Tag Archives: plugins

Saturday: projects, reading, markdown plugins

Greatly enjoyed see­ing this per­spec­tive on power laws Or as Richard McEl­reath put even more con­cisely, Peo­ple get amazed by power laws but never by nor­mal dis­tri­b­u­tions. Seems like some max ent out­comes aston­ish while oth­ers don’t. When so many mech­a­nisms aggre­gate to com­mon den­si­ties, I’d hope we’d stop try­ing to argue that we can …

February 12, 2012 – 1:40 pm | By Carl | Posted in Logistics | Tagged | Comments (0)

Monday

Wrote method2 test func­tions out in knitr/sweave. Sent doc­u­ment to Peter. Move my ropen­sci git ori­gins to the ropen­sci github page. Ropen­sci com­ments on \don­trun: rec­om­mended for any­thing non-trivial, includ­ing web calls. Richer tests should be put into test­that. Reply to Charles Jervis, biol­ogy high school teacher inter­ested in tools to teach math/modeling in ecol­ogy.  Sounds …

December 12, 2011 – 7:00 pm | By Carl | Posted in Logistics | Tagged | Comments (1)

Wednesday: ESA presentation, manuscript/appendix edits

Misc morn­ing Site trou­ble, again.  requested migrat­ing servers.  Done.  hope we’re more sta­ble now. Check­ing in with Peter about migrat­ing site domain.  Sent request to Matt. Look­ing over NERSC PI appli­ca­tion, see first allo­ca­tion instruc­tions.  Emailed Mary Ann w/ ques­tions on forms. SMB 2012 is at NIM­BioS! Nick to join ropen­sci.  Coor­di­nat­ing launch, advis­ers, etc.   Karthik and …

July 27, 2011 – 4:22 pm | By Carl | Posted in Stochastic Population Dynamics | Tagged | Comments (2)

Monday

Power in Phy­lo­ge­nies  Paper (PMC) Work­ing through / incor­po­rated Graham’s edits Added con­fi­dence inter­vals dis­cus­sion tweaks to asso­ci­ated pmc pack­age Explor­ing con­fi­dence inter­vals (and lack thereof) in lit­er­a­ture on com­par­a­tive meth­ods.  Pagel (1999)  includes them, but few other papers do.  He does not include any dis­cus­sion about how these are cal­cu­lated. Seems Sweave makes sense for …

May 30, 2011 – 11:44 pm | By Carl | Posted in Phylogenetics | Tagged | Comments (0)

MathJax the smart way: Child Themes

Adding math­jax by mod­i­fy­ing the header.php file in my word­press theme, as rec­om­mended by Math­Jax web­site, isn’t sta­ble to upgrades of the theme, which sim­ply replace the header.php file with a fresh ver­sion.  The “cor­rect” way to do this is using child themes, which are pretty sim­ple, even though this got me writ­ing my first …

May 16, 2011 – 12:54 pm | By Carl | Posted in Open Notebook Thoughts | Tagged | Comments (1)

Monday: meetings, notebook

Coop & Moore 270: Species Trees Dis­cussing Bucky paper Approach of BEST and *BEAST (last time): Prior prob­a­bil­ity on gene trees P(G|S), given species trees.  Goal: Pos­te­rior of species trees, Uses a Dirch­let process model for clus­ter­ing genes by topolo­gies.  All genes in a clus­ter agree to share a com­mon topol­ogy.  Com­par­isons to BEST and *BEAST …

May 9, 2011 – 11:56 pm | By Carl | Posted in Phylogenetics | Tagged , | Comments (0)

Building a semantic notebook

What would a seman­tic lab note­book look like?  What would be pos­si­ble with such a struc­ture, ide­ally?  What is already pos­si­ble now?  There’s a lot that can be done with an elec­tronic note­book that adds value over a paper note­book: brows­ing by cat­e­gories and tags, embed­ding links, time-stamping entries, search­ing the full text, and hav­ing …

May 8, 2011 – 6:39 pm | By Carl | Posted in Open Notebook Thoughts | Tagged | Comments (1)

Weds: Parrotfish data set analysis

Par­rot­fish Need bet­ter con­ver­gence error han­dling. Need to rem­edy: “Func­tion can­not be eval­u­ated at ini­tial para­me­ters” errors — Occur when attempt­ing very large val­ues of alpha, result­ing in NaN out­put (trou­ble with expo­nen­tials of alpha in cal­cu­la­tions). Changed sum­maries to group by paint­ing, so com­pare mod­els and traits.  Less nat­ural than com­par­ing across paint­ing for …

May 4, 2011 – 11:16 pm | By Carl | Posted in Phylogenetics | Tagged | Comments (0)