Files in openpharma/mmrm
Mixed Models for Repeated Measures
.Rbuildignore
.github/CODEOWNERS
.github/CONTRIBUTING.Rmd
.github/CONTRIBUTING.md
.github/FUNDING.yml
.github/ISSUE_TEMPLATE/add_function.md
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/PULL_REQUEST_TEMPLATE.md
.github/workflows/check.yaml
.github/workflows/docs.yaml
.github/workflows/release.yaml
.github/workflows/rhub.yaml
.github/workflows/scheduled.yaml
.gitignore
.lintr
.pre-commit-config.yaml
DESCRIPTION
NAMESPACE
NEWS.md
R/between-within.R
R/catch-routine-registration.R
R/component.R
R/cov_struct.R
R/data.R
R/empirical.R
R/fit.R
R/interop-car.R
R/interop-emmeans.R
R/interop-parsnip.R
R/kenwardroger.R
R/mmrm-methods.R
R/mmrm-package.R
R/residual.R
R/satterthwaite.R
R/skipping.R
R/testing.R
R/tidiers.R
R/tmb-methods.R
R/tmb.R
R/utils-formula.R
R/utils-nse.R
R/utils.R
R/zzz.R
README.Rmd
README.md
_pkgdown.yml
data-raw/bcva-helpers.R
data-raw/bcva_data.R
data-raw/mmrm_review.R
data/bcva_data.rda
data/cached_mmrm_results.rda
data/fev_data.rda
design/R/R_weighted.R
design/R/R_weighted_mmrm.txt
design/R/R_weighted_nlme.txt
design/R/mmrm_ad.R
design/R/mmrm_ad_ml.txt
design/R/mmrm_ad_reml.txt
design/Robust/empirical.Rmd
design/Robust/empirical_adh.txt
design/Robust/empirical_adh_covb.csv
design/Robust/empirical_adh_lsmean.csv
design/Robust/empirical_adh_weighted.txt
design/Robust/empirical_adh_weighted_covb.csv
design/Robust/empirical_adh_weighted_lsmean.csv
design/Robust/empirical_ar1.txt
design/Robust/empirical_ar1_covb.csv
design/Robust/empirical_ar1_lsmean.csv
design/Robust/empirical_ar1_weighted.txt
design/Robust/empirical_ar1_weighted_covb.csv
design/Robust/empirical_ar1_weighted_lsmean.csv
design/Robust/empirical_arh1.txt
design/Robust/empirical_arh1_covb.csv
design/Robust/empirical_arh1_lsmean.csv
design/Robust/empirical_arh1_weighted.txt
design/Robust/empirical_arh1_weighted_covb.csv
design/Robust/empirical_arh1_weighted_lsmean.csv
design/Robust/empirical_cs.txt
design/Robust/empirical_cs_covb.csv
design/Robust/empirical_cs_lsmean.csv
design/Robust/empirical_cs_weighted.txt
design/Robust/empirical_cs_weighted_covb.csv
design/Robust/empirical_cs_weighted_lsmean.csv
design/Robust/empirical_csh.txt
design/Robust/empirical_csh_covb.csv
design/Robust/empirical_csh_lsmean.csv
design/Robust/empirical_csh_weighted.txt
design/Robust/empirical_csh_weighted_covb.csv
design/Robust/empirical_csh_weighted_lsmean.csv
design/Robust/empirical_spexp.txt
design/Robust/empirical_spexp_covb.csv
design/Robust/empirical_spexp_lsmean.csv
design/Robust/empirical_spexp_weighted.txt
design/Robust/empirical_spexp_weighted_covb.csv
design/Robust/empirical_spexp_weighted_lsmean.csv
design/Robust/empirical_toep.txt
design/Robust/empirical_toep_covb.csv
design/Robust/empirical_toep_lsmean.csv
design/Robust/empirical_toep_weighted.txt
