Merge pull request #86 from juliangehring/develop

Merge changes for v0.3.0

Author: juliangehring

.appveyor.yml

@@ -1,7 +1,11 @@
 environment:
   matrix:
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.5/julia-0.5-latest-win64.exe"
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.6-latest-win64.exe"  
+  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.6-latest-win64.exe"
+  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
+
+matrix:
+  allow_failures:
+    - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
 
 notifications:
   - provider: Email

.codecov.yml

@@ -17,7 +17,7 @@ coverage:
 
 flags:
   julia_0_6:
-    joined: false
+    joined: true
 
 parsers:
   gcov:

.travis.yml

@@ -4,8 +4,12 @@ os:
   - linux
 
 julia:
-  - 0.5
   - 0.6
+  - nightly
+
+matrix:
+  allow_failures:
+    - julia: nightly
 
 notifications:
   email:

NEWS.md

@@ -1,5 +1,49 @@
 # MultipleTesting.jl News and Changes
 
+## Version 0.3.0
+
+### New Features
+
+- Convex decreasing density estimator for π0 (#56)
+- Higher criticism scores (`HigherCriticismScores`) and threshold (`HigherCriticismThreshold`) estimation (#55)
+- List of publications which describe the implemented statistical methods (#54, #65, #81, #83)
+
+
+### Changes
+
+#### User-facing changes
+
+- Fix p-value adjustments with unsorted inputs (#66)
+- Speed up p-value combinations (#75)
+- Define return types for p-value combinations (#76)
+- Unify methods for weighted Stouffer combination (#84)
+- Update documentation notebooks (#67)
+- Drop support for julia 0.5, require julia 0.6 as the minimum version (#52, #64, #58, #82)
+
+
+#### Internal changes
+
+- Simplify the step functions for p-value adjustments (#77)
+- Simplify the method structure (#74)
+- Switch to new julia syntax, with preliminary support for julia 0.7 (#71, #78)
+- Update tests and references for p-value combinations (#70)
+- Use `clamp` for better bounding of estimates (#85, #82)
+- Support the new `Distributions` interface (#52)
+- Drop the `Compat` dependency (#53)
+- Link comic logo in the readme file as an external resource (#69)
+
+
+### Removed
+
+- Drop `qvalues` in favour of BH-adjusted p-values (#73).
+
+
+### Support
+
+- Requires julia 0.6
+- Preliminary support for julia 0.7 nightly builds
+
+
 ## Version 0.2.3
 
 ### Changes
@@ -79,7 +123,7 @@
 ### New Features
 
 - New π0 estimators: BUM, Censored BUM, Flat Grenander
-- New p-value adjustment methods: Forward Step, Benjamini-Liu
+- New p-value adjustment methods: Forward Stop, Benjamini-Liu
 - BUM model for simulating p-value distributions
 - Fast isotonic regression
 - Reference list of related software packages in documentation

README.md

@@ -1,8 +1,10 @@
 # MultipleTesting
 
-The `MultipleTesting` package offers common algorithms for p-value adjustment and combination as well as the estimation of the proportion π₀ of true null hypotheses.
+The `MultipleTesting` package offers common algorithms for p-value adjustment
+and combination as well as the estimation of the proportion π₀ of true null
+hypotheses.
 
-![xkcd p-value guide](pvalues.png)
+![xkcd p-value guide](https://imgs.xkcd.com/comics/p_values.png)
 
 
 ## Features
@@ -92,6 +94,17 @@ combine(pvals, MinimumCombination(PValueAdjustment()))
 ```
 
 
+### Higher criticism
+
+* Higher criticism scores
+* Higher criticism threshold
+
+```julia
+estimate(pvals, HigherCriticismScores())
+estimate(pvals, HigherCriticismThreshold())
+```
+
+
 ## Installation
 
 The `MultipleTesting` package is part of the Julia ecosphere and the latest
@@ -102,7 +115,7 @@ 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)
+[package section](https://docs.julialang.org/en/stable/manual/packages/#adding-and-removing-packages)
 of the Julia documentation.
 
 
@@ -114,12 +127,11 @@ requests or issues with your questions or ideas.
 
 ## Package Status
 
-The package is actively developed and uses [semantic versioning](http://semver.org/).
+The package is actively developed and uses [semantic versioning](https://semver.org/).
 
 [![DOI](https://zenodo.org/badge/27935122.svg)](https://zenodo.org/badge/latestdoi/27935122)
 
-[![Package Status](http://pkg.julialang.org/badges/MultipleTesting_0.6.svg)](http://pkg.julialang.org/?pkg=MultipleTesting)
-[![Package Status](http://pkg.julialang.org/badges/MultipleTesting_0.5.svg)](http://pkg.julialang.org/?pkg=MultipleTesting)
+[![Package Status](https://pkg.julialang.org/badges/MultipleTesting_0.6.svg)](https://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)

REQUIRE

@@ -1,4 +1,4 @@
-julia 0.5
+julia 0.6
 StatsBase 0.15.0
-Distributions
-Compat 0.19.0
+Distributions 0.14.1
+SpecialFunctions 0.3.8