Carl Boettiger

In the spirit of repro­ducible research and the Sci­ence Code Man­i­festo (http://dx.doi.org/10.1038/467753a), all codes I write are open source and per­ma­nently archived on Github. Sev­eral of these projects have become sup­ported R soft­ware pack­ages on CRAN. You will find ref­er­ences to many of these projects in the pages of my Lab Note­book.

Excel­lent data for eco­log­i­cal research is read­ily avail­able through pub­lic data­bases, which are rapidly grow­ing thanks to recent require­ments by pro­fes­sional jour­nals and the NSF. To facil­i­tate the use of this data, I’ve cre­ated sev­eral R pack­ages that allow the user to directly access and manip­u­late, and link up data from such repos­i­to­ries from within R. To fur­ther this, I’ve recently helped launch a project called rOpen­Sci.

Plat­forms

Ubuntu Linux is my oper­at­ing sys­tem of choice. The Linux ker­nel runs most of the devices I use: phone, kin­dle, lap­top, 16 core devel­op­ment server, web­server, 500 core uni­ver­sity clus­ter, and 10,000 core super­com­puter.

Lan­guages

R, C, OpenMP, C++, XML, LaTeX, SWeave, bash, octave/matlab

Some python, html, php.

Devel­op­ment Practices

I was for­tu­nate to be exposed to some good devel­op­ment prac­tices through inter­ac­tions with folks at the National Labs and a course by Dun­can Tem­ple Lang (R Core Team), and the Soft­ware Car­pen­try courses, includ­ing ver­sion man­age­ment, lit­er­ate pro­gram­ming, effec­tive visu­al­iza­tion, par­al­lel pro­cess­ing, and style con­ven­tions. For R users I highly rec­om­mend Hadley Wickam’s dev­tools for pack­age devel­op­ment and doc­u­men­ta­tion, and ggplot2, which pro­vides a graph­i­cal gram­mar cap­tur­ing ideas of Tufte & Wilkinson.

Active Projects

• pdg_control

  Pretty Darn Good Con­trol: appli­ca­tions in opti­mal con­trol

• lab­note­book

  Source code for my Jekyll-based web­site.

• ear­ly­warn­ing

  Meth­ods for detect­ing early warn­ing sig­nals of crit­i­cal tran­si­tions

• knitc­i­ta­tions

  Gen­er­ate cita­tions for knitr mark­down and html files

• sand­box

  Sand­box for explor­ing var­i­ous things

• warn­ingsig­nals

• pop­u­la­tion­dy­nam­ics

  Tools to sim­u­late var­i­ous pop­u­la­tion dynam­ics mod­els in ecol­ogy

• cboettig.github.com

  A mir­ror of my Jekyll site (post-build, see jekyll-source for orig­i­nal source)

• wrightscape

  Infer adap­tive land­scapes from phy­lo­ge­netic trees

• socialR

  func­tions for mak­ing R inter­act with social media

• cboettig.ruhoh.com

  Exper­i­men­tal Ruhoh web­site

• pmc

  Phy­lo­ge­netic Monte Carlo: a method for esti­mat­ing power and uncer­tainty in Phy­lo­ge­netic Com­par­a­tive Meth­ods (now on CRAN)

• geiger

  My development/experimental fork of the geiger pack­age

• fluc­tu­a­tion­Do­mains

  Code for “Fluc­tu­a­tion Domains in Adap­tive Evo­lu­tion”, pub­lished in TPB

• rfish­base

  an R inter­face to the fishbase.org data­base (now on CRAN)

• mcm­c­Tools

  tools for Markov Chain Monte Carlo in R

• tree­BASE

  An R inter­face to the tree­BASE API (now on CRAN)

• structured-populations

  Sto­chas­tic Pop­u­la­tion Dynam­ics in Ecol­ogy with Age and Stage Struc­ture

• com­mu­ni­ty­Phylo

• adg

  algo­rithms dis­cus­sion group code

• Comparative-Phylogenetics

  Research and Meth­ods Devel­op­ment in Com­par­a­tive Phy­lo­ge­net­ics

• Adap­tive­Dy­nam­ics

  Indi­vid­ual based sim­u­la­tions of adap­tive dynam­ics

(this list is gen­er­ated auto­mat­i­cally from Github)

Bib­li­og­ra­phy