Merge branch 'develop' into barber-candes-#81

Author: juliangehring

.gitignore

@@ -1 +1,2 @@
 **/.ipynb_checkpoints/
+docs/build/

.travis.yml

@@ -23,3 +23,5 @@ script:
 
 after_success:
   - julia -e 'cd(Pkg.dir("MultipleTesting")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder(), flags="julia_$(VERSION.major)_$(VERSION.minor)")'
+  - julia -e 'Pkg.add("Documenter")'
+  - julia -e 'cd(Pkg.dir("MultipleTesting")); include(joinpath("docs", "make.jl"))'

Makefile

@@ -0,0 +1,12 @@
+COLOR := yes
+
+.PHONY: test docs
+
+all: test docs
+
+test:
+	julia --color=$(COLOR) test/runtests.jl
+
+docs:
+	julia --color=$(COLOR) docs/make.jl
+

NEWS.md

@@ -69,7 +69,7 @@
 ### Changes
 
 - Adds compatibility with julia 0.6 development versions, including automated tests
-- Fixes Censored BUM π0 edge case when all p-values are equal to 1
+- Fixes Censored BUM π₀ edge case when all p-values are equal to 1
 - Updates test cases and reference values for `qValues`
 - Introduces `Compat` as a new dependency
 - Separates test coverage reports for different julia versions
@@ -122,7 +122,7 @@
 
 ### New Features
 
-- New π0 estimators: BUM, Censored BUM, Flat Grenander
+- New π₀ estimators: BUM, Censored BUM, Flat Grenander
 - New p-value adjustment methods: Forward Stop, Benjamini-Liu
 - BUM model for simulating p-value distributions
 - Fast isotonic regression
@@ -153,7 +153,7 @@
 
 ### New features
 
-- New π0 estimators: Two Step, Right Boundary
+- New π₀ estimators: Two Step, Right Boundary
 - New p-value adjustment methods: Benjamini-Hochberg Adaptive, Oracle, Sidak
 - Package precompilation
 

docs/make.jl

@@ -0,0 +1,32 @@
+using Documenter
+using MultipleTesting
+
+makedocs(
+    modules = [MultipleTesting],
+    format = :html,
+    sitename = "MultipleTesting.jl",
+    doctest = true,
+    checkdocs = :exports,
+    linkcheck = true,
+    html_disable_git = true, # disable source and edit links to github
+    html_canonical = "https://juliangehring.github.io/MultipleTesting.jl/stable/",
+    pages = [
+        "Home" => "index.md",
+        "Library" => Any[
+            "adjustment.md",
+            "combination.md",
+            "pi0.md",
+            "higher-criticism.md",
+            "models.md",
+        ]
+    ]
+)
+
+deploydocs(
+    repo = "github.com/juliangehring/MultipleTesting.jl.git",
+    julia = "0.6",
+    target = "build",
+    latest = "develop",
+    deps   = nothing,
+    make   = nothing
+)

docs/src/adjustment.md

@@ -0,0 +1,31 @@
+# Adjustment of p-Values
+
+```@meta
+CurrentModule = MultipleTesting
+DocTestSetup = quote
+    using MultipleTesting
+end
+```
+
+## Methods
+
+```@docs
+adjust
+```
+
+
+## Types
+
+```@docs
+Bonferroni
+BenjaminiHochberg
+BenjaminiHochbergAdaptive
+BenjaminiYekutieli
+BenjaminiLiu
+Hochberg
+Holm
+Hommel
+Sidak
+ForwardStop
+BarberCandes
+```

docs/src/combination.md

@@ -0,0 +1,27 @@
+# Combination of p-Values
+
+```@meta
+CurrentModule = MultipleTesting
+DocTestSetup = quote
+    using MultipleTesting
+end
+```
+
+## Methods
+
+```@docs
+combine
+```
+
+
+## Types
+
+```@docs
+FisherCombination
+LogitCombination
+StoufferCombination
+TippettCombination
+SimesCombination
+WilkinsonCombination
+MinimumCombination
+```

docs/src/higher-criticism.md

@@ -0,0 +1,14 @@
+# Higher Criticism
+
+```@meta
+CurrentModule = MultipleTesting
+DocTestSetup = quote
+    using MultipleTesting
+end
+```
+
+
+```@docs
+HigherCriticismScores
+HigherCriticismThreshold
+```

docs/src/index.md

@@ -0,0 +1,16 @@
+# MultipleTesting.jl
+
+```@meta
+CurrentModule = MultipleTesting
+DocTestSetup = quote
+    using MultipleTesting
+end
+```
+
+
+## Package Features
+
+## Manual
+
+```@contents
+```

docs/src/models.md

@@ -0,0 +1,13 @@
+# Modelling of p-Value Distributions
+
+```@meta
+CurrentModule = MultipleTesting
+DocTestSetup = quote
+    using MultipleTesting
+end
+```
+
+
+```@docs
+BetaUniformMixtureModel
+```