Wednesday, March 14, 2012

Re: XKCD 979

Life imitates XKCD.
  1. Get cryptic error from Libre Office
  2. Realize this is one package I never want to understand.  It's an MS Office replacement which faithfully replicates the whole anti-UNIX philosophy of MS Office.  Down to some of the Excel statistics bugs.
  3. Google for "Extension manager: exception in synchronize" 
  4. Find this record of an chat session in German
  5. Find a reference to this bug at 8:25 pm in the chat
  6. ls /usr/lib/libreoffice/share/uno_packages/cache/uno_packages
  7. chmod a+rx /usr/lib/libreoffice/share/uno_packages/cache/uno_packages
  8. It works again!
I'm glad Vassar at least taught me to use primary sources....

Monday, March 12, 2012

Math in biology manuscripts

Steps for co-authors helping out with the math on a manuscript: 
  1. look at equations (and text), dig up references;
  2. figure out the equations are wrong;
  3. try to figure out why they're right;
  4. fail;
  5. start to write email explaining your logic about the (potential) mistake (don't fill in recipient at this stage);
  6. find your mistake;
  7. discard draft email;
  8. repeat 1-6 until step 6 fails;
  9. fill in recipient and send;
  10. rinse and repeat, try not to look like a douche 
Step 10 is the hardest.  I suppose failing at step 2 is eventually the way out.

Tuesday, March 6, 2012

Bane of my existence

 That little "12031" is a life-saver though.

> source('adjustData.R'); source('runModel.R')
Compiling model graph
   Declaring variables
   Resolving undeclared variables
   Allocating nodes
   Graph Size: 1724335

Initializing model
Deleting model

Error in jags.model(file = "unroll-wbATS-DCJS.bugs", data =,  :
  Error in node alive[12031]
Unobserved node inconsistent with unobserved parents at initialization

Bad habits

If you're a biologist and there's crazy weather, your first thought is "I wonder what my study site(s) look(s) like?"... the second is inevitably whether it was sensible to go driving on dirt roads to find out.

Figure 1: No, it was not sensible, but it was beautiful.

Victory! (Domestic)

Sometimes you got to take the small ones.  Especially when the large ones are at the mercy of the JAGS sampler fairy.

Figure 1: victory, small.