PROJECTNAME = nmix
#BD = BUGS
#RD = R
AD = ADMB
WD = WRITEUP
LCMD = pdflatex
ROPTS = --vanilla
RCMD = $(REXE) $(ROPTS) CMD
RSCRIPT = Rscript $(ROPTS)


runR = R CMD BATCH --vanilla 

.PHONY = all clean admb bugs r

all: admb
#all: bugs r admb

## clean ALL to get rid of fit.RData?
clean: 
	cd $(AD); rm -f $(PROJECTNAME)_$(AD)_run.Rout *~ *.plt .RData .Rhistory  nmix.dat  nmix.pin  nmix.std nmix nmix.par
#	cd $(RD); rm -f $(PROJECTNAME)_$(RD)_run.Rout *~ .RData .Rhistory
#	cd $(BD); rm -f $(PROJECTNAME)_$(BD)_run.Rout *~ .RData .Rhistory
#	cd $(WD); rm -f $(PROJECTNAME).tex $(PROJECTNAME).log $(PROJECTNAME).bbl \
# $(PROJECTNAME).aux $(PROJECTNAME).blg $(PROJECTNAME).out $(PROJECTNAME)-*.eps $(PROJECTNAME)-*.pdf Rplots.pdf

admb: $(AD)/fit.RData

$(AD)/fit.RData: $(AD)/$(PROJECTNAME)_$(AD)_run.R
	cd $(AD); $(runR) $(PROJECTNAME)_$(AD)_run.R

#bugs: $(BD)/fit.RData

#$(BD)/fit.RData: $(BD)/$(PROJECTNAME)_$(BD)_run.R
#	cd $(BD); $(runR) $(PROJECTNAME)_$(BD)_run.R

#r: $(RD)/fit.RData

#$(RD)/fit.RData: $(RD)/$(PROJECTNAME)_$(RD)_run.R
#	cd $(RD); $(runR) $(PROJECTNAME)_$(RD)_run.R

##$(RD)/fit.RData: $(RD)/fit_fits.RData
##	cd $(RD); $(runR) $(PROJECTNAME)_$(RD)_sum.R

##writeup: $(WD)/$(PROJECTNAME).pdf
##
##$(WD)/$(PROJECTNAME).pdf: $(WD)/$(PROJECTNAME).tex
##	cd $(WD); $(LCMD) $(PROJECTNAME).tex
##
#$(WD)/$(PROJECTNAME).tex: $(WD)/$(PROJECTNAME).Rnw
##	cd $(WD); R CMD Sweave $(PROJECTNAME).Rnw

## failed attempt at using odfWeave for weave -> odt -> doc conversion
## $(WD)/$(PROJECTNAME).odt: $(WD)/$(PROJECTNAME)_in.odt
##	cd $(WD); $(RSCRIPT) -e "library(odfWeave); odfWeave(\"$*_in.odt\",\"$*.odt\");"
##  http://sourceforge.net/projects/ooconvert/>
##
## $(WD)/$(PROJECTNAME).doc: $(WD)/$(PROJECTNAME).odt
##	cd $(WD); ooconvert $(PROJECTNAME).odt $(PROJECTNAME).doc