Patch.dwt analysis

- Does a shift in the balance between productivity and decomposition translate into a difference in total Patch Dry Weight?
	- Maybe, but the trend is not statistically significant.

Signed-off-by: Jonathan A. Whiteley <jonathan.whiteley@mail.mcgill.ca>
Specified Decomposition units as a rate: % mass loss / year

Signed-off-by: Jonathan A. Whiteley <jonathan.whiteley@mail.mcgill.ca>
Added a little data exploration to H2O analysis

Turned out not to be very useful, because I was hoping to compare H2O to temperature, and then realized I really don't have that kind of Temperature data.
*shrug*

Signed-off-by: Jonathan A. Whiteley <jonathan.whiteley@mail.mcgill.ca>
Moss_biomass analysis of dead tissue; Net Production update.

Signed-off-by: Jonathan A. Whiteley <jonathan.whiteley@mail.mcgill.ca>
Fixed miscalculation of patch area (re-run CH1)

Yeah, I'm an idiot. I had been calculating patch area using the diameter, not the radius (*face slap*).
The calculation has been fixed in `SECC.functions.R`, and everywhere else I could find it.
Just to be safe, I blocked out many of the definitions of these constants, to allow the values in `SECC.functions.R` to be used instead.
I re-ran analyses for Chapter 1 just to be sure: no major changes or errors.
Thankfully, it appears that this value was never really used until now (in CH3).


Signed-off-by: Jonathan A. Whiteley <jonathan.whiteley@mail.mcgill.ca>
Re-ran CH2 (Fauna) analyses to check for effect of patch area calculation

Any differences appear to be due to permutations.

Signed-off-by: Jonathan A. Whiteley <jonathan.whiteley@mail.mcgill.ca>
Re-ran CH3 (Productivity - Decomposition) with new patch area calculations

Wow, those values are much more similar to the literature.  *sigh* :)


Signed-off-by: Jonathan A. Whiteley <jonathan.whiteley@mail.mcgill.ca>
Reviewed Moss-growth analyses for more robust results

+ generally getting re-acquainted in preparation for writing results.
+ adjusted diagnostic plots in nested lm script to check for heterogeneity
+ added xtable() output of model anova table
+ added Tukey HSD output of differences between treatment levels.

Productivity analysis across years ("split-plot in time"):
+ tried accounting for heterogeneity between years
+ backward model-selection to confirm approximate p-values from F-tests of main model terms
+ Tukey's HSD for differences between levels of Chamber:Position:Year is working again!



Signed-off-by: Jonathan A. Whiteley <jonathan.whiteley@mail.mcgill.ca>
Check for Block effects in Productivity model

They are statistically significant, although barely.
They may be marginal.
The point is that I don't care about variation across Blocks, that's expected.
I'm more worried about possible interaction, which appears significant, but not serious in terms of magnitude (the basic pattern is the same, it's just weaker in some blocks).
Check effect of "Time" (replicates) on Moss Growth

There is a significant interaction term between 'Time' and the usual Chamber x Frag,
But this is only significant in the second interval (grow12),
and seems to have more to do with smaller differences in t3 patches,
but with the same overall trend.
I'm hand-waving this "effect" away as spurious, given that there really shouldn't *be* an effect of replicate ID in this situation.


Signed-off-by: Jonathan A. Whiteley <jonathan.whiteley@mail.mcgill.ca>
Some Model selection to verify Net Production (PD.bal) model

Accounting for heterogeneity across Frag treatments makes for a *slightly*
better fit (according to AIC< but not BIC), and renders Frag treatments NS.
(residuals look just as normal).
BUT, this throws errors with the `effects` package, and makes plotting pretty much impossible.
I'm calling the Frag effect (and interaction terms) NS, and using the regular model for plotting.

Signed-off-by: Jonathan A. Whiteley <jonathan.whiteley@mail.mcgill.ca>
Include Tukey tests for treatment means vs. 0 (in nested lm script): re-ran moss growth analyses.

Signed-off-by: Jonathan A. Whiteley <jonathan.whiteley@mail.mcgill.ca>