diff --git a/developer/index.html b/developer/index.html
index 0f55ba0f9..a5d7f1f04 100644
--- a/developer/index.html
+++ b/developer/index.html
@@ -96,23 +96,23 @@
Developer’s Guide
@@ -124,16 +124,16 @@ Developer’s Guide
diff --git a/developer/setup/netbeans.html b/developer/setup/netbeans.html
index 644be8f13..873da7bd0 100644
--- a/developer/setup/netbeans.html
+++ b/developer/setup/netbeans.html
@@ -55,7 +55,7 @@
- Last modified on March 11, 2018
+ Last modified on March 10, 2018
Conventions: File paths are relative to the repository root.
diff --git a/developer/setup/vim.html b/developer/setup/vim.html
index 1dcb83e9b..1e3e87b91 100644
--- a/developer/setup/vim.html
+++ b/developer/setup/vim.html
@@ -55,7 +55,7 @@
Setting up vim for RevBayes development
- Last modified on March 11, 2018
+ Last modified on March 10, 2018
Vim is a text editor that some people love.
diff --git a/developer/tutorial/index.html b/developer/tutorial/index.html
index feb4d7a12..bdf72afed 100644
--- a/developer/tutorial/index.html
+++ b/developer/tutorial/index.html
@@ -55,7 +55,7 @@
Contributing a RevBayes tutorial
- Last modified on May 31, 2019
+ Last modified on May 30, 2019
diff --git a/tutorials/biogeo/biogeo_simple.html b/tutorials/biogeo/biogeo_simple.html
index 698cb2e45..c9e0f6613 100644
--- a/tutorials/biogeo/biogeo_simple.html
+++ b/tutorials/biogeo/biogeo_simple.html
@@ -55,7 +55,7 @@
Simple Phylogenetic Analysis of Historical Biogeography
Estimating ancestral ranges using the Dispersal-Extirpation-Cladogenesis (DEC) model
Michael J. Landis
- Last modified on February 28, 2022
+ Last modified on February 27, 2022
diff --git a/tutorials/chromo/index.html b/tutorials/chromo/index.html
index 37ac587a8..bfeb832bf 100644
--- a/tutorials/chromo/index.html
+++ b/tutorials/chromo/index.html
@@ -55,7 +55,7 @@
Chromosome Evolution
Modeling chromosome evolution with ChromEvol, BiChroM, and ChromoSSE
William A. Freyman and Sebastian Höhna
- Last modified on February 28, 2022
+ Last modified on February 27, 2022
diff --git a/tutorials/cont_traits/relaxed_bm.html b/tutorials/cont_traits/relaxed_bm.html
index c95a91603..813725e63 100644
--- a/tutorials/cont_traits/relaxed_bm.html
+++ b/tutorials/cont_traits/relaxed_bm.html
@@ -99,14 +99,14 @@ Data files and scripts
- primates_tree.nex
-
primates_tree.nex
primates_tree.nex
primates_tree.nex
+ primates_tree.nex
+
@@ -121,10 +121,10 @@ Data files and scripts
primates_cont_traits.nex
- primates_tree.nex
-
primates_tree.nex
+ primates_tree.nex
+
diff --git a/tutorials/cont_traits/relaxed_ou.html b/tutorials/cont_traits/relaxed_ou.html
index 30065d08f..72b9da274 100644
--- a/tutorials/cont_traits/relaxed_ou.html
+++ b/tutorials/cont_traits/relaxed_ou.html
@@ -99,14 +99,14 @@ Data files and scripts
- primates_tree.nex
-
primates_tree.nex
primates_tree.nex
primates_tree.nex
+ primates_tree.nex
+
@@ -121,10 +121,10 @@ Data files and scripts
primates_cont_traits.nex
- primates_tree.nex
-
primates_tree.nex
+ primates_tree.nex
+
diff --git a/tutorials/cont_traits/simple_bm.html b/tutorials/cont_traits/simple_bm.html
index 9f96e4027..a98daceec 100644
--- a/tutorials/cont_traits/simple_bm.html
+++ b/tutorials/cont_traits/simple_bm.html
@@ -97,14 +97,14 @@ Data files and scripts
- primates_tree.nex
-
primates_tree.nex
primates_tree.nex
primates_tree.nex
+ primates_tree.nex
+
@@ -121,10 +121,10 @@ Data files and scripts
primates_cont_traits.nex
- primates_tree.nex
-
primates_tree.nex
+ primates_tree.nex
+
diff --git a/tutorials/cont_traits/simple_ou.html b/tutorials/cont_traits/simple_ou.html
index 13cf54154..69f77c6fa 100644
--- a/tutorials/cont_traits/simple_ou.html
+++ b/tutorials/cont_traits/simple_ou.html
@@ -97,14 +97,14 @@ Data files and scripts
- primates_tree.nex
-
primates_tree.nex
primates_tree.nex
primates_tree.nex
+ primates_tree.nex
+
@@ -123,10 +123,10 @@ Data files and scripts
primates_cont_traits.nex
- primates_tree.nex
-
primates_tree.nex
+ primates_tree.nex
+
diff --git a/tutorials/divrate/branch_specific.html b/tutorials/divrate/branch_specific.html
index 2567c18fe..2d44c8f3b 100644
--- a/tutorials/divrate/branch_specific.html
+++ b/tutorials/divrate/branch_specific.html
@@ -97,10 +97,10 @@ Data files and scripts
primates_tree.nex
- primates_tree.nex
-
primates_tree.nex
+ primates_tree.nex
+
primates_tree.nex
diff --git a/tutorials/divrate/data/crocs_taxa.txt b/tutorials/divrate/data/crocs_taxa.txt
deleted file mode 100644
index a18870546..000000000
--- a/tutorials/divrate/data/crocs_taxa.txt
+++ /dev/null
@@ -1,143 +0,0 @@
-taxon age
-Eothoracosaurus 68.3215
-Thoracosaurus 60.9215
-Eosuchus 52.2
-Gryposuchus 13.885
-Piscogavialis 6.289
-Gavialis 0
-Eogavialis 35.55
-Borealosuchus_formidabilis 58.75
-Borealosuchus_threensis 66.15
-Borealosuchus_sternbergii 64.6715
-Boverisuchus_vorax 45.35
-Boverisuchus_magnifrons 44.5
-Planocrania_datengensis 58.785
-Planocrania_hengdongensis 57.25
-Alligator_mississippiensis 0
-Alligator_thompsoni 18.2
-Alligator_prenasalis 35.55
-Allognathosuchus 43.1
-Eocaiman 44.85
-Paleosuchus 0
-Purussaurus 9.566
-Mourasuchus 10.651
-Melanosuchus 0
-Caiman_crocodilis 0
-Caiman_yacare 0
-Brachychampsa 68.3215
-Diplocynodon 42.1
-Leidyosuchus 77.75
-Prodiplocynodon 68.3215
-Crocodylus_affinis 48.25
-Brachyuranochampsa 43.3
-Tomistoma 0
-Gavialosuchus_eggenburgensis 18.2
-Gavialosuchus_americanus 7.1
-Thecachampsa 25.715
-Dollosuchoides 44.5
-Maroccosuchus 52.2
-Qunikana 20.004
-Kambara 41.25
-Australosuchus 22.185
-Euthecodon 19.5
-Voay 0.006
-Osteolaemus 0
-Mecistops 0
-Crocodylus_porosus 0
-Crocodylus_siamensis 0
-Crocodylus_rhombifer 0
-Crocodylus_acutus 0
-Crocodylus_niloticus 0
-Allodaposuchus_precedens 68.3215
-Lohuecosuchus 68.3215
-Arenysuchus 68.3215
-Hylaeochampsa 126.23
-Acynodon_adriaticus 75.4715
-Acynodon_iberoccitanus 68.3215
-Paralligator 94.5
-Shamosuchus 77.75
-Bernissartia 135.475
-Calsoyasuchus 189.75
-Goniopholis_simus 142.85
-Goniopholis_baryglypheaus 153.25
-Eutretauranosuchus 153.25
-Elosuchus 97
-Vectisuchus 126.23
-Cerrejonisuchus 60.2
-Anthracosuchus 58.75
-Chenanisuchus 63.2
-Guarinisuchus 63.8715
-Rhabdognathus 66.15
-Atlantosuchus 63.8715
-Dyrosaurus 52.2
-Sokotosuchus 68.3215
-Meridiosaurus 150.6
-Sarcosuchus 106.15
-Pholidosaurus 142.85
-Oceanosuchus 97
-Terminonaris_browni 91.8
-Terminonaris_robusta 91.8
-Theriosuchus_pusilis 142.85
-Theriosuchus_guimarotae 153.25
-Mahajangasuchus 68.3215
-Kaprosuchus 97
-Stolokrosuchus 112.575
-Lomasuchus 90.05
-Uberabasuchus 68.3215
-Peirosaurus 68.3215
-Araripesuchus_gomesii 110.8
-Araripesuchus_patagonicus 97
-Urugaysuchus 105.175
-Libycosuchus 97
-Simosuchus 68.3215
-Malawisuchus 119.025
-Notosuchus 85.35
