update the remiagning vignettes and DESCRIPTION

Author: Georgi Boshnakov

DESCRIPTION

@@ -2,7 +2,7 @@ Package: Countr
 Type: Package
 Title: Flexible Univariate Count Models Based on Renewal Processes
 Version: 3.5.3
-Date: 2019-08-13
+Date: 2019-08-15
 Authors@R: c( person(given = "Tarak", family = "Kharrat",
                      role = c("aut", "cre"), 
                      email = "[email protected]"),
@@ -16,7 +16,7 @@ Description: Flexible univariate count models based on renewal
     of Statistical Software <10.18637/jss.v090.i13> (included as
     vignette 'Countr_guide' in the package).
 License: GPL (>= 2)
-URL: https://github.com/GeoBosh/Countr
+URL: https://github.com/GeoBosh/Countr  https://geobosh.github.io/Countr/
 BugReports: https://github.com/GeoBosh/Countr/issues
 Depends:
     R (>= 3.3.0)

Org/countr_guide_paper_Rnw/CountrJSSArticle.bib

@@ -0,0 +1,10 @@
+@Article{CountrJssArticle,
+    title = {Flexible Regression Models for Count Data Based on Renewal Processes: The {Countr} Package},
+    author = {Tarak Kharrat and Georgi N. Boshnakov and Ian McHale and Rose Baker},
+    journal = {Journal of Statistical Software},
+    year = {2019},
+    volume = {90},
+    number = {13},
+    pages = {1--35},
+    doi = {10.18637/jss.v090.i13},
+}

