Files in sahirbhatnagar/ggmix
A General Framework for Variable Selection in Linear Mixed Models with Applications to Genetic Studies with Structured Populations

.DS_Store
.Rbuildignore
.gitignore
.travis.yml
CONDUCT.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/constructors.R R/data.R R/eta.R R/fitting.R R/functions.R R/ggmix.R R/gic.R R/kkt.R R/lambda.R R/lmmlasso.R R/loglik.R R/methods.R R/plot.R R/ranef.R R/sigma2.R R/utils.R README.md
RealData/GAW20-RMSE-Nactive.RData
RealData/Mice-200Bootstrap.RData
RealData/mice.RData
_pkgdown.yml
codecov.yml
cran-comments.md
data-raw/Scenario0.RData
data-raw/bnpsd-data.R data-raw/karim-data.R
data/admixed.rda
data/karim.rda
docs/CONDUCT.html
docs/LICENSE-text.html
docs/articles/alternative-kinship-input.html
docs/articles/alternative-kinship-input_files/figure-html/unnamed-chunk-1-1.png
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docs/articles/alternative-kinship-input_files/figure-html/unnamed-chunk-4-1.png
docs/articles/index.html
docs/articles/introduction-to-ggmix.html
docs/articles/introduction-to-ggmix_files/figure-html/unnamed-chunk-11-1.png
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docs/articles/prior-annotation-weights.html
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docs/authors.html
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docs/docsearch.json
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docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/admixed.html
docs/reference/gen_structured_model.html
docs/reference/ggmix-1.png
docs/reference/ggmix-2.png
docs/reference/ggmix.html
docs/reference/ggmix_data_object.html
docs/reference/gic.html
docs/reference/gr_eta_lasso_fullrank.html
docs/reference/index.html
docs/reference/karim.html
docs/reference/kkt_check.html
docs/reference/lambdalasso.html
docs/reference/lmmlasso.html
docs/reference/logliklasso.html
docs/reference/plot.ggmix_fit.html
docs/reference/plot.ggmix_gic.html
docs/reference/predict.ggmix_fit.html
docs/reference/predict.ggmix_gic.html
docs/reference/print.ggmix_fit.html
docs/reference/ranef.html
docs/reference/sigma2lasso.html
docs/sitemap.xml
ggmixGit.Rproj
man/admixed.Rd man/gen_structured_model.Rd man/ggmix.Rd man/ggmix_data_object.Rd man/gic.Rd man/gr_eta_lasso_fullrank.Rd man/karim.Rd man/kkt_check.Rd man/lambdalasso.Rd man/lmmlasso.Rd man/logliklasso.Rd man/plot.ggmix_fit.Rd man/plot.ggmix_gic.Rd man/predict.ggmix_fit.Rd man/predict.ggmix_gic.Rd man/print.ggmix_fit.Rd man/ranef.Rd man/sigma2lasso.Rd
manuscript/.DS_Store
manuscript/bin/ADNI.R manuscript/bin/RealData.R manuscript/bin/intro.R manuscript/bin/setup.R manuscript/bin/simulation.R manuscript/comments/07092018_122713.pdf manuscript/comments/07092018_122748.pdf manuscript/comments/07092018_122825.pdf manuscript/comments/07092018_122858.pdf manuscript/comments/07092018_122925.pdf manuscript/comments/07092018_122951.pdf
manuscript/source/.DS_Store
manuscript/source/figure/GAW20-prediction-RMSE-activeVariable-1.pdf manuscript/source/figure/Mice-comparison-fixTPR-1.pdf manuscript/source/figure/Mice-comparison-fixTPR.pdf manuscript/source/figure/ggmix-bic-1.pdf manuscript/source/figure/ggmix-hdbic-1.pdf manuscript/source/figure/ggmix-obs-pred-1.pdf manuscript/source/figure/ggmix-popkin-1.pdf manuscript/source/figure/ggmix-qqplot-1.pdf manuscript/source/figure/ggmix-qqplot-2.pdf manuscript/source/figure/ggmix-solution-path-1.pdf manuscript/source/figure/ggmix-tukey-1.pdf manuscript/source/figure/plot-correct-sparsity-sim-1.pdf manuscript/source/figure/plot-correct-sparsity-sim-1p-causal-1.pdf