-Mariliasuchus 75.4715
-Sphagesaurus 77.75
-Chimaerasuchus 112.575
-Comahuesuchus 85.35
-Pissarrachampsa 80.1715
-Stratiotosuchus 75.4715
-Hsisosuchus_dashanpuensis 166.4
-Hsisosuchus_chungkingensis 153.35
-Protosuchus 199.05
-Orthosuchus 195.6
-Edentosuchus 111.08
-Sichuanosuchus 122.6
-Shantungosuchus 122.6
-Zosuchus 77.75
-Fruitachampsa 150.6
-Zaraasuchus 77.75
-Gobiosuchus 77.75
-Pelagosaurus 182.5
-Teleidosaurus_calvadosi 168.15
-Eoneustes_bathonicus 166.2
-Eoneustes_gaudryi 166.2
-Zoneait 172
-Metriorhynchus_superciliosus 157.75
-Metriorhynchus_leedsi 157.75
-Cricosaurus_suevicus 153.25
-Metriorhynchus_durobrivensis 162.95
-Metriorhynchus_casamiquelai 162.95
-Geosaurus_grandis 148.15
-Geosaurus_giganteus 148.15
-Dakosaurus_maximus 148.15
-Dakosaurus_andiniensis 142.85
-Steneosaurus_gracilirostris 179.3
-Teleosaurus 159.25
-Peipehsuchus 178.4
-Thai_teleosaurid 148.55
-Platysuchus_multiscrobiculatus 182.5
-Steneosaurus_bollensis 182.5
-Steneosaurus_brevior 182.5
-Steneosaurus_durobrivensis 162.95
-Machimosaurus 153.25
-Steneosaurus_leedsi 162.95
-Kayentasuchus 189.75
-Junggarsuchus 162.95
-Almadasuchus 158.45
-Dibothrosuchus 192.6
-Sphenosuchus 195.6
-Hesperosuchus 213.55
-Postosuchus 213.55
-Gracilisuchus 238.5
diff --git a/tutorials/divrate/div_rate_intro.html b/tutorials/divrate/div_rate_intro.html
index 0a8a8ad6f..d0c1c5990 100644
--- a/tutorials/divrate/div_rate_intro.html
+++ b/tutorials/divrate/div_rate_intro.html
@@ -362,14 +362,14 @@ Höhna S. 2014. Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling. PLoS One. 9:e84184.
+Höhna S. 2015. The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events. Journal of Theoretical Biology. 380:321–331.
-10.1371/journal.pone.0084184
+http://dx.doi.org/10.1016/j.jtbi.2015.06.005
-Höhna S. 2015. The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events. Journal of Theoretical Biology. 380:321–331.
+Höhna S. 2014. Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling. PLoS One. 9:e84184.
-http://dx.doi.org/10.1016/j.jtbi.2015.06.005
+10.1371/journal.pone.0084184
Höhna S., Freyman W.A., Nolen Z., Huelsenbeck J.P., May M.R., Moore B.R. 2019. A Bayesian Approach for Estimating Branch-Specific Speciation and Extinction Rates. bioRxiv.
diff --git a/tutorials/divrate/ebd.html b/tutorials/divrate/ebd.html
index f0e0bd84f..8640b6d52 100644
--- a/tutorials/divrate/ebd.html
+++ b/tutorials/divrate/ebd.html
@@ -97,18 +97,18 @@ Data files and scripts
- primates.tre
-
primates.tre
- primates_tree.nex
-
- primates_tree.nex
+ primates.tre
primates_tree.nex
+ primates_tree.nex
+
primates_tree.nex
+ primates_tree.nex
+
@@ -498,14 +498,14 @@ Exercise 2
10.1093/sysbio/syw021
-Höhna S. 2014. Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling. PLoS One. 9:e84184.
+Höhna S. 2015. The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events. Journal of Theoretical Biology. 380:321–331.
-10.1371/journal.pone.0084184
+http://dx.doi.org/10.1016/j.jtbi.2015.06.005
-Höhna S. 2015. The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events. Journal of Theoretical Biology. 380:321–331.
+Höhna S. 2014. Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling. PLoS One. 9:e84184.
-http://dx.doi.org/10.1016/j.jtbi.2015.06.005
+10.1371/journal.pone.0084184
Höhna S., Heath T.A., Boussau B., Landis M.J., Ronquist F., Huelsenbeck J.P. 2014. Probabilistic Graphical Model Representation in Phylogenetics. Systematic Biology. 63:753–771.
diff --git a/tutorials/divrate/efbdp_me.html b/tutorials/divrate/efbdp_me.html
index fb9b81021..c1b2837e2 100644
--- a/tutorials/divrate/efbdp_me.html
+++ b/tutorials/divrate/efbdp_me.html
@@ -55,7 +55,7 @@
Mass Extinction Estimation
Estimating Mass Extinctions from Phylogenies with Fossil and Extant Taxa
Andrew Magee and Sebastian Höhna
- Last modified on March 11, 2022
+ Last modified on April 2, 2024
@@ -99,8 +99,6 @@ Data files and scripts
crocs_T1.tre
- crocs_taxa.txt
-
@@ -177,9 +175,10 @@ Read the data
Begin by reading in the ``observed’’ tree.
T <- readTrees("data/crocs_T1.tre")[1]
-When the tree has fossils, it is best to read in the taxa from a taxon data file.
-This is absolutely required if the tree is to be simultaneously inferred.
-taxa <- readTaxonData("data/crocs_taxa.txt",delim=TAB)
+Here, we extract the fossil ages directly from the tree. If we were to simultaneously
+infer the tree instead, these ages would have to be read in from a taxon data file.
+(You can find an example of such a file in the Episodic Diversification Rate Estimation tutorial.)
+
Additionally, we initialize a variable for our vector of moves and monitors.
moves = VectorMoves()
@@ -556,14 +555,14 @@ Exercise 2
Carvalho C.M., Polson N.G., Scott J.G. 2010. The horseshoe estimator for sparse signals. Biometrika. 97:465–480.
-Höhna S. 2014. Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling. PLoS One. 9:e84184.
+Höhna S. 2015. The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events. Journal of Theoretical Biology. 380:321–331.
-10.1371/journal.pone.0084184
+http://dx.doi.org/10.1016/j.jtbi.2015.06.005
-Höhna S. 2015. The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events. Journal of Theoretical Biology. 380:321–331.
+Höhna S. 2014. Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling. PLoS One. 9:e84184.
-http://dx.doi.org/10.1016/j.jtbi.2015.06.005
+10.1371/journal.pone.0084184
Höhna S., Stadler T., Ronquist F., Britton T. 2011. Inferring speciation and extinction rates under different species sampling schemes. Molecular Biology and Evolution. 28:2577–2589.
diff --git a/tutorials/divrate/env.html b/tutorials/divrate/env.html
index e89dbf50d..4b578d77a 100644
--- a/tutorials/divrate/env.html
+++ b/tutorials/divrate/env.html
@@ -101,14 +101,14 @@ Data files and scripts
primates.tre
- primates_tree.nex
-
primates_tree.nex
- primates_tree.nex
+ primates_tree.nex
primates_tree.nex
+ primates_tree.nex
+
diff --git a/tutorials/divrate/modules/efbdp_me_estimation.md b/tutorials/divrate/modules/efbdp_me_estimation.md
index b3215606d..b0cd6dcd3 100644
--- a/tutorials/divrate/modules/efbdp_me_estimation.md
+++ b/tutorials/divrate/modules/efbdp_me_estimation.md
@@ -6,10 +6,11 @@ Begin by reading in the ``observed'' tree.
```
T <- readTrees("data/crocs_T1.tre")[1]
```
-When the tree has fossils, it is best to read in the taxa from a taxon data file.
-This is absolutely required if the tree is to be simultaneously inferred.
+Here, we extract the fossil ages directly from the tree. If we were to simultaneously
+infer the tree instead, these ages would have to be read in from a taxon data file.
+(You can find an example of such a file in the {% page_ref divrate/ebd %} tutorial.)