Org/countr_guide_paper_Rnw/Countr_guide_paper.Rnw

@@ -0,0 +1,349 @@
+@Article{RpackageFormula,
+    title = {{Extended Model Formulas in \proglang{R}: Multiple Parts and
+      Multiple Responses}},
+    author = {Achim Zeileis and Yves Croissant},
+    journal = {Journal of Statistical Software},
+    year = {2010},
+    volume = {34},
+    number = {1},
+    pages = {1--13},
+    doi = {10.18637/jss.v034.i01},
+  }
+
+@Article{BB2009,
+    title = {{\pkg{BB}: An \proglang{R} Package for Solving a Large System of Nonlinear Equations and for Optimizing a High-Dimensional Nonlinear Objective Function}},
+    author = {Ravi Varadhan and Paul Gilbert},
+    journal = {Journal of Statistical Software},
+    year = {2009},
+    volume = {32},
+    number = {4},
+    pages = {1--26},
+    url = {http://www.jstatsoft.org/v32/i04/},
+  }
+
+@article{stacy1962generalization,
+  title={{A Generalization of the Gamma Distribution}},
+  author={Stacy, Eo W},
+  journal={The Annals of Mathematical Statistics},
+  pages={1187--1192},
+  year={1962},
+  publisher={JSTOR}
+}
+
+
+@Manual{Rcore,
+  title = {{\proglang{R}: A Language and Environment for Statistical Computing}},
+  author = {{R Core Team}},
+  organization = {R Foundation for Statistical Computing},
+  address = {Vienna, Austria},
+  year = {2017},
+  url = {https://www.R-project.org/},
+}
+
+@article{tadikamalla1980look,
+  title={{A Look at the Burr and Related Distributions}},
+  author={Tadikamalla, Pandu R},
+  journal={International Statistical Review/Revue Internationale de Statistique},
+  pages={337--344},
+  year={1980},
+  publisher={JSTOR}
+}
+
+
+@book{mccullagh1989generalized,
+ title={Generalized Linear Models, 2nd ed.,
+        no. 37 in Monograph on Statistics and Applied Probability},
+ author={McCullagh, Peter and Nelder, John A},
+  year={1989},
+  publisher={CRC press/Chapman \& Hall}
+}
+
+@Article{flexsurv2016,
+    title = {\pkg{flexsurv}: A Platform for Parametric Survival Modeling in
+      \proglang{R}},
+    author = {Christopher Jackson},
+    journal = {Journal of Statistical Software},
+    year = {2016},
+    volume = {70},
+    number = {8},
+    pages = {1--33},
+    doi = {10.18637/jss.v070.i08},
+  }
+
+
+@Article{optimx2014,
+    title = {Unifying Optimization Algorithms to Aid Software System
+      Users: \pkg{optimx} for \proglang{R}},
+    author = {John C. Nash and Ravi Varadhan},
+    journal = {Journal of Statistical Software},
+    year = {2011},
+    volume = {43},
+    number = {9},
+    pages = {1--14},
+    url = {http://www.jstatsoft.org/v43/i09/},
+  }
+
+
+@book{eddelbuettel2013seamless,
+  title={Seamless \proglang{R} and \proglang{C++} Integration With Rcpp},
+  author={Eddelbuettel, Dirk},
+  year={2013},
+  publisher={Springer-Verlag}
+}
+
+@Manual{RpackageCountr,
+  title = {\pkg{Countr}: Flexible Univariate Count Models Based on Renewal Processes},
+  author = {Tarak Kharrat and Georgi N. Boshnakov},
+  year = {2016},
+  note = {R package version 3.2.7},
+  url = {https://cran.r-project.org/web/packages/Countr/index.html}
+}
+
+
+@article{winkelmann1995duration,
+  title={Duration Dependence and Dispersion in Count-Data Models},
+  author={Winkelmann, Rainer},
+  journal={Journal of Business \& Economic Statistics},
+  volume={13},
+  number={4},
+  pages={467--474},
+  year={1995},
+  publisher={Taylor \& Francis}
+}
+
+@article{baker2016Renewal,
+  title={Event Count Distributions from Renewal Processes: Fast Computation of Probabilities},
+  author={Baker, Rose and Kharrat, Tarak},
+  journal={IMA Journal of Management Mathematics},
+  year={2017},
+  url = {http://dx.doi.org/10.1093/imaman/dpx008},
+  publisher={Oxford University Press}
+}
+
+@book{press2007numerical,
+  title={Numerical Recipes: The Art of Scientific Computing (3rd ed.)},
+  author={Press, W H and Teukolsky, S A and Vetterling, W T and Flannery, B P},
+  year={2007},
+  publisher={Cambridge University Press}
+}
+
+@Manual{Rlang2015,
+    title = {\proglang{R}: A Language and Environment for Statistical Computing},
+    author = {{R Core Team}},
+    organization = {R Foundation for Statistical Computing},
+    address = {Vienna, Austria},
+    year = {2016},
+    url = {https://www.R-project.org/},
+  }
+
+@article{McShane2008Count,
+  title={Count Models Based on Weibull Inter-Arrival Times},
+  author={McShane, Blake and Adrian, Moshe and Bradlow, Eric T and Fader, Peter S},
+  journal={Journal of Business \& Economic Statistics},
+  volume={26},
+  number={3},
+  year={2008}
+}
+
+@article{jose2011count,
+  title={A Count Model Based on Mittag-Leffler Inter-Arrival Times},
+  author={Jose, Kanichukattu K and Abraham, Bindu},
+  journal={Statistica},
+  volume={71},
+  number={4},
+  pages={501--514},
+  year={2011},
+  publisher={Department of Statistics, University of Bologna}
+}
+
+@article{Jose2013Gumbel,
+  author = {Jose, K and Bindu Abraham},
+  title = {A Counting Process with Gumbel Inter-Arrival Times for Modeling Climate Data},
+  journal = {Journal of Environmental Statistics},
+  volume = {4},
+  number = {5},
+  year ={2013},
+  CODEN = {JESOBK},
+  ISSN ={1945-1296},
