Initial commit

.gitignore

@@ -0,0 +1,134 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# Jekyll
+_site/
+
+# XPP
+*.ode
+
+# C
+*.o
+*.c
+*.cpp
+
+# Fortran
+*.f
+
+# R
+*.Rhistory
+Rplots.pdf
+
+# Result files
+*.out
+
+# VFGEN
+*.vf
+
+# Matlab
+*.m
+
+# Scilab
+*.sci

CNAME.bak

@@ -0,0 +1 @@
+epirecip.es/epicookbook

Dockerfile

@@ -0,0 +1,4 @@
+FROM sdwfrost/epirecipes:latest
+
+LABEL maintainer="Simon Frost <[email protected]>"
+

Gemfile

@@ -0,0 +1,27 @@
+source "https://rubygems.org"
+
+# Hello! This is where you manage which Jekyll version is used to run.
+# When you want to use a different version, change it below, save the
+# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
+#
+#     bundle exec jekyll serve
+#
+# This will help ensure the proper Jekyll version is running.
+# Happy Jekylling!
+
+gem "github-pages", group: :jekyll_plugins
+gem 'jekyll-redirect-from'
+
+# If you want to use Jekyll native, uncomment the line below.
+# To upgrade, run `bundle update`.
+
+# gem "jekyll"
+
+gem "wdm", "~> 0.1.0" if Gem.win_platform?
+
+# If you have any plugins, put them here!
+group :jekyll_plugins do
+  # gem "jekyll-archives"
+  gem "jekyll-feed"
+  gem 'jekyll-sitemap', :github => 'jekyll/jekyll-sitemap', :branch => 'master'
+end

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Chris Holdgraf
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Makefile

@@ -0,0 +1,20 @@
+.PHONY: help textbook clean serve
+
+help:
+	@echo "Please use 'make <target>' where <target> is one of:"
+	@echo "  textbook    to convert the `notebooks/` folder into Jekyll markdown in `chapters/`"
+	@echo "  clean       to clean out site build files"
+	@echo "  runall      to run all notebooks in-place, capturing outputs with the notebook"
+	@echo "  serve       to serve the repository locally with Jekyll"
+
+textbook:
+	python scripts/generate_textbook.py
+
+runall:
+	python scripts/execute_all_notebooks.py
+
+clean:
+	python scripts/clean.py
+
+serve:
+	bundle exec jekyll serve

README.md

@@ -0,0 +1,4 @@
+# epicookbook
+
+This repository / website is based on a template for hosting a textbook using
+Jupyter Notebooks and Jekyll.

Rakefile

@@ -0,0 +1,76 @@
+require "bundler/gem_tasks"
+require "jekyll"
+require "listen"
+
+def listen_ignore_paths(base, options)
+  [
+    /_config\.ya?ml/,
+    /_site/,
+    /\.jekyll-metadata/
+  ]
+end
+
+def listen_handler(base, options)
+  site = Jekyll::Site.new(options)
+  Jekyll::Command.process_site(site)
+  proc do |modified, added, removed|
+    t = Time.now
+    c = modified + added + removed
+    n = c.length
+    relative_paths = c.map{ |p| Pathname.new(p).relative_path_from(base).to_s }
+    print Jekyll.logger.message("Regenerating:", "#{relative_paths.join(", ")} changed... ")
+    begin
+      Jekyll::Command.process_site(site)
+      puts "regenerated in #{Time.now - t} seconds."
+    rescue => e
+      puts "error:"
+      Jekyll.logger.warn "Error:", e.message
+      Jekyll.logger.warn "Error:", "Run jekyll build --trace for more information."
+    end
+  end
+end
+
+task :preview do
+  base = Pathname.new('.').expand_path
+  options = {
+    "source"        => base.join('test').to_s,
+    "destination"   => base.join('test/_site').to_s,
+    "force_polling" => false,
+    "serving"       => true,
+    "theme"         => "minimal-mistakes-jekyll"
+  }
+
+  options = Jekyll.configuration(options)
+
+  ENV["LISTEN_GEM_DEBUGGING"] = "1"
+  listener = Listen.to(
+    base.join("_data"),
+    base.join("_includes"),
+    base.join("_layouts"),
+    base.join("_sass"),
+    base.join("assets"),
+    options["source"],
+    :ignore => listen_ignore_paths(base, options),
+    :force_polling => options['force_polling'],
+    &(listen_handler(base, options))
+  )
+
+  begin
+    listener.start
+    Jekyll.logger.info "Auto-regeneration:", "enabled for '#{options["source"]}'"
+
+    unless options['serving']
+      trap("INT") do
+        listener.stop
+        puts "     Halting auto-regeneration."
+        exit 0
+      end
+
+      loop { sleep 1000 }
+    end
+  rescue ThreadError
+    # You pressed Ctrl-C, oh my!
+  end
+
+  Jekyll::Commands::Serve.process(options)
+end

