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Makefile
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RM = rm -f
all: sweave stangle makeRfiles pdf
sweave:
"$(R_HOME)/bin/R" CMD Sweave EMDerivation.Rnw
"$(R_HOME)/bin/R" CMD Sweave Quick_Start.Rnw
"$(R_HOME)/bin/R" CMD Sweave UserGuide.Rnw
"$(R_HOME)/bin/R" CMD Sweave Residuals.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/Quick_Examples.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/Case_Study_1.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/Case_Study_2.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/Case_Study_3.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/Case_Study_4.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/Case_Study_5.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/Case_Study_6.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/Case_Study_7.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/Case_Study_8.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/Case_Study_dlm1.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/Case_Study_mlr.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/Setting_Inits.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/MARp.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/Covariates.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/Structural_TS.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/KFAS.Rnw
"$(R_HOME)/bin/R" CMD Sweave ./manual_files/Manual.Rnw
stangle:
Rscript -e "Stangle('./manual_files/Quick_Examples.Rnw')"
Rscript -e "Stangle('./manual_files/Case_Study_1.Rnw')"
Rscript -e "Stangle('./manual_files/Case_Study_2.Rnw')"
Rscript -e "Stangle('./manual_files/Case_Study_3.Rnw')"
Rscript -e "Stangle('./manual_files/Case_Study_4.Rnw')"
Rscript -e "Stangle('./manual_files/Case_Study_5.Rnw')"
Rscript -e "Stangle('./manual_files/Case_Study_6.Rnw')"
Rscript -e "Stangle('./manual_files/Case_Study_7.Rnw')"
Rscript -e "Stangle('./manual_files/Case_Study_8.Rnw')"
Rscript -e "Stangle('./manual_files/Case_Study_dlm1.Rnw')"
Rscript -e "Stangle('./manual_files/Case_Study_mlr.Rnw')"
Rscript -e "Stangle('./manual_files/Setting_Inits.Rnw')"
Rscript -e "Stangle('./manual_files/Covariates.Rnw')"
Rscript -e "Stangle('./manual_files/MARp.Rnw')"
Rscript -e "Stangle('./manual_files/Structural_TS.Rnw')"
Rscript -e "Stangle('./manual_files/KFAS.Rnw')"
makeRfiles:
cat ./figures/QE--Cs*.R > ../inst/doc/Quick_Examples.R
cat ./figures/CS1--Cs1_*.R > ../inst/doc/Chapter_PVA.R
cat ./figures/CS2--Cs2_*.R > ../inst/doc/Chapter_SealTrend.R
cat ./figures/CS3--Cs*_*.R > ../inst/doc/Chapter_SealPopStructure.R
cat ./figures/CS4--Cs*.R > ../inst/doc/Chapter_DFA.R
cat ./figures/CS5--Cs*.R > ../inst/doc/Chapter_AnimalTracking.R
cat ./figures/CS6--Cs*.R > ../inst/doc/Chapter_StructuralBreaks.R
cat ./figures/CS7--Cs*.R > ../inst/doc/Chapter_SpeciesInteractions.R
cat ./figures/CS8--Cs*.R > ../inst/doc/Chapter_CombiningTrendData.R
cat ./figures/CSDLM--Cs_*.R > ../inst/doc/Chapter_UnivariateDLM.R
cat ./figures/Covar--Covar_*.R > ../inst/doc/Chapter_Covariates.R
cat ./figures/MLR--Cs_*.R > ../inst/doc/Chapter_MLR.R
cat ./figures/MCI--Cs_mci_*.R > ../inst/doc/Chapter_inits.R
cat ./figures/ARMAp--Cs_*.R > ../inst/doc/Chapter_MARp.R
cat ./figures/STS--Cs*.R > ../inst/doc/Chapter_Structural_TS.R
cat ./figures/KFAS--Cs*.R > ../inst/doc/Chapter_KFAS.R
pdf:
pdflatex EMDerivation.tex
pdflatex Quick_Start.tex
pdflatex Manual.tex
pdflatex Residuals.tex
bibtex EMDerivation
bibtex Manual
bibtex Residuals
pdflatex EMDerivation.tex
pdflatex Quick_Start.tex
pdflatex Residuals.tex
pdflatex Manual.tex
pdflatex EMDerivation.tex
pdflatex Quick_Start.tex
pdflatex Residuals.tex
pdflatex Manual.tex
makeindex Manual
pdflatex Manual.tex
cat Manual.pdf > UserGuide.pdf
clean:
$(RM) *.log *.aux *.ilg *.ind *.idx *.blg *.bbl *.out *.Rout *.toc *.lof *.lot Rplots.ps Rplots.pdf
$(RM) *.sty *.bst *.cls
$(RM) *.tex
$(RM) *.R
$(RM) ../README.md ../_config.yml ../favicon.ico ../logo.jpg ../logot.png ../License.md ../hexlogo.png ../mars.png
$(RM) ../_layouts/*.*
$(RM) Manual.pdf
$(RM) ./tables/*.*
$(RM) ./tex/*.*
$(RM) ./figures/*.*
$(RM) ./manual_files/*.*
$(RM) debug_manual.R debugger_template.Rnw
cat ./index.html > ../inst/doc/index.html
$(RM) ./index.html
rm -rf ./manual_files
rm -rf ./tex
rm -rf ./figures
rm -rf ./tables
rm -rf ../_layouts
$(RM) ../inst/WORDLIST
$(RM) ../man/MARSS_out.Rd