```
-taxa <- readTaxonData("data/crocs_taxa.txt",delim=TAB)
+taxa <- T.taxa()
```
Additionally, we initialize a variable for our vector of moves and monitors.
```
diff --git a/tutorials/divrate/sampling.html b/tutorials/divrate/sampling.html
index fe8bb869e..f3189fc7d 100644
--- a/tutorials/divrate/sampling.html
+++ b/tutorials/divrate/sampling.html
@@ -55,7 +55,7 @@
Diversification Rate Estimation with Missing Taxa
How to estimate diversification rates with incomplete taxon sampling
Sebastian Höhna, Will Freyman and Mike May
- Last modified on February 28, 2022
+ Last modified on February 27, 2022
@@ -97,8 +97,6 @@
Data files and scripts
crocs_T1.tre
-
crocs_taxa.txt
-
primates.tre
primates_tree.nex
diff --git a/tutorials/divrate/scripts/mcmc_CRFBD.Rev b/tutorials/divrate/scripts/mcmc_CRFBD.Rev
index db11b0551..0922e4fab 100644
--- a/tutorials/divrate/scripts/mcmc_CRFBD.Rev
+++ b/tutorials/divrate/scripts/mcmc_CRFBD.Rev
@@ -6,8 +6,7 @@
T <- readTrees("data/crocs_T1.tre")[1]
# Get some useful variables from the data. We need these later on.
-taxa <- readTaxonData("data/crocs_taxa.txt",delim=TAB)
-
+taxa <- T.taxa()
# Create some vector for the moves and monitors of this analysis
moves = VectorMoves()
diff --git a/tutorials/divrate/scripts/mcmc_EFBD_mass_extinctions.Rev b/tutorials/divrate/scripts/mcmc_EFBD_mass_extinctions.Rev
index c584d8ada..d86876758 100644
--- a/tutorials/divrate/scripts/mcmc_EFBD_mass_extinctions.Rev
+++ b/tutorials/divrate/scripts/mcmc_EFBD_mass_extinctions.Rev
@@ -16,8 +16,7 @@
T <- readTrees("data/crocs_T1.tre")[1]
# Get some useful variables from the data. We need these later on.
-taxa <- readTaxonData("data/crocs_taxa.txt",delim=TAB)
-
+taxa <- T.taxa()
# Create some vector for the moves and monitors of this analysis
moves = VectorMoves()
diff --git a/tutorials/divrate/simple.html b/tutorials/divrate/simple.html
index 39ab1299d..2a1ef71aa 100644
--- a/tutorials/divrate/simple.html
+++ b/tutorials/divrate/simple.html
@@ -95,10 +95,10 @@
Data files and scripts
-
primates.tre
-
primates.tre
+
primates.tre
+
primates_tree.nex
primates_tree.nex
@@ -596,14 +596,14 @@
Exercise 3
Aldous D.J. 2001. Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today. Statistical Science.:23–34.
-Höhna S. 2014. Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling. PLoS One. 9:e84184.
+Höhna S. 2015. The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events. Journal of Theoretical Biology. 380:321–331.
-10.1371/journal.pone.0084184
+http://dx.doi.org/10.1016/j.jtbi.2015.06.005
-Höhna S. 2015. The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events. Journal of Theoretical Biology. 380:321–331.
+Höhna S. 2014. Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling. PLoS One. 9:e84184.
-http://dx.doi.org/10.1016/j.jtbi.2015.06.005
+10.1371/journal.pone.0084184
Höhna S., Heath T.A., Boussau B., Landis M.J., Ronquist F., Huelsenbeck J.P. 2014. Probabilistic Graphical Model Representation in Phylogenetics. Systematic Biology. 63:753–771.
diff --git a/tutorials/fbd/fbd_specimen.html b/tutorials/fbd/fbd_specimen.html
index b88cb5ec6..5b2addc6d 100644
--- a/tutorials/fbd/fbd_specimen.html
+++ b/tutorials/fbd/fbd_specimen.html
@@ -55,7 +55,7 @@
Combined-Evidence Analysis and the Fossilized Birth-Death Process for Analysis of Extant Taxa and Fossil Specimens
Joint inference of divergence times and phylogenetic relationships of fossil and extant taxa
Tracy A. Heath, April M. Wright, and Walker Pett
- Last modified on April 9, 2020
+ Last modified on April 8, 2020
diff --git a/tutorials/fbd_range/index.html b/tutorials/fbd_range/index.html
index f9c8843fe..65a0e1f94 100644
--- a/tutorials/fbd_range/index.html
+++ b/tutorials/fbd_range/index.html
@@ -55,7 +55,7 @@
Macroevolutionary Analysis of Stratigraphic Range Data
Inference of diversification rates using the fossilized birth-death range process
Rachel Warnock and Walker Pett
- Last modified on February 28, 2022
+ Last modified on February 27, 2022
diff --git a/tutorials/index.html b/tutorials/index.html
index aef942733..d99d8f6fd 100644
--- a/tutorials/index.html
+++ b/tutorials/index.html
@@ -634,7 +634,7 @@
Joint inference of divergence times and phylogenetic relationships of fossil and extant taxa
@@ -649,7 +649,7 @@
Joint inference of divergence times and phylogenetic relationships of fossil and extant taxa
@@ -890,6 +890,9 @@
Comparative methods
+
+
+
Diversification Rate Estimation
diff --git a/tutorials/intro/revgadgets.html b/tutorials/intro/revgadgets.html
index f78d43f52..f5e57bd5e 100644
--- a/tutorials/intro/revgadgets.html
+++ b/tutorials/intro/revgadgets.html
@@ -117,13 +117,13 @@
Data files and scripts
primates_cytb_GTR_MAP.tre
-
primates_tree.nex
-
primates_tree.nex
+
primates_tree.nex
+
primates_tree.nex
-
primates_tree.nex
+
primates_tree.nex
relaxed_OU_MAP.tre
diff --git a/tutorials/intro_posterior_prediction/index.html b/tutorials/intro_posterior_prediction/index.html
index f9c754c40..4e24115fb 100644
--- a/tutorials/intro_posterior_prediction/index.html
+++ b/tutorials/intro_posterior_prediction/index.html
@@ -411,14 +411,14 @@
Phyloseminar
10.1093/oxfordjournals.molbev.a004175
-
Brown J.M. 2014. Predictive approaches to assessing the fit of evolutionary models. Systematic Biology. 63:289–292.
+Brown J.M. 2014. Detection of implausible phylogenetic inferences using posterior predictive assessment of model fit. Systematic Biology. 63:334–348.
-10.1093/sysbio/syu009
+10.1093/sysbio/syu002
-
Brown J.M. 2014. Detection of implausible phylogenetic inferences using posterior predictive assessment of model fit. Systematic Biology. 63:334–348.
+Brown J.M. 2014. Predictive approaches to assessing the fit of evolutionary models. Systematic Biology. 63:289–292.
-10.1093/sysbio/syu002
+10.1093/sysbio/syu009
Brown J.M., Thomson R.C. 2018. Evaluating model performance in evolutionary biology. Annual Review of Ecology, Evolution, and Systematics. 49:95–114.
