update NobBS for CRAN release

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+NEWS.Rmd
+README.Rmd

DESCRIPTION

@@ -1,15 +1,20 @@
 Package: NobBS
 Title: Nowcasting by Bayesian Smoothing
-Version: 0.0.0.9000
-Author: Sarah McGough
-Maintainer: Sarah McGough <sfm341@gmail.com>
-Description: Make real-time estimates of cases based on incomplete time-stamped reporting data.
-Depends: R (>= 3.3.2)
+Version: 0.1.0
+Authors@R: c(
+    person("Sarah", "McGough", email = "sfm341@mail.harvard.edu", role = c("aut", "cre")),
+    person("Nicolas", "Menzies", email = "nmenzies@hsph.harvard.edu", role = "aut"),
+    person("Marc", "Lipsitch", email = "mlipsitc@hsph.harvard.edu", role = "aut"),
+    person("Michael", "Johansson", email = "mjohansson@cdc.gov", role = "aut")
+    )
+Description: A Bayesian approach to estimate the number of occurred-but-not-yet-reported cases from incomplete, time-stamped reporting data for disease outbreaks. NobBS learns the reporting delay distribution and the time evolution of the epidemic curve to produce smoothed nowcasts in both stable and time-varying case reporting settings. 
+Depends: R (>= 3.3.0)
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Imports:
 	dplyr,
 	rjags,
-	coda
+	coda,
+	magrittr
 RoxygenNote: 6.1.1

NAMESPACE

@@ -3,7 +3,15 @@
 export(NobBS)
 import(coda)
 import(rjags)
+importFrom(dplyr,group_by_)
+importFrom(dplyr,last)
+importFrom(dplyr,left_join)
+importFrom(dplyr,n)
 importFrom(dplyr,select)
 importFrom(dplyr,select_vars)
 importFrom(dplyr,starts_with)
+importFrom(dplyr,summarise)
 importFrom(magrittr,"%>%")
+importFrom(stats,median)
+importFrom(stats,quantile)
+importFrom(stats,update)

NEWS.Rmd

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+---
+output: github_document
+---
+
+
+# NobBS v. 0.1.0 (Initial Release)
+See `README.md` for a full tutorial on using the NobBS package.
+
+Updates to the development version include:
+
+* An argument to specify the `proportion_reported` and inflate the estimated cases by that factor, important in outbreaks with severe under-reporting or asymptomatic cases.
+* Additional checks on impossible temporal combinations of moving window sizes, maximum delay D, and the length of the time series.
+* Warning issued when a case onset week is skipped in the time series or is missing reports altogether.
+* Plot examples
+
+# NobBS v. 0.0.0.9000 (Development)
+
+NobBS (Nowcasting by Bayesian Smoothing) is a new R package that produces smooth Bayesian nowcasts of incomplete, time-stamped reporting data implemented from [McGough et al. 2019](https://www.biorxiv.org/content/10.1101/663823v1.full).
+

NEWS.md

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+
+NobBS v. 0.1.0 (Initial Release)
+================================
+
+See `README.md` for a full tutorial on using the NobBS package.
+
+Updates to the development version include:
+
+-   An argument to specify the `proportion_reported` and inflate the estimated cases by that factor, important in outbreaks with severe under-reporting or asymptomatic cases.
+-   Additional checks on impossible temporal combinations of moving window sizes, maximum delay D, and the length of the time series.
+-   Warning issued when a case onset week is skipped in the time series or is missing reports altogether.
+-   Plot examples
+
+NobBS v. 0.0.0.9000 (Development)
+=================================
+
+NobBS (Nowcasting by Bayesian Smoothing) is a new R package that produces smooth Bayesian nowcasts of incomplete, time-stamped reporting data implemented from [McGough et al. 2019](https://www.biorxiv.org/content/10.1101/663823v1.full).

NobBS_Git.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source