Merge pull request #34 from juliangehring/develop

Merge changes for v2.0.0 release

.appveyor.yml

@@ -1,6 +1,13 @@
 environment:
   matrix:
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.6-latest-win64.exe"
+  - julia_version: 0.7
+  - julia_version: 1
+
+platform:
+  - x64
+
+matrix:
+  fast_finish: true
 
 notifications:
   - provider: Email
@@ -9,19 +16,12 @@ notifications:
     on_build_status_changed: false
 
 install:
-  - ps: "[System.Net.ServicePointManager]::SecurityProtocol = [System.Net.SecurityProtocolType]::Tls12"
-# Download most recent Julia Windows binary
-  - ps: (new-object net.webclient).DownloadFile(
-        $env:JULIA_URL,
-        "C:\projects\julia-binary.exe")
-# Run installer silently, output to C:\projects\julia
-  - C:\projects\julia-binary.exe /S /D=C:\projects\julia
+  - ps: iex ((new-object net.webclient).DownloadString("https://raw.githubusercontent.com/JuliaCI/Appveyor.jl/version-1/bin/install.ps1"))
 
 build_script:
-# Need to convert from shallow to complete for Pkg.clone to work
-  - IF EXIST .git\shallow (git fetch --unshallow)
-  - C:\projects\julia\bin\julia -e "versioninfo();
-      Pkg.clone(pwd(), \"Bootstrap\"); Pkg.build(\"Bootstrap\")"
+  - echo "%JL_BUILD_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_BUILD_SCRIPT%"
 
 test_script:
-  - C:\projects\julia\bin\julia --check-bounds=yes -e "Pkg.test(\"Bootstrap\")"
+  - echo "%JL_TEST_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_TEST_SCRIPT%"

.codecov.yml

@@ -16,7 +16,7 @@ coverage:
     project: true
 
 flags:
-  julia_0_6:
+  julia_1_0:
     joined: true
 
 parsers:

.travis.yml

@@ -2,18 +2,20 @@ language: julia
 
 os:
   - linux
+  - osx
 
 julia:
-  - 0.6
+  - 0.7
+  - 1.0
+
+matrix:
+  fast_finish: true
 
 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("Bootstrap"); Pkg.test("Bootstrap"; coverage=true)'
-
 after_success:
-  - julia -e 'cd(Pkg.dir("Bootstrap")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder(), flags="julia_$(VERSION.major)_$(VERSION.minor)")'
+  - julia -e 'using Pkg; Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder(), flags="julia_$(VERSION.major)_$(VERSION.minor)")'
+  - julia -e 'using Pkg; Pkg.add("Documenter"); include(joinpath("docs", "make.jl"))'

NEWS.md

@@ -1,5 +1,22 @@
 # Bootstrap.jl News and Changes
 
+## Version 2.0.0
+
+### Interface changes
+
+- Put the function argument first in the signatures (#26): Changes the bootstrap signature to have the function argument come first: `bootstrap(statistic::Function, data, sampling)`. The old syntax has been deprecated and will be removed in a future version.
+- Integrate better with StatsBase function names (#24): Integrates with the naming of the equivalent functions in StatsBase.jl: Renames ci to confint and se to stderror. The old function names have been deprecated, and will be supported until the next major release. The motivation for these change is outlined in #23.
+
+### Changes
+
+- Build the html documentation directly with Documenter (#28, #25)
+- Support julia v0.7 and v1.0, drop support for julia v0.6 (#33)
+
+### Support
+
+- Requires julia 0.7 or v1.0
+
+
 ## Version 1.2.0
 
 ### New features
@@ -9,7 +26,7 @@
 
 ### Changes
 
-- Transition tests from ``FactCheck`` to `Base.Test`.
+- Transition tests from `FactCheck` to `Base.Test`.
 - Introduces `StatsModels` as a new dependency which is now the new home of `Formula`s.
 - Use vectorized function calls for `Distribution` functions.
 - Removes the dependency on `Compat`.
@@ -25,13 +42,13 @@
 
