tring a merge

Merge branch 'developement' of https://github.com/kkmann/cme into developement

Conflicts:
	R/cme.R
	R/sim.R
	demo/regularization.R
	doc/presentation/bias-concordance.tex
	inst/doc/presentation/bias.pdf
	inst/doc/presentation/bias.tex
	out.txt
merging

Merge branch 'master' of https://github.com/kkmann/cme

Conflicts:
	doc/presentation/bias-concordance.tex
	inst/doc/presentation/bias.pdf
	inst/doc/presentation/bias.tex
merging

Merge branch 'master' of https://github.com/kkmann/cme

Conflicts:
	doc/presentation/bias-concordance.tex
	inst/doc/presentation/bias.pdf
	inst/doc/presentation/bias.tex
Merge branch 'master' of https://github.com/kkmann/cme

Conflicts:
	doc/presentation/bias-concordance.tex
Merge branch 'master' of https://github.com/kkmann/cme

Conflicts:
	doc/presentation/bias-concordance.tex
Merge branch 'master' of https://github.com/kkmann/cme
cleaning up temporary files from knitr
added a monitor() function calling the respective shiny app directly
Create README.md
reorganizing stuff