Merge pull request #2 from bjoelle/master

Updated tutorial for TtB Canada
Taming-the-BEAST · Jul 17, 2019 · 227c734 · 227c734
2 parents 08f9712 + 8e1c001
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diff --git a/.gitignore b/.gitignore
@@ -8,3 +8,6 @@ main-blx.bib
 main.pdf
 /figures_raw/
 .texpadtmp/
+.DS_Store
+main.bcf
+main.synctex.gz
diff --git a/README.md b/README.md
@@ -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. 

diff --git a/figures/bearsTree_icytree.pdf b/figures/bearsTree_icytree.pdf
diff --git a/figures/geoscaled_bears.pdf b/figures/geoscaled_bears.pdf
diff --git a/figures/geoscaled_bears_ext.pdf b/figures/geoscaled_bears_ext.pdf
diff --git a/figures/prior_tip.png b/figures/prior_tip.png
diff --git a/figures/priors_all_tips.png b/figures/priors_all_tips.png
diff --git a/figures/ts_tip.png b/figures/ts_tip.png
diff --git a/main.tex b/main.tex
diff --git a/master-refs.bib b/master-refs.bib
@@ -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},

diff --git a/preamble.tex b/preamble.tex
@@ -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}
 
 % Page margins

diff --git a/precooked_runs/bearsDivtime_FBD.1.log.gz b/precooked_runs/bearsDivtime_FBD.1.log.gz
diff --git a/precooked_runs/bearsDivtime_FBD.2.log.gz b/precooked_runs/bearsDivtime_FBD.2.log.gz
diff --git a/precooked_runs/bearsDivtime_FBD.prior.log.gz b/precooked_runs/bearsDivtime_FBD.prior.log.gz
diff --git a/precooked_runs/bearsDivtime_FBD.prior.trees.gz b/precooked_runs/bearsDivtime_FBD.prior.trees.gz
diff --git a/precooked_runs/bearsDivtime_FBD.2.trees.gz → precooked_runs/bearsTree.1.trees.gz b/precooked_runs/bearsDivtime_FBD.2.trees.gz → precooked_runs/bearsTree.1.trees.gz
diff --git a/precooked_runs/bearsDivtime_FBD.1.trees.gz → precooked_runs/bearsTree.2.trees.gz b/precooked_runs/bearsDivtime_FBD.1.trees.gz → precooked_runs/bearsTree.2.trees.gz
diff --git a/scripts/plot_geoscaled_tree.R b/scripts/plot_geoscaled_tree.R
@@ -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)

diff --git a/xml/bearsDivtime_FBD.1.xml b/xml/bearsDivtime_FBD.1.xml
diff --git a/xml/bearsDivtime_FBD.2.xml b/xml/bearsDivtime_FBD.2.xml
diff --git a/xml/bearsDivtime_FBD.prior.xml b/xml/bearsDivtime_FBD.prior.xml