manuscript/source/figure/plot-correct-sparsity-sim-null-model-1.pdf manuscript/source/figure/plot-errorvar-sim-1.pdf manuscript/source/figure/plot-errorvar-sim-1p-causal-1.pdf manuscript/source/figure/plot-errorvar-sim-null-model-1.pdf manuscript/source/figure/plot-eta-sim-1.pdf manuscript/source/figure/plot-eta-sim-1p-causal-1.pdf manuscript/source/figure/plot-eta-sim-null-model-1.pdf manuscript/source/figure/plot-kinship-sim-1.pdf manuscript/source/figure/plot-me-nactive-sim-1.pdf manuscript/source/figure/plot-me-nactive-sim-1p-causal-1.pdf manuscript/source/figure/plot-me-nactive-sim-null-1.pdf manuscript/source/figure/plot-mse-nactive-sim-1.pdf manuscript/source/figure/plot-mse-nactive-sim-1p-causal-1.pdf manuscript/source/figure/plot-mse-nactive-sim-1p-causal-zoom-in-1.pdf manuscript/source/figure/plot-mse-nactive-sim-null-1.pdf manuscript/source/figure/plot-nactive-sim-1.pdf manuscript/source/figure/plot-nactive-sim-1p-causal-1.pdf manuscript/source/figure/plot-nactive-sim-null-model-1.pdf manuscript/source/figure/plot-pc-sim-1.pdf manuscript/source/figure/plot-runtime-sim-1p-causal-1.pdf manuscript/source/figure/plot-runtime-sim-null-model-1.pdf manuscript/source/figure/plot-sigma2-sim-1.pdf manuscript/source/figure/plot-structure-pc-sim-1.pdf manuscript/source/figure/plot-tpr-fpr-sim-1.pdf manuscript/source/figure/plot-tpr-fpr-sim-1p-causal-1.pdf manuscript/source/figure/plot-tpr-fpr-sim-null-model-1.pdf manuscript/source/figure/unnamed-chunk-10-1.pdf manuscript/source/figure/unnamed-chunk-15-1.pdf manuscript/source/figure/unnamed-chunk-16-1.pdf manuscript/source/figure/unnamed-chunk-16-2.pdf manuscript/source/figure/unnamed-chunk-17-1.pdf manuscript/source/figure/unnamed-chunk-2-1.pdf manuscript/source/figure/unnamed-chunk-4-1.pdf manuscript/source/figure/unnamed-chunk-8-1.pdf
manuscript/source/ggmix_manuscript_v1-concordance.tex
manuscript/source/ggmix_manuscript_v1.Rnw
manuscript/source/ggmix_manuscript_v1.pdf
manuscript/source/ggmix_manuscript_v1.tex
manuscript/source/ggmixbib.bib
penfam.Rproj
rda/GAW20/Cov_confounder_714_samples.RData
rda/GAW20/kinship_matrix.R rda/mice/mice.R rda/mice/rmse_for_3_methods.R rda/mice/rmse_individual_for_3_methods.R reports/kkt.Rmd reports/lmm_example.Rmd reports/lmm_example.md reports/popkin.Rmd reports/report.Rmd
simulation/.DS_Store
simulation/UKB_simulations_sent_to_KO_May30_2018 (2).html
simulation/eval_functions.R simulation/functions.R simulation/main.R simulation/method_functions.R simulation/model_functions.R simulation/packages.R simulation/popkin.R simulation/scrap.R simulation/sim-data.R simulation/sim_trait.R
simulation/simulation_results/july_12_2018_results_with_null_model.rds
simulation/simulation_results/july_12_2018_results_with_null_model_VC.rds
simulation/simulation_results/july_12_2018_results_with_null_model_VC_lasso_has_proper_MSE.rds
simulation/simulation_results/july_1_2018_results.rds
simulation/simulation_results/july_1_2018_results_with_twostepY.rds
simulation/simulation_results/june_29_2018_results.rds
simulation/simulation_results/may_02_2019_results.rds
simulation/simulation_results/may_05_2019_results.rds
simulation/simulation_results/may_06_2019_results.rds
simulation/simulation_results/may_07_2019_results.rds
simulation/writeup.Rmd tests/testthat.R tests/testthat/test-KKT.R tests/testthat/test-constructors.R tests/testthat/test-ggmix.R tests/testthat/test-predict.R tests/testthat/test-ranef.R
vignettes/.gitignore
vignettes/alternative-kinship-input.Rmd vignettes/introduction-to-ggmix.Rmd vignettes/prior-annotation-weights.Rmd
sahirbhatnagar/ggmix documentation built on May 29, 2019, 9:10 a.m.