Increased summary.mulTree coverage and added new release

TGuillerme · May 8, 2018 · 123c4d6 · 123c4d6
1 parent c881727
commit 123c4d6
Show file tree

Hide file tree

Showing 5 changed files with 30 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,8 @@ Package: mulTree
 Title: Performs MCMCglmm on Multiple Phylogenetic Trees
 Author: Thomas Guillerme <guillert@tcd.ie> & Kevin Healy <heaylke@tcd.ie>
 Maintainer: Thomas Guillerme <guillert@tcd.ie>
-Version: 1.3.3
-Date: 2018-03-14
+Version: 1.3.4
+Date: 2018-05-08
 Description: Allows to run a MCMCglmm on multiple phylogenetic trees to take into account phylogenetic uncertainty.
 Depends:
     R (>= 3.0.0),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,14 @@
+mulTree 1.3.4 (2018-05-08)
+=========================
+
+### NEW FEATURES
+
+  * Increased test coverage for all functions.
+
+### MINOR IMPROVEMENTS
+
+  * Improved optional arguments handling for `mulTree` (following [Eldar Rakhimberdiev](https://github.com/eldarrak)'s contribution)
+
 mulTree 1.3.3 (2018-03-14)
 =========================
 
@@ -13,6 +24,7 @@ mulTree 1.3.2 (2017/10/19)
 =========================
 
 ### NEW FEATURES
+
   * Complex formula management in `mulTree` and `as.mulTree`.
 
 ### MINOR IMPROVEMENTS

diff --git a/R/summary.mulTree_fun.R b/R/summary.mulTree_fun.R
@@ -27,7 +27,7 @@ smooth.hdr <- function(hdr_out, prob, name) {
         }
         hdr_out$hdr <- new_hdr
         ## Print some warning!
-        message("Warning message:\n", name, " has multiple highest density regions (hdr) for some probabilities.\nOnly the maximum and the minimum hdr were used for each probabilities.", sep="")
+        warning(name, " has multiple highest density regions (hdr) for some probabilities.\nOnly the maximum and the minimum hdr were used for each probabilities.", sep="")
     }
     return(hdr_out)
 }

diff --git a/README.md b/README.md
@@ -48,7 +48,7 @@ Authors
 -------
 [Thomas Guillerme](http://tguillerme.github.io) and [Kevin Healy](http://healyke.github.io)
 
-##Contributors
+## Contributors
 
 [Eldar Rakhimberdiev](https://github.com/eldarrak).
 

diff --git a/tests/testthat/test-summary.mulTree.R b/tests/testthat/test-summary.mulTree.R
@@ -90,11 +90,10 @@ test_that("lapply.hdr works", {
     expect_is(smooth_simple, "list")
     expect_equal(names(smooth_simple), c("hdr", "mode", "falpha"))
 
-    expect_message(smooth_bimod <- smooth.hdr(hdrcde::hdr((c(rnorm(50, 1, 1), rnorm(50, 10, 1))), prob=c(50,95)), prob=c(50,95), "test_hrd"))
+    expect_warning(smooth_bimod <- smooth.hdr(hdrcde::hdr((c(rnorm(50, 1, 1), rnorm(50, 10, 1))), prob=c(50,95)), prob=c(50,95), "test_hrd"))
     expect_is(smooth_bimod, "list")
     expect_equal(names(smooth_bimod), c("hdr", "mode", "falpha"))
 
-
     # Errors
     expect_error(
     	lapply.hdr("X", prob=c(50,95))
@@ -160,6 +159,19 @@ test_that("example works", {
     expect_error(
     	summary(lifespan.mcmc, use.hdr=FALSE, cent.tend=matrix)
     	)
+    expect_error(
+        summary(lifespan.mcmc, prob = 101)
+        )
+    test <- lifespan.mcmc
+    test$Intercept <- 1
+    test$mass <- 1
+    test$volancy <- 1
+    test$phy.var <- 1
+    test$res.var <- 1
+    expect_error(
+        summary(test)
+        )
+
     # Default example
     test_example <- summary(lifespan.mcmc)
     expect_is(