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Welcome to the BAMM Google Groups page!

BAMM (Bayesian Analysis of Macroevolutionary Mixtures) is a program for modeling complex dynamics of speciation, extinction, and trait evolution on phylogenetic trees. Please visit bamm-project.org for more information about BAMM.

Please post any questions, comments, suggestions, possible bugs, etc. here. If you are reporting a problem, please include (if possible):

Data files that led to the problem
Control file
Operating system version and computer architecture
Compiler and version (if used)
run_info.txt (if BAMM was able to run)

0 selected

Humberto Nappo, pasca...@gmail.com5

2/19/24

Function plotRateThroughTime malfunctioning

Well, if the problem is on my PC I will try and plot the figure in a different machine. I will come

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Function plotRateThroughTime malfunctioning

Well, if the problem is on my PC I will try and plot the figure in a different machine. I will come

2/19/24

Sander de Backer2

9/14/23

logLik = 0 throughout analysis

I've discovered the problem. In the control file, sampleFromPriorOnly was set to 0, meaning

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logLik = 0 throughout analysis

I've discovered the problem. In the control file, sampleFromPriorOnly was set to 0, meaning

9/14/23

7/26/23

how can i improve effective size of log likelihood in a phenotypic rates analysis?

hello, i am running phenotypic rates on a large tree (>10000 taxa), and did not expect either

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how can i improve effective size of log likelihood in a phenotypic rates analysis?

hello, i am running phenotypic rates on a large tree (>10000 taxa), and did not expect either

7/26/23

ljq...@gmail.com, pasca...@gmail.com3

7/2/23

bamm converging too quick

Thank you, Pascal, for your comment. The three is relatively large (344 tips). Given the size, I

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bamm converging too quick

Thank you, Pascal, for your comment. The three is relatively large (344 tips). Given the size, I

7/2/23

Jamie T, pasca...@gmail.com3

6/30/23

Get best shift configuration does not work on combined eventdatas

Hi Pascal, It is the angiosperms tree analysed by Igea and Tanentzap (2020) (https://onlinelibrary.

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Get best shift configuration does not work on combined eventdatas

Hi Pascal, It is the angiosperms tree analysed by Igea and Tanentzap (2020) (https://onlinelibrary.

6/30/23

felipe lamarca, pasca...@gmail.com6

6/16/23

diversification analysis

In the R package BAMMtools, you need to run the function setBAMMpriors with your tree. It will

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diversification analysis

In the R package BAMMtools, you need to run the function setBAMMpriors with your tree. It will

6/16/23

Centurion Cacau, Dan Rabosky2

6/14/23

question about studying virus evolution using BAMM

Hi Cacau- I would say that BAMM, and most other diversification models, are poorly suited to studying

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question about studying virus evolution using BAMM

Hi Cacau- I would say that BAMM, and most other diversification models, are poorly suited to studying

6/14/23

Nachiket Shankar, … Juan Daniel Vásquez-Restrepo3

5/5/23

Phenotypic trait evolution - running MCMC - very low Effective sample sizes

Dear Dr. Rabosky. I found this answer from 2014 to be really helpful. Currently, I am using BAMM to

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Phenotypic trait evolution - running MCMC - very low Effective sample sizes

Dear Dr. Rabosky. I found this answer from 2014 to be really helpful. Currently, I am using BAMM to

5/5/23

Daniel David Díaz Contreras Díaz, pasca...@gmail.com3

3/16/23

How to overlay RateThroughTime plots

Hi Daniel, The examples in the help for plotRateThroughTime() show how to do this. I would recommend

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How to overlay RateThroughTime plots

Hi Daniel, The examples in the help for plotRateThroughTime() show how to do this. I would recommend

3/16/23

Daniel David Díaz Contreras Díaz

2/13/23

In-Credible Shift Sets

Hi everyone! I generated the credible shifts set based on the edata of a Diversification analysis run

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In-Credible Shift Sets

Hi everyone! I generated the credible shifts set based on the edata of a Diversification analysis run

2/13/23

1/24/23

Presenting phylgenies with zero rate shifts

Hello, I recently ran a diversification analysis on BAMM. Turns out, there is greatest support for a

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Presenting phylgenies with zero rate shifts

Hello, I recently ran a diversification analysis on BAMM. Turns out, there is greatest support for a

1/24/23

Daniel David Díaz Contreras Díaz

1/9/23

Trees with negative branches

Hi all! I would like to know if there is a way of bypassing or correcting a negative branch in the

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Trees with negative branches

Hi all! I would like to know if there is a way of bypassing or correcting a negative branch in the

1/9/23

Laura van Holstein

1/1/23

Fossil BAMM - preservationModel problem

Hi Dan, First of all a massive thank you for BAMM & all the helpful documentation! Just wondering

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Fossil BAMM - preservationModel problem

Hi Dan, First of all a massive thank you for BAMM & all the helpful documentation! Just wondering

1/1/23

12/7/22

getting "nan" values for loglik

Hi, I am trying to run a BAMM analysis on the attached tree after generating the attached control

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getting "nan" values for loglik

Hi, I am trying to run a BAMM analysis on the attached tree after generating the attached control

12/7/22

11/28/22

How to plot clade names in bammdata figures?

