Whitebark 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). Ehren Moler recently completed an MS project to to ascertain the effect of native endophytic (within-leaf) fungal community structure, and community assembly on C. ribicola infection.
Figs (left). Whitebark pine study sites in the mountains of South-Central Oregon. (L to R) Parent trees representing a specific type of genetic vulnerability to blister rust infection, view of Crater Lake from Watchman's Peak along the caldera rim
(photos: E. Moler, 2013).
Fig (right). The figure shows Certhomas Tan and Connor Newman at the top Bonneville Peak near Pocatello, ID, collecting limber pine (P. flexilis) needles. P. flexilis is a close relative of P. albicaulis (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). Roy Hill recently completed an MS project 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-devel
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.
MAC OS X users please use the newest R, and download the most recent version of XQuartz to allow implementation of tcltk GUIs.
Releases
Zipped or tarballed folders can be unzipped directly into an R "library" folder, or a personal user R-library folder. Note that asbio >= 0.3-43 requires R >= 2.15.1. Note also that asbio requires tcltk, and imports functions from a number of packages (see the CRAN asbio html) These packages and functions will be downloaded with a download of asbio from CRAN.
plant.ecol-devel
This is a stripped down package containing functions for plant community ecology. It is only available at this website. It requires plotrix, mvtnorm, and vegan.
Releases
Biostatistical consulting
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
