Copied over from bitbucket epiforecast repo

.gitignore

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+# begin license for material from https://github.com/github/gitignore/**
+
+# Copyright (c) 2015 GitHub, Inc.
+
+# 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.
+
+# end license for material from https://github.com/github/gitignore/**
+
+
+
+# begin material from https://github.com/github/gitignore/blob/master/Global/Emacs.gitignore
+
+*~
+\#*\#
+/.emacs.desktop
+/.emacs.desktop.lock
+*.elc
+auto-save-list
+tramp
+.\#*
+
+# Org-mode
+.org-id-locations
+*_archive
+
+# flymake-mode
+*_flymake.*
+
+# eshell files
+/eshell/history
+/eshell/lastdir
+
+# elpa packages
+/elpa/
+
+# reftex files
+*.rel
+
+# AUCTeX auto folder
+/auto/
+
+# cask packages
+.cask/
+
+# end material from https://github.com/github/gitignore/blob/master/Global/Emacs.gitignore
+
+
+
+
+
+# begin material from https://github.com/github/gitignore/blob/master/Global/Vim.gitignore
+
+[._]*.s[a-w][a-z]
+[._]s[a-w][a-z]
+*.un~
+Session.vim
+.netrwhist
+*~
+
+# end material from https://github.com/github/gitignore/blob/master/Global/Vim.gitignore
+
+
+
+# begin material from https://github.com/github/gitignore/blob/master/R.gitignore
+
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# Example code in package build process
+*-Ex.R
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# end material from https://github.com/github/gitignore/blob/master/R.gitignore
+
+
+
+# begin material from https://github.com/github/gitignore/blob/master/C%2B%2B.gitignore
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+# end material from https://github.com/github/gitignore/blob/master/C%2B%2B.gitignore
+
+# Assume contents of man page directories are automatically generated:
+man/**
+
+# Ignore copy of delphi_epidata.R:
+# /R_pkg/epiforecast/R/delphi_epidata.R
+# /R_pkg/epiforecast/R/RcppExports.R
+# /R_pkg/epiforecast/src/RcppExports.cpp
+
+# Ignore epiforecast package data folder (it should be generated by scripts in data-raw):
+/R_pkg/epiforecast/data/**
+
+
+# (For now) offline copies of data that was fetched
+*.csv
+*.Rdata
+
+# R documentatation
+*.Rd
+
+# Personal todo lists
+*todo-justin.org

demo/demo.R

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+library(epiforecast)
+
+## Make dummy csv
+area.name = "hhs1"
+hhs1.dat = fetchEpidataFullDat("fluview", area.name, "wili",
+                               min.points.in.season=52L,
+                               first.week.of.season = 21L,
+                               cache.file=sprintf("fluview_%s_fetch.Rdata", area.name))
+
+## Create a csv in the correct, desirable format
+filename="./correct.csv"
+hhs1.dat = lapply(hhs1.dat, function(myvec){ if(length(myvec)<53) return(c(myvec,NA))  else {return(myvec)}})
+correct.hhs1.dat = do.call(cbind, hhs1.dat)
+correct.hhs1.dat = correct.hhs1.dat[-53,]
+write.csv(correct.hhs1.dat, file = filename,row.names=FALSE)
+full.dat = read.from.file(filename)
+
+
+## Try EB with basic options
+mysim = eb.sim(full.dat, n.sims=1000)
+epiforecast:::plot.sim(mysim)
+targets = epiforecast:::forecast.sim(mysim,'pht')
+
+
+## Try EB with more simulation settings
+control.list = get.eb.control.list(sd.option="prior",max.match.length=5)
+mysim = eb.sim(full.dat, n.sims=100, control.list=control.list)
+epiforecast:::plot.sim(mysim)
+
+
+## Try BR
+mysim = br.sim(full.dat, n.sims=100, bootstrap=T)
+epiforecast:::plot.sim(mysim)
+epiforecast:::print.sim(mysim,verbose=TRUE)
+targets = epiforecast:::forecast.sim(mysim, "pht")
+
+## Try BR with more simulation settings
+control.list = get_br_control_list(df=5, cv.rule="1se")
+mysim = br.sim(full.dat, n.sims=100, bootstrap=T, control.list=control.list)
+epiforecast:::plot.sim(mysim)
+epiforecast:::print.sim(mysim,verbose=TRUE)
+targets = epiforecast:::forecast.sim(mysim, "pht", plot.hist=TRUE)
+targets = epiforecast:::forecast.sim(mysim, "pwk", plot.hist=TRUE)
+
+
+
+## Try twkde
+mysim = twkde.sim(full.dat)
+epiforecast:::plot.sim(mysim)