diff --git a/tutorials/mcmc/binomial.html b/tutorials/mcmc/binomial.html
index a12514685..f0e529195 100644
--- a/tutorials/mcmc/binomial.html
+++ b/tutorials/mcmc/binomial.html
@@ -55,7 +55,7 @@
Introduction to MCMC using RevBayes
Introduction to MCMC Simulation using a simple Binomial Model
Mike May, Brian Moore and Sebastian Höhna
- Last modified on February 28, 2022
+ Last modified on February 27, 2022
diff --git a/tutorials/morph_ase/ase_mammals.html b/tutorials/morph_ase/ase_mammals.html
index a49d96f1e..d415692b6 100644
--- a/tutorials/morph_ase/ase_mammals.html
+++ b/tutorials/morph_ase/ase_mammals.html
@@ -55,7 +55,7 @@
Discrete morphology - Ancestral State Estimation (Mammals & Placenta Type)
Ancestral State Estimation and Testing for Irreversibility
Sebastian Höhna
- Last modified on February 28, 2022
+ Last modified on February 27, 2022
diff --git a/tutorials/morph_ase/corr.html b/tutorials/morph_ase/corr.html
index bfda8fc3c..e49eabbdb 100644
--- a/tutorials/morph_ase/corr.html
+++ b/tutorials/morph_ase/corr.html
@@ -55,7 +55,7 @@
Discrete morphology - Correlation among Characters
Testing for Correlation
Sebastian Höhna
- Last modified on February 28, 2022
+ Last modified on February 27, 2022
diff --git a/tutorials/partition/index.html b/tutorials/partition/index.html
index 45f837b26..c55fc0704 100644
--- a/tutorials/partition/index.html
+++ b/tutorials/partition/index.html
@@ -55,7 +55,7 @@
Partitioned data analysis
Current Protocols in Bioinformatics - Phylogenetic Inference using RevBayes (Protocol #2)
Sebastian Höhna, Michael J. Landis and Tracy A. Heath
- Last modified on October 13, 2023
+ Last modified on October 12, 2023
diff --git a/tutorials/pomobalance/data/great_apes_BS_10000.txt b/tutorials/pomobalance/data/great_apes_BS_10000.txt
new file mode 100644
index 000000000..79d8ac955
--- /dev/null
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@@ -0,0 +1,5 @@
+HUMAN 0 2 0 1 3 2 0 0 44 44 1 1 3 1 0 3 2 0 3 3 1 1 3 2 3 3 2 8 0 0 3 2 3 1 3 3 2 1 3 2 3 44 3 3 35 1 2 3 0 0 1 53 3 0 0 1 1 2 35 1 0 1 2 2 0 1 2 1 3 1 3 26 0 3 3 0 1 1 35 0 0 2 3 3 0 1 3 0 2 44 35 3 3 2 0 3 1 3 2 1 3 1 2 3 3 2 3 2 8 3 1 2 0 17 3 1 0 3 2 2 3 1 1 2 2 0 2 3 44 1 3 26 2 0 0 1 3 3 1 17 3 1 3 1 3 2 17 1 3 2 0 2 0 0 0 0 0 1 1 3 1 2 0 0 0 1 0 2 1 2 1 8 2 2 2 0 2 1 17 3 3 2 3 1 1 0 3 0 0 0 1 2 1 3 1 0 2 2 2 2 0 1 0 26 1 0 2 3 1 1 0 0 3 0 2 1 3 2 2 1 3 3 1 1 1 2 2 2 3 3 1 2 3 26 0 26 2 0 0 2 0 0 3 3 1 1 0 2 3 44 2 0 0 3 3 44 1 3 3 0 3 3 1 2 3 2 0 0 44 3 2 3 2 3 2 26 1 1 2 1 2 2 2 35 3 17 1 3 3 2 0 1 3 0 2 3 44 1 1 0 0 0 3 2 1 53 1 2 2 0 0 1 0 0 1 1 0 26 2 0 3 1 0 2 2 0 1 3 2 0 0 3 0 2 2 1 2 1 1 0 3 0 1 3 8 0 1 3 2 17 3 2 26 1 1 0 8 0 2 1 2 3 3 2 0 1 17 0 1 0 0 2 1 3 3 2 0 35 0 3 26 0 1 3 2 3 2 2 2 17 2 1 2 0 0 0 0 8 0 2 0 2 3 2 2 3 2 2 0 35 1 1 2 3 0 1 1 3 0 3 0 3 2 3 0 3 2 3 1 3 1 1 3 0 1 1 0 3 3 3 0 26 3 3 3 1 2 2 17 3 1 0 0 3 2 0 1 3 1 53 0 0 0 3 2 2 3 17 2 2 2 2 0 2 1 3 1 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0 3 0 2 3 2 1 3 0 0 1 1 2 3 1 0 0 2 1 3 2 3 3 2 0 3 2 0 8 3 0 35 1 2 35 44 17 1 0 1 2 2 0 0 3 2 2 0 2 53 3 35 1 0 3 2 1 17 35 3 3 3 1 3 0 0 2 8 1 0 0 1 1 35 1 1 0 0 0 0 2 3 0 3 0 1 0 0 3 0 2 1 3 1 35 17 3 0 35 0 2 1 3 2 0 2 3 1 1 2 3 1 3 2 2 2 0 3 2 2 2 2 0 0 8 2 0 3 17 2 2 0 2 0 3 8 1 3 1 0 3 3 1 1 3 3 8 2 1 2 3 0 0 0 0 2 3 0 53 2 1 0 1 0 3 1 0 2 2 2 2 2 0 1 2 2 3 3 0 2 1 2 0 3 3 0 2 26 1 0 2 3 0 3 0 3 3 1 1 1 17 53 2 1 0 2 1 0 2 2 1 1 0 35 1 2 53 3 1 2 17 3 0 1 2 2 1 44 3 1 3 1 3 0 2 44 2 0 0 2 2 1 2 0 2 0 2 2 8 3 2 2 2 0 3 2 1 3 8 1 2 2 3 3 1 35 0 0 3 3 1 2 2 2 3 0 1 3 2 26 0 2 0 0 35 44 1 3 3 2 2 0 2 3 2 2 2 0 0 1 0 26 26 1 3 1 2 2 3 53 1 3 1 2 0 2 1 3 1 8 2 0 3 1 1 1 2 2 3 3 44 2 2 0 1 1 1 35 0 3 0 2 2 3 0 2 0 0 2 1 3 2 2 0 0 2 3 0 2 2 2 3 1 3 35 3 1 1 2 3 3 2 53 2 3 2 3 3 1 2 1 0 3 0 3 44 3 1 2 0 0 0 1 2 2 2 1 3 3 3 0 8 2 3 3 3 0 0 2 2 3 3 0 3 1 2 3 2 0 3 1 3 1 3 2 3 26 1 2 2 0 3 0 1 2 2 26 1 0 1 1 2 0 53 0 44 1 2 2 1 3 0 0 1 2 2 0 3 1 1 0 35 1 0 0 1 3 3 2 3 2 26 3 2 2 2 1 0 3 3 1 3 2 0 0 17 0 2 3 2 3 1 1 35 2 0 2 3 2 3 26 1 2 44 2 3 0 0 3 3 3 44 2 2 2 1 3 17 44 3 3 1 2 2 2 2 44 35 2 0 3 0 1 44 3 1 0 1 3 2 2 2 3 1 0 1 0 0 2 53 0 26 1 3 3 2 0 1 0 0 8 1 2 3 0 0 2 3 2 1 2 53 3 2 3 0 0 1 2 1 0 3 0 1 1 0 3 1 2 1 3 3 0 1 0 2 2 3 0 2 2 2 0 0 3 2 17 1 3 1 1 1 1 1 2 1 0 53 3 0 2 0 53 3 0 2 8 1 1 0 0 2 3 1 3 1 2 3 1 17 0 1 1 2 0 0 1 2 0 1 3 1 2 2 44 3 1 8 1 2 0 3 2 3 3 3 2 1 8 2 2 0 3 3 3 3 2 3 0 3 3 3 2 3 3 0 3 2 44 1 0 0 2 2 17 1 44 17 44 1 3 3 0 3 3 26 3 2 2 1 1 1 3 0 3 26 1 1 2 1 0 0 2 3 2 0 0 3 3 1 1 1 2 2 8 0 2 3 2 3 2 1 3 1 0 26 2 0 2 3 1 3 2 2 2 1 0 2 0 2 1 0 2 2 2 0 1 2 3 2 1 2 0 0 3 3 2 2 1 3 0 0 1 1 3 1 0 2 1 8 26 0 2 1 0 0 3 