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Makefile
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RAWLLIDS := data/llids.txt
VARLLIDS := $(shell cat ${RAWLLIDS})
.PHONY: data all figures
all: tables manuscript/figures.pdf data/dt.rds manuscript/combined.pdf
data: data/ep.rds \
data/usgs/usgs.rds \
data/cdl/cdl.csv \
data/cdl/cdl_summary.csv \
data/gssurgo/gssurgo.rds \
data/census/census.rds \
data/gis.gpkg \
data/llids.txt \
data/buffer_lulc.csv \
data/mcmc/re_brms.rds \
data/dt.rds
gssurgo: data/gssurgo/gssurgo.rds
cdl: data/cdl/cdl_summary.csv
usgs: data/usgs/usgs.rds
data/gis.gpkg: scripts/00_get_gis.R data/ep.rds
Rscript $<
data/ep.rds: scripts/00_get_ep.R \
data/iws_lulc.rds \
data/county_lulc.rds
Rscript $<
data/llids.txt: scripts/00_list_llids.R data/ep.rds
Rscript $<
data/predictor_key.csv: scripts/99_make_predictor_key.R
Rscript $<
buffer_lulc: $(VARLLIDS)
echo buffers pulled
data/buffer_lulc/%.csv: scripts/00_get_buffers.R
Rscript $< $(basename $@)
data/buffer_lulc.csv: scripts/01_process_buffers.R
Rscript $<
data/iws_lulc.rds: scripts/00_get_lulc.R
Rscript $<
data/county_lulc.rds: scripts/00_get_lulc.R
Rscript $<
data/usgs/usgs.rds: scripts/00_get_usgs.R data/ep.rds
Rscript $<
data/cdl/cdl.csv: scripts/00_get_cdl.R data/ep.rds
Rscript $< 'data/cdl/'
data/cdl/cdl_summary.csv: scripts/01_process_cdl.R \
data/cdl/cdl.csv \
data/cdl/cdl_key.csv
Rscript $<
data/cdl/cdl_key.csv: scripts/99_make_cdl_key.R
Rscript $<
data/gssurgo/gssurgo_key.csv: scripts/99_make_ssurgo_key.R
Rscript $<
data/gssurgo/gssurgo.csv: scripts/00_get_ssurgo.R data/ep.rds
Rscript $< 'data/gssurgo/'
data/gssurgo/gssurgo.rds: scripts/01_process_ssurgo.R data/gssurgo/gssurgo.csv
Rscript $<
data/census/census.rds: scripts/00_get_census.R
Rscript $<
data/macroag/tillage.gpkg: scripts/00_get_tillage.R
Rscript $<
data/macroag/crp.rds: scripts/00_get_crp.R
Rscript $<
data/dt.rds: scripts/02_aggregate_predictors.R \
data/ep.rds \
data/cdl/cdl_summary.csv \
data/iws_lulc.rds \
data/usgs/usgs.rds \
data/gssurgo/gssurgo.rds \
data/buffer_lulc.csv
Rscript $<
data/buffer_stats.csv: scripts/00_get_buffers.R
Rscript $<
data/mcmc/re_brms.rds: scripts/03_model.R
Rscript $<
data/mcmc/fe_brms_nolulc.rds: scripts/03_model_nolulc.R
Rscript $<
data/tile_drainage.rds: scripts/00_get_tile_drainage.R
Rscript $<
manuscript/combined.pdf: manuscript/figures.pdf manuscript/appendix.pdf
pdftk manuscript/figures.pdf manuscript/appendix.pdf cat output manuscript/combined.pdf
manuscript/figures.pdf: manuscript/figures.Rmd \
tables/01_predictors.pdf \
tables/03_model_summary.pdf \
figures/11_map-1.pdf \
figures/re-comparison-1.pdf \
figures/fe-1.pdf \
figures/re-1.pdf \
figures/tn_re_hu4-1.pdf \
figures/tn_re_compare-1.pdf
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
-pdftk manuscript/figures.pdf cat 2-end output manuscript/figures2.pdf
-mv manuscript/figures2.pdf manuscript/figures.pdf
#cd figures && make pnglatest
manuscript/appendix.pdf: manuscript/appendix.Rmd \
data/tile_drainage.rds \
figures/cdl_vs_nlcd-1.pdf \
tables/02_cdl_key.pdf \
figures/fe_nolulc-1.pdf \
figures/08_exploratory_dotplot-1.pdf
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
-pdftk manuscript/appendix.pdf cat 2-end output manuscript/appendix2.pdf
-mv manuscript/appendix2.pdf manuscript/appendix.pdf
