### Miscellaneous - Added `Rcpp` specific flag to avoid warnings when using the upcoming new version of `Rcpp`. ## What's Changed * Prevent Rcpp from masking valid uses of Rf_error by @Enchufa2 in https://github.com/openpharma/mmrm/pull/556 * New minor release by @danielinteractive in https://github.com/openpharma/mmrm/pull/557 ## New Contributors * @Enchufa2 made their first contribution in https://github.com/openpharma/mmrm/pull/556 **Full Changelog**: https://github.com/openpharma/mmrm/compare/v0.3.16...v0.3.17

### New Features - `mmrm` now returns score per subject in empirical covariance. It can be accessed by `component(obj, name = "score_per_subject")`. ### Bug Fixes - Previously, when fitting a model with empirical covariance matrix estimation to a data set with a large number of subjects and/or a large number of coefficients, the model fitting could take very long and exhaust the memory in the worst case. This was due to an inefficient implementation of a matrix needed only in case of Satterthwaite degrees of freedom adjustment. This is fixed now, by returning the matrix `empirical_g_mat` in the `mmrm` object, instead of the previous `empirical_df_mat` matrix. The model fit is now much faster and does not exhaust the memory anymore. If old model fit objects are used, the `empirical_df_mat` will still be used correctly, however a deprecation warning will be issued. Please consider re-fitting the model to get the new `empirical_g_mat` matrix. - Previously, when compiling `mmrm` from source using a `TMB` version below 1.9.15, and installing a newer `TMB` of version 1.9.15 or above, would render the `mmrm` package unusable. This is fixed now, by checking in the dynamic library of `mmrm` whether the version of `TMB` has been sufficient. ## What's Changed * 476: be more robust against TMB version/order by @danielinteractive in https://github.com/openpharma/mmrm/pull/478 * return meat per subject when computing empirical covariance matrix of coefficients by @zhangh12 in https://github.com/openpharma/mmrm/pull/495 * Update DESCRIPTION by @clarkliming in https://github.com/openpharma/mmrm/pull/498 * 506: optimize empirical vcov / Satterthwaite d.f. calculations by @danielinteractive in https://github.com/openpharma/mmrm/pull/507 * Fix AR correlation structure in `gls` calls by @KonstantinLang in https://github.com/openpharma/mmrm/pull/512 * 515: release 0.3.15 by @danielinteractive in https://github.com/openpharma/mmrm/pull/516 ## New Contributors * @zhangh12 made their first contribution in https://github.com/openpharma/mmrm/pull/495 * @KonstantinLang made their first contribution in https://github.com/openpharma/mmrm/pull/512 **Full Changelog**: https://github.com/openpharma/mmrm/compare/v0.3.14...v0.3.15

### Bug Fixes - In version 0.3.13, when the tape optimizer from `TMB` was switched on, a warning would be given by `fit_mmrm()`, instructing users to turn off the tape optimizer. However, this is not necessary for reproducible results. Instead, it is now checked whether the deterministic hash for the `TMB` tape optimizer is used, and a warning is issued otherwise. - In version 0.3.13, the above described warning by `fit_mmrm()` was not visible to the user when calling `mmrm()` because it was caught internally, causing the first fit in each session to fail for the first tried optimizer and falling back to the other optimizers. The warning is now issued directly by `mmrm()`. This change ensures that the first model fit is consistent regarding the chosen optimizer (and thus numeric results) with subsequent model fits, avoiding discrepancies observed in version 0.3.13. ## What's Changed * 472: fix TMB option warning by @danielinteractive in https://github.com/openpharma/mmrm/pull/473 * add Lukas as contributor, bump up version, polish news by @danielinteractive in https://github.com/openpharma/mmrm/pull/475 **Full Changelog**: https://github.com/openpharma/mmrm/compare/v0.3.13...v0.3.14