53 44 0 1 2 2 1 1 3 0 1 3 2 2 2 1 3 1 0 2 1 3 1 0 2 3 1 0 2 0 2 2 0 0 3 1 0 2 2 3 0 2 1 8 8 1 2 1 2 2 2 3 0 2 2 1 3 2 1 3 26 26 3 0 1 1 1 1 3 0 2 2 0 0 1 1 3 1 1 3 2 0 1 1 2 0 3 0 2 3 2 1 3 1 1 3 3 2 35 0 1 1 2 3 3 0 1 1 3 2 3 1 3 1 1 3 2 1 3 3 2 3 2 1 1 1 0 2 0 2 3 3 3 1 3 2 3 0 3 0 2 3 0 2 3 3 0 0 2 3 3 1 3 1 17 8 3 3 2 2 44 3 3 8 3 1 2 2 1 0 2 53 2 3 1 0 2 1 1 1 0 26 0 2 2 0 2 2 3 26 3 2 2 3 1 2 1 1 3 53 1 3 0 2 2 2 2 3 44 17 0 0 3 0 3 1 1 35 3 2 1 3 3 44 0 3 3 35 1 8 0 2 35 3 0 2 0 3 2 26 1 3 2 17 26 1 2 44 0 2 3 3 3 3 1 1 1 1 22 0 0 0 3 2 2 2 0 0 8 1 1 22 0 2 2 1 3 3 3 0 2 44 3 1 3 1 1 0 0 0 2 2 3 1 2 0 3 3 1 2 0 2 3 0 2 1 0 2 3 2 0 3 0 0 2 1 2 3 3 1 0 2 3 2 3 3 0 0 2 3 1 3 3 1 3 0 0 2 2 35 44 1 0 1 2 3 0 1 2 3 44 0 0 0 1 2 3 1 3 3 3 1 0 2 3 0 3 0 1 0 0 2 1 1 2 3 53 3 2 1 0 1 1 3 1 44 2 0 3 1 0 0 8 2 2 0 1 1 1 3 2 0 1 2 0 3 0 3 2 3 0 0 3 26 3 3 1 0 1 3 1 1 3 1 1 3 3 0 3 2 3 3 2 1 0 2 3 2 0 1 3 1 1 2 1 3 2 2 17 3 1 1 35 1 0 0 3 2 3 1 2 17 3 2 3 35 2 3 1 35 2 0 1 3 0 0 0 1 3 3 0 2 0 1 0 2 0 3 2 2 53 1 2 35 1 3 1 2 0 1 0 2 1 0 0 1 2 8 3 2 0 2 26 3 2 0 1 2 2 1 1 1 2 3 3 8 2 0 1 2 3 1 0 1 0 1 1 0 1 3 8 0 2 1 3 0 0 3 2 2 3 2 2 2 1 2 2 2 0 8 8 26 1 1 1 3 2 0 2 0 35 2 0 3 2 2 2 1 2 1 1 2 1 1 2 2 3 2 0 0 2 1 3 0 2 3 3 1 2 1 2 2 2 1 3 0 8 2 0 0 17 44 2 1 2 0 1 1 2 8 3 3 2 3 0 44 2 2 0 2 3 3 1 2 0 1 2 1 1 2 2 3 1 2 2 2 8 1 3 2 0 3 0 3 0 2 3 1 1 3 2 0 3 3 1 3 1 3 26 2 35 1 3 3 3 2 1 1 1 1 3 1 3 1 26 0 26 2 0 0 3 44 3 2 0 2 44 3 1 26 1 2 3 0 44 3 0 26 2 35 0 44 8 3 1 3 2 1 3 2 0 1 2 35 0 1 2 3 3 2 1 1 3 0 3 2 17 1 2 3 3 0 2 1 2 0 0 3 2 1 0 2 3 3 1 8 3 26 2 1 0 0 3 3 3 3 1 8 3 1 2 0 3 2 0 1 3 2 0 3 44 0 3 0 0 1 3 0 53 2 3 2 0 2 2 2 2 44 0 3 2 1 2 0 3 2 3 1 3 1 3 0 3 3 0 2 17 1 3 1 0 1 0 1 1 2 0 3 3 2 3 0 8 2 0 1 3 1 2 3 0 3 1 2 2 3 1 0 1 2 2 0 0 1 3 3 3 3 2 35 3 3 3 3 0 1 1 0 0 26 2 26 1 44 2 0 2 1 35 1 1 3 3 44 1 2 0 0 35 3 3 2 2 2 1 1 2 0 0 2 0 2 0 2 2 2 3 0 1 2 2 2 17 0 0 3 2 17 0 0 3 2 2 3 3 2 0 2 26 0 3 3 2 3 3 2 44 1 1 1 1 2 1 44 2 0 1 1 0 3 0 3 1 2 1 3 1 35 1 1 1 3 0 2 2 3 2 3 0 1 3 3 1 0 2 3 0 0 35 0 0 2 1 0 3 3 0 0 1 3 2 0 2 3 3 3 8 3 3 3 2 2 0 3 2 2 3 3 0 0 2 0 0 1 0 0 8 53 0 0 1 0 2 1 3 3 0 1 0 2 2 0 1 2 0 53 1 0 2 8 3 8 1 1 3 8 1 53 2 1 1 44 3 3 1 3 0 0 1 0 1 1 3 2 3 1 1 3 1 44 1 3 3 1 3 17 2 3 2 0 2 1 1 1 1 3 0 0 35 3 3 44 1 0 0 3 1 0 1 1 0 0 8 8 0 2 1 3 3 26 1 26 2 3 1 1 3 3 53 2 3 3 0 2 1 2 3 0 2 0 0 2 0 0 2 1 1 0 0 2 3 0 8 26 3 0 3 35 2 3 1 0 1 0 3 1 2 0 3 2 2 0 0 1 0 2 2 0 44 1 2 2 0 0 3 1 3 8 35 3 2 1 3 1 3 2 2 3 1 35 1 3 2 3 2 1 3 0 0 3 1 2 1 2 2 3 1 0 0 26 17 0 2 0 2 0 2 0 2 3 1 0 0 3 0 3 3 3 0 3 1 2 3 3 3 1 8 0 0 1 0 3 2 44 3 2 2 2 2 1 2 53 0 0 1 0 1 2 17 2 3 2 3 0 2 3 3 3 0 35 2 2 0 3 0 2 1 1 0 2 3 1 0 3 3 1 0 35 1 0 2 1 2 2 3 35 0 3 1 1 0 1 2 3 3 1 1 3 0 0 1 26 2 2 2 44 2 1 1 0 3 3 3 3 2 0 1 2 3 44 2 1 1 2 2 2 0 1 0 3 3 3 3 0 0 44 2 8 0 2 1 3 26 0 1 1 2 1 1 3 0 2 2 2 2 3 0 0 3 3 1 1 0 0 1 3 3 0 2 0 26 1 1 1 2 2 2 2 1 3 3 35 1 35 1 1 3 2 2 3 3 0 0 17 1 0 1 3 0 2 2 2 3 3 0 1 2 0 3 1 3 3 2 35 0 2 35 26 2 1 3 3 3 8 1 26 3 44 1 1 1 3 2 3 0 1 3 0 1 3 2 3 0 1 1 1 2 0 0 3 35 1 0 0 3 1 2 0 2 3 0 0 0 1 1 0 0 1 3 3 1 0 2 35 1 3 2 0 0 2 2 2 1 3 0 3 2 1 1 0 26 3 1 2 44 35 2 3 1 1 0 1 3 0 3 17 26 2 3 8 2 0 35 2 2 2 26 1 2 3 0 1 1 3 1 26 1 1 26 1 53 2 2 2 2 0 3 0 1 2 3 1 3 0 3 1 1 3 0 2 0 1 26 0 0 1 1 3 0 1 1 1 1 3 1 2 1 17 3 1 0 53 1 1 0 3 1 3 0 1 1 3 2 2 1 0 3 3 3 1 1 0 3 2 1 3 2 0 3 0 0 26 3 3 2 2 1 1 0 0 26 2 3 1 0 0 1 0 1 3 3 0 0 1 0 0 26 1 1 1 1 1 1 1 44 0 2 2 0 3 2 44 1 3 0 0 8 0 1 1 1 1 1 1 3 0 3 44 3 1 1 0 1 3 8 2 1 2 1 0 0 26 2 2 1 3 1 1 2 3 2 1 0 3 1 26 2 2 0 2 2 1 0 0 3 1 1 3 0 3 2 0 3 3 0 3 35 1 0 2 1 0 2 3 2 17 2 0 3 8 1 3 3 2 1 3 53 0 0 0 2 0 0 1 0 0 0 53 2 3 2 3 3 3 1 3 3 1 0 0 26 1 0 44 3 3 3 1 2 1 3 0 3 44 1 57 35 0 0 1 1 2 2 3 1 3 1 21 0 0 2 3 3 0 0 3 1 1 0 0 3 1 44 0 2 0 0 0 3 1 53 3 2 0 1 2 2 3 3 0 3 1 3 0 2 3 1 8 1 3 3 0 1 0 0 3 3 2 1 2 1 2 3 3 3 3 0 0 1 1 0 53 0 2 35 3 3 1 2 3 0 3 3 0 0 0 1 3 2 0 2 0 1 2 2 3 2 2 0 44 3 1 2 2 2 0 3 0 0 0 2 3 3 3 2 3 3 2 2 0 3 0 0 3 1 0 3 0 2 0 0 1 0 0 2 44 35 1 0 3 3 1 2 3 0 1 1 17 3 2 2 3 2 2 3 53 8 44 3 2 3 1 2 0 2 1 2 0 2 0 3 3 0 1 1 1 3 0 0 1 0 0 44 3 0 2 2 3 0 2 0 0 2 1 2 1 0 3 2 1 2 1 0 2 0 0 2 0 2 2 26 0 2 3 2 44 0 0 44 3 1 3 3 0 1 1 0 3 2 17 1 0 0 3 0 1 1 0 1 0 0 3 2 0 2 1 1 8 2 2 3 17 3 0 2 1 1 1 3 8 2 35 1 1 1 2 2 3 2 1 1 3 3 3 1 2 0 1 1 3 1 3 35 1 1 3 2 17 0 53 1 2 2 0 2 3 3 2 3 1 3 3 0 2 1 3 2 1 0 1 2 2 2 2 0 1 2 1 3 1 53 2 3 2 3 1 3 3 2 1 3 2 0 1 0 1 3 1 0 1 0 3 1 3 0 0 1 0 8 3 0 2 8 0 2 2 2 1 2 2 3 1 8 1 1 2 3 1 2 0 2 3 53 2 0 0 1 0 8 3 2 0 0 1 0 0 0 0 0 2 2 1 3 0 2 1 0 2 2 3 3 0 3 3 1 2 1 1 3 1 0 3 3 1 53 3 1 0 2 2 0 2 2 2 0 3 2 0 1 1 2 3 2 3 3 3 1 2 3 0 1 3 0 44 3 0 2 2 3 2 