Merge pull request #19 from sahirbhatnagar/fix-sims

PRS rda scripts and proofs. The proofs however still might change. Note that the manuscript hasnt been updated to reflect the PRS rda yet.
sahirbhatnagar · Oct 20, 2019 · a151e96 · a151e96
2 parents ffe8a26 + 1b41571
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diff --git a/manuscript/bin/ADNI.R b/manuscript/bin/ADNI.R
@@ -2,9 +2,9 @@
 
 source("/home/sahir/git_repositories/sail/my_sims/plot_functions_rda_ADNI.R")
 
-amy_mat <- read.csv("/home/sahir/git_repositories/sail/data-nogit/adni_new/csf_amyloid_final.csv",
+amy_mat <- read.csv("/home/sahir/git_repositories/sail/rda/csf_amyloid_final.csv",
                     stringsAsFactors = FALSE)
-covr <- read.csv("/home/sahir/git_repositories/sail/data-nogit/adni_new/covariates.csv",
+covr <- read.csv("/home/sahir/git_repositories/sail/rda/covariates.csv",
                  stringsAsFactors = FALSE, sep = ";")
 
 # these are used for plotting. we use the entire data set for the plots

diff --git a/manuscript/source/GEbib.bib b/manuscript/source/GEbib.bib
@@ -1,3 +1,36 @@
+@article{zou2009adaptive,
+	title={On the adaptive elastic-net with a diverging number of parameters},
+	author={Zou, Hui and Zhang, Hao Helen},
+	journal={Annals of statistics},
+	volume={37},
+	number={4},
+	pages={1733},
+	year={2009},
+	publisher={NIH Public Access}
+}
+
+@article{nardi2008asymptotic,
+	title={On the asymptotic properties of the group lasso estimator for linear models},
+	author={Nardi, Yuval and Rinaldo, Alessandro and others},
+	journal={Electronic Journal of Statistics},
+	volume={2},
+	pages={605--633},
+	year={2008},
+	publisher={The Institute of Mathematical Statistics and the Bernoulli Society}
+}
+
+@article{wang2007regression,
+	title={Regression coefficient and autoregressive order shrinkage and selection via the lasso},
+	author={Wang, Hansheng and Li, Guodong and Tsai, Chih-Ling},
+	journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
+	volume={69},
+	number={1},
+	pages={63--78},
+	year={2007},
+	publisher={Wiley Online Library}
+}
+
+
 @article{connors1995controlled,
   title={A controlled trial to improve care for seriously iII hospitalized patients: The study to understand prognoses and preferences for outcomes and risks of treatments (SUPPORT)},
   author={Connors, Alfred F and Dawson, Neal V and Desbiens, Norman A and Fulkerson, William J and Goldman, Lee and Knaus, William A and Lynn, Joanne and Oye, Robert K and Bergner, Marilyn and Damiano, Anne and others},
@@ -9,6 +42,7 @@ @article{connors1995controlled
   publisher={American Medical Association}
 }
 
+
 @article{huang2010variable,
 	title={Variable selection in nonparametric additive models},
 	author={Huang, Jian and Horowitz, Joel L and Wei, Fengrong},

diff --git a/manuscript/source/figure/error-crosses-adni-1.pdf b/manuscript/source/figure/error-crosses-adni-1.pdf
diff --git a/manuscript/source/figure/plot-fpr-sim-1.pdf b/manuscript/source/figure/plot-fpr-sim-1.pdf
diff --git a/manuscript/source/figure/plot-inter-adni-1.pdf b/manuscript/source/figure/plot-inter-adni-1.pdf
diff --git a/manuscript/source/figure/plot-mse-nactive-sim-1.pdf b/manuscript/source/figure/plot-mse-nactive-sim-1.pdf
diff --git a/manuscript/source/figure/plot-mse-sim-1.pdf b/manuscript/source/figure/plot-mse-sim-1.pdf
diff --git a/manuscript/source/figure/plot-nactive-sim-1.pdf b/manuscript/source/figure/plot-nactive-sim-1.pdf
diff --git a/manuscript/source/figure/plot-tpr-fpr-sim-1.pdf b/manuscript/source/figure/plot-tpr-fpr-sim-1.pdf
diff --git a/manuscript/source/figure/plot-tpr-sim-1.pdf b/manuscript/source/figure/plot-tpr-sim-1.pdf
diff --git a/manuscript/source/figure/sail-cv-1.pdf b/manuscript/source/figure/sail-cv-1.pdf
diff --git a/manuscript/source/figure/sail-expand-false-1.pdf b/manuscript/source/figure/sail-expand-false-1.pdf
diff --git a/manuscript/source/figure/sail-inter-eff-1.pdf b/manuscript/source/figure/sail-inter-eff-1.pdf
diff --git a/manuscript/source/figure/sail-main-eff-1.pdf b/manuscript/source/figure/sail-main-eff-1.pdf
diff --git a/manuscript/source/figure/sail-pf-path-1.pdf b/manuscript/source/figure/sail-pf-path-1.pdf
diff --git a/manuscript/source/figure/sail-plot-cv-design-1.pdf b/manuscript/source/figure/sail-plot-cv-design-1.pdf
diff --git a/manuscript/source/figure/sail-solution-path-1.pdf b/manuscript/source/figure/sail-solution-path-1.pdf
diff --git a/manuscript/source/figure/sail-solution-path-linear-1.pdf b/manuscript/source/figure/sail-solution-path-linear-1.pdf
diff --git a/manuscript/source/figure/toy-effects-1.pdf b/manuscript/source/figure/toy-effects-1.pdf
diff --git a/manuscript/source/figure/toy-solution-path-1.pdf b/manuscript/source/figure/toy-solution-path-1.pdf
diff --git a/manuscript/source/sail_manuscript_v2.Rnw b/manuscript/source/sail_manuscript_v2.Rnw
diff --git a/manuscript/source/sail_manuscript_v2.pdf b/manuscript/source/sail_manuscript_v2.pdf
diff --git a/manuscript/source/sail_manuscript_v2.tex b/manuscript/source/sail_manuscript_v2.tex
diff --git a/my_sims/rda_results/rda_IQ_4yrs_cond2_s2_4.rds b/my_sims/rda_results/rda_IQ_4yrs_cond2_s2_4.rds
diff --git a/my_sims/rda_results/rda_IQ_4yrs_cond2_s2_4_data.rds b/my_sims/rda_results/rda_IQ_4yrs_cond2_s2_4_data.rds