Added genlasso to Suggests; compressed data sets; other various impro…

…vements and revisions throughout.

.Rbuildignore

@@ -7,3 +7,7 @@
 ^\.Rproj\.user$
 ^\.travis\.yml$
 ^.*\.Rproj$
+^data/N3finemapping\.CAVIAR\.RData$
+^data/N3finemapping\.DAP\.RData$
+^data/N3finemapping\.FINEMAP\.RData$
+

DESCRIPTION

@@ -15,7 +15,7 @@ Description: Implements methods for variable selection in linear
     and fast, allowing the SuSiE model be fit to large data sets
     (thousands of samples and hundreds of thousands of variables).
 Date: 2020-06-30
-Version: 0.9.5
+Version: 0.9.6
 Authors@R: c(person("Gao","Wang",role="aut",email="[email protected]"),
              person("Yuxin","Zou",role="aut"),
              person("Kaiqian","Zhang",role="aut"),
@@ -40,7 +40,8 @@ Suggests:
     microbenchmark,
     knitr,
     rmarkdown,
-    L0Learn
+    L0Learn,
+    genlasso
 LazyData: true
 NeedsCompilation: no
 RoxygenNote: 7.1.0

NAMESPACE

@@ -53,4 +53,5 @@ importFrom(stats,sd)
 importFrom(stats,summary.lm)
 importFrom(stats,uniroot)
 importFrom(stats,var)
+importFrom(utils,head)
 importFrom(utils,modifyList)

R/elbo.R

@@ -1,24 +1,24 @@
-#' @title Get objective function from data and susie fit object.
-#' @param data A flash data object.
-#' @param f A flash fit object.
-#' @keywords internal
+# @title Get objective function from data and susie fit object.
+# @param data A flash data object.
+# @param f A flash fit object.
+# @keywords internal
 get_objective = function(X, Y, s) {
   return(Eloglik(X,Y,s)-sum(s$KL))
 }
 
-# @title expected loglikelihood for a susie fit
+# Expected loglikelihood for a susie fit.
 Eloglik = function(X,Y,s){
   n = nrow(X)
-  result =  -(n/2) * log(2*pi* s$sigma2) - (1/(2*s$sigma2)) * get_ER2(X,Y,s)
+  result = -(n/2) * log(2*pi* s$sigma2) - (1/(2*s$sigma2)) * get_ER2(X,Y,s)
   return(result)
 }
 
-# expected squared residuals
+# Expected squared residuals.
 get_ER2 = function(X,Y,s){
   # Xr_L is L by N matrix
   # s$Xr is column sum of Xr_L
   Xr_L = compute_MXt(s$alpha*s$mu, X)
-  postb2 = s$alpha * s$mu2 #posterior second moment
+  postb2 = s$alpha * s$mu2 # posterior second moment
   return(sum((Y-s$Xr)^2) - sum(Xr_L^2) + sum(attr(X, "d")*t(postb2)))
 }
 
@@ -30,5 +30,7 @@ get_ER2 = function(X,Y,s){
 # @param Eb2 the posterior second moment of b (p vector) (alpha * mu2)
 SER_posterior_e_loglik = function(X,Y,s2,Eb,Eb2){
   n = nrow(X)
-  return(-0.5*n*log(2*pi*s2)  - (0.5/s2) * (sum(Y*Y) - 2*sum(Y*compute_Xb(X, Eb)) + sum(attr(X,'d')*Eb2)))
+  return(-0.5*n*log(2*pi*s2)
+         - (0.5/s2) * (sum(Y*Y) - 2*sum(Y*compute_Xb(X, Eb))
+                       + sum(attr(X,'d')*Eb2)))
 }

R/susie.R

@@ -253,7 +253,6 @@ susie <- function(X,Y,L = min(10,ncol(X)),scaled_prior_variance = 0.2,
   elbo[1] = -Inf;
   tracking = list()
 
-
   for(i in 1:max_iter){
     #s = add_null_effect(s,0)
     if (track_fit)

R/susie_ss.R

@@ -77,8 +77,8 @@
 #' X        <- matrix(rnorm(n*p),nrow=n,ncol=p)
 #' y        <- c(X %*% beta + rnorm(n))
 #' input_ss <- compute_ss(X,y,standardize = TRUE)
-#' ss = susieR:::univariate_regression(X, y)
-#' R = with(input_ss, cov2cor(XtX))
+#' ss <- susieR:::univariate_regression(X, y)
+#' R <- with(input_ss, cov2cor(XtX))
 #' res1      <- with(input_ss,susie_suff_stat(XtX = XtX,Xty = Xty, yty = yty,n=n))
 #' coef(res1)
 #' res2      <- with(ss,susie_suff_stat(bhat = betahat, shat = sebetahat, R = R, n=n, var_y = var(y)))

