Re: error dividing tree with timeperiods

[Nick Matzke]

On Tue, Dec 5, 2017 at 12:56 AM, Gabriel Ferreira <gsferr...@gmail.com> wrote:

Hi Nick,

I am running an analysis with a fossil-only tree, of a Devonian-Silurian clade and when I try to divide up the tree into 5 periods with my timeperiods file BioGeoBEARS returns the following error message:

Error in scan(file = file, what = "", sep = "\n", quiet = TRUE, skip = skip, : 'file' must be a character string or connection

I tried using a timeperiods table with the real ages (i.e., varying from 377.4 to 430.5) and with ages scaled to 0 (i.e., varying from 0.1 - 53.1) but on both cases, I get the same message. I also tried to use only two periods (to avoid potential few taxa problems), but it happens the same

Hi -- this error is about something else, it indicates that some file is not being found.

E.g. you would probably get it if you had:

BioGeoBEARS_run_object$timesfn = timeperiods.txt

...instead of:

BioGeoBEARS_run_object$timesfn = "timeperiods.txt"

...or if the file was misnamed, not in your working directory, etc.

Re: time scaling, BioGeoBEARS (and any other program) will treat the highest tip in the tree as time 0, whatever the absolute time, so yes, you should scale the times accordingly.

Cheers!

Nick

 

Hope you can help me.

Thanks in advance.

Best wishes,

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Gabriel S. Ferreira - PhD Student

Phone: +55-16-3315 4984

PaleoLab, Uni. São Paulo, Ribeirão Preto, Brazil

Eberhard Karls Universität Tübingen/Germany

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'Die Gestalt ist ein bewegliches, ein werdendes, ein vergehendes. Gestaltenlehre ist Verwandlungslehre. Die Lehre der Metamorphose ist der Schlüssel zu allen Zeichen der Natur.'

(Form is a moving, a becoming, a passing thing. The doctrine of forms is the doctrine of transformation. The doctrine of metamorphosis is the key to all signs of nature'

J.W. von Goethe

[Gabriel Ferreira]

Hi Nick,

thank you very much for your answer! It was indeed a wrong path but for the tree file, not the timeperiods.

Cheers,

-----------------------------------------------------------------

Gabriel S. Ferreira - PhD Student

Phone: +55-16-3315 4984

PaleoLab, Uni. São Paulo, Ribeirão Preto, Brazil

Eberhard Karls Universität Tübingen/Germany

-----------------------------------------------------------------

'Die Gestalt ist ein bewegliches, ein werdendes, ein vergehendes. Gestaltenlehre ist Verwandlungslehre. Die Lehre der Metamorphose ist der Schlüssel zu allen Zeichen der Natur.'

(Form is a moving, a becoming, a passing thing. The doctrine of forms is the doctrine of transformation. The doctrine of metamorphosis is the key to all signs of nature'

J.W. von Goethe