### Bug Fixes - When running with `TMB` package versions below 1.9.15, MMRM fit results are not completely reproducible. While this may not be relevant for most applications, because the numerical differences are very small, we now issue a warning to the user if this is the case. We advise users to upgrade their `TMB` package versions to 1.9.15 or higher to ensure reproducibility. - Previously, `mmrm` ignored contrasts defined for covariates in the input data set. This is fixed now. - Previously, `predict` always required the response to be valid, even for unconditional predictions. This is fixed now and unconditional prediction does not require the response to be valid or present any longer. - `model.frame` has been updated to ensure that the `na.action` works correctly. - Previously `emmeans::emmeans` returned `NA` for spatial covariance structures. This is fixed now. - Previously `car::Anova` gave incorrect results if an interaction term is included and the covariate of interest was not the first categorical variable. This is fixed now. - Previously `car::Anova` failed if the model did not contain an intercept. This is fixed now. ### Miscellaneous - Upon fitting an MMRM, it is checked whether a not reproducible optimization feature of `TMB` is turned on. If so, a warning is issued to the user once per session. - `mmrm` now checks on the positive definiteness of the covariance matrix `theta_vcov`. If it is not positive definite, non-convergence is messaged appropriately. - `model.matrix` has been updated to ensure that the `NA` values are dropped. Additionally, an argument `use_response` is added to decide whether records with `NA` values in the response should be discarded. - `predict` has been updated to allow duplicated subject IDs for unconditional prediction. ## What's Changed * fix emmeans on spatial covariance by @clarkliming in https://github.com/openpharma/mmrm/pull/450 * clean up simulations by @clarkliming in https://github.com/openpharma/mmrm/pull/456 * keep contrast using droplevels by @clarkliming in https://github.com/openpharma/mmrm/pull/455 * fix anova type 3 by @clarkliming in https://github.com/openpharma/mmrm/pull/460 * 464: TMB warnings by @danielinteractive in https://github.com/openpharma/mmrm/pull/466 * make unconditional prediction default by @clarkliming in https://github.com/openpharma/mmrm/pull/463 * signal non-convergence if theta_vcov is not positive definite by @danielinteractive in https://github.com/openpharma/mmrm/pull/468 * Create FUNDING.yml by @danielinteractive in https://github.com/openpharma/mmrm/pull/471 * 469 cran by @danielinteractive in https://github.com/openpharma/mmrm/pull/470 **Full Changelog**: https://github.com/openpharma/mmrm/compare/v0.3.12...v0.3.13

### New Features - Add parameter `conditional` for `predict` method to control whether the prediction is conditional on the observation or not. ### Bug Fixes - Previously if the left hand side of a model formula is an expression, `predict` and `simulate` will fail. This is fixed now. ## What's Changed * add rhub workflow by @danielinteractive in https://github.com/openpharma/mmrm/pull/436 * add conditional arg for predict by @clarkliming in https://github.com/openpharma/mmrm/pull/438 * Adapt missing data sims by @danielinteractive in https://github.com/openpharma/mmrm/pull/443 * docs: Link the coverage badge to the HTML report by @cicdguy in https://github.com/openpharma/mmrm/pull/444 * change email, bump version by @danielinteractive in https://github.com/openpharma/mmrm/pull/447 **Full Changelog**: https://github.com/openpharma/mmrm/compare/v0.3.11...v0.3.12

### Bug Fixes - Previously if a secondary optimizer fails `mmrm` will fail. This is fixed now. - Previously character covariate variables will make `Anova` fail. This is fixed now. ## What's Changed * fix issue of h_record_all_outputs by @clarkliming in https://github.com/openpharma/mmrm/pull/424 * fix anova error by @clarkliming in https://github.com/openpharma/mmrm/pull/427 * remove biocVer by @clarkliming in https://github.com/openpharma/mmrm/pull/429 * update docs by @clarkliming in https://github.com/openpharma/mmrm/pull/428 * Missing data simulations by @danielinteractive in https://github.com/openpharma/mmrm/pull/430 * fix eigen deprecated warning by @clarkliming in https://github.com/openpharma/mmrm/pull/432 * add tests for residual.R, bump up version by @danielinteractive in https://github.com/openpharma/mmrm/pull/433 **Full Changelog**: https://github.com/openpharma/mmrm/compare/v0.3.10...v0.3.11

### Miscellaneous - Fix internal test skipping functions for MacOS R. ## What's Changed * 419: make skipping code more general to also run on old R versions by @danielinteractive in https://github.com/openpharma/mmrm/pull/420 **Full Changelog**: https://github.com/openpharma/mmrm/compare/v0.3.8...v0.3.10

### Miscellaneous - In documentation of `mmrm_control()`, the allowed vcov definition is corrected to "Empirical-Jackknife" (CR3), and "Empirical-Bias-Reduced" (CR2). - Fix a compiler warning related to missing format specification in error message function call. ## What's Changed * swapped CR2 and CR3 by @clarkliming in https://github.com/openpharma/mmrm/pull/379 * 377: Fix compiler warning for new CRAN hotfix by @danielinteractive in https://github.com/openpharma/mmrm/pull/381 **Full Changelog**: https://github.com/openpharma/mmrm/compare/v0.3.6...v0.3.7