makefile: use rmarkdown package for conversion of knit.md instead of calling pandoc directly

Makefile

@@ -1,4 +1,4 @@
-all: knit.md knit.pandoc.docx knit.pandoc.html knit.markdown.html knit.rmarkdown.html knit.pandoc.pdf
+all: knit.md knit.rmarkdown.html knit.rmarkdown.pdf
 
 # avoid loading dependencies defined in .RData or ~/.Rprofile
 # http://kbroman.org/knitr_knutshell/pages/reproducible.html
@@ -7,28 +7,27 @@ R_OPTS=--no-save --no-restore --no-init-file --no-site-file --quiet
 knit.md : main.Rmd
 	R ${R_OPTS} -e "library(knitr); knit(input='$<', output='$@')"
 
-knit.pandoc.docx : knit.md
-	pandoc --output=$@ $^
-
-knit.pandoc.html : knit.md
-	pandoc --standalone --output=$@ $^
-
-knit.markdown.html : knit.md
-	R ${R_OPTS} -e "library(markdown); markdownToHTML(file='$<', output='$@')"
-
 knit.rmarkdown.html : knit.md
 	R ${R_OPTS} -e "library(rmarkdown); render(input='$<', output_format='html_document', output_file='$@')"
 
-knit.pandoc.pdf : knit.md
-	pandoc --output=$@ $^
+# equivalent to knit.rmkardown.html:
+# rmarkdown.html : main.Rmd
+# 	R ${R_OPTS} -e "library(rmarkdown); render(input='$<', output_format='html_document', output_file='$@')"
+
+knit.rmarkdown.pdf : knit.md
+	R ${R_OPTS} -e "library(rmarkdown); render(input='$<', output_format='pdf_document', output_file='$@')"
+
+# equivalent to knit.rmarkdown.pdf
+# rmarkdown.pdf : main.Rmd
+# 	R ${R_OPTS} -e "library(rmarkdown); render(input='$<', output_format='pdf_document', output_file='$@')"
 
 clean :
 	-trash figures
-	-trash knit.markdown.html
 	-trash knit.md
-	-trash knit.pandoc.docx
-	-trash knit.pandoc.html
-	-trash knit.pandoc.pdf
 	-trash knit.rmarkdown.html
+	-trash knit.rmarkdown.pdf
+	# -trash rmarkdown.html
+	# -trash rmarkdown.pdf
 
 # https://www.gnu.org/software/make/manual/html_node/Automatic-Variables.html
+# https://www.rdocumentation.org/packages/rmarkdown/versions/1.3/topics/render