Comments for Palaeontology 2.0

Comment on MrBayes and Ubuntu by Ross Mounce (@rmounce)

Ross Mounce (@rmounce) — Tue, 20 Dec 2011 14:08:18 +0000

PS I compiled it from source too on my Ubuntu 64-bit machine! Does the software centre install method correctly compile and install the optional BEAGLE libraries? I couldn’t correctly do this bit when I compiled and installed from source so I’m apparently not making full use of all my cores :/

http://code.google.com/p/beagle-lib/

Comment on TNT and Ubuntu by Ross Mounce (@rmounce)

Ross Mounce (@rmounce) — Tue, 20 Dec 2011 14:04:15 +0000

Hi Matthew,

Good to see people posting helpful tutorials on how to use TNT. It’s not the easiest program to get to grips with, in my experience.

However, a small note of correction – your method is not the only one with which you can calculate (Goodman)Bremer support in TNT. On the official TNT wiki manual website, under the “scripts” page there’s a nice little script written by Goloboff that’ll calculate it for you: http://tnt.insectmuseum.org/index.php/Scripts

Note also; scripts to calculate partitioned (Goodman)Bremer support, the Incongruence Length Difference test, and other useful data exploration tools. I’ve written a post of my own, (along with my research poster) on how to do these tests in TNT here: http://sites.google.com/site/rossmounce/palass2011

I hope it might be of some use to someone out there – I certainly think these are useful and interesting methods.

Comment on pdflatex errors and R by andrewgriffin

andrewgriffin — Mon, 26 Sep 2011 17:42:17 +0000

Cheers for the information. I had a similar problem with R on a Fedora 15 distribution and this pointed me in the right direction.

The culprit in this case was the texinfo-tex (4.13a-15.fc15) package.

Comment on MrBayes and multicore processors by mvavrek

mvavrek — Wed, 17 Aug 2011 01:53:05 +0000

I’ll check it out. Another one of those things that I never really thought about though, since palaeo data usually consist of a few hundred values, not hundred thousand.

Comment on MrBayes and multicore processors by Julien

Julien — Wed, 17 Aug 2011 01:49:41 +0000

Thanks for the spp.est package. Very useful. I use it in microbial ecology and I have a suggestion (if its feasible and if it makes sense!). There exist a package called mothur (oriented for microbial ecology) into which there is a rarefaction module. I think its basically the same module as spp.est but with an extra parameter which is the frequency. For instance if you only want to output the data every n species). So Lets say we have a table representing a total of 500,000 species and we want only 10 points on our rarefaction curve we would calculate values every 50,000 values. The resulting rarefaction curve would not be as detailed as if using every value, but would still give a good idea… and be faster.
Cheers!

Comment on pdflatex errors and R by synapseandsyntax

synapseandsyntax — Fri, 12 Aug 2011 20:19:38 +0000

Hi. Thanks for this post– it helped me to discover that I was missing a texlive package when I encountered the same problem. For what it’s worth, it’s probably not necessary to install texlive-full, which is over 1GB. It’s (at least one of) the following packages:

Installed the following packages:
debiandoc-sgml (1.2.15)
libroman-perl (1.23-1)
libsgmls-perl (1.03ii-32)
libsp1c2 (1.3.4-1.2.1-47build3)
libtext-format-perl (0.52-21)
sgmlspl (1.03ii-32)
sp (1.3.4-1.2.1-47build3)
texinfo (4.13a.dfsg.1-6ubuntu3)
texlive-formats-extra (2009-10ubuntu1)
texlive-generic-extra (2009-10ubuntu1)
texlive-lang-other (2009-3)
texlive-plain-extra (2009-10ubuntu1)
texlive-xetex (2009-11)

Cheers.

Comment on Reproducible Results: Not Likely by hawright

hawright — Mon, 01 Aug 2011 11:24:44 +0000

Unfortunately, I agree with this post. In general, it seems that certain fields in science are using open access and others could take a lesson. Also missing from this is the discrepancy between the computer science field and ecoinformatics or bioinformatics in general…where is the source code used for analysis that others can apply to their own data sets? I hope to incorporate my code and unique scripts for analysis into my project.

Comment on MrBayes and multicore processors by mvavrek

mvavrek — Fri, 15 Jul 2011 17:57:17 +0000

I’m using 10.10, because I didn’t find 11.04 to be stable enough for my purposes yet. What error messages?

Comment on MrBayes and multicore processors by Martina

Martina — Fri, 15 Jul 2011 10:41:35 +0000

What version of Ubuntu do you use? I just get error messages while ‘make’ is running on Ubuntu 11.04.

Comment on MrBayes and multicore processors by James

James — Thu, 19 May 2011 15:56:00 +0000

Thank you for this post and sharing your experience. It certainly made things easy for me. I can now make decent runs on my laptop. The one thing I notice a loss of, is the tab complete with file names and interrupting a run with Ctrl+C causes the program to exit. Nothing major and certainly an acceptable sacrifice for the increase in speeeeeeeeeeeeeeeeeeeeeeeeeed.