Make 5aaf344472 changes without html tags

-5aaf344472 introduced html tags, which makes the raw file unusable
-Raw code copied from http://jonlefcheck.net/2013/03/13/r2-for-linear-mixed-effects-models/ (visited on 01/22/14)
Test for any object inheriting from [g]lmerMod

- This allows testing on objects generated by lmerTest, blme, etc
Prepend namespaces to avoid name clashes

- Functions like VarCorr are declared in multiple packages including nlme, lme4, ordinal, etc.
- Prepending the namespace will ensure the appropriate function for each class is called
Split into a generic + methods, and an internal calculation function

- `.rsquared.glmm` does all the r-squared calculations based on variances
- `r.squared.*` methods extract variances to pass to the calculation function
- This allows to reuse more code, separate calculations from class specific commands,
  and make it easier to add implementations for new models.
- Current methods are implemented for `lm`, `merMod`, and `lme` objects
- The `rsquared.glmm` function is only a wrapper for the generic `r.squared` which works on lists
- Also fixes jslefche/rsquared.glmer#2
- Did some style mods including changing `=` for `<-` and adding spaces after commas
Move examples to README

- The readme also contains some information about the code
- Verified examples and added new example for blme
- Fixed the documentation for r.squared.lm
Document the varCorr parameter in .rsquared.glmm

- Also, calculate VarCorr in merMod only for lmerMod objects
  (glmerMod objects don't use this for the r-squared calculations)
- Fix some small issues of style
- Minor change in examples to display output of lme.models
Add probit and sqrt link functions for binomial and poisson, update examples

- Change of link requires a change in the distribution specific variance,
  the values are taken from Nakagawa and Schielzeth (2013).
- Updated the .rsquared.glmm signature to require link specification
- .rsquared.glmm now checks for unknown families or links.
- Updated the README to show examples of binomial+probit and poisson+sqrt links.
Project files
Merge branch 'before_casallas'