Got documents to work in subdirs

Author: zimolzak

makefile

@@ -1,30 +1,18 @@
-files = README.pdf Rplots_outpat.pdf Routputs_inpat_v4.txt README.docx thoughts-notes-appendix.pdf Routputs_inpat_v5.txt Routputs_inpat.txt
+files = Rplots_outpat.pdf Routputs_inpat_v4.txt Routputs_inpat_v5.txt Routputs_inpat.txt
 files_unmentioned = Routputs_outpat.txt Rplots_inpat_v4.pdf Rplots_inpat.pdf
+
 .PHONY: all clean upload
-infiles_outpat = PATIENT.txt PAT_ORDERS_PROCEDURES.txt PAT_ENC_DX.txt PAT_PRBL_LIST.txt Pat_FlowSheet_PulseOx.txt
-infile_bsl = COVID_1_SLH.tab
 
 all: $(files)
-
-%.pdf: %.txt
-	pandoc -o $@ $<
-
-%.pdf: %.md
-	pandoc -o $@ $<
-
-%.docx: %.txt
-	pandoc -o $@ $<
-
-%.docx: %.md
-	pandoc -o $@ $<
+	$(MAKE) -C outputs
 
 #### Analyses
 
-Rplots_outpat.pdf: analysis_outpat.R $(infiles_outpat)
+Rplots_outpat.pdf: analysis_outpat.R
 	Rscript $< > Routputs_outpat.txt
 	mv -f Rplots.pdf Rplots_outpat.pdf
 
-Routputs_inpat.txt: analysis_inpat.R $(infile_bsl)
+Routputs_inpat.txt: analysis_inpat.R # COVID_1....
 	Rscript $< > $@
 
 Routputs_inpat_v4.txt: bslmc_v4_DataSets_pipe.R # infiles_v4, sadly 15 of them

outputs/makefile

@@ -0,0 +1,13 @@
+files = README.pdf README.docx thoughts-notes-appendix.pdf
+
+.PHONY: all
+
+all: $(files)
+
+#### Documents
+
+%.pdf: ../%.md
+	pandoc -o $@ $<
+
+%.docx: ../%.md
+	pandoc -o $@ $<