include DOI for references

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: phylopomp
 Type: Package
 Title: Phylodynamic Inference for POMP Models
-Version: 0.14.2.3
-Date: 2024-06-11
+Version: 0.14.2.4
+Date: 2024-07-04
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa@umich.edu",comment=c(ORCID="0000-0001-6159-3207")),
 	  person(given=c("Qianying"),family="Lin",role=c("aut"),comment=c(ORCID="0000-0001-8620-9910"))
 	  )
@@ -17,7 +17,7 @@ LazyData: true
 Contact: kingaa at umich dot edu
 Encoding: UTF-8
 Roxygen: list(roclets = c("collate", "namespace", "rd"))
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Collate: 
     'package.R'
     'geneal.R'

man/macros/citations.Rd

@@ -1,16 +1,16 @@
 % unlike in latex, new lines within \newcommand end the command (even using %)
-\newcommand{\Moran1958}{P.A.P. Moran. Random processes in genetics.  \emph{Mathematical Proceedings of the Cambridge Philosophical Society} \bold{54}, 60--71, 1958.  DOI:10.1017/s0305004100033193}
+\newcommand{\Moran1958}{P.A.P. Moran. Random processes in genetics.  \emph{Mathematical Proceedings of the Cambridge Philosophical Society} \bold{54}, 60--71, 1958. \doi{10.1017/s0305004100033193}.}
 
-\newcommand{\Arulampalam2002}{M.S. Arulampalam, S. Maskell, N. Gordon, & T. Clapp. A Tutorial on Particle Filters for Online Nonlinear, Non-Gaussian Bayesian Tracking. \emph{IEEE Transactions on Signal Processing} \bold{50}, 174--188, 2002. DOI:10.1109/78.978374}
+\newcommand{\Arulampalam2002}{M.S. Arulampalam, S. Maskell, N. Gordon, & T. Clapp. A Tutorial on Particle Filters for Online Nonlinear, Non-Gaussian Bayesian Tracking. \emph{IEEE Transactions on Signal Processing} \bold{50}, 174--188, 2002. \doi{10.1109/78.978374}.}
 
-\newcommand{\He2010}{D. He, E.L. Ionides, & A.A. King. Plug-and-play inference for disease dynamics: measles in large and small populations as a case study.  \emph{Journal of the Royal Society Interface} \bold{7}, 271--283, 2010. DOI:10.1098/rsif.2009.0151}
+\newcommand{\He2010}{D. He, E.L. Ionides, & A.A. King. Plug-and-play inference for disease dynamics: measles in large and small populations as a case study.  \emph{Journal of the Royal Society Interface} \bold{7}, 271--283, 2010. \doi{10.1098/rsif.2009.0151}.}
 
-\newcommand{\Ionides2015}{E.L. Ionides, D. Nguyen, Y. \ifelse{latex}{\out{Atchad\'e}}{\ifelse{html}{\out{Atchadé}}{Atchade}}, S. Stoev, and A.A. King. Inference for dynamic and latent variable models via iterated, perturbed Bayes maps. \emph{Proceedings of the National Academy of Sciences} \bold{112}, 719--724, 2015. DOI:10.1073/pnas.1410597112}
+\newcommand{\Ionides2015}{E.L. Ionides, D. Nguyen, Y. \ifelse{latex}{\out{Atchad\'e}}{\ifelse{html}{\out{Atchadé}}{Atchade}}, S. Stoev, and A.A. King. Inference for dynamic and latent variable models via iterated, perturbed Bayes maps. \emph{Proceedings of the National Academy of Sciences} \bold{112}, 719--724, 2015. \doi{10.1073/pnas.1410597112}.}
 
-\newcommand{\King2016}{A. A. King, D. Nguyen, and E. L. Ionides. Statistical Inference for Partially Observed Markov Processes via the Package \pkg{pomp}. \emph{Journal of Statistical Software} \bold{69}(12), 1--43, 2016.  DOI:10.18637/jss.v069.i12. An updated version of this paper is available on the \href{https://kingaa.github.io/pomp/docs.html}{\pkg{pomp} package website}.}
+\newcommand{\King2016}{A. A. King, D. Nguyen, and E. L. Ionides. Statistical inference for partially observed Markov processes via the R package \pkg{pomp}. \emph{Journal of Statistical Software} \bold{69}(12), 1--43, 2016. \doi{10.18637/jss.v069.i12}. An updated version of this paper is available on the \href{https://kingaa.github.io/pomp/docs.html}{\pkg{pomp} package website}.}
 
-\newcommand{\Stadler2010}{T. Stadler. Sampling-through-time in birth-death trees. \emph{Journal of Theoretical Biology} \bold{267}, 396--404, 2010. DOI:10.1016/j.jtbi.2010.09.010}
+\newcommand{\Stadler2010}{T. Stadler. Sampling-through-time in birth-death trees. \emph{Journal of Theoretical Biology} \bold{267}, 396--404, 2010. \doi{10.1016/j.jtbi.2010.09.010}.}
 
-\newcommand{\King2024}{A. A. King, Q. Lin, and E. L. Ionides. Exact phylodynamic likelihood via structured Markov genealogy processes. \emph{arXiv} 2405.17032, 2024. DOI:10.48550/arxiv.2405.17032}
+\newcommand{\King2024}{A. A. King, Q. Lin, and E. L. Ionides. Exact phylodynamic likelihood via structured Markov genealogy processes. \emph{arXiv} 2405.17032, 2024. \doi{10.48550/arxiv.2405.17032}.}
 
-\newcommand{\King2022}{A. A. King, Q. Lin, and E. L. Ionides. Markov genealogy processes. \emph{Theoretical Population Biology} \bold{143}, 77--91, 2022. DOI:10.1016/j.tpb.2021.11.003}
+\newcommand{\King2022}{A. A. King, Q. Lin, and E. L. Ionides. Markov genealogy processes. \emph{Theoretical Population Biology} \bold{143}, 77--91, 2022. \doi{10.1016/j.tpb.2021.11.003}.}