Moved R Markdown to top-level
Does having the R markdown script stored in the top-level work for you?
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Makefile
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route_analysis: R/route_analysis.Rmd
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route_analysis: route_analysis.Rmd
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R -e 'library("rmarkdown"); old_path <- Sys.getenv("PATH"); Sys.setenv(PATH = paste(old_path, "/usr/local/bin", sep = ":")); rmarkdown::render(knit_root_dir = "./../", output_dir = "./html", input = "./R/route_analysis.Rmd", output_file = "./html/route_analysis.html")'
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R -e 'library("rmarkdown"); old_path <- Sys.getenv("PATH"); Sys.setenv(PATH = paste(old_path, "/usr/local/bin", sep = ":")); rmarkdown::render(knit_root_dir = "./", output_dir = "./html", input = "./route_analysis.Rmd", output_file = "./html/route_analysis.html")'
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clean: clean-data clean-figure clean-script
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clean: clean-data clean-figure clean-script
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