BioGeoBEARS

Contact owners and managers

1–30 of 457

0 selected

Jonathan Drury, … Nick Matzke15

Nov 26

New update to BioGeoBEARS and stochastic map objects

Thanks folks -- sorry I missed this before, I will check; at some point R got more picky about is.na

unread,

New update to BioGeoBEARS and stochastic map objects

Thanks folks -- sorry I missed this before, I will check; at some point R got more picky about is.na

Nov 26

Nov 23

package vctrs vs devtools

Hi all, I see I missed a report on these packages having conflicting version numbers or something:

unread,

package vctrs vs devtools

Hi all, I see I missed a report on these packages having conflicting version numbers or something:

Nov 23

Nov 23

update: rexpokit 0.26.6.14

Hi all, I fixed one more fortran LTO warning for rexpokit; the new rexpokit 0.26.6.14 is now accepted

unread,

update: rexpokit 0.26.6.14

Hi all, I fixed one more fortran LTO warning for rexpokit; the new rexpokit 0.26.6.14 is now accepted

Nov 23

Nov 21

Fwd: [CRAN-pretest-newbies] CRAN Submission rexpokit 0.26.6.14

A new version of rexpokit is going on CRAN, it fixes one remaining warning (LTO) that was occurring

unread,

Fwd: [CRAN-pretest-newbies] CRAN Submission rexpokit 0.26.6.14

A new version of rexpokit is going on CRAN, it fixes one remaining warning (LTO) that was occurring

Nov 21

Natalia Ossa Hernández, Ivan Magalhães2

Nov 20

Hi Natalia, In order to make this kind of inference, first you need to perform biogeographic

unread,

Hi Natalia, In order to make this kind of inference, first you need to perform biogeographic

Nov 20

Sander de Backer, … Nick Matzke7

Nov 6

num_cores_to_use ignored

Thanks for this link, I had forgotten that discussion from mid-pandemic! On Tue, Nov 7, 2023 at 1:27

unread,

num_cores_to_use ignored

Thanks for this link, I had forgotten that discussion from mid-pandemic! On Tue, Nov 7, 2023 at 1:27

Nov 6

Nicole Mitidieri, … Nick Matzke17

Nov 1

Rexpokit removed from CRAN

Sweet! Thank you, Nick! I had a spooky installation following your Github page. I installed "

unread,

Rexpokit removed from CRAN

Sweet! Thank you, Nick! I had a spooky installation following your Github page. I installed "

Nov 1

Nick Matzke, … Nicole Mitidieri3

Oct 29

Fwd: CRAN Submission rexpokit 0.26.6.11

Thank you, Nick! Looking forward to working with BioGeoBEARS. El domingo, 29 de octubre de 2023 a las

unread,

Fwd: CRAN Submission rexpokit 0.26.6.11

Thank you, Nick! Looking forward to working with BioGeoBEARS. El domingo, 29 de octubre de 2023 a las

Oct 29

Alma Melisa Vázquez López

Sep 4

dispersal vs. range expansion

Hi! I ran a basic model of BioGeoBears, is possible with the parameter D infer if the species reached

unread,

dispersal vs. range expansion

Hi! I ran a basic model of BioGeoBears, is possible with the parameter D infer if the species reached

Sep 4

mpnogu...@gmail.com

Aug 30

optimx vs optim vs GenSa in trait-dependent time-stratified models

Hi everyone, I hope you're all doing well. I'm currently encountering a problem with my

unread,

optimx vs optim vs GenSa in trait-dependent time-stratified models

Hi everyone, I hope you're all doing well. I'm currently encountering a problem with my

Aug 30

Daniel Eusebio Quintero Vallejo, Nick Matzke3

Jul 31

it is possible not to test a model if it does not make sense with the biological group

Thanks! I have send you all the files by mail (because they are large files and I just could do it by

unread,

it is possible not to test a model if it does not make sense with the biological group

Thanks! I have send you all the files by mail (because they are large files and I just could do it by

Jul 31

Daniel Eusebio Quintero Vallejo, Nick Matzke4

Jun 20

DIVALIKE+J runs very slow compared to other models

Hi -- yes, exactly... Cheers! Nick On Wed, Jun 21, 2023 at 11:33 AM Daniel Eusebio Quintero Vallejo

unread,

DIVALIKE+J runs very slow compared to other models

Hi -- yes, exactly... Cheers! Nick On Wed, Jun 21, 2023 at 11:33 AM Daniel Eusebio Quintero Vallejo

Jun 20

Frank Koehler, … Nick Matzke8

Jun 19

Stochastic mapping (stratified): "Error in condprobs_branch_bot %*% independent_likelihoods_on_root"

On Tue, Jun 20, 2023 at 10:38 AM José Ribeiro <jozeca...@gmail.com> wrote: Ok, NIck. Thank

unread,

Stochastic mapping (stratified): "Error in condprobs_branch_bot %*% independent_likelihoods_on_root"

On Tue, Jun 20, 2023 at 10:38 AM José Ribeiro <jozeca...@gmail.com> wrote: Ok, NIck. Thank

Jun 19

José Ribeiro, Nick Matzke4

Jun 16

plotting issues

Hi -- OK I think I see the issue... On Sat, Jun 17, 2023 at 5:10 AM José Ribeiro <jozecaricardo@

unread,

plotting issues

Hi -- OK I think I see the issue... On Sat, Jun 17, 2023 at 5:10 AM José Ribeiro <jozecaricardo@

