BioGeoBEARS Output

[Carissa Lim]

Hi there,

I've just got a question regarding the output in BioGeoBEARS - is there any way I can format it so that the states don't overlap and obscure each other? I know this is probably a result of my phylogeny, but any help would be greatly appreciated!

I've attached my output as above.

Thank you so much!

Carissa.

[Chris Buddenhagen]

I have found that you can edit the pdf in illustrator or inkscape and move the components of the graphic around.....

On a side note:

Although your phylogeny has time units it does not look like a typical chronogram (unless those are fossils?) A chronogram normally has all the tips lined up at time zero.  That would probably help spread out some of the nodes.

Chris Buddenhagen
cbudde...@gmail.com

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[Nick Matzke]

On Fri, Mar 11, 2016 at 8:06 AM, Chris Buddenhagen <cbudde...@gmail.com> wrote:

I have found that you can edit the pdf in illustrator or inkscape and move the components of the graphic around.....

On a side note:

Although your phylogeny has time units it does not look like a typical chronogram (unless those are fossils?) A chronogram normally has all the tips lined up at time zero.  That would probably help spread out some of the nodes.

Chris Buddenhagen
cbudde...@gmail.com

Yeah, good points.  Other tips:

1. You can increase the size of the PDF, look at the pdf() command in the script, and edit the height/width.  Set runslow=FALSE so you don't re-run the whole ML analysis, just re-do the PDF plots

2. The various "cex" (character expansion) options in the BioGeoBEARS plot function let you grow/shrink the various items.

3. you can also change xlims and ylims (see a recent post in this group).

Regarding the issue of Did You Really Mean To Use That Tree, see:

http://phylo.wikidot.com/biogeobears-mistakes-to-avoid#use_dated_phylogenies

Cheers!

Nick

 

On Thu, Mar 10, 2016 at 2:51 PM, Carissa Lim <caris...@gmail.com> wrote:

Hi there,

I've just got a question regarding the output in BioGeoBEARS - is there any way I can format it so that the states don't overlap and obscure each other? I know this is probably a result of my phylogeny, but any help would be greatly appreciated!

I've attached my output as above.

Thank you so much!

Carissa.

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