design/Robust/empirical_toep_weighted_covb.csv
design/Robust/empirical_toep_weighted_lsmean.csv
design/Robust/empirical_toeph.txt
design/Robust/empirical_toeph_covb.csv
design/Robust/empirical_toeph_lsmean.csv
design/Robust/empirical_toeph_weighted.txt
design/Robust/empirical_toeph_weighted_covb.csv
design/Robust/empirical_toeph_weighted_lsmean.csv
design/Robust/empirical_us.txt
design/Robust/empirical_us_covb.csv
design/Robust/empirical_us_lsmean.csv
design/Robust/empirical_us_weighted.txt
design/Robust/empirical_us_weighted_covb.csv
design/Robust/empirical_us_weighted_lsmean.csv
design/Robust/robust.R
design/SAS/estimates.R
design/SAS/sas.R
design/SAS/sas_adh.R
design/SAS/sas_adh_ml.txt
design/SAS/sas_adh_reml.txt
design/SAS/sas_ar1.R
design/SAS/sas_ar1_ml.txt
design/SAS/sas_ar1_reml.txt
design/SAS/sas_ar1h.R
design/SAS/sas_ar1h_ml.txt
design/SAS/sas_ar1h_reml.txt
design/SAS/sas_coef_ci_ml_ar1.txt
design/SAS/sas_coef_ci_ml_un.txt
design/SAS/sas_coef_ci_reml_ar1.txt
design/SAS/sas_coef_ci_reml_un.txt
design/SAS/sas_cs.R
design/SAS/sas_cs_ml.txt
design/SAS/sas_cs_reml.txt
design/SAS/sas_csh.R
design/SAS/sas_csh_ml.txt
design/SAS/sas_csh_reml.txt
design/SAS/sas_group_adh_ml.txt
design/SAS/sas_group_adh_reml.txt
design/SAS/sas_group_ar1_ml.txt
design/SAS/sas_group_ar1_reml.txt
design/SAS/sas_group_ar1h_ml.txt
design/SAS/sas_group_ar1h_reml.txt
design/SAS/sas_group_cs_ml.txt
design/SAS/sas_group_cs_reml.txt
design/SAS/sas_group_csh_ml.txt
design/SAS/sas_group_csh_reml.txt
design/SAS/sas_group_toeph_ml.txt
design/SAS/sas_group_toeph_reml.txt
design/SAS/sas_log.txt
design/SAS/sas_log_nonconvergence.txt
design/SAS/sas_log_nonconvergence_reml.txt
design/SAS/sas_log_reml.txt
design/SAS/sas_log_simple.txt
design/SAS/sas_log_simple_reml.txt
design/SAS/sas_resid_spatial.txt
design/SAS/sas_resid_un.txt
design/SAS/sas_resid_un_grp.txt
design/SAS/sas_resid_un_weighted.txt
design/SAS/sas_sp_exp.R
design/SAS/sas_sp_exp2_ml.txt
design/SAS/sas_sp_exp2_reml.txt
design/SAS/sas_sp_exp_ml.txt
design/SAS/sas_sp_exp_reml.txt
design/SAS/sas_toep.sas
design/SAS/sas_toep_ml.rtf
design/SAS/sas_toep_reml.rtf
design/SAS/sas_toeph.R
design/SAS/sas_toeph_ml.txt
design/SAS/sas_toeph_reml.txt
design/SAS/sas_weighted.R
design/SAS/sas_weighted.txt
design/SAS/sas_weighted_mmrm.sas
design/SAS/sas_weighted_mmrm_ml.rtf
design/SAS/sas_weighted_mmrm_reml.rtf
design/SAT_autodiff/efficiency_compare.Rmd
design/TMB/TMB_mixed.R
design/TMB/TMB_mixed.cpp
design/TMB/TMB_mmrm.Rmd
design/TMB/TMB_mmrm.cpp
design/TMB/TMB_mmrm2.cpp
design/TMB/TMB_mmrm3.cpp
design/TMB/check_autodiff.R
design/TMB/check_autodiff.cpp
design/TMB/sas_log.txt
design/anova/anova.Rmd
design/anova/anova.sas
design/anova/test2_1.csv
design/anova/test2_2.csv
design/anova/test3_1.csv
design/anova/test3_2.csv
design/ddfm_covtype/ddfm_covtype.R