Jun 16

Jun 15

plotting issues

Hello everyone, I have got some issues concerning the plot of the tree with ranges after running an

unread,

plotting issues

Hello everyone, I have got some issues concerning the plot of the tree with ranges after running an

Jun 15

Ivan Magalhães, … Nick Matzke9

Jun 6

Stratified analyses resulting in unexpected estimates

Hi -- yes, this was fixed back in 2020, and yes it's on GitHub. Cheers, Nick On Wed, Jun 7, 2023

unread,

Stratified analyses resulting in unexpected estimates

Hi -- yes, this was fixed back in 2020, and yes it's on GitHub. Cheers, Nick On Wed, Jun 7, 2023

Jun 6

Juan Daniel Vásquez-Restrepo2

Mar 15

STOP ERROR in section_the_tree():

Figured out! My code missing the readfiles_BioGeoBEARS_run(BioGeoBEARS_run_object) before

unread,

STOP ERROR in section_the_tree():

Figured out! My code missing the readfiles_BioGeoBEARS_run(BioGeoBEARS_run_object) before

Mar 15

Tobias Van Elst

Feb 8

Comparing different classification schemes in BioGeoBEARS

Hi everyone, I am studying mouse lemur diversification in Madagascar. We use BioGeoBEARS to

unread,

Comparing different classification schemes in BioGeoBEARS

Hi everyone, I am studying mouse lemur diversification in Madagascar. We use BioGeoBEARS to

Feb 8

Feb 1

Hi all, Apologies I missed the questions about "Mnumeric". I have given 2 workshops

unread,

Hi all, Apologies I missed the questions about "Mnumeric". I have given 2 workshops

Feb 1

Alexander Sáchez Rojas

Jan 9

Can I remove states from the pie chart?

Dear Dr Matzke, Thanks for add me. I have been using this code segment to obtain the pie charts of 5

unread,

Can I remove states from the pie chart?

Dear Dr Matzke, Thanks for add me. I have been using this code segment to obtain the pie charts of 5

Jan 9

Alessandro, … davidca...@gmail.com3

11/19/22

Error: object 'tipranges' not found"

For what it's worth, I've encountered the same "tipranges not found" error recently

unread,

Error: object 'tipranges' not found"

For what it's worth, I've encountered the same "tipranges not found" error recently

11/19/22

Tae-Kun Seo, Nick Matzke5

11/2/22

trouble with optimizing with DEC+J model

Hi -- yes, sometimes on rare occasions I've found that GenSA does weird things, but then, I'

unread,

trouble with optimizing with DEC+J model

Hi -- yes, sometimes on rare occasions I've found that GenSA does weird things, but then, I'

11/2/22

Bruna Guarabyra

10/21/22

BioGeoBEARS through RASP

Hey everyone! I'm pretty new to biogeography, especially with the BioGeoBEARS package. I'm

unread,

BioGeoBEARS through RASP

Hey everyone! I'm pretty new to biogeography, especially with the BioGeoBEARS package. I'm

10/21/22

10/20/22

Probabilities of per-area probability table do not sum to one

Dear Dr. Matzke, I hope you are well. I have a question about the output tables of biogeobears

unread,

Probabilities of per-area probability table do not sum to one

Dear Dr. Matzke, I hope you are well. I have a question about the output tables of biogeobears

10/20/22

mpnogu...@gmail.com, Nick Matzke3

9/19/22

Error running models with adjacent areas with disjunct distributions

Hi Nick, thanks for the response! I will send this link to her. Thanks once again for your help!

unread,

Error running models with adjacent areas with disjunct distributions

Hi Nick, thanks for the response! I will send this link to her. Thanks once again for your help!

9/19/22

José Ribeiro, Nick Matzke11

9/16/22

running SSE_simtrait simulation

Once again, thank you so much. Cheers. On Wednesday, September 14, 2022 at 6:54:58 PM UTC-3 nickmat..

unread,

running SSE_simtrait simulation

Once again, thank you so much. Cheers. On Wednesday, September 14, 2022 at 6:54:58 PM UTC-3 nickmat..

9/16/22

Nicolas F. Brignone, Nick Matzke2

9/2/22

BSM - how to change number of iterations

I think you need to change this: maxnum_maps_to_try=100, nummaps_goal=50, maxtries_per_branch=40000 .

unread,

BSM - how to change number of iterations

I think you need to change this: maxnum_maps_to_try=100, nummaps_goal=50, maxtries_per_branch=40000 .

9/2/22

Sébastien Mirolo, … Nick Matzke4

8/16/22

max_range_size Fatal Error

Meant to add as a PS: (PS 10 areas for a 16-tip tree is physically possible on the computer, the

unread,

max_range_size Fatal Error

Meant to add as a PS: (PS 10 areas for a 16-tip tree is physically possible on the computer, the

8/16/22

Justin Bernstein, Julia Dupin2

8/16/22

error: tip range not allowed in states_list

Hi, I've never seen this error, but it could be because you have tips with the same name. Did you

unread,

error: tip range not allowed in states_list

Hi, I've never seen this error, but it could be because you have tips with the same name. Did you

8/16/22

Nicolas F. Brignone, stub...@gmail.com2

5/25/22

how to obtain the PP or each range in the node pies?

I just had to look this up. Code is provided on the wikidot page (which is back up). Provides a table

unread,

how to obtain the PP or each range in the node pies?

I just had to look this up. Code is provided on the wikidot page (which is back up). Provides a table

5/25/22

Search

Clear search

Close search

Google apps

Main menu