syntaxHighligher isn’t working. no idea why, posted to forums.
Still no luck compiling gsl on carver. Can’t install gsl R package or compile wrightscape C code. posted C issue to NERSC, R issue to statscicomp.
Commits to taxize pushed to Scott.
wrightscape
parrotfish example
Convergence test: with simple (common) initial values (alpha=.1, sigma=1), the different methods behave mostly appropriately: outer nested models out-perform inner ones, and likelihoods roughly agree between ouch package methods and wrightscape equivalents:
[gist id=1179079]
values agree with those from the sigma=40 starting condition (biased to explain variation by sigma instead of alpha). Note that with fixed alpha, the sigmas-indep is doing just slightly worse than the sigmas-global model, and the sigmas-indep model with sigma=40 starting condition did substantially worse than this.
So, it looks like good evidence for selection at least (non-zero alpha). Next run should see if there’s any evidence of two different selection strengths.
- Running ou vs 2 alphas on farm, 64 nodes
Some evidence, thought difference in alphas seems very small relative to the resolution:
Running alphas vs sigmas2, an OU model with sigmas indep vs one with indep alphas. Likely not distinquishable: parrotfish2. 64 cores, farm.
Also running the fully general model against the indep sigmas, second-best scoring. May be distinguishable: parrotfish_indep, 128 cores, farm.
Primates example
A much larger tree, routine is much slower. For some reason, MLE on the brownie-style models do the worse. Primates dataset shows release of constraint over OU:
Waiting on primates2.R to compare this to brownie result.
Wrightscape/gsl compile on carver!
Automatic configuration failed, but was able to set libraries manually in Makevars:
PKG_CPPFLAGS=-I/usr/common/usg/gsl/1.13/include -Wall -O3
PKG_LIBS=-L/usr/common/usg/gsl/1.13/lib -lm -lgsl -lgslcblas Then removing all the configure files and loading the intel modules (R wants the intel compilers for carver I guess):
module swap pgi intel
module swap openmpi openmpi-intel
module load gsl
module load R/2.12.1
R CMD INSTALL wrightscapeand we’re live!