Fwd: Geography File Errors - BioGeoBEARS

[Nick Matzke]

Quick answer that worked on this one -- the geography file had extra spaces/tabs at the end of the lines.

Cheers,

Nick

---------- Forwarded message ----------

Date: Sun, Nov 29, 2015 at 1:53 PM
Subject: Re: Geography File Errors - BioGeoBEARS
To: Nick Matzke <mat...@nimbios.org>

Hello Nick,

Thank you so much for your speedy response, the geography file is working now!

Kind regards,

X

On Sun, Nov 29, 2015 at 2:31 AM, Nick Matzke <mat...@nimbios.org> wrote:

Hi! It looks like your geog file has spaces/tabs at the end of many lines (see attaches PNG). If you remove these it should work.

Cheers,

Nick

On Sun, Nov 29, 2015 at 1:20 PM, XXX wrote:

Hello Nick,

I am new to BioGeoBEARS and have been going through the example script provided. Thank you also for providing the public forum, which I have been reading through. I unfortunately, seem to be running into some errors with the geography data. I have tried two different formats to see if I could get it running properly (I have attached both). I have also attached the phylogeny file. For both geography files I receive the following error for tip ranges:

> tipranges = getranges_from_LagrangePHYLIP(lgdata_fn=geogfn)

Read 9 items

Read 132 items

STOP ERROR in read_PHYLIP_data():

The first line of data file 'Crocsgeog1.txt' says that you have 44 tips and 7 characters/columns/areas.

However, 43 rows have the wrong number.

Printing these out:

(I have attached the 43 row error message print out)

Error in read_PHYLIP_data(lgdata_fn) : 

  STOPPING on ERROR in read_PHYLIP_data().

> tipranges

Error: object 'tipranges' not found

I have also been having an issue with core BioGeoBEARS functions and producing the pdf files, (not sure if it is because of the errors in my files or me failing to load required functions). I will review your tips on making sure library(BioGeoBEARS) is loaded in addition to the other packages. Thank you very much for your time and help.

Kind regards,

XXX