1 1 3 1 2 3 53 2 35 2 2 12 1 0 0 2 1 3 0 0 2 2 3 3 3 0 2 2 2 1 2 1 2 0 2 2 3 3 1 35 2 0 1 2 2 3 3 3 1 2 2 2 1 2 1 3 3 2 0 3 2 3 2 44 2 2 1 3 8 3 2 0 1 2 1 17 0 44 0 0 0 35 2 0 17 3 0 0 0 2 1 1 3 44 0 17 0 3 0 3 35 0 2 0 2 1 0 0 1 1 1 0 3 3 0 53 17 2 2 1 1 2 35 0 3 0 3 1 3 0 1 3 3 1 3 3 0 2 3 0 3 1 1 0 3 17 2 1 1 1 3 3 3 1 2 1 2 1 2 8 1 3 2 2 2 44 1 1 35 1 1 3 2 3 1 2 2 2 2 1 0 1 1 3 0 0 1 1 1 2 17 3 2 1 1 2 3 2 0 0 1 2 2 2 0 3 53 0 2 3 3 1 3 1 2 44 1 0 2 35 1 1 0 2 35 26 0 17 3 2 2 1 0 1 2 0 44 0 0 1 2 2 3 0 3 0 3 1 1 1 0 1 44 1 1 0 26 0 53 0 2 1 3 2 0 8 1 2 0 2 2 0 1 0 2 2 1 3 35 1 3 1 0 0 0 8 0 0 2 2 3 2 53 2 0 2 3 2 3 3 17 3 1 2 2 17 1 26 3 3 2 1 0 0 3 8 2 17 2 3 2 3 1 1 1 2 0 0 2 1 1 3 8 1 1 1 3 2 0 0 2 1 0 0 1 3 0 1 2 3 2 1 0 0 1 1 1 0 0 0 2 1 0 1 1 2 1 2 17 1 1 1 1 53 2 2 0 1 2 0 3 3 0 1 26 0 0 1 1 3 2 0 3 53 2 3 0 3 1 3 0 2 3 44 0 0 1 0 3 0 2 0 0 2 3 1 2 3 1 3 1 2 1 2 0 3 1 35 0 1 3 2 2 2 1 2 2 1 1 0 1 3 0 1 3 0 2 0 3 2 2 2 1 3 0 1 3 0 1 1 3 3 1 3 2 2 3 0 0 3 3 2 1 1 0 2 3 2 1 2 0 0 44 1 3 0 2 2 0 0 3 0 1 0 0 1 2 2 0 0 2 2 1 0 2 2 3 3 1 2 2 3 3 3 44 3 17 0 0 1 0 3 0 0 2 0 2 2 2 0 1 2 8 0 8 3 2 1 0 3 1 1 0 3 2 2 44 2 0 2 1 1 0 2 1 2 2 1 2 2 2 2 3 0 2 44 17 53 35 0 53 2 2 2 3 3 2 2 1 1 0 1 1 3 3 1 1 53 3 44 3 1 0 2 2 0 2 0 0 1 2 35 2 1 2 2 3 53 2 0 8 1 1 0 3 1 1 2 0 8 3 2 3 3 3 0 8 3 0 0 3 44 3 2 17 0 0 2 2 3 3 2 1 3 26 1 1 3 3 3 2 2 1 2 3 1 1 0 3 3 1 0 44 2 0 2 35 1 3 1 2 44 3 44 1 3 2 2 2 2 1 3 0 0 2 1 0 1 2 0 0 2 2 3 2 44 35 2 0 0 8 0 3 3 0 3 53 3 0 3 3 2 26 1 0 0 2 0 3 2 3 2 1 3 0 44 3 1 3 3 2 2 3 1 2 3 2 2 2 3 0 1 2 53 1 3 1 53 1 53 0 2 0 0 3 0 3 0 3 1 1 3 2 1 3 3 0 1 0 2 0 2 1 8 1 2 1 3 3 2 1 3 1 3 2 2 2 2 1 1 3 44 8 0 3 2 8 3 0 17 0 3 0 1 3 1 26 0 1 1 1 8 0 2 1 0 2 2 0 2 2 1 0 1 3 1 2 0 1 1 53 2 8 0 1 0 0 26 2 3 1 2 1 1 1 1 3 44 3 2 0 2 26 3 3 0 2 3 0 35 3 2 1 3 3 1 1 2 2 0 3 3 1 17 44 3 2 44 1 0 0 1 3 1 2 2 3 0 2 2 2 1 3 3 2 0 2 3 2 2 0 1 2 3 1 0 0 0 44 1 2 3 0 1 0 2 3 0 3 2 1 2 1 1 3 0 2 3 3 1 1 3 2 2 1 35 3 2 2 2 1 0 0 0 3 0 0 0 3 8 1 1 0 0 1 3 35 3 3 0 2 0 2 3 35 2 1 0 1 0 35 2 2 3 0 2 3 3 8 2 1 3 1 1 35 0 0 8 2 1 2 1 3 2 2 2 1 2 3 0 1 0 3 2 3 0 17 3 3 8 2 0 3 2 2 0 2 0 3 2 0 0 0 2 26 3 3 3 0 2 1 0 0 3 3 2 0 3 0 0 2 2 3 3 3 1 3 1 1 2 3 3 2 0 3 3 2 2 0 0 1 1 2 0 1 2 0 0 3 2 2 1 0 0 3 3 44 0 2 2 2 2 26 1 1 1 2 8 0 44 3 3 1 1 3 3 1 3 0 2 35 2 3 2 1 2 2 1 0 3 2 0 3 3 3 0 1 3 0 1 1 2 3 3 0 0 3 3 1 3 0 2 0 0 2 2 2 3 0 2 3 3 26 2 1 0 3 1 8 1 0 0 1 0 0 0 2 0 2 1 2 0 44 2 0 2 3 0 3 2 2 2 2 1 1 0 3 3 0 2 35 2 2 2 3 0 1 0 3 1 3 3 1 1 1 0 2 17 0 1 0 3 1 0 2 3 2 44 53 2 3 0 0 2 53 3 0 1 3 3 3 44 0 3 8 1 3 2 1 2 2 2 3 53 2 1 0 3 1 0 2 0 0 3 1 44 1 3 0 3 2 3 0 2 2 3 17 3 2 0 26 3 1 0 3 1 1 2 2 0 17 0 1 0 0 26 1 1 2 0 17 1 3 2 0 0 1 3 3 0 1 3 0 2 2 0 44 1 3 0 0 2 2 1 3 1 2 3 3 44 35 0 1 53 0 0 26 17 0 1 35 0 1 3 0 1 3 1 1 2 3 2 2 1 1 0 0 26 35 53 2 8 3 1 26 0 1 3 3 3 3 2 3 2 0 2 2 0 1 0 1 0 3 1 3 3 0 1 1 3 0 2 2 2 0 1 1 3 0 3 3 2 3 17 3 3 8 0 3 0 0 3 2 2 1 0 3 2 3 2 0 2 8 0 2 2 0 3 0 1 2 26 3 0 44 0 2 2 0 0 2 3 26 3 3 0 2 1 0 2 2 3 3 3 0 2 2 1 0 3 1 2 26 1 3 0 0 0 3 26 0 2 44 1 2 1 2 44 3 1 0 0 1 2 3 0 1 53 0 0 1 3 8 2 2 1 1 3 2 0 0 44 35 2 0 1 1 3 0 1 1 1 26 1 0 0 2 1 35 1 2 1 2 0 2 0 1 2 1 2 0 2 0 1 3 1 3 0 1 0 2 2 17 1 3 2 2 3 0 35 3 2 2 1 44 8 17 2 44 1 0 1 3 3 3 1 1 3 3 3 0 1 0 1 0 0 1 2 0 3 3 1 0 2 2 3 53 35 2 0 0 3 0 0 2 3 2 1 2 0 3 0 2 1 3 0 1 0 0 1 3 1 2 26 2 3 1 2 2 2 3 1 1 44 2 1 53 0 53 1 3 0 1 1 3 0 1 1 35 2 3 3 1 0 1 8 0 1 0 1 0 3 26 3 44 44 1 3 1 1 2 2 0 1 0 0 3 0 2 3 2 3 0 3 3 1 3 3 3 2 0 0 0 3 2 3 3 2 2 0 3 2 3 0 2 2 2 1 3 1 17 1 0 2 3 2 1 2 0 3 3 0 0 3 0 3 3 2 3 1 0 2 1 0 2 0 3
+
diff --git a/tutorials/pomobalance/index.html b/tutorials/pomobalance/index.html
index e03d1cd6a..401853f7c 100644
--- a/tutorials/pomobalance/index.html
+++ b/tutorials/pomobalance/index.html
@@ -55,7 +55,7 @@
Polymorphism-aware phylogenetic models with balancing selection
Species tree inference and identification of preferred allele frequency for balancing selection in RevBayes
Svitlana Braichenko, Rui Borges, and Carolin Kosiol
- Last modified on August 24, 2023
+ Last modified on April 21, 2024
@@ -99,6 +99,8 @@ Data files and scripts
great_apes_BS_10000.cf
+ great_apes_BS_10000.txt
+
@@ -107,8 +109,12 @@ Data files and scripts
+ counts_to_pomo_states_converter.R
+
great_apes_pomobalance.Rev
+ weighted_sampled_method.cpp
+
@@ -120,6 +126,8 @@ Data files and scripts
Polymorphism-aware phylogenetic models with balancing selection
+NB! Please note that the current version of the code has been tested in the development version of RevBayes built from the dev_PoMo_bs_master
branch. PoMoBalance will be added to the main functionality in the next release.