design/ddfm_covtype/kr1_adh.csv
design/ddfm_covtype/kr1_adh.txt
design/ddfm_covtype/kr1_ar1.csv
design/ddfm_covtype/kr1_ar1.txt
design/ddfm_covtype/kr1_arh1.csv
design/ddfm_covtype/kr1_arh1.txt
design/ddfm_covtype/kr1_cs.csv
design/ddfm_covtype/kr1_cs.txt
design/ddfm_covtype/kr1_csh.csv
design/ddfm_covtype/kr1_csh.txt
design/ddfm_covtype/kr1_spexp.csv
design/ddfm_covtype/kr1_spexp.txt
design/ddfm_covtype/kr1_toep.csv
design/ddfm_covtype/kr1_toep.txt
design/ddfm_covtype/kr1_toeph.csv
design/ddfm_covtype/kr1_toeph.txt
design/ddfm_covtype/kr1_us.csv
design/ddfm_covtype/kr1_us.txt
design/ddfm_covtype/kr_adh.csv
design/ddfm_covtype/kr_adh.txt
design/ddfm_covtype/kr_ar1.csv
design/ddfm_covtype/kr_ar1.txt
design/ddfm_covtype/kr_arh1.csv
design/ddfm_covtype/kr_arh1.txt
design/ddfm_covtype/kr_cs.csv
design/ddfm_covtype/kr_cs.txt
design/ddfm_covtype/kr_csh.csv
design/ddfm_covtype/kr_csh.txt
design/ddfm_covtype/kr_numderiv.R
design/ddfm_covtype/kr_spexp.csv
design/ddfm_covtype/kr_spexp.txt
design/ddfm_covtype/kr_toep.csv
design/ddfm_covtype/kr_toep.txt
design/ddfm_covtype/kr_toeph.csv
design/ddfm_covtype/kr_toeph.txt
design/ddfm_covtype/kr_us.csv
design/ddfm_covtype/kr_us.txt
design/design_fit.Rmd
design/predict_interval/ar(1)_kenwardroger.csv
design/predict_interval/ar(1)_satterthwaite.csv
design/predict_interval/cs_kenwardroger.csv
design/predict_interval/cs_satterthwaite.csv
design/predict_interval/predict_interval.Rmd
design/predict_interval/sp(exp)(VISITN VISITN2)_kenwardroger.csv
design/predict_interval/sp(exp)(VISITN VISITN2)_satterthwaite.csv
design/predict_interval/toep_kenwardroger.csv
design/predict_interval/toep_satterthwaite.csv
design/predict_interval/un_kenwardroger_linear.csv
design/predict_interval/un_satterthwaite.csv
design/unstructured_optimization.Rmd
inst/REFERENCES.bib
inst/WORDLIST
inst/jss.csl
man/Anova.mmrm.Rd
man/COV_TYPES.Rd
man/as.cov_struct.Rd
man/bcva_data.Rd
man/cached_mmrm_results.Rd
man/car_add_mmrm.Rd
man/check_package_version.Rd
man/component.Rd
man/cov_struct.Rd
man/cov_type_abbr.Rd
man/cov_type_name.Rd
man/covariance_types.Rd
man/df_1d.Rd
man/df_md.Rd
man/drop_elements.Rd
man/emit_tidymodels_register_msg.Rd
man/emmeans_support.Rd
man/emp_start.Rd
man/fev_data.Rd
man/figures/lifecycle-archived.svg
man/figures/lifecycle-defunct.svg
man/figures/lifecycle-deprecated.svg
man/figures/lifecycle-experimental.svg
man/figures/lifecycle-maturing.svg
man/figures/lifecycle-questioning.svg
man/figures/lifecycle-stable.svg
man/figures/lifecycle-superseded.svg
man/figures/logo.png
man/figures/logo.svg
man/fill_names.Rd
man/fit_mmrm.Rd
man/fit_single_optimizer.Rd
man/flat_expr.Rd
man/format.cov_struct.Rd
man/format_symbols.Rd
man/formula_rhs.Rd
man/h_add_covariance_terms.Rd
man/h_add_terms.Rd
man/h_coef_table.Rd
man/h_confirm_large_levels.Rd
