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Makefile
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R_OPTS=--vanilla --no-save
pdf_with_diff: paper/latex/revision.tex
cd paper/latex/;\
pdflatex revision.tex;\
bibtex revision;\
pdflatex revision.tex;\
pdflatex revision.tex;\
latexdiff submitted.tex revision.tex > diff.tex;\
pdflatex diff.tex;\
bibtex diff;\
pdflatex diff.tex;\
pdflatex diff.tex
pdf: paper/latex/ref.bib paper/latex/revision.tex
cd paper/latex/;\
pdflatex revision.tex;\
bibtex revision;\
pdflatex revision.tex;\
pdflatex revision.tex
sim_normal: sim/normal/nbiom10/simulate.R
cd sim/normal/nbiom10/; nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom20/; nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom50/; nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom100/; nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom1000/; nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ../..; cd normal_block/nbiom10/; nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ../..; cd normal_corr/nbiom10/; nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom20/; nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom50/; nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom100/; nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ../..; cd normal_tol.beta0/nbiom10/; nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom20/; nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom50/; nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom100/; nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom1000/; nohup R CMD BATCH $(R_OPTS) simulate.R;\
sim_survival:
cd sim/survival/0predictive/;\
nohup R CMD BATCH $(R_OPTS) "--args 100" simulate.R simulate100.Rout;\
nohup R CMD BATCH $(R_OPTS) "--args 400" simulate.R simulate400.Rout;\
nohup R CMD BATCH $(R_OPTS) "--args 700" simulate.R simulate700.Rout;\
nohup R CMD BATCH $(R_OPTS) "--args 1000" simulate.R simulate1000.Rout;\
nohup R CMD BATCH $(R_OPTS) summary.R;\
cd ..; cd 2predictive/;\
nohup R CMD BATCH $(R_OPTS) "--args 100" simulate.R simulate100.Rout;\
nohup R CMD BATCH $(R_OPTS) "--args 400" simulate.R simulate400.Rout;\
nohup R CMD BATCH $(R_OPTS) "--args 700" simulate.R simulate700.Rout;\
nohup R CMD BATCH $(R_OPTS) "--args 1000" simulate.R simulate1000.Rout;\
nohup R CMD BATCH $(R_OPTS) summary.R
sim:
cd sim/normal/nbiom10/;\nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom20/;\ nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom50/;\ nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom100/;\ nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom1000/;\ nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ../..; cd normal_block/nbiom10/;\ nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ../..; cd normal_corr/nbiom10/;\ nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom20/;\ nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom50/;\ nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom100/;\ nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ../..; cd normal_tol.beta0/nbiom10/;\ nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom20/;\ nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom50/;\ nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom100/;\ nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ..; cd nbiom1000/;\ nohup R CMD BATCH $(R_OPTS) simulate.R;\
cd ../..;\ cd survival/0predictive/;\
nohup R CMD BATCH $(R_OPTS) "--args 100" simulate.R simulate100.Rout;\
nohup R CMD BATCH $(R_OPTS) "--args 400" simulate.R simulate400.Rout;\
nohup R CMD BATCH $(R_OPTS) "--args 700" simulate.R simulate700.Rout;\
nohup R CMD BATCH $(R_OPTS) "--args 1000" simulate.R simulate1000.Rout;\
nohup R CMD BATCH $(R_OPTS) summary.R;\
cd ..; cd 2predictive/;\
nohup R CMD BATCH $(R_OPTS) "--args 100" simulate.R simulate100.Rout;\
nohup R CMD BATCH $(R_OPTS) "--args 400" simulate.R simulate400.Rout;\
nohup R CMD BATCH $(R_OPTS) "--args 700" simulate.R simulate700.Rout;\
nohup R CMD BATCH $(R_OPTS) "--args 1000" simulate.R simulate1000.Rout;\
nohup R CMD BATCH $(R_OPTS) summary.R
figs: paper/figures/Rcode/Fig1.R paper/figures/Rcode/Fig2and3.R paper/figures/Rcode/Fig4and5.R paper/figures/Rcode/Fig6and7.R
cd paper/figures/Rcode/;\
nohup R CMD BATCH $(R_OPTS) Fig1.R;\
nohup R CMD BATCH $(R_OPTS) Fig2and3.R;\
nohup R CMD BATCH $(R_OPTS) Fig4and5.R;\
nohup R CMD BATCH $(R_OPTS) Fig6and7.R;\
cd ..; zip figures_pdf.zip *pdf; zip figures_eps.zip *eps
tables: paper/tables/Rcode/Table1.R paper/tables/Rcode/Table2.R
cd paper/tables/Rcode/;\
nohup R CMD BATCH $(R_OPTS) Table1.R;\
nohup R CMD BATCH $(R_OPTS) Table2.R
supplementary_srv:
cd paper/SupplementaryMaterial/;\
Rscript -e "Sys.setenv(PATH = '/usr/lib/rstudio-server/bin/pandoc/:$PATH');rmarkdown::render('SuppMaterial_v2.Rmd')"
supplementary:
cd paper/SupplementaryMaterial/;\
Rscript -e "rmarkdown::render('SuppMaterial_v2.Rmd')"
submission: paper/latex/revision.tex
mkdir paper/submission
cp paper/latex/revision.pdf paper/submission/
cp paper/latex/diff.pdf paper/submission/
cp paper/figures/*eps paper/submission/
cp paper/SupplementaryMaterial/SuppMaterial_v2.pdf paper/submission/
cd paper/;\zip -r submission submission/;\rm -r submission/
clean:
find . -name "nohup.out" -type f -delete
find . -name "Rplots.pdf" -type f -delete