Files in plmmr

Penalized Linear Mixed Models for Correlated Data

NEWS.md README.md R/cv-plmm.R R/rotate_filebacked.R R/name_and_count_bigsnp.R R/untransform.R R/find_example_data.R R/standardize_matrix.R R/create_log.R R/predict-plmm.R R/count_cores.R R/estimate_eta.R R/plmm_checks.R R/index_samples.R R/summary-cv-plmm.R R/check_for_file_extension.R R/relatedness_mat.R R/cvf.R R/plot-plmm.R R/plmm_prep.R R/print-summary-cv-plmm.R R/pretty_time.R R/read_plink_files.R R/coef-cv-plmm.R R/data.R R/count_constant_features.R R/eigen_K.R R/fbm2bm.R R/plmmr-package.R R/penalties.R R/untransform_delim.R R/add_predictors.R R/get_data.R R/create_design_filebacked.R R/untransform_in_memory.R R/coef-plmm.R R/impute_snp_data.R R/plmm.R R/read_data_files.R R/lam_names.R R/process_plink.R R/log_lik.R R/create_design.R R/get_hostname.R R/construct_variance.R R/print-summary-plmm.R R/setup_lambda.R R/zzz.R R/predict_within_cv.R R/plmm_format.R R/process_delim.R R/untransform_plink.R R/loss-plmm.R R/standardize_filebacked.R R/subset_bigsnp.R R/align_ids.R R/create_design_in_memory.R R/big_cbind.R R/plmm_fit.R R/plot-cv-plmm.R R/summary-plmm.R inst/doc/getting-started.R inst/doc/getting-started.Rmd inst/tinytest/_debug_standardization.R inst/tinytest/_penncath_mid_test.R inst/tinytest/_sign_flip_issue.R inst/tinytest/_test_fbm.R inst/tinytest/_test_process_plink.R inst/tinytest/_test_rotation_approach.R inst/tinytest/test_cv.R inst/tinytest/test_plmm.R inst/tinytest/_test_big_cbind.R tests/test.R vignettes/getting-started.Rmd man/pretty_time.Rd man/unzip_example_data.Rd man/setup_lambda.Rd man/create_design.Rd man/construct_variance.Rd man/create_design_filebacked.Rd man/rotate_filebacked.Rd man/summary.plmm.Rd man/plmm_loss.Rd man/impute_snp_data.Rd man/plmm_prep.Rd man/big_cbind.Rd man/predict_within_cv.Rd man/plmm_checks.Rd man/untransform_in_memory.Rd man/add_predictors.Rd man/summary.cv_plmm.Rd man/find_example_data.Rd man/eigen_K.Rd man/print.summary.plmm.Rd man/check_for_file_extension.Rd man/relatedness_mat.Rd man/count_constant_features.Rd man/predict.plmm.Rd man/MCP.Rd man/lam_names.Rd man/plot.plmm.Rd man/create_design_in_memory.Rd man/get_data.Rd man/untransform.Rd man/count_cores.Rd man/untransform_plink.Rd man/read_data_files.Rd man/index_samples.Rd man/get_hostname.Rd man/log_lik.Rd man/coef.cv_plmm.Rd man/fbm2bm.Rd man/print.summary.cv_plmm.Rd man/create_log.Rd man/lasso.Rd man/read_plink_files.Rd man/process_delim.Rd man/estimate_eta.Rd man/standardize_filebacked.Rd man/cv_plmm.Rd man/plmm.Rd man/align_ids.Rd man/cvf.Rd man/process_plink.Rd man/SCAD.Rd man/name_and_count_bigsnp.Rd man/plmm_fit.Rd man/plmmr-package.Rd man/standardize_in_memory.Rd man/coef.plmm.Rd man/untransform_delim.Rd man/plot.cv_plmm.Rd man/subset_filebacked.Rd man/admix.Rd man/plmm_format.Rd