Fwd: biogeobears: time stratified analysis

[Nick Matzke]

I have fixed this bug in the screen output for reporting changing numbers of states in different time bins.

Cheers!

Nick

---------- Forwarded message ----------
From: Nick Matzke <mat...@nimbios.org>
Date: Mon, May 23, 2016 at 11:23 AM
Subject: Re: biogeobears: time stratified analysis
To: XXX

Hi -- I think it's working fine, I probably just have the message mis-reading the stratum ages by one slot, I'll see if I can fix that, but you should be good to go.

Cheers!

Nick

On Mon, May 23, 2016 at 5:35 AM, XXX wrote:

Dear Nick,

I'm using your great program BioGeoBEARS and have a question about stratified analyses. In my analysis I have defined 9 regions whereof one didn't appear before 140 mya (the whole tree is dated to 350 mya). This means that I have two strata: 0-140 mya and 140-400 mya.

This is what is output in the terminal:

===================================================================
1- top: 0, bot: 140, rel_bot: 140

2- top: 140, bot: 400, rel_bot: 260
Read 11 items
Read 576 items
Read 11 items
Read 576 items

bears_optim_run() note: overall states_list has 256 states/ranges. In stratum #1 (140-400 mya), states_list_for_this_stratum has 256 states/ranges, due to areas_allowed and/or areas_adjacency matrices. See BioGeoBEARS_run_object$lists_of_states_lists_0based.
bears_optim_run() note: overall states_list has 256 states/ranges. In stratum #2 (400-Inf mya), states_list_for_this_stratum has 163 states/ranges, due to areas_allowed and/or areas_adjacency matrices. See BioGeoBEARS_run_object$lists_of_states_lists_0based.

===================================================================

I think "1- top: ... etc. " looks good, but I wonder why it outputs "In stratum #1 (140-400 mya)" ..."In stratum #2 (400-Inf mya)" further down, because that doesn't sound right?


And a second, connected question:
In my stratified analysis I have a timeperiod-file and an areas-allowed-file. I haven't included a manual_dispersal_multipliers-file. In my analysis I have put the relative
probability of dispersal between each region to 1 all over (i.e. the default settings) for both time strata, and then I figured it would be enough just to include an areas-allowed-file for the stratified analysis. I compared my case to the one in this example (https://groups.google.com/forum/#!topic/biogeobears/XXaJqmI232o).
Have I set up my analysis correctly (at least it runs ...)?

Thanks a lot for your help!

XXX