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Example project

An example analysis, which follows my project template.

Some data redacted.

Makefile

makefile controls all code (except the Rmd notebooks)

all: clean data process pool

clean:
	rm -rf cache derived

.PHONY: data
data:
	mkdir -p data/...
	Rscript code/get_data_from_bce.R

process:
	mkdir -p cache/...
	Rscript code/process_study1.R
	Rscript code/process_study2.R
	Rscript code/process_study3.R

pool:
	mkdir -p derived/adam
	echo "analysis.csv consists of only analysis-ready variables from the ADAM datasets (it includes a subset of the variables from the ADAM datasets, all in a single dataset for analysis)" > derived/README.md
	Rscript code/pool.R

adhoc:
	Rscript code/obtain_prior_cancer_treatment.R

specs:
	# [this copies some files to /data]
	scp ..

local:    # this is to copy server data to local, for quicker development
	mkdir -p data/...
	scp -r ...

tweak:
	git commit -m 'Tweak'; git push

directories

/cache
/code
/data
/derived
/notebooks
/output
/references

important directories are /code (ETL, data munging), /notebooks (data summaries and results), and /derived for analysis datasets

/code

get_data_from_*.R
make_specs_from_sas_files.sas
obtain_prior_*.R
pool.R
process_*.R
process_*.R
process_*.R

helpers.R
README.md

/notebooks

checks.Rmd
checks.md
checks_cache
data-report.Rmd
predictive-prognostic.Rmd
predictive-prognostic.html
predictive-prognostic.md
predictive-prognostic_files
summary-full.Rmd
summary-full.md
summary.Rmd
summary.html
summary.md
t*-comparison.Rmd
t*-comparison.md
validation.Rmd
validation.html
validation.md

README.md
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