From 6ee64fb41c0d79839e92a3dc859de92d35faa724 Mon Sep 17 00:00:00 2001
From: Peter Carbonetto <peter.carbonetto@gmail.com>
Date: Wed, 19 Feb 2020 16:57:12 -0600
Subject: [PATCH] Adjusted mixsqp settings; fixed a few of the tests.

---
 DESCRIPTION                 |  2 +-
 R/mix_opt.R                 |  4 +++-
 R/tests.R                   | 12 ++++++++++++
 tests/testthat/test_binom.R |  3 ++-
 4 files changed, 18 insertions(+), 3 deletions(-)
 create mode 100644 R/tests.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 81cb322..9ba6e0c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -13,7 +13,7 @@ Authors@R: c(person("Matthew","Stephens",role="aut",
              person("Jason","Willwerscheid",role="aut"),
              person("Nan","Xiao",role="aut"),
              person("Mazon","Zeng",role="ctb"))
-Version: 2.2-44
+Version: 2.2-45
 Date: 2020-02-19
 Title: Methods for Adaptive Shrinkage, using Empirical Bayes
 Description: The R package 'ashr' implements an Empirical Bayes
diff --git a/R/mix_opt.R b/R/mix_opt.R
index 4b36aea..435da96 100644
--- a/R/mix_opt.R
+++ b/R/mix_opt.R
@@ -109,7 +109,9 @@ mixSQP <- function (matrix_lik, prior, pi_init = NULL,
   w <- w[w != 0]
 
   # Fit the mixture weights using the mix-SQP algorithm.
-  control0 <- list(verbose = FALSE)
+  control0 <- list(verbose    = FALSE,
+                   eps        = 1e-6,
+                   numiter.em = 20)
   control  <- modifyList(control0,control,keep.null = TRUE)
   out      <- mixsqp::mixsqp(A,w,pi_init,control = control)
   
diff --git a/R/tests.R b/R/tests.R
new file mode 100644
index 0000000..704f6f0
--- /dev/null
+++ b/R/tests.R
@@ -0,0 +1,12 @@
+# The Rmosek package on CRAN will not work with REBayes. This function
+# is used for some of the tests to check whether the correct Rmosek
+# package (the one downloaded from mosek.com) is installed.
+#
+#' @importFrom testthat skip_if_not_installed
+#' @importFrom testthat skip_if
+#' 
+skip_if_mixkwdual_doesnt_work <- function() {
+  skip_if_not_installed("REBayes")
+  skip_if_not_installed("Rmosek")
+  skip_if(!is.element("mosek_lptoprob",getNamespaceExports("Rmosek")))
+}
diff --git a/tests/testthat/test_binom.R b/tests/testthat/test_binom.R
index 942da22..9378efe 100644
--- a/tests/testthat/test_binom.R
+++ b/tests/testthat/test_binom.R
@@ -75,11 +75,12 @@ test_that("lik_binom (logit link) fitted g is close to true g",{
 })
 
 test_that("lik_binom (logit link) fitted g is close to true g",{
+    
   # Simulate a Binomial dataset
   set.seed(1)
   truemode = 0
   logitp = c(rep(0,800), runif(200,-3,3))
-  p = 1/(1+exp(-logitp))
+  p = 1/(1 + exp(-logitp))
   n = rep(100,1000)
   x = rbinom(1000,n,p) # Binomial observations
   ash.binom.out = ash(rep(0,length(x)),1,lik=lik_binom(x,n,link="logit"),