figures/11_map-1.pdf: figures/11_map.Rmd data/gis.gpkg
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
pdfcrop $@ $@
figures/re-comparison-1.pdf: figures/07_model-selection.Rmd data/mcmc/re_brms.rds
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
pdfcrop $@ $@
figures/re-1.pdf: figures/07_model-selection.Rmd data/mcmc/re_brms.rds
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
pdfcrop $@ $@
figures/fe-1.pdf: figures/07_model-selection.Rmd data/mcmc/re_brms.rds
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
pdfcrop $@ $@
figures/fe_40-1.pdf: figures/07_model-selection_40.Rmd data/mcmc/re_brms_40.rds
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
pdfcrop $@ $@
figures/fe_nolulc-1.pdf: figures/07_model-selection_nolulc.Rmd data/mcmc/fe_brms_nolulc.rds
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
pdfcrop $@ $@
figures/tn_re_hu4-1.pdf: figures/07_model-selection.Rmd data/mcmc/re_brms.rds
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
pdfcrop $@ $@
figures/tn_re_compare-1.pdf: figures/07_model-selection.Rmd data/mcmc/re_brms.rds
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
pdfcrop $@ $@
figures/tptn_maps-1.pdf: figures/01_county_extent.Rmd scripts/explore_lagos_ag.R data/ep.rds
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
figures/02_hierarchical_demo-1.pdf: figures/02_hierarchical_demo.Rmd
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
figures/03_wetland_potential-1.pdf: figures/03_wetland_potential.Rmd
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
figures/04_nlcd-versus-cdl-1.pdf: figures/04_nlcd-versus-cdl.Rmd
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
figures/08_exploratory_dotplot-1.pdf: figures/08_exploratory_dotplot.Rmd data/dt.rds data/predictor_key.csv
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
figures/09_stream_buffer-1.pdf: figures/09_stream_buffer.Rmd data/dt.rds
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
tables: manuscript/tables.pdf manuscript/appendix.pdf
manuscript/tables.pdf: tables/01_predictors.pdf \
tables/02_cdl_key.pdf \
tables/03_model_summary.pdf
# tables/03_model_summary.pdf
pdftk $^ cat output manuscript/tables.pdf
tables/01_predictors.pdf: tables/01_predictors.Rmd \
data/dt.rds \
data/dt_units.rds \
data/predictor_key.csv
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
pdfcrop $@ $@
tables/02_cdl_key.pdf: tables/02_cdl_key.Rmd
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
pdfcrop $@ $@
tables/03_model_summary.pdf: tables/03_model_summary.Rmd data/mcmc/re_brms.rds
Rscript -e "rmarkdown::render('$<', output_format = 'pdf_document')"
pdfcrop $@ $@
manuscript/reviewer_comments.pdf: manuscript/reviewer_comments.md
pandoc $< -H manuscript/quote_setup.tex -o $@
manuscript/manuscript.pdf: manuscript/manuscript.Rmd \
manuscript/pinp.cls \
manuscript/lagosag.bib \
manuscript/jsta.bst
cd manuscript && make manuscript.pdf
docker: Dockerfile
docker build -f Dockerfile.debug -t jsta/beyond_land_use:test .
check:
rm manuscript/appendix.pdf \
manuscript/figures.pdf \
tables/03_model_summary.pdf \
tables/01_predictors.pdf \
figures/11_map-1.pdf \
figures/re-comparison-1.pdf \
figures/fe-1.pdf \
figures/re-1.pdf \
figures/tn_re_hu4-1.pdf \
figures/tn_re_compare-1.pdf \
tables/02_cdl_key.pdf \
figures/fe_nolulc-1.pdf \
figures/08_exploratory_dotplot-1.pdf
make all