Merge pull request #38 from juliangehring/dev

Merge v0.2.0 changes into master

Author: juliangehring

.codecov.yml

@@ -0,0 +1,23 @@
+codecov:
+  notify:
+    require_ci_to_pass: true
+comment: off
+coverage:
+  precision: 2
+  range:
+  - 70.0
+  - 100.0
+  round: down
+  status:
+    changes: false
+    patch: true
+    project: true
+parsers:
+  gcov:
+    branch_detection:
+      conditional: true
+      loop: true
+      macro: false
+      method: false
+  javascript:
+    enable_partials: false

.travis.yml

@@ -1,9 +1,12 @@
 language: julia
 os:
   - linux
-  - osx
 julia:
   - 0.5
+notifications:
+  email:
+    on_success: never
+    on_failure: change
 script:
   - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
   - julia --check-bounds=yes -e 'Pkg.clone(pwd()); Pkg.build("MultipleTesting"); Pkg.test("MultipleTesting"; coverage=true)'

NEWS.md

@@ -1,5 +1,43 @@
 # MultipleTesting.jl News and Changes
 
+## Version 0.2.0
+
+### New Features
+
+- Combination of p-values through the `combine` interface:
+  * Fisher
+  * Stouffer
+  * Logit
+  * Wilkinson
+  * Simes
+  * Tippett
+  * Minimum of adjusted p-values
+- Analysis notebook for p-value combinations
+- `PValues` type: Representation of vectors with p-values
+- Adjustments of p-values support specifying the total number of tests
+- Barber-Candès p-value adjustment
+
+
+### Changes
+
+- Optimised Benjamini-Liu p-value adjustment and test cases
+- Estimator types are now immutables
+- Harmonised type names
+- Restructed readme
+- Simplified method signatures
+- Various performance improvements
+
+
+### Removed
+
+- Export of lower-level functions for p-value adjustment
+
+
+### Support
+
+- Requires julia 0.5
+
+
 ## Version 0.1.0
 
 ### New Features

README.md

@@ -5,14 +5,6 @@ The `MultipleTesting` package offers common algorithms for p-value adjustment an
 ![xkcd p-value guide](pvalues.png)
 
 
-## Package Status
-
-[![Package Status](http://pkg.julialang.org/badges/MultipleTesting_0.5.svg)](http://pkg.julialang.org/?pkg=MultipleTesting)
-[![Linux/Mac Build Status](https://travis-ci.org/juliangehring/MultipleTesting.jl.svg?branch=master)](https://travis-ci.org/juliangehring/MultipleTesting.jl)
-[![Windows Build Status](https://ci.appveyor.com/api/projects/status/1ld0ppptisirryt1/branch/master?svg=true)](https://ci.appveyor.com/project/juliangehring/multipletesting-jl/branch/master)
-[![Coverage Status](https://codecov.io/gh/juliangehring/MultipleTesting.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/juliangehring/MultipleTesting.jl)
-
-
 ## Features
 
 ### Adjustment of p-values
@@ -27,6 +19,7 @@ The `MultipleTesting` package offers common algorithms for p-value adjustment an
 * Hommel
 * Sidak
 * Forward Stop
+* Barber-Candès
 
 ```julia
 adjust(pvals, Bonferroni())
@@ -40,6 +33,13 @@ adjust(pvals, Holm())
 adjust(pvals, Hommel())
 adjust(pvals, Sidak())
 adjust(pvals, ForwardStop())
+adjust(pvals, BarberCandes())
+```
+
+The adjustment can also be performed on the `k` smallest out of `n` p-values:
+
+```julia
+adjust(pvals, n, PValueAdjustmentMethod)
 ```
 
 
@@ -68,3 +68,57 @@ estimate_pi0(pvals, BUM())
 estimate_pi0(pvals, FlatGrenander())
 estimate_pi0(pvals, Oracle(0.9))
 ```
+
+
+### Combination of p-values
+
+* Fisher
+* Stouffer, optionally with weights
+* Logit
+* Tippett
+* Simes
+* Wilkinson
+* Minimum of adjusted p-values
+
+```julia
+combine(pvals, FisherCombination())
+combine(pvals, StoufferCombination())
+combine(pvals, weights, StoufferCombination())
+combine(pvals, LogitCombination())
+combine(pvals, TippettCombination())
+combine(pvals, SimesCombination())
+combine(pvals, WilkinsonCombination(rank))
+combine(pvals, MinimumCombination(PValueAdjustment()))
+```
+
+
+## Installation
+
+The `MultipleTesting` package is part of the Julia ecosphere and the latest
+release version can be installed with
+
+```julia
+Pkg.add("MultipleTesting")
+```
+
+More details on packages and how to manage them can be found in the
+[package section](http://docs.julialang.org/en/stable/manual/packages/#adding-and-removing-packages)
+of the Julia documentation.
+
+
+## Feedback and Contributions
+
+Contributions of any kind are very welcome. Please feel free to open pull
+requests or issues with your questions or ideas.
+
+
+## Package Status
+
+The package is actively developed and uses [semantic versioning](http://semver.org/).
+
+[![DOI](https://zenodo.org/badge/27935122.svg)](https://zenodo.org/badge/latestdoi/27935122)
+
+[![Package Status](http://pkg.julialang.org/badges/MultipleTesting_0.5.svg)](http://pkg.julialang.org/?pkg=MultipleTesting)
+[![Linux/Mac Build Status](https://travis-ci.org/juliangehring/MultipleTesting.jl.svg?branch=master)](https://travis-ci.org/juliangehring/MultipleTesting.jl)
+[![Windows Build Status](https://ci.appveyor.com/api/projects/status/1ld0ppptisirryt1/branch/master?svg=true)](https://ci.appveyor.com/project/juliangehring/multipletesting-jl/branch/master)
+[![Coverage Status](https://codecov.io/gh/juliangehring/MultipleTesting.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/juliangehring/MultipleTesting.jl)