+
The polymorphism-aware phylogenetic models with balancing selection (PoMoBalance) is a natural extension of polymorphism-aware phylogenetic models (De Maio et al. 2013; De Maio et al. 2015; Schrempf et al. 2016; Borges et al. 2019; Borges et al. 2022; Borges et al. 2022) including all previous capabilities as well as detection of preferred allele frequencies and strength of balancing selection as shown in .
@@ -185,7 +193,25 @@ Loading the data
Similarly to PoMos , we are using count files in the same format. File great_apes_BS_10000.cf
contains an example of heterozygote advantage simulation with the preferred frequency in the middle in $4$ great ape populations performed with the evolutionary simulation framework SLiM (Haller and Messer 2019) . We generated $10000$ sites, however, normally balancing selection happens in small regions containing only a few genes or around a thousand nucleotides. Thus, to improve the accuracy of the method we recommend increasing the virtual population size. In the current example, we use $N = 10$ and it can be further increased taking into account the interplay between the number of sites and the computational cost.
-First, we convert the allelic counts into PoMo states. Open the terminal and copy the data and script into the corresponding subfolders data and scripts of your working directory, for example, call it, PoMoBalance . Inside PoMoBalance create output folder to store the results. Open the great_apes_pomobalance.Rev
file using an appropriate text editor so you can follow what each command is doing. Then run RevBayes :
+First, we convert the allelic counts into PoMo states. Open the terminal and copy the data and script into the corresponding subfolders data and scripts of your working directory, for example, call it, PoMoBalance . Inside PoMoBalance create output folder to store the results.
+
+PoMo state-space includes fixed and polymorphic states. However, sampled fixed sites might not be necessarily fixed in the original population. We might just have been unlucky and only sampled individuals with the same allele from a locus that is polymorphic. It is typically the case that the real genetic diversity is undersampled in population genetic studies. The fewer the number of sampled individuals or the rarer are the alleles in the original population (i.e., singletons, doubletons), the more likely are we to observe fake fixed sites in the sequence alignment. The sampled-weighted method helps us to correct for such bias by attributing to each of the allelic counts an appropriate PoMo state (0-based coding). For a population size of 3 virtual individuals, we expect 16 states (coded 0-15), while for a population of 2 virtual individuals, we expected 10 states (coded 0-9).
+
+The script weighted_sampled_method.cpp
is implemented in C++ , and we will run it using the Rcpp package in R . Open the counts_to_pomo_states_converter.R
file and make the appropriate changes to obtain your PoMo alignments suited for PoMoBalance.
+
+name <- "great_apes_BS_10000" # name of the count file
+ count_file <- paste0 ( "../data/" , name , ".cf" ) # path to the count file
+ n_alleles <- 4 # the four nucleotide bases A, C, G and T
+ N <- 10 # virtual population size
+
+ alignment <- counts_to_pomo_states_converter ( count_file , n_alleles , N ) # Create the alignment
+
+ writeLines ( alignment , paste0 ( "../data/" , name , ".txt" )) # writeg the PoMo alignment
+
+
+We place the produced alignments inside the data folder. The output files follow the NaturalNumbers
character type of RevBayes and can easily read by it.
+
+Open the great_apes_pomobalance.Rev
file using an appropriate text editor so you can follow what each command is doing. Then run RevBayes :
./rb great_apes_pomobalance.Rev
@@ -262,7 +288,7 @@ Setting up the model
The strength of balancing selection beta
is also exponential and for the same reason as rho
combines two kinds of moves. The preferred frequency B
must be a discrete positive value between 0 and N
, thus, we set up variable Num
with a uniform prior and two kinds of standard movesmvSlide
and mvScale
with high weights to enhance exploration of parameter space. We round Num
on each iteration to obtain discrete B
-# Strenths of the balancing selection
+# Strengths of the balancing selection
for (i in 1:6){
@@ -343,6 +369,10 @@ Set
monitors.append( mnScreen(printgen=10) )
+Run burn-in tuning the weights of the parameters
+
+pbalance_mcmc.burnin(generations=2000,tuningInterval=200)
+
Finally, set up mcmc
moves with four independent MCMC runs to ensure proper convergence and mixing.
diff --git a/tutorials/pomobalance/scripts/counts_to_pomo_states_converter.R b/tutorials/pomobalance/scripts/counts_to_pomo_states_converter.R
new file mode 100644
index 000000000..3e0e7d3f0
--- /dev/null
+++ b/tutorials/pomobalance/scripts/counts_to_pomo_states_converter.R
@@ -0,0 +1,20 @@
+# This script reads a count file and creates a PoMo alignment in the "NaturalNumbers" type that can be uploaded into RevBayes.
