initializing with lots of code

Author: christacaggiano

.gitignore

@@ -34,3 +34,5 @@ vignettes/*.pdf
 
 # Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
 rsconnect/
+
+.DS_Store

TreeWAS/.Rbuildignore

@@ -0,0 +1,13 @@
+# R project
+^.*\.Rproj$
+^\.Rproj\.user$
+
+# bash scripts
+^buildLocally.sh$
+
+# git
+^\.gitignore$
+^\.gitattributes$
+
+# testthat
+^tests/testthat/Rplots.pdf$

TreeWAS/.gitignore

@@ -0,0 +1,2 @@
+TreeWAS.Rcheck/
+TreeWAS_*.tar.gz

TreeWAS/DESCRIPTION

@@ -0,0 +1,23 @@
+Package: TreeWAS
+Type: Package
+Title: Bayesian analysis of genetic association across tree-structured routine
+    healthcare data in the UK Biobank
+Version: 0.1.0
+Authors@R: c(
+    person("Adrian", "Cortes", role = c("aut", "cre", "cph"), email="[email protected]"),
+    person("Joe", "Zhu", role=c("ctb"), email="[email protected]")
+    )
+Description: Method employs a novel Bayesian analysis framework that exploits
+    the hierarchical structure of diagnosis classifications to jointly analyse
+    genetic variants against UK Biobank healthcare phenotypes.
+URL: https://github.com/mcveanlab/TreeWAS
+License: MIT
+BugReports: https://github.com/mcveanlab/TreeWAS/issues
+Depends:
+    R (>= 3.0.0)
+Suggests:
+    data.table,
+    mvtnorm,
+    testthat (>= 0.9.0)
+LazyData: true
+RoxygenNote: 6.0.1

TreeWAS/NAMESPACE

@@ -0,0 +1,22 @@
+importFrom("graphics", "abline", "image", "plot")
+importFrom("stats", "dnorm", "uniroot")
+
+export(calculate.integrated.llk_scaled)
+export(calculate.integrated.llk_scaled_additive)
+export(calculate.integrated_1d_llk_scaled)
+export(calculate.llk.grid.wrapper)
+export(calculate.llk.grid_scaled)
+export(calculate.llk.grid_scaled_additive)
+export(calculate_1d_llk_grid_scaled)
+export(calculate_1d_prior)
+export(calculate_prior_2d)
+export(cc_d.llk)
+export(cc_d.llk_additive)
+export(cc_llk)
+export(cc_llk_additive)
+export(get.posterior.node)
+export(get.posterior.node_1d)
+export(get.posterior.node_additive)
+export(prepare_count_table)
+export(prepare_tree_table)
+export(prepare_tree_table_grs)