more sub-model comparisons
wrightscape sub-models:
a1 independent alphas, global theta, sigmas
bm “brownie” (alpha = 0, indep sigmas)
a2 independent alpha, theta, global sigma
s1 indep sigma, global alpha, theta
s2 indep sigma, theta, global alpha
Basic Nelder Mead
![](https://farm8.staticflickr.com/7142/6402641965_cf632aa2cf_o.png)
Simulated annealing
associated parameter estimates
![](https://farm8.staticflickr.com/7015/6403260959_04a0f06d73_o.png)
This approach is really not finding a very robust solution.
![](https://farm7.staticflickr.com/6119/6402646435_b77d7d2548_o.png)
Plotting with stats_summary()
Using stats_summary instead of melt and cast computations and line and ribbon geometries for adding statistical layers to plots. For instance, from plots.R in SDP code:
ggplot(data = subset(dat, variable == "unharvested"),
aes(time, value, group = L1)) + geom_line(alpha=.2) +
# shows the mean +/i mult * sd , requires Hmisc
stat_summary(fun.data = mean_sdl, geom="smooth", mapping=aes(group = 1), mult=1)
Note that this needs thee aesthetic mapping (group=1) to know what to do. I’m not clear exactly why.
Note also that “mult” is an additional option, and is passed to the function, mean_sdl, specifying the multiplier in front of the standard deviation.
The documentation of possible function definitions in stat_summary aren’t entirely clear. This can take fun.y to apply the function across y values, for instance, to calculate just the mean:
ggplot(data = subset(dat, variable == "unharvested"),
aes(time, value, group = L1)) + geom_line(alpha=.2) +
stat_summary(fun.y = mean, geom="line", mapping=aes(group = 1))
Note that we’ve also changed the geometry to line, since we’re not returning ymin/ymax information.
We could add separate functions for the lower and upper bounds, fun.ymin and fun.ymax instead. Again we’d need a geometry that knew what to do with these – for instance, “smooth” or “errorbar”.
There’s quite a collection of convenient functions whose wrappers are provided through the package Hmisc, such as the mean_sdl choice shown here, which are illustrated well in the stat_summary examples.
Wordpress memory management
tcp-memory-usage plugin
Increased available memory in wp-config.php (instructions).
Wow, my saga continues for RStudio server running on Debian Lenny…