fix Makefile for docs

.gitignore

@@ -12,4 +12,4 @@ figs
 *.html
 *.Rdata
 *.rds
-site_description.md
+docs/metadata/sites

R/metadata/Makefile

+SITES := BCI Canada France Fushan NSW NVS Paracou Spain Sweden Swiss US 
+OBJDIR := ../../docs/metadata/sites
+OBJS := $(addsuffix .md, $(addprefix $(OBJDIR)/, $(SITES))) 
+     
+all: $(OBJS)
+
+%.md:
+	Rscript knit_site_description.R $@
+	
+.PHONY: all 

R/metadata/knit_site_description.R

@@ -5,11 +5,12 @@ library(markdown, quietly  = TRUE)
 library(rjson, quietly =TRUE)
 library(pander, quietly =TRUE)
 
+args <- commandArgs(TRUE)
 
-# Generate tables for each file
-for(DIR in dir("metadata", full.names = TRUE)){
-	cat(paste("\n", DIR))	
-	fname <- "site_description" 
-	mdfile <- knit(paste0(fname, ".Rmd"), output = file.path(DIR, paste0(fname, ".md")))  # produces the md file		
-	system(paste0("pandoc -V geometry:a4paper -V geometry:margin=1in ", mdfile, " -o ", file.path(DIR, paste0(fname, ".pdf"))))
-}
+TARGET <- args[1]  # accepts argument from command line
+SITE = basename(tools::file_path_sans_ext(TARGET))
+DIR <- file.path("../../data/metadata/sites", SITE) # this variable required by knitr script
+cat(DIR)
+
+knit("site_description.Rmd", output = TARGET)
+# produces the md file		

docs/Makefile

-all: metadata base meeting
-
-base: data.format.pdf
-
-meeting:
-	make -C meeting
- 
-%.pdf: %.md
-	pandoc $< -V linkcolor:black -V geometry:a4paper -V geometry:margin=0.5in --listings --include-in-header=include.tex -o $@
-
-
-metadata: meta_data_all.pdf
-
-INPUTS=metadata/BCI/site_description.md metadata/Canada/site_description.md metadata/France/site_description.md metadata/Fushan/site_description.md metadata/NSW/site_description.md metadata/NVS/site_description.md metadata/Paracou/site_description.md metadata/Spain/site_description.md metadata/Sweden/site_description.md metadata/Swiss/site_description.md metadata/US/site_description.md 
-
-${INPUTS}: 
-	Rscript knit_site_description.R
+all: analysis agenda
 	
-meta_data_all.pdf: ${INPUTS}
-	pandoc -V linkcolor:black -V geometry:a4paper -V geometry:margin=0.5in --listings --include-in-header=include.tex ${INPUTS} -o $@
-
-clean:
-	find . -name '*.pdf' -delete
-	find . -name 'site_description.md' -delete
+analysis:
+	make -C analysis.plan
+ 
+agenda:
+	make -C meeting.agenda
 
 .PHONY: all base metadata clean

docs/analysis.plan/Makefile

+TARGETS = $(subst md,pdf,$(shell ls *.md))
+
+all: $(TARGETS)
+
+%.pdf: %.md
+	pandoc $< -V linkcolor:black -V geometry:a4paper -V geometry:margin=1in --listings --include-in-header=../include.tex -o $@
+
+clean:
+	rm -f *.pdf

docs/metadata/Makefile

+all: metadata
+	
+metadata: all.pdf
+
+INPUTS=metadata/BCI/site_description.md metadata/Canada/site_description.md metadata/France/site_description.md metadata/Fushan/site_description.md metadata/NSW/site_description.md metadata/NVS/site_description.md metadata/Paracou/site_description.md metadata/Spain/site_description.md metadata/Sweden/site_description.md metadata/Swiss/site_description.md metadata/US/site_description.md 
+
+${INPUTS}: 
+	Rscript ../../knit_site_description.R
+	
+meta_data_all.pdf: ${INPUTS}
+	pandoc -V linkcolor:black -V geometry:a4paper -V geometry:margin=0.5in --listings --include-in-header=include.tex ${INPUTS} -o $@
+
+clean:
+	find . -name '*.pdf' -delete
+	find . -name 'site_description.md' -delete
+
+.PHONY: all base metadata clean