epiforecast/.gitignore

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+inst/doc

epiforecast/DESCRIPTION

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+Package: epiforecast
+Type: Package
+Title: Tools for forecasting semi-regular seasonal epidemic curves and similar
+    time series
+Version: 0.0.1
+Date: 2015-12-09
+Author: Logan C. Brooks, David C. Farrow, Sangwon Hyun, Ryan J. Tibshirani, Roni
+    Rosenfeld
+Maintainer: Logan C. Brooks <lcbrooks@cs.cmu.edu>
+Imports:
+    stats,
+    utils,
+    lubridate,
+    splines,
+    glmgen,
+    glmnet,
+    httr,
+    Rcpp,
+    rlist,
+    RColorBrewer,
+    data.table,
+    hexbin,
+    plotrix
+Description: Tools for forecasting semi-regular seasonal epidemic curves and
+    similar time series. Includes an empirical Bayes approach that forms a prior
+    by transforming historical curves, a basis regression approach that balances
+    matching observations from the current season and matching historical
+    seasons' measurements for future weeks, and timestep-by-timestep weighted
+    kernel density estimation on backward differences parameterized by both the
+    time series measurments and the current time.
+License: GPL-2
+RoxygenNote: 5.0.1.9000
+Collate:
+    'RcppExports.R'
+    'match.R'
+    'utils.R'
+    'br.R'
+    'checks.R'
+    'cv.R'
+    'delphi_epidata.R'
+    'eb_dists.R'
+    'weeks.R'
+    'loaders.R'
+    'interface.R'
+    'eb.R'
+    'holidays.R'
+    'read.R'
+    'simclass.R'
+    'todo-by-file.R'
+    'twkde.R'
+LinkingTo: Rcpp
+SystemRequirements: C++14
+Suggests:
+    testthat

epiforecast/NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(DateToYearWeekWdayDF)
+export(DatesOfSeason)
+export(Seq)
+export(augmentWeeklyDF)
+export(br.sim)
+export(br.smoothedCurve)
+export(dat.to.matrix)
+export(eb.createForecasts)
+export(eb.fitSmoothCurves)
+export(eb.sim)
+export(fetchEpidataDF)
+export(fetchEpidataFullDat)
+export(get.latest.time)
+export(get_br_control_list)
+export(get_eb_control_list)
+export(is_christmas)
+export(is_newyear)
+export(is_thanksgiving)
+export(lastWeekNumber)
+export(match.arg.else.default)
+export(match.dat)
+export(match.integer)
+export(match.new.dat.sim)
+export(match.single.na.or.numeric)
+export(match.single.nonna.integer)
+export(match.single.nonna.integer.or.null)
+export(read.from.file)
+export(seasonModelWeekDFToYearWeekDF)
+export(seasonModelWeekToYearWeekDF)
+export(seasonModelWeekWdayDFToDate)
+export(seasonModelWeekWdayToDate)
+export(seasonOfDate)
+export(seasonOfYearWeek)
+export(trimPartialPastSeasons)
+export(twkde.markovian.sim)
+export(twkde.sim)
+export(unifChoicePrior)
+export(weekConventions)
+export(yearWeekDFToSeasonModelWeekDF)
+export(yearWeekWdayDFToDate)
+export(yearWeekWdayListsToDate)
+export(yearWeekWdayVecsToDate)
+import(RColorBrewer)
+import(Rcpp)
+import(data.table)
+import(glmgen)
+import(hexbin)
+import(httr)
+import(plotrix)
+import(rlist)
+useDynLib(epiforecast)

epiforecast/R/RcppExports.R

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+# This file was generated by Rcpp::compileAttributes
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+