man/h_construct_model_frame_inputs.Rd
man/h_default_value.Rd
man/h_df_1d_bw.Rd
man/h_df_1d_kr.Rd
man/h_df_1d_res.Rd
man/h_df_1d_sat.Rd
man/h_df_bw_calc.Rd
man/h_df_md_bw.Rd
man/h_df_md_from_1d.Rd
man/h_df_md_kr.Rd
man/h_df_md_res.Rd
man/h_df_md_sat.Rd
man/h_df_min_bw.Rd
man/h_df_to_tibble.Rd
man/h_drop_covariance_terms.Rd
man/h_drop_levels.Rd
man/h_extra_levels.Rd
man/h_extract_covariance_terms.Rd
man/h_first_contain_categorical.Rd
man/h_get_contrast.Rd
man/h_get_cov_default.Rd
man/h_get_empirical.Rd
man/h_get_index.Rd
man/h_get_kr_comp.Rd
man/h_get_na_action.Rd
man/h_get_optimizers.Rd
man/h_get_prediction.Rd
man/h_get_prediction_variance.Rd
man/h_get_sim_per_subj.Rd
man/h_get_theta_from_cov.Rd
man/h_gradient.Rd
man/h_jac_list.Rd
man/h_kr_df.Rd
man/h_md_denom_df.Rd
man/h_mmrm_tmb_assert_start.Rd
man/h_mmrm_tmb_check_conv.Rd
man/h_mmrm_tmb_data.Rd
man/h_mmrm_tmb_extract_cov.Rd
man/h_mmrm_tmb_fit.Rd
man/h_mmrm_tmb_formula_parts.Rd
man/h_mmrm_tmb_parameters.Rd
man/h_newdata_add_pred.Rd
man/h_obtain_lvls.Rd
man/h_optimizer_fun.Rd
man/h_partial_fun_args.Rd
man/h_print_aic_list.Rd
man/h_print_call.Rd
man/h_print_cov.Rd
man/h_quad_form.Rd
man/h_reconcile_cov_struct.Rd
man/h_record_all_output.Rd
man/h_register_s3.Rd
man/h_residuals_normalized.Rd
man/h_residuals_pearson.Rd
man/h_residuals_response.Rd
man/h_split_control.Rd
man/h_summarize_all_fits.Rd
man/h_tbl_confint_terms.Rd
man/h_test_1d.Rd
man/h_test_md.Rd
man/h_tmb_version_sufficient.Rd
man/h_tmb_warn_non_deterministic.Rd
man/h_tr.Rd
man/h_valid_formula.Rd
man/h_var_adj.Rd
man/h_warn_na_action.Rd
man/h_within_or_between.Rd
man/is_infix.Rd
man/mmrm-package.Rd
man/mmrm.Rd
man/mmrm_control.Rd
man/mmrm_methods.Rd
man/mmrm_tidiers.Rd
man/mmrm_tmb_methods.Rd
man/parsnip_add_mmrm.Rd
man/position_symbol.Rd
man/print.cov_struct.Rd
man/reexports.Rd
man/refit_multiple_optimizers.Rd
man/register_on_load.Rd
man/std_start.Rd
man/tmb_cov_type.Rd
man/validate_cov_struct.Rd
mmrm.Rproj
simulations/chols/README.Rmd
simulations/csh-benchmarks/.gitignore
simulations/csh-benchmarks/R/dgp-functions.R
simulations/csh-benchmarks/R/eval-functions.R
simulations/csh-benchmarks/R/meal.R
simulations/csh-benchmarks/R/method-functions.R
simulations/csh-benchmarks/R/tests/evalulator-tests.R
simulations/csh-benchmarks/R/tests/method-tests.R
simulations/csh-benchmarks/R/visualizer-functions.R
simulations/csh-benchmarks/README.Rmd
simulations/csh-benchmarks/results/hom_rct-het_rct/Varying num_part-num_part/.gitignore
simulations/csh-benchmarks/results/hom_rct-het_rct/Varying num_part-num_part/eval_results.rds
simulations/csh-benchmarks/results/hom_rct-het_rct/Varying num_part-num_part/experiment.rds
simulations/csh-benchmarks/results/hom_rct-het_rct/Varying num_part-num_part/viz_results.rds
simulations/csh-benchmarks/slurm/meal.sh
simulations/csh-benchmarks/vignette/summary.Rmd
