Office: LS 419, Phone: (208)-282-3391, email: firstname.lastname@example.org
Figs. Alpine study sites in the Absaroka-Beartooth mountains. (L to R) E. face of Cutoff Pk., looking NW from the summit of the Thunderer, looking NW from the summit of Mineral Pk., and looking S from the summit plateau of Amphitheatre Pk (photos: S. Contor, 2008-2009).
White bark pine endophytic ecology
Whitebark pine (Pinus albicaulis), a species of treeline environments in the Western US, is in rapid decline due in part to the exotic fungal pathogen whitebark pine blister rust (Cronartium ribicola). We are conducting research to ascertain the effect of native endophytic (within-leaf) fungal community structure, and community assembly on C. ribicola infection.
Fig (right). A number of undergraduate researchers (Connor Newman, Certhomas Tan, Jillian Buttici, Aaron Harnsberger, Courtney Dial) are currently helping Dr. Scot Kelchner and I in establishing procedures to extract fungal DNA from the interior of five needle pines. The group members has been given the name PEEPs --for Pine Endophyte Education Project(s). The figure shows Certhomas Tan and Connor Newman at the top Bonneville Peak near Pocatello, ID, collecting limber pine (P. flexilis) needles (photo: K. Aho).
Dwarf mistletoe population ecology
Lodgepole pine dwarf mistletoe (Arceuthobium americanum), is an obligate parasite of lodgepole pine (Pinus contorta). The patterns of genetic variation within A. americanum populations are largely unexplored, and of interest because of the poor gene flow characteristics of the species, due to limited dispersal abilities, and specificity to P. contorta (which itself is limited to montane islands). We are exploring the genetic diversity and phylogeny A. americanum populations using microsatellite markers developed specifically for this species.
The R computational environment
R is a computer language and an open source environment for statistics, data management, computation and graphics. Documentation and software can be downloaded for free here.
Asbio (applied statistics for
biologists) is an R package that contains functions for statistical
pedagogy and biological research. Of particular interest are hundreds of graphical functions for depicting statistical concepts, many with interactive GUIs. Asbio also serves as a software companion
to a biostatistical textbook I am completing: "Foundational and Applied Statistics for Biologists Using R". Developmental versions of the software for Windows and Unix/Linux can be found in the table below. Bolded versions are available at the Comprehensive R Archive Network (CRAN). I generally clean out versions older than the newest CRAN release since CRAN archives these.
Zipped or tarballed folders can be unzipped directly into an R "library" folder (in my computer this is currently located in C:/Program Files/R/R-2.15.2/library), or a personal user R-library folder (i.e., C:/Program Files(x86)/R/R-2.15.2/library). Note that asbio >= 0.3-43 requires R >= 2.15.1. Note also that asbio requires tcltk, and imports functions from the packages plotrix, mvtnorm, deSolve, scatterplot3d, pixmap, tkrplot, plotrix, multcompView and lattice. These packages can be found at CRAN, and all come with a download of asbio from CRAN. Packages can also be installed during an R-session using pulldown menus (non-Linux only) or with install.packages().
Some of my recent biostatistical consulting work can be found below.
ASD associated protein-protein network analysis
In vivo intestinal and placental transfer of carbamazepine at typical environmental concentrations from drinking water to the developing fetus brain