+
+# setting the working directory
+setwd(getwd())
+
+# install.packages("Rcpp")
+library("Rcpp")
+
+# uploading the function counts_to_pomo_states_converter
+sourceCpp("weighted_sampled_method.cpp")
+
+name <- "great_apes_BS_10000"
+count_file <- paste0("../data/", name, ".cf") # count file
+n_alleles <- 4 # the four nucleotide bases A, C, G and T
+N <- 10 # virtual population size
+
+alignment <- counts_to_pomo_states_converter(count_file,n_alleles,N)
+
+# writing the PoMo alignment
+writeLines(alignment,paste0("../data/", name, ".txt"))
diff --git a/tutorials/pomobalance/scripts/great_apes_pomobalance.Rev b/tutorials/pomobalance/scripts/great_apes_pomobalance.Rev
index 4f8cb3472..002563f12 100644
--- a/tutorials/pomobalance/scripts/great_apes_pomobalance.Rev
+++ b/tutorials/pomobalance/scripts/great_apes_pomobalance.Rev
@@ -6,7 +6,7 @@
N <- 10
-data <- readPoMoCountFile(countFile="data/great_apes_BS_10000.cf", virtualPopulationSize=N, format="PoMo")
+data <- readCharacterDataDelimited("../data/great_apes_BS_10000.txt", stateLabels=58, type="NaturalNumbers", delimiter=" ", header=FALSE)
taxa <- data.taxa()
@@ -55,7 +55,7 @@ moves.append(mvAVMVN(sigma) )
phi := [1.0,1.0+sigma,1.0+sigma,1.0]
-# Strenths of the balancing selection
+# Strength of the balancing selection
for (i in 1:6){
@@ -110,7 +110,7 @@ psi := treeAssembly(topology, branch_lengths)
# Create the substitution model and clamp with our observed data
-sequences ~ dnPhyloCTMC(psi,Q=Q,type="PoMo")
+sequences ~ dnPhyloCTMC(psi,Q=Q,type="NaturalNumbers")
sequences.clamp(data)
diff --git a/tutorials/pomobalance/scripts/weighted_sampled_method.cpp b/tutorials/pomobalance/scripts/weighted_sampled_method.cpp
new file mode 100644
index 000000000..92d1362ff
--- /dev/null
+++ b/tutorials/pomobalance/scripts/weighted_sampled_method.cpp
@@ -0,0 +1,256 @@
+#include
+#include
+#include
+#include
+#include
+#include
+#include
+
+#include
+using namespace Rcpp;
+
+
+// samples a state from a pomo edge 0:(N-1) givent the weights of a
+// binomal distribution B(m|n/N,M)
+// based on equation (13) of Schrempf et al. (2016) JTB
+int sample_weight(int M, int m, int N){
+
+ std::vector weights(N+1);
+ double prob;
+
+ // calculating the weight vector
+ for (int i=0; i < N+1; ++i){
+ prob = 1.0*i/N;
+ weights[i] = pow(prob,m)*pow(1-prob,M-m);
+ }
+
+ // sampling a pomo state from the weight vector
+ std::random_device rd;
+ std::mt19937 gen(rd());
+ std::discrete_distribution<> d(weights.begin(), weights.end());
+
+ return d(gen);
+
+}
+
+// samples a pomo edge from a matrix of allele_indexes*edge_indexes matrix
+// the matrix estipulates wich edges contain the allele allele_index
+int sample_edge(int allele_index, std::vector vector){
+
+ // setting the appropriate sub vector to sample from
+ // the edge matrix is indexed as [allele_index,edge_index]
+ // the sub vector pics the allele_index line
+ std::vector sub_vector = {vector.begin() + allele_index*6, vector.begin() + allele_index*6 + 6};
+
+ // sampling a pomo edge
+ std::random_device rd;
+ std::mt19937 gen(rd());
+ std::discrete_distribution<> d( sub_vector.begin(), sub_vector.end() );
+
+ return d(gen);
+
+}
+
+
+// gets the edge of an observed polymorphic count
+int get_index(std::vector vector, std::string element) {
+
+ for (int i=0; i matrix_edges(n_alleles*n_edges,0);
+ std::vector vector_edges(n_edges);
+
+
+ // generating all the possible pairwise combinations of alleles
+ int edge = 0;
+ for (int i=0; i> content;
+ if (content != "COUNTSFILE"){
+ std::cout << "\n " << count_file << " does not seem to be properly formatted. First line: COUNTSFILE NPOP # NSITES #";
+ }
+
+ inFile >> content;
+ if (content != "NPOP"){
+ std::cout << "\n " << count_file << " does not seem to be properly formatted. First line: COUNTSFILE NPOP # NSITES #";
+ }
+
+ inFile >> n_taxa;
+
+ inFile >> content;
+ if (content != "NSITES"){
+ std::cout << "\n " << count_file << " does not seem to be properly formatted. First line: COUNTSFILE NPOP # NSITES #";
+ }
+
+ inFile >> n_sites;
+
+ std::vector taxa(n_taxa);
+
+ inFile >> content;
+ if (content != "CHROM"){
+ std::cout << "\n " << count_file << " does not seem to be properly formatted. Second line: CHROM POS TaxaName1 TaxaName2 ...";
+ }
+
+ inFile >> content;
+ if (content != "POS"){
+ std::cout << "\n " << count_file << " does not seem to be properly formatted. Second line: CHROM POS TaxaName1 TaxaName2 ...";
+ }
+
+ // getting the taxa names
+ for (int i=0; i> taxa[i];
+ }
+
+
+ // going through the number of sites
+ for (int i=0; i> content;
+ inFile >> content;
+
+ // some important initializations
+ int value,state,int_index,M,m,weight,n_counts;
+
+ // going through the number of taxa
+ for (int j=0; j> counts;
+ std::stringstream ss( counts );
+ std::string count,str_index;
+
+ // setting total counts, the last postive count (why last? important for state indexing), and number of non-null counts to 0
+ M = 0;
+ n_counts = 0;
+
+ // goes through the number of alleles
+ // counts are comma separated
+ for (int k=0; k 0) {
+ M += value;
+ m = value;
+ n_counts += 1;
+ int_index = k;
+ str_index = str_index + std::to_string(k);
+ }
+
+ }
+
+ // pointing out some typical invalid counts: null counts (e.g., 0,0,0,0) and >2-allelic counts (e.g., 0,1,1,1)
+ if (n_counts==0){
+ std::cout << "\n Unexpected count pattern: " << counts << ". PoMos require at least one postive count.\n\n";
+ return "\n";
+ }
+ if (n_counts>2){
+ std::cout << "\n Unexpected count pattern: " << counts << ". PoMos only accept monoallelic or biallelic counts.\n\n";
+ return "\n";
+ }
+
+ // sampling a 0:N frequency from the weight vector
+ weight = sample_weight(M, m, N);
+
+ // determining the pomo state
+ // three possible situations
+ // if the count is monoallelic & likely "sampled" from a fixed state
+ if (weight==N){
+
+ state = int_index;
+ //std::cout << " " << state << "\n";
+
+ // if the count is monoallelic & likely "sampled" from a polymoprhic state
+ } else if (n_counts==1 & weight1) {
+
+ edge = get_index(vector_edges,str_index);
+ state = n_alleles+edge*N-edge+weight-1;
+ //std::cout << " " << state << "\n";
+
+ }
+
+ std::cout << "Pattern: " << counts << " State: " << state << "\n";
+
+ // creating the NaturalNumber type file for RevBayes
+ taxa[j] += " " + std::to_string(state);
+
+ }
+
+ }
+
+ // summarizing
+ std::cout << "\n\n Number of alleles " << n_alleles <<
+ "\n Number of sites " << n_sites <<
+ "\n Number of virtual individuals " << N <<
+ "\n Number of PoMo states " << n_alleles*(1.0+(n_alleles-1.0)*(N-1.0)*0.5) <<
+ "\n Number of taxa " << n_taxa << "\n\n";
+
+
+ // creating the alignment and returning it
+ std::string alignment = "";
+ for (int i=0; iEq
10.1093/sysbio/syp067
-FitzJohn R.G. 2010. Quantitative Traits and Diversification. Systematic Biology. 59:619–633.
+FitzJohn R.G. 2012. Diversitree: Comparative Phylogenetic Analyses of Diversification in R. Methods in Ecology and Evolution. 3:1084–1092.
-10.1093/sysbio/syq053
+10.1111/j.2041-210X.2012.00234.x
-FitzJohn R.G. 2012. Diversitree: Comparative Phylogenetic Analyses of Diversification in R. Methods in Ecology and Evolution. 3:1084–1092.
+FitzJohn R.G. 2010. Quantitative Traits and Diversification. Systematic Biology. 59:619–633.
-10.1111/j.2041-210X.2012.00234.x
+10.1093/sysbio/syq053
Freyman W.A., Höhna S. 2018. Cladogenetic and anagenetic models of chromosome number evolution: a Bayesian model averaging approach. Systematic Biology. 67:1995–215.
diff --git a/tutorials/sse/bisse.html b/tutorials/sse/bisse.html
index 93c61c30c..281a9619a 100644
--- a/tutorials/sse/bisse.html
+++ b/tutorials/sse/bisse.html
@@ -125,10 +125,10 @@ Data files and scripts
primates_activity_period.nex
- primates_mating_system.nex
-
primates_mating_system.nex
+ primates_mating_system.nex
+
primates_solitariness.nex
primates_solitariness.nex
diff --git a/tutorials/sse/classe.html b/tutorials/sse/classe.html
index e0ee8f8eb..7d7e2d280 100644
--- a/tutorials/sse/classe.html
+++ b/tutorials/sse/classe.html
@@ -127,10 +127,10 @@ Data files and scripts
primates_activity_period.nex
- primates_mating_system.nex
-
primates_mating_system.nex
+ primates_mating_system.nex
+
primates_solitariness.nex
primates_solitariness.nex
diff --git a/tutorials/sse/hisse.html b/tutorials/sse/hisse.html
index f546ec157..9cfb026b7 100644
--- a/tutorials/sse/hisse.html
+++ b/tutorials/sse/hisse.html
@@ -127,10 +127,10 @@ Data files and scripts
primates_activity_period.nex
- primates_mating_system.nex
-
primates_mating_system.nex
+ primates_mating_system.nex
+
primates_solitariness.nex
primates_solitariness.nex