SUMMARY.md

@@ -0,0 +1,50 @@
+# Summary
+
+* [Simple deterministic models](notebooks/simple.md)
+  * [SIR model](notebooks/sir/intro.md)
+    * [Python using SciPy](notebooks/sir/python.ipynb)
+    * [R using deSolve](notebooks/sir/r_desolve.ipynb)
+    * [R using odin](notebooks/sir/r_odin.ipynb)
+    * [Julia](notebooks/sir/julia.ipynb)
+    * [Octave](notebooks/sir/octave.ipynb)
+    * [Scilab](notebooks/sir/scilab.ipynb)
+    * [C++](notebooks/sir/cpp.ipynb)
+    * [xppaut](notebooks/sir/xpp.ipynb)
+    * [VFGEN](notebooks/sir/vfgen.ipynb)
+    * [Javascript](notebooks/sir/js.ipynb)
+    * [Javascript using Observable](notebooks/sir/js_observable.md)
+* [Simple stochastic models](notebooks/stochastic.md)
+  * [Continuous time](notebooks/sir-stochastic-discretestate-continuoustime/intro.md)
+    * [R](notebooks/sir-stochastic-discretestate-continuoustime/r.ipynb)
+    * [R using GillespieSSA](notebooks/sir-stochastic-discretestate-continuoustime/r-gillespiessa.ipynb)
+    * [R using Rcpp](notebooks/sir-stochastic-discretestate-continuoustime/r-rcpp.ipynb)
+    * [Julia](notebooks/sir-stochastic-discretestate-continuoustime/julia.ipynb)
+  * [Discrete time](notebooks/sir-stochastic-discretestate-discretetime/intro.md)
+    * [R using POMP](notebooks/sir-stochastic-discretestate-discretetime/r_pomp.ipynb)
+    * [R using LibBi](notebooks/sir-stochastic-discretestate-discretetime/r_rbi.ipynb)
+    * [Julia](notebooks/sir-stochastic-discretestate-discretetime/julia.ipynb)
+* [Final size of an epidemic](notebooks/finalsize.md)
+  * [Exact recursive expressions](notebooks/blackross2015/intro.md)
+    * [Original Matlab code](notebooks/blackross2015/matlab.md)
+    * [Julia](notebooks/blackross2015/julia.ipynb)
+    * [Octave](notebooks/blackross2015/octave.ipynb)
+    * [Scilab](notebooks/blackross2015/scilab.ipynb)
+* [Time-varying parameters](notebooks/timevarying.md)
+  * [Seasonally forced deterministic model](notebooks/sirforced/intro.md)
+    * [R](notebooks/sirforced/r.ipynb)
+* [Network models](notebooks/network.md)
+  * [An edge based SIR model on a configuration network](notebooks/sircn/intro.md)
+    * [R](notebooks/sircn/r.ipynb)    
+* [Applications](notebooks/applications.md)
+  * [Acute HIV infection](notebooks/acutehiv/intro.md)
+    * [R](notebooks/acutehiv/r.ipynb)
+  * [A model of HIV with two risk groups](notebooks/diffrisk/intro.md)
+    * [R](notebooks/diffrisk/r.ipynb)
+* [Keeling and Rohani 2008](notebooks/kr08.md)
+  * [Program 2.1](notebooks/kr08/2_1/intro.md)
+    * [Original C](notebooks/kr08/2_1/c_original.ipynb)
+    * [Original Fortran](notebooks/kr08/2_1/fortran_original.ipynb)
+    * [Original Python](notebooks/kr08/2_1/python_original.ipynb)
+    * [Original Matlab/Octave](notebooks/kr08/2_1/octave_original.ipynb)
+* [Appendices](notebooks/appendices.md)
+  * [Style guide for notebooks](notebooks/style.md)

_chapters/acutehiv/intro.md

@@ -0,0 +1,13 @@
+---
+title: 'Acute HIV infection'
+permalink: 'chapters/acutehiv/intro'
+previouschapter:
+  url: chapters/applications
+  title: 'Applications'
+nextchapter:
+  url: chapters/acutehiv/r
+  title: 'R'
+redirect_from:
+  - 'chapters/acutehiv/intro'
+---
+## A model of acute HIV infection