Closed gowerc closed 4 months ago
Filename Stmts Miss Cover Missing
------------------------------- ------- ------ ------- --------------------------------
R/brier_score.R 167 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 34 4 88.24% 52, 396, 416, 471
R/Grid.R 27 1 96.30% 173
R/GridEven.R 32 0 100.00%
R/GridEvent.R 22 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 126 10 92.06% 146-151, 201, 205, 247, 293, 299
R/JointModelSamples.R 66 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/LongitudinalClaretBruno.R 88 6 93.18% 164-168, 183
R/LongitudinalGSF.R 89 0 100.00%
R/LongitudinalModel.R 19 0 100.00%
R/LongitudinalQuantities.R 71 0 100.00%
R/LongitudinalRandomSlope.R 44 5 88.64% 102-106
R/LongitudinalSteinFojo.R 80 5 93.75% 155-159
R/Parameter.R 14 0 100.00%
R/ParameterList.R 42 1 97.62% 184
R/Prior.R 254 6 97.64% 507, 651-665
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/SimLongitudinalClaretBruno.R 52 0 100.00%
R/SimLongitudinalGSF.R 60 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 144 2 98.61% 13, 335
R/zzz.R 28 25 10.71% 3, 8-12, 14-35, 47
TOTAL 3009 120 96.01%
Filename Stmts Miss Cover
--------------------------- ------- ------ --------
R/generics.R +1 0 +0.36%
R/LongitudinalClaretBruno.R +5 0 +0.41%
R/LongitudinalGSF.R +5 0 +100.00%
R/LongitudinalRandomSlope.R +2 0 +0.54%
R/LongitudinalSteinFojo.R +4 0 +0.33%
R/Prior.R +18 -2 +1.03%
TOTAL +35 -2 +0.11%
Results for commit: a0a8a6f923382015dd019b1a77ec3f93d03a50d7
Minimum allowed coverage is 80%
:recycle: This comment has been updated with latest results
1 files 160 suites 6m 26s :stopwatch: 139 tests 136 :white_check_mark: 3 :zzz: 0 :x: 1 052 runs 1 048 :white_check_mark: 4 :zzz: 0 :x:
Results for commit a9c9f1ab.
:recycle: This comment has been updated with latest results.
Test Suite | $Status$ | Time on main |
$±Time$ | $±Tests$ | $±Skipped$ | $±Failures$ | $±Errors$ |
---|---|---|---|---|---|---|---|
JointModelSamples | 💔 | $30.05$ | $+2.01$ | $0$ | $0$ | $0$ | $0$ |
extract_quantities | 💚 | $7.52$ | $-2.56$ | $0$ | $0$ | $0$ | $0$ |
misc_models | 💔 | $0.84$ | $+4.40$ | $0$ | $0$ | $0$ | $0$ |
model_multi_chain | 💚 | $4.54$ | $-1.41$ | $0$ | $0$ | $0$ | $0$ |
Results for commit 39f98f9d0aea465204c30d16b05357d316fc90bf
♻️ This comment has been updated with latest results.
Closes #268
Generally tried to shield the user from this as much as possible and pushed all code to the behind the scenes. Each model (e.g.
LongitudinalGSF
) is responsible for setting the constraints on the priors which is done viaset_limits()
.initialValues()
then attempts to draw 100 values and discards any that do not meet the constraint. If there is more than 1 value that meets the constraint then 1 of these is sampled at random.For random effects parameters that were having their distribution set based on the initial value of the parent I've tried to reduce the variance of the values being produced by implementing a
median
function. In short this just generates 250 values following the above described method and then just takes the median across these. Originally we were just taking the centre point of the distribution but as users can now specify distributions whose centre point is potentially not a valid value this alternative was required.Misc changes
prior@init
slot toprior@centre
which better represents what this parameter is doing (its meant to denote the centre of the distribution or more accurately the point at which we shrink our initial values towards).test_data_01
which is generated by a helper function started throwing errors when the unit tests were run in parallel. I've had to change the code slightly such that the environment is now individually created in each file that needs it. This does unfortunately add some run time but I couldn't find another solution :(