predict / autoplot methods
• new as.data.frame method to return the raw samples
• predict has been re-named as summary which I felt better reflected what was happening
• Renamed the underlying object as SurvivalQuantities (think this slightly better represents what they are)

Currently marked as "draft" as I still need to update the documentation / unit tests

[danielinteractive]

Thanks @gowerc , sounds good - one thought on shorter naming, how about survival() instead of extractSurvivalQuantities() ? I think when applied to a samples object it is clear that we will get survival samples then.

[gowerc]

@danielinteractive - Pending CICD corrections this is now ready for review.

Regarding the function name I feel very conflicted. General convention for methods is to be verb focused "extract", "as", "sample", "get". Part of me wonders if survival is too generic in that this is really reducing the model down to pure the generated-quantities no other part of the survival model is left. In theory you could handle this with another layer but that feels a bit unnecessary in terms of user interactions e.g.

survsamps <- survival(jointsamples)
survquant <- quantities(survsamps, time_grid = ...)

I do appreciate / agree the current method name is a bit excessively verbose but the alternative doesn't quite feel "right" to me.

[danielinteractive]

Ok yeah good thoughts on the naming. Not super important so can leave as is

[danielinteractive]

Thanks @gowerc I browsed through it and looks good to me, only found some typos

[gowerc]

Another alternative is to move the implementation to the constructor so that the call is slightly shorter e.g.

samps <- SurvivalQuantities(stan_samples)

[github-actions]

Unit Tests Summary

    1 files    25 suites   3m 8s ⏱️
  57 tests   56 ✔️ 1 💤 0 ❌
228 runs  227 ✔️ 1 💤 0 ❌

Results for commit ee032e0.

♻️ 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                  46       0  100.00%
R/defaults.R                      11       6  45.45%   27, 57-84, 111
R/generics.R                      11       1  90.91%   173
R/JointModel.R                    46       5  89.13%   85-99
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                     12       0  100.00%
R/ParameterList.R                 28       0  100.00%
R/Prior.R                         58       9  84.48%   127-135
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                      7       0  100.00%
R/StanModule.R                   145       5  96.55%   185-186, 202, 235, 246
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%   179-202
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                           1191      91  92.36%

Diff against main

Filename                  Stmts    Miss  Cover
----------------------  -------  ------  -------
R/SurvivalQuantities.R     +156     +23  +85.26%
TOTAL                      +156     +23  -1.77%

Results for commit: 5971760

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results