Tag Archives: fishbase

rfishbase Tutorial — updated & extended

Updated rfish­base pack­age. Include query­ing for a list of sci­en­tific names and the addi­tion of more quan­ti­ta­tive traits, though the selec­tion is still some­what lim­ited. Demo includes how to grab some data to match a phy­lo­ge­netic tree, and some reg­u­lar expres­sion (grep) searches for feed­ing behav­ior. Source code Win­dows binary also available.

October 12, 2011 – 11:59 am | By Carl | Posted in Computation | Tagged | Comments (0)

rfishbase demo: Are there more Goby or Labrid species on reefs?

I have updated the pack­age to 0.0–3 alpha, hav­ing all the tar­get func­tion­al­ity now.  Improved error han­dling, down­load­ing of data, pro­cess­ing.  Get the source or win­dows binary here. I now down­load the full data­base and cache it locally for faster query­ing. Just about any kind of manip­u­la­tion is then pos­si­ble and fast. For instance, here’s a …

September 2, 2011 – 12:59 pm | By Carl | Posted in Phylogenetics | Tagged | Comments (1)

rfishbase and some taxonomy in R with taxize

rfish­base Went through demo of rfish­base with Tomomi.  Improved error han­dling, added a few data types and a few use cases. I always for­get that I have to drop nulls by index­ing, not my return val­ues of sap­ply. Very annoyed with fish­base id num­bers (being dis­con­tin­u­ous list­ings and unable to query xml by any­thing more intel­li­gent). …

August 26, 2011 – 11:16 pm | By Carl | Posted in Computation, Phylogenetics | Tagged | Comments (0)

FishBASE from R: some XML parsing

cross-posted from Wain­wright Lab blog, archiv­ing in the note­book here. This early tuto­r­ial includes some back­ground on XML pars­ing from R using XPath. See the later rfish­base tuto­r­ial for more func­tion­al­ity. In lab known for its qual­ity data col­lec­tion, high-speed video style, writ­ing the weekly blog post can be a bit of a chal­lenge for …

August 26, 2011 – 10:51 am | By Carl | Posted in Computation | Tagged | Comments (0)

Tuesday: rfishbase, Rmpi, manuscripts, …

rfish­base In answer to Tomomi’s ques­tion from last week, have basic func­tion­al­ity as an R pack­age on github, rfish­base. Learned some slightly richer XML pars­ing in the process. XML Notes Had to iden­tify blocks by a child node that spec­i­fies the iden­tity, and then find the sib­ling node that con­tains the con­tent I needed. Goes …

August 23, 2011 – 3:10 pm | By Carl | Posted in Computation, Phylogenetics | Tagged | Comments (0)

Thursday: reviewing edits, fishbase, computers.

Gra­ham & Peter meet­ing Going over review and fig­ur­ing out how to address issues.  Plan: Will write our line-by-line responses under the reviewer com­ments in the Google Doc.  Peter and I will imple­ment remain­ing changes on the .tex file, then we’ll com­pose the reply let­ter from the notes under the com­ments and include the latex-diff. …

August 18, 2011 – 3:03 pm | By Carl | Posted in Phylogenetics | Tagged | Comments (3)