 ### Changes
 
-- Adds compatibility with julia 0.6 development versions, inc- Supports formula macros for DataFrame formulas (required for using [`DataFrames`](https://github.com/JuliaStats/DataFrames.jl/pull/1170) v0.9.0 or newer)
+- Adds compatibility with julia 0.6 development versions, inc- Supports formula macros for DataFrame formulas (required for using [`DataFrames`](https://github.com/JuliaData/DataFrames.jl/pull/1170) v0.9.0 or newer)
 - Fixes convergence errors of GLM models in parametric bootstrap test cases
 - Modernise automated test and coverage setup (also thanks to [Tony Kelman](https://github.com/tkelman) for contributions)
 - Improves the readme (also thanks to [Patrick Kofod Mogensen](https://github.com/pkofod) for contributions)
 luding automated tests.
 - Introduces `Compat` as a new dependency
-- Supports formula macros for DataFrame formulas (required for using [`DataFrames`](https://github.com/JuliaStats/DataFrames.jl/pull/1170) v0.9.0 or newer)
+- Supports formula macros for DataFrame formulas (required for using [`DataFrames`](https://github.com/JuliaData/DataFrames.jl/pull/1170) v0.9.0 or newer)
 - Fixes convergence errors of GLM models in parametric bootstrap test cases
 - Modernise automated test and coverage setup (also thanks to [Tony Kelman](https://github.com/tkelman) for contributions)
 - Improves the readme (also thanks to [Patrick Kofod Mogensen](https://github.com/pkofod) for contributions)

README.md

@@ -5,10 +5,10 @@
 
 Bootstrapping is a widely applicable technique for statistical estimation.
 
-![img](docs/src/bootstraps.png)
+![img](docs/src/assets/logo.png)
 
 
-# Functionality
+## Functionality
 
 - Bootstrapping statistics with different resampling methods:
   - Random resampling with replacement (`BasicSampling`)
@@ -32,7 +32,7 @@ Bootstrapping is a widely applicable technique for statistical estimation.
 Reports on package builds for all platforms and test coverage are collected on
 the [package status page](status.md).
 
-The package is under active development and uses [semantic versioning](http://semver.org/).
+The package uses [semantic versioning](https://semver.org/).
 
 
 ## Installation
@@ -41,15 +41,16 @@ The `Bootstrap` package is part of the Julia ecosphere and the latest release
 version can be installed with
 
 ```julia
+using Pkg
 Pkg.add("Bootstrap")
 ```
 
-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.
+More details on packages and how to manage them can be found in the [package
+section](https://docs.julialang.org/en/v1/stdlib/Pkg/) of the Julia
+documentation.
 
 
-# Examples
+## Examples
 
 This example illustrates the basic usage and cornerstone functions of the package.
 More elaborate cases are covered in the documentation notebooks.
@@ -58,51 +59,53 @@ More elaborate cases are covered in the documentation notebooks.
   using Bootstrap
 ```
 
-Our observations `r` are sampled from a standard normal distribution.
+Our observations in `some_data` are sampled from a standard normal distribution.
 
 ```julia
-  r = randn(100);
+  some_data = randn(100);
 ```
 
 Let's bootstrap the standard deviation (`std`) of our data, based on 1000
 resamples and with different bootstrapping approaches.
 
 ```julia
+  using Statistics  # the `std` methods live here
+
   n_boot = 1000
 
   ## basic bootstrap
-  bs1 = bootstrap(r, std, BasicSampling(n_boot))
+  bs1 = bootstrap(std, some_data, BasicSampling(n_boot))
 
   ## balanced bootstrap
-  bs2 = bootstrap(r, std, BalancedSampling(n_boot))
+  bs2 = bootstrap(std, some_data, BalancedSampling(n_boot))
 ```
 
-We can explore the properties of the bootstrapped samples, for example estimated
-bias and standard error of our statistic.
+We can explore the properties of the bootstrapped samples, for example, the
+estimated bias and standard error of our statistic.
 