R/susie_utils.R

@@ -294,6 +294,8 @@ calc_z = function(X,Y,center=FALSE,scale=FALSE){
 #' @param b for simulated data, specify b = true effects (highlights in red).
 #' @param max_cs the biggest CS to display, based on purity (set max_cs in between 0 and 1) or size (>1).
 #' @param add_legend if TRUE, add a legend to annotate the size and purity of each CS discovered.
+#'
+#' @importFrom utils head
 #' @importFrom stats pnorm
 #' @importFrom graphics plot
 #' @importFrom graphics segments
@@ -505,4 +507,4 @@ susie_get_posterior_sd = function(res){
 #' @export
 susie_get_niter = function(res) {
   return(res$niter)
-}
+}

README.md

@@ -30,7 +30,7 @@ but they are too correlated to be sure which one.
 
 The package is developed by Gao Wang, Peter Carbonetto, Yuxin Zou,
 Kaiqian Zhang, and Matthew Stephens from the
-[Stephens Lab](http://stephenslab.uchicago.edu/) at the University of
+[Stephens Lab](http://stephenslab.uchicago.edu) at the University of
 Chicago.
 
 This is very much work in progress. Please
@@ -39,7 +39,7 @@ questions, get our support or provide us feedback; please
 [send pull requests](https://github.com/stephenslab/susieR/pulls) if
 you have helped fixing bugs or making improvements to the source code.
 
-## Setup
+## Quick Start
 
 To automatically retrieve and install `susieR` from this repository,
 with the vignettes included, run:
@@ -48,8 +48,6 @@ with the vignettes included, run:
 devtools::install_github("stephenslab/[email protected]")
 ```
 
-## Quick Start
-
 See [here](https://stephenslab.github.io/susieR/articles/mwe.html) for
 a brief illustration of `susieR`.  For more documentation and examples
 please visit https://stephenslab.github.io/susieR
@@ -59,23 +57,15 @@ please visit https://stephenslab.github.io/susieR
 If you find the `susieR` package or any of the source code in this
 repository useful for your work, please cite:
 
-> G Wang, A K Sarkar, P Carbonetto and M Stephens. A simple new approach to variable selection in regression, with application to genetic fine-mapping.
-> [bioRxiv](https://www.biorxiv.org/content/10.1101/501114v2) doi:10.1101/501114.
+> G Wang, A K Sarkar, P Carbonetto and M Stephens. [A simple new
+> approach to variable selection in regression, with application to
+> genetic fine-mapping.][susie-preprint] *bioRxiv* doi:10.1101/501114.
 
 ## Developer notes
 
-+ When any changes are made to `roxygen2` markup, simply run
-`devtools::document()` to update package `NAMESPACE`
-and documentation files.
-
-+ To install and test the development version of susieR, run the
-following commands in the shell:
-
-    ```bash
-    R CMD build --resave-data --no-build-vignettes susieR
-    R CMD INSTALL susieR_0.9.0.tar.gz
-    R CMD check --as-cran --ignore-vignettes susieR_0.9.0.tar.gz
-    ```
++ When any changes are made to `roxygen2` markup, run
+`devtools::document()` to update package `NAMESPACE` and documentation
+files.
 
 + Run `pkgdown::build_site()` to build the website. Getting `pkgdown`
 to work properly can be frustrating due to numerous & fragile dependencies.
@@ -87,3 +77,5 @@ docker run --rm --security-opt label:disable -t -P -w $PWD -v $PWD:$PWD \
   -u $UID:${GROUPS[0]} -e HOME=/home/$USER -e USER=$USER gaow/susie \
   R --slave -e "pkgdown::build_site(lazy=TRUE, examples=FALSE)"
 ```
+
+[susie-preprint]: https://doi.org/10.1101/501114

TODO.txt

@@ -1,5 +1,11 @@
 to do
 =====
 
-+ Improve Description in DESCRIPTION.
++ Update (and shorten) description in README.
+
++ Fill out roxygen2 docs for N2finemapping data set.
+
++ Fill out roxygen2 docs for N3finemapping data set.
+
++ Update pkgdown site.