simulations/missing-data-benchmarks/README.md
simulations/missing-data-benchmarks/Snakefile
simulations/missing-data-benchmarks/aggregate_all_results.R
simulations/missing-data-benchmarks/config.yaml
simulations/missing-data-benchmarks/process_sas.R
simulations/missing-data-benchmarks/programs/analyze_data.R
simulations/missing-data-benchmarks/programs/generate_data.R
simulations/missing-data-benchmarks/run_analysis.R
simulations/missing-data-benchmarks/run_analysis.sas
simulations/missing-data-benchmarks/simulate_data.R
src/.gitignore
src/Makevars
src/chol_cache.h
src/covariance.h
src/derivatives.h
src/empirical.cpp
src/exports.cpp
src/jacobian.cpp
src/kr_comp.cpp
src/mmrm.cpp
src/predict.cpp
src/test-chol_cache.cpp
src/test-covariance.cpp
src/test-derivatives.cpp
src/test-runner.cpp
src/test-utils.cpp
src/testthat-helpers.h
src/tmb.cpp
src/tmb_includes.h
src/utils.h
tests/testthat.R
tests/testthat/_snaps/between-within.md
tests/testthat/_snaps/car.md
tests/testthat/_snaps/emmeans.md
tests/testthat/_snaps/empirical.md
tests/testthat/_snaps/fit.md
tests/testthat/_snaps/kenwardroger.md
tests/testthat/_snaps/mmrm-methods.md
tests/testthat/_snaps/testing.md
tests/testthat/_snaps/tmb-methods.md
tests/testthat/helper-examples.R
tests/testthat/helper-skipping.R
tests/testthat/test-between-within.R
tests/testthat/test-car.R
tests/testthat/test-component.R
tests/testthat/test-cov-struct.R
tests/testthat/test-cpp-covariance.R
tests/testthat/test-cpp-utils.R
tests/testthat/test-cpp.R
tests/testthat/test-emmeans.R
tests/testthat/test-empirical.R
tests/testthat/test-fit.R
tests/testthat/test-interop-parsnip.R
tests/testthat/test-interop.R
tests/testthat/test-kenwardroger.R
tests/testthat/test-mmrm-methods.R
tests/testthat/test-residual.R
tests/testthat/test-satterthwaite.R
tests/testthat/test-skipping.R
tests/testthat/test-testing.R
tests/testthat/test-tidiers.R
tests/testthat/test-tmb-methods.R
tests/testthat/test-tmb.R
tests/testthat/test-utils-formula.R
tests/testthat/test-utils-nse.R
tests/testthat/test-utils.R
vignettes/.gitignore
vignettes/algorithm.Rmd
vignettes/between_within.Rmd
vignettes/coef_vcov.Rmd
vignettes/covariance.Rmd
vignettes/empirical_wls.Rmd
vignettes/hypothesis_testing.Rmd
vignettes/introduction.Rmd
vignettes/kenward.Rmd
vignettes/methodological_introduction.Rmd
vignettes/mmrm_review_methods.Rmd
vignettes/mmrm_review_refs.bib
vignettes/package_structure.Rmd
vignettes/predict.Rmd
vignettes/satterthwaite.Rmd
vignettes/subsections/_intro-acknowledgments.Rmd
vignettes/subsections/_intro-customizations.Rmd
vignettes/subsections/_intro-getting_started.Rmd
vignettes/subsections/_intro-hypothesis_testing.Rmd
vignettes/subsections/_intro-lower_level.Rmd
vignettes/subsections/_intro-model_features.Rmd
vignettes/subsections/_intro-tidymodels.Rmd
