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

-

Automated building and testing in RevBayes

+

Using Docker with RevBayes

-

Quick automated feedback on code changes

+

Containerized debugging and executeables

-

Best practices in RevBayes

+

Integration Tests in RevBayes

-

Coding and documentation guidelines

+

Ensuring that code changes did not unexpectedly alter the software

-

Using Docker with RevBayes

+

Contributing a RevBayes tutorial

-

Containerized debugging and executeables

+

How to write and host a tutorial on this website

@@ -124,16 +124,16 @@

Developer’s Guide

-

Integration Tests in RevBayes

+

Best practices in RevBayes

-

Ensuring that code changes did not unexpectedly alter the software

+

Coding and documentation guidelines

-

Contributing a RevBayes tutorial

+

Automated building and testing in RevBayes

-

How to write and host a tutorial on this website

+

Quick automated feedback on code changes

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 @@

    The birth-death br 10.1093/bioinformatics/btt153 -
  • 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.)

    +
    taxa <- T.taxa()
     

    Additionally, we initialize a variable for our vector of moves and monitors.

    moves    = VectorMoves()
    @@ -556,14 +555,14 @@ 

    Exercise 2

    1. Carvalho C.M., Polson N.G., Scott J.G. 2010. The horseshoe estimator for sparse signals. Biometrika. 97:465–480.
    2. -
    3. Höhna S. 2014. Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling. PLoS One. 9:e84184. +
    4. 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
    5. -
    6. Höhna S. 2015. The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events. Journal of Theoretical Biology. 380:321–331. +
    7. 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
    8. 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

    9. primates.tre
    10. -
    11. primates_tree.nex
    12. -
    13. primates_tree.nex
    14. -
    15. primates_tree.nex
    16. +
    17. primates_tree.nex
    18. primates_tree.nex
    19. +
    20. primates_tree.nex
    21. + 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

    1. Aldous D.J. 2001. Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today. Statistical Science.:23–34.
    2. -
    3. Höhna S. 2014. Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling. PLoS One. 9:e84184. +
    4. 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
    5. -
    6. Höhna S. 2015. The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events. Journal of Theoretical Biology. 380:321–331. +
    7. 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
    8. 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 @@

    Complex hierarchical models for phylogenetic inference -

    Combined-Evidence Analysis and the Fossilized Birth-Death Process for Analysis of Extant Taxa and Fossil Specimens

    +

    Combined-Evidence Analysis and the Fossilized Birth-Death Process for Stratigraphic Range Data

    Joint inference of divergence times and phylogenetic relationships of fossil and extant taxa

    @@ -649,7 +649,7 @@

    Complex hierarchical models for phylogenetic inference -

    Combined-Evidence Analysis and the Fossilized Birth-Death Process for Stratigraphic Range Data

    +

    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

    @@ -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

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    Discrete morphology - Ancestral State Estimation (Mammals & Placenta Type)

    Ancestral State Estimation and Testing for Irreversibility

    Sebastian Höhna

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    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

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    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

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    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 +++ b/tutorials/pomobalance/data/great_apes_BS_10000.txt @@ -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 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53 0 1 3 8 0 2 0 0 2 2 1 1 3 0 1 8 0 0 0 1 8 2 0 2 1 1 2 3 1 0 0 44 2 3 3 1 0 0 2 0 1 1 2 3 1 17 1 1 2 1 3 53 1 2 3 53 1 1 3 0 1 0 0 2 3 0 2 1 0 3 3 1 0 0 0 2 1 3 3 0 2 1 44 35 26 2 3 2 1 2 1 3 17 0 0 2 1 3 3 8 1 3 1 1 0 2 2 0 2 35 1 1 8 0 2 0 3 3 1 2 2 3 3 0 53 3 1 3 2 0 2 0 2 2 1 0 3 0 17 1 3 2 0 1 53 2 1 2 3 2 2 0 0 1 1 0 0 1 1 17 1 2 2 3 2 1 1 3 0 2 1 1 2 3 2 53 53 1 1 2 3 1 1 2 3 0 1 2 0 3 0 0 2 1 1 3 35 0 3 1 1 0 0 3 17 1 2 26 1 17 0 3 0 2 3 0 0 1 35 2 0 2 1 53 3 1 3 2 2 1 1 3 3 0 26 0 2 1 0 2 0 0 44 2 2 3 44 0 2 3 1 2 2 1 1 17 1 1 3 3 1 1 0 1 0 2 0 2 1 0 0 1 0 0 3 1 0 3 1 3 0 0 3 3 17 44 3 0 8 2 2 1 2 1 2 0 3 0 0 0 2 2 0 3 2 1 2 44 3 0 0 1 2 0 2 8 1 2 2 3 0 2 2 2 2 0 2 3 1 3 2 1 26 1 0 1 1 3 1 3 2 3 1 3 0 2 1 17 2 0 3 2 3 26 2 0 0 3 0 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 @@

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