+  bibdate = {2012-09-17},
+  URL = {http://jes.stat.ucla.edu/v04/i05},
+  accepted = {2012-09-17},
+  submitted = {2012-03-14},
+}
+
+@book{chambers1992statistical,
+  title={Statistical Models in \proglang{S}},
+  author={Chambers, J M and Hastie, T J},
+  year={1992},
+  publisher={Wadsworth \& Brooks/Cole, Pacific Grove, California},
+}
+
+@article{zeileis2008regression,
+  title={Regression Models for Count Data in \proglang{R}},
+  author={Zeileis, Achim and Kleiber, Christian and Jackman, Simon},
+  journal={Journal of statistical software},
+  volume={27},
+  number={8},
+  pages={1--25},
+  year={2008},
+  publisher={Foundation for Open Access Statistics}
+}
+
+@article{prentice1974log,
+  title={A Log Gamma Model and Its Maximum Likelihood Estimation},
+  author={Prentice, Ross L},
+  journal={Biometrika},
+  volume={61},
+  number={3},
+  pages={539--544},
+  year={1974},
+  publisher={Biometrika Trust}
+}
+
+@book{winkelmann2013econometric,
+  title={Econometric Analysis of Count Data, 4th ed.},
+  author={Winkelmann, Rainer},
+  year={2013},
+  publisher={Springer-Verlag, Berlin Heidelberg},
+}
+
+@book{cameron2013regression,
+  title={Regression Analysis of Count Data, 2nd ed.},
+  author={Cameron, A Colin and Trivedi, Pravin K},
+  year={2013},
+  publisher={Cambridge University Press}
+}
+
+@article{depril,
+  title={Recursions for Convolutions of Arithmetic Distributions},
+  author={De Pril, Nelson},
+  journal={Astin Bulletin},
+  volume={15},
+  number={02},
+  pages={135--139},
+  year={1985},
+  publisher={Cambridge Univ Press}
+}
+
+@book{feller1970,
+  author = {Feller, William},
+  title = {An Introduction to Probability Theory and Its Applications; 2nd ed.},
+  publisher = {John Wiley \& Sons},
+  address = "New York, NY",
+  year = "1971",
+}
+
+@book{TarakPhd,
+  title={A Journey Across Football Modelling with Application to Algorithmic Trading (PhD Thesis)},
+  author={Kharrat, Tarak},
+  year={2016},
+  publisher={University of Manchester}
+}
+
+
+@article{bittner2007self,
+  title={Self-Affirmation Model for Football Goal Distributions},
+  author={Bittner, Elmar and Nussbaumer, Andreas and Janke, Wolfhard and Weigel, Martin},
+  journal={EPL (Europhysics Letters)},
+  volume={78},
+  number={5},
+  pages={58002},
+  year={2007},
+  publisher={IOP Publishing}
+}
+
+@Article{RcppArmadillo2014,
+    title = {RcppArmadillo: Accelerating \proglang{R} With High-Performance \proglang{C++}
+      Linear Algebra},
+    author = {Dirk Eddelbuettel and Conrad Sanderson},
+    journal = {Computational Statistics and Data Analysis},
+    year = {2014},
+    volume = {71},
+    month = {March},
+    pages = {1054--1063},
+    url = {http://dx.doi.org/10.1016/j.csda.2013.02.005},
+  }
+
+@Manual{dplyr2016,
+    title = {dplyr: A Grammar of Data Manipulation},
+    author = {Hadley Wickham and Romain Francois},
+    year = {2016},
+    note = {R package version 0.5.0},
+    url = {https://CRAN.R-project.org/package=dplyr},
+  }
+
+@Manual{xtable2016,
+    title = {xtable: Export Tables to LaTeX or HTML},
+    author = {David B. Dahl},
+    year = {2016},
+    note = {R package version 1.8-2},
+    url = {https://CRAN.R-project.org/package=xtable},
+}
+
+@article{boshnakov2017bivariate,
+  title={A Bivariate Weibull Count Model for Forecasting Association Football Scores},
+  author={Boshnakov, Georgi and Kharrat, Tarak and McHale, Ian G},
+  journal={International Journal of Forecasting},
+  volume={33},
+  number={2},
+  pages={458--466},
+  year={2017},
+  publisher={Elsevier}
+}
+
+@article{dixon1998birth,
+  title={A Birth Process Model for Association Football Matches},
+  author={Dixon, Mark and Robinson, Michael},
+  journal={Journal of the Royal Statistical Society D (The Statistician)},
+  volume={47},
+  number={3},
+  pages={523--538},
+  year={1998},
+  publisher={Wiley Online Library}
+}
+
+@Manual{boot2017,
+    title = {boot: Bootstrap R (S-PLUS) Functions},
+    author = {Angelo Canty and B. D. Ripley},
+    year = {2017},
+    note = {R package version 1.3-20},
+  }
+
+@article{aitkin1978analysis,
+  title={The Analysis of Unbalanced Cross-Classifications},
+  author={Aitkin, Murray},
+  journal={Journal of the Royal Statistical Society A (General)},
+  pages={195--223},
+  year={1978},
+  publisher={JSTOR}
+}
+
+@Book{Venables20102MASS,
+    title = {Modern Applied Statistics with S},
+    author = {W. N. Venables and B. D. Ripley},
+    publisher = {Springer-Verlag},
+    edition = {Fourth},
+    address = {New York},
+    year = {2002},
+    note = {ISBN 0-387-95457-0},
+    url = {http://www.stats.ox.ac.uk/pub/MASS4},
+  }
+
+@Book{car2011,
+    title = {An \proglang{R} Companion to Applied Regression},
+    edition = {Second},
+    author = {John Fox and Sanford Weisberg},
+    year = {2011},
+    publisher = {Sage},
+    address = {Thousand Oaks {CA}},
+    url = {http://socserv.socsci.mcmaster.ca/jfox/Books/Companion},
+}
+
+@book{davison1997bootstrap,
+  title={Bootstrap Methods and Their Application},
+  author={Davison, Anthony Christopher and Hinkley, David Victor},
+  volume={1},
+  year={1997},
+  publisher={Cambridge University Press}
+}
+