I've seen in figures of a few papers bamm data is plotted with branches coloured by rates, and

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How to plot clade names in bammdata figures?

I've seen in figures of a few papers bamm data is plotted with branches coloured by rates, and

11/28/22

Jamie T, pasca...@gmail.com3

11/23/22

Extract a tree from an event data

Thank you! Much appreciated On Thursday, October 13, 2022 at 9:23:22 PM UTC+1 pasca...@gmail.com

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Extract a tree from an event data

Thank you! Much appreciated On Thursday, October 13, 2022 at 9:23:22 PM UTC+1 pasca...@gmail.com

11/23/22

Francis Nge, Dan Rabosky3

11/21/22

no core rate shift in BAMM run?

Hi Dan, great thanks for the clarification. I noticed in the figure though the colours are different

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no core rate shift in BAMM run?

Hi Dan, great thanks for the clarification. I noticed in the figure though the colours are different

11/21/22

Matthew Olson, pasca...@gmail.com2

11/8/22

traitDependentBAMM error

You need to get your traits object to be a vector of trait values, named according to the tip labels

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traitDependentBAMM error

You need to get your traits object to be a vector of trait values, named according to the tip labels

11/8/22

Chao Shen, pasca...@gmail.com2

9/21/22

parameter for BAMM

Hi Shen, The poisson rate prior was replaced with the expected number of rate shifts. See the

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parameter for BAMM

Hi Shen, The poisson rate prior was replaced with the expected number of rate shifts. See the

9/21/22

8/27/22

How to decide which model is "best" when they differ by priors

My analyses seem sensitive to the expected number of rate shifts, with the RTT and BSC changing quite

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How to decide which model is "best" when they differ by priors

My analyses seem sensitive to the expected number of rate shifts, with the RTT and BSC changing quite

8/27/22

8/8/22

Question about Trait Evolution - BAMM

I hope you are doing very well. I am writing because I am doing an analysis on the evolution of body

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Question about Trait Evolution - BAMM

I hope you are doing very well. I am writing because I am doing an analysis on the evolution of body

8/8/22

JET, pasca...@gmail.com5

8/8/22

Extracting the mean phylorate plot number (PP) for a branch

Fantastic. That is quite easy and straightforward. I did getMarginalBranchRateMatrix(), but didn'

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Extracting the mean phylorate plot number (PP) for a branch

Fantastic. That is quite easy and straightforward. I did getMarginalBranchRateMatrix(), but didn'

8/8/22

6/28/22

fossil BAMM for phenotype evolutionary rate

Hi, everyone, I was wondering if you could help to estimate rate of phenotypic evolution using the

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fossil BAMM for phenotype evolutionary rate

Hi, everyone, I was wondering if you could help to estimate rate of phenotypic evolution using the

6/28/22

Perry Wood, pasca...@gmail.com2

5/10/22

Extracting Individual branch rates

Hi Perry, Yeah, getCladeRates() generally makes more sense for monophyletic groups, although you can

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Extracting Individual branch rates

Hi Perry, Yeah, getCladeRates() generally makes more sense for monophyletic groups, although you can

5/10/22

Jamie T, pasca...@gmail.com4

4/27/22

Plot density of rate shifts in the entire sample

The formula for lam(t) calculates the rate at any point in time within a particular rate regime,

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Plot density of rate shifts in the entire sample

The formula for lam(t) calculates the rate at any point in time within a particular rate regime,

4/27/22

MSerrano, … pasca...@gmail.com4

4/26/22

Understanding best$eventData

No, lam1 and lam2 are the parameters of the exponential change model for that rate regime. See

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Understanding best$eventData

No, lam1 and lam2 are the parameters of the exponential change model for that rate regime. See

4/26/22

Jamie T, pasca...@gmail.com3

4/26/22

How to save plot.bammdata plots

Thank you! On Tuesday, April 26, 2022 at 1:23:15 PM UTC+1 pasca...@gmail.com wrote: Hi Jamie,

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How to save plot.bammdata plots

Thank you! On Tuesday, April 26, 2022 at 1:23:15 PM UTC+1 pasca...@gmail.com wrote: Hi Jamie,

4/26/22

Jamie T, pasca...@gmail.com3

4/26/22

Plot.bammdata with time scale?

Hi, Thanks for this! Jamie On Wednesday, April 20, 2022 at 2:00:55 PM UTC+1 pasca...@gmail.com wrote:

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Plot.bammdata with time scale?

Hi, Thanks for this! Jamie On Wednesday, April 20, 2022 at 2:00:55 PM UTC+1 pasca...@gmail.com wrote:

4/26/22

Daniel David Díaz Contreras Díaz, pasca...@gmail.com4

4/14/22

plot.bammdata Missing function

Thanks for your response! I will look into these examples. Daniel El domingo, 10 de abril de 2022 a

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plot.bammdata Missing function

Thanks for your response! I will look into these examples. Daniel El domingo, 10 de abril de 2022 a

4/14/22

3/16/22

It is not immediately apparent to me how I would go about citing BAMM in my dissertation, I need to

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It is not immediately apparent to me how I would go about citing BAMM in my dissertation, I need to

3/16/22

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