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Merge pull request #2 from bjoelle/master

Updated tutorial for TtB Canada
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rachelwarnock committed Jul 17, 2019
2 parents 08f9712 + 8e1c001 commit 227c734549d69ca0e1be0097a6b1f8f32247c923
@@ -8,3 +8,6 @@ main-blx.bib
main.pdf
/figures_raw/
.texpadtmp/
.DS_Store
main.bcf
main.synctex.gz
@@ -3,7 +3,7 @@ author: Tracy A. Heath
level: Intermediate
title: Divergence Time Estimation using BEAST v2.x
subtitle: Dating Species Divergences with the Fossilized Birth-Death Process
beastversion: 2.4.4
beastversion: 2.5.2
---

Central among the questions explored in biology are those that seek to understand the timing and rates of evolutionary processes. Accurate estimates of species divergence times are vital to understanding historical biogeography, estimating diversification rates, and identifying the causes of variation in rates of molecular evolution.
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285 main.tex

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@@ -117,6 +117,17 @@ @ARTICLE{birney07
pages = {799--816}
}

@article{baridosottani2019,
author = {Joëlle Barido-Sottani and Gabriel Aguirre-Fernández and Melanie J. Hopkins and Tanja Stadler and Rachel Warnock },
title = {Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth\&\#x2013;death process},
journal = {Proceedings of the Royal Society B: Biological Sciences},
volume = {286},
number = {1902},
pages = {20190685},
year = {2019},
doi = {10.1098/rspb.2019.0685}
}

@ARTICLE{abella12,
author = {Juan Abella and David M. Alba and Josep M. Robles and Alberto Valenciano
and Cheyenn Rotgers and Ra\"ul Carmona and Plinio Montoya and Jorge
@@ -809,16 +820,6 @@ @ARTICLE{bell2014strap
publisher = {Wiley Online Library}
}

@ARTICLE{bell2014strap,
author = {Bell, Mark A and Lloyd, Graeme T},
title = {{strap}: an {R} package for plotting phylogenies against stratigraphy
and assessing their stratigraphic congruence},
journal = {Palaeontology},
year = {2014},
pages = {in press},
publisher = {Wiley Online Library}
}

@ARTICLE{benton03,
author = {M. J. Benton and F. J. Ayala},
title = {Dating the tree of life},
@@ -34,7 +34,7 @@


% References
\usepackage[backend=bibtex,hyperref=true,citestyle=authoryear,bibstyle=authortitle,firstinits=true,terseinits=true,doi=false,url=false,eprint=false,maxbibnames=10,maxcitenames=2]{biblatex}
\usepackage[backend=bibtex,hyperref=true,citestyle=authoryear,bibstyle=authortitle,giveninits=true,terseinits=true,doi=false,url=false,eprint=false,maxbibnames=10,maxcitenames=2]{biblatex}
\input{biblatex_macros}

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@@ -3,7 +3,7 @@ library("phyloch")
library("strap")
library("coda")

t <- read.beast("bearsDivtime_FBD.summary.tre")
t <- read.beast("bearsTree.summary.tre")
t$root.time <- t$height[1]

log_data1 <- read.table("bearsDivtime_FBD.1.log",header=T)

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