example of a makefile that runs an r job and sends an email when done.

makefile

EMAIL=youremail@gmail.com
SERVER=username@yourserver.com
mode=standard # e.g., quick, standard, publication

all:
	make models mode=$(mode)
	make ppc mode=$(mode)
	make standard-figures mode=$(mode)
	make yhat mode=$(mode)

models:
	Rscript -e "library(knitr); analysis_mode = '$(mode)'; knit('reports/bayesian-models.rmd')"
	echo "Models on $(mode) is complete." | mail -s "Models on $(mode) is complete."  $(EMAIL) 

ppc:
	Rscript -e "library(knitr); analysis_mode = '$(mode)'; knit('reports/bayesian-ppc.rmd')"
	echo "ppc on $(mode) is complete." | mail -s "ppc on $(mode) is complete."  $(EMAIL) 

figures:
	Rscript -e "library(knitr); analysis_mode = '$(mode)'; knit('reports/bayesian-figures.rmd')"
	echo "standard-figures on $(mode) is complete." | mail -s "standard-figures on $(mode) is complete."  $(EMAIL) 

yhat:
	Rscript -e "library(knitr); analysis_mode = '$(mode)'; knit('reports/mu_y.rmd')"
	echo "yhat on $(mode) is complete." | mail -s "yhat on $(mode) is complete."  $(EMAIL) 
 
updatelocal:
	rsync -av --update $(SERVER):~/dynamic-pwi-analysis/ .
	
updateserver:
	rsync -av --update . $(SERVER):~/dynamic-pwi-analysis/