 ```julia
   bias(bs1)
-  se(bs1)
+  stderror(bs1)
 ```
 
-Further, we can estimate confidence intervals for our statistic of interest,
-based on the bootstrapped samples.
+Furthermore, we can estimate confidence intervals (CIs) for our statistic of
+interest, based on the bootstrapped samples.
 
 ```julia
   ## calculate 95% confidence intervals
   cil = 0.95;
 
   ## basic CI
-  bci1 = ci(bs1, BasicConfInt(cil));
+  bci1 = confint(bs1, BasicConfInt(cil));
 
   ## percentile CI
-  bci2 = ci(bs1, PercentileConfInt(cil));
+  bci2 = confint(bs1, PercentileConfInt(cil));
 
   ## BCa CI
-  bci3 = ci(bs1, BCaConfInt(cil));
+  bci3 = confint(bs1, BCaConfInt(cil));
 
   ## Normal CI
-  bci4 = ci(bs1, NormalConfInt(cil));
+  bci4 = confint(bs1, NormalConfInt(cil));
 ```
 
 
@@ -113,8 +116,8 @@ is a comprehensive introduction into the topic.  An extensive description of the
 bootstrap is the focus of the book *Davison and Hinkley (1997):
 [Bootstrap Methods and Their Application](http://statwww.epfl.ch/davison/BMA/)*.
 Most of the methodology covered in the book is implemented in the
-[boot](http://cran.r-project.org/web/packages/boot/index.html) package for the
-[R programming language](http://www.r-project.org/). [More references](docs/src/references.md)
+[boot](https://cran.r-project.org/web/packages/boot/index.html) package for the
+[R programming language](https://www.r-project.org/). [More references](docs/src/references.md)
 are listed in the documentation for further reading.
 
 

REQUIRE

@@ -1,5 +1,5 @@
-julia 0.6
-StatsBase 0.15.0
-Distributions 0.14.1
-DataFrames 0.11.0
+julia 0.7
+StatsBase 0.24.0
+Distributions 0.16.1
+DataFrames 0.14.0
 StatsModels 0.2.0

docs/make.jl

@@ -1,10 +1,27 @@
 using Documenter
 using Bootstrap
 
-makedocs()
+makedocs(
+    modules = [Bootstrap],
+    format = :html,
+    sitename = "Bootstrap.jl",
+    doctest = true,
+    checkdocs = :exports,
+    linkcheck = true,
+    html_disable_git = true, # disable source and edit links to github
+    html_canonical = "https://juliangehring.github.io/Bootstrap.jl/stable/",
+    pages = [
+        "Home" => "index.md",
+        "Library" => "library.md",
+        "Changelog" => "NEWS.md",
+        "License" => "LICENSE.md"
+    ]
+)
 
 deploydocs(
     repo = "github.com/juliangehring/Bootstrap.jl.git",
-    julia  = "0.4",
-    deps = Deps.pip("mkdocs", "python-markdown-math", "pygments", "mkdocs-material")
+    julia = "1.0",
+    target = "build",
+    deps   = nothing,
+    make   = nothing
 )

docs/src/index.md

@@ -1,19 +1,14 @@
 # Motivation
 
-```
-{meta}
-CurrentModule = Bootstrap
-```
-
 Bootstrapping is a widely applicable technique for statistical estimation.
 
-![img](bootstraps.png)
+![img](assets/logo.png)
 
 
 # References
 
 The [bootstrapping wikipedia article](https://en.wikipedia.org/wiki/Bootstrapping_(statistics)) is a comprehensive summary of the topic.  An
 extensive description of the bootstrap is the focus of the book *Davison and
 Hinkley (1997): [Bootstrap Methods and Their Application](http://statwww.epfl.ch/davison/BMA/)*.  Most of the
-methodology covered in the book is implemented in the [boot](http://cran.r-project.org/web/packages/boot/index.html) package for the [R
-programming language](http://www.r-project.org/).
+methodology covered in the book is implemented in the [boot](https://cran.r-project.org/web/packages/boot/index.html) package for the [R
+programming language](https://www.r-project.org/).