Merge pull request #100 from juliangehring/v0.4.0

Prepare for v0.4.0 release

Author: juliangehring

NEWS.md

@@ -1,5 +1,20 @@
 # MultipleTesting.jl News and Changes
 
+## Version 0.4.0
+
+### Changes
+
+#### User-facing changes
+
+- Require julia v0.7 as the minimum version, drop support for julia v0.6 
+- Describe package features in the documentation
+
+
+### Support
+
+- Requires julia 0.7
+
+
 ## Version 0.3.1
 
 ### New Features

docs/src/index.md

@@ -8,7 +8,110 @@ end
 ```
 
 
-## Package Features
+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](https://imgs.xkcd.com/comics/p_values.png)
+
+
+## Features
+
+### Adjustment of p-values
+
+* Bonferroni
+* Benjamini-Hochberg
+* Adaptive Benjamini-Hochberg with known π₀ or π₀ estimation method (see section below)
+* Benjamini-Yekutieli
+* Benjamini-Liu
+* Hochberg
+* Holm
+* Hommel
+* Sidak
+* Forward Stop
+* Barber-Candès
+
+```julia
+adjust(pvals, Bonferroni())
+adjust(pvals, BenjaminiHochberg())
+adjust(pvals, BenjaminiHochbergAdaptive(0.9))
+adjust(pvals, BenjaminiHochbergAdaptive(Storey()))
+adjust(pvals, BenjaminiYekutieli())
+adjust(pvals, BenjaminiLiu())
+adjust(pvals, Hochberg())
+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)
+```
+
+
+### Estimation of π₀
+
+* Storey
+* Storey's closed-form bootstrap
+* Least Slope
+* Two Step
+* RightBoundary (Storey's estimate with dynamically chosen λ)
+* Beta-Uniform Mixture (BUM)
+* Censored BUM
+* Flat Grenander
+* Oracle for known π₀
+
+```julia
+estimate_pi0(pvals, Storey())
+estimate_pi0(pvals, StoreyBootstrap())
+estimate_pi0(pvals, LeastSlope())
+estimate_pi0(pvals, TwoStep())
+estimate_pi0(pvals, TwoStep(0.05))
+estimate_pi0(pvals, TwoStep(0.05, BenjaminiHochbergAdaptive(0.9))
+estimate_pi0(pvals, RightBoundary())
+estimate_pi0(pvals, CensoredBUM())
+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()))
+```
+
+
+### Higher criticism
+
+* Higher criticism scores
+* Higher criticism threshold
+
+```julia
+estimate(pvals, HigherCriticismScores())
+estimate(pvals, HigherCriticismThreshold())
+```
+
 
 ## Manual