updating for html output too

R/strip_mdpi.R

@@ -1,4 +1,4 @@
-strip_mdpi_render = function(in_rmd = "doc/peakcharacterization_manuscript.Rmd", out_rmd = "doc/peakcharacterization_nostyle.Rmd"){
+strip_mdpi_render = function(in_rmd = "doc/peakcharacterization_manuscript.Rmd", out_rmd = "doc/peakcharacterization_nostyle.Rmd", out_file = here::here("doc/peakcharacterization_nostyle.docx"), output_format = "word_document"){
   rmd_doc = readLines(in_rmd)
 
   template_line = grepl("metabolites-template", rmd_doc)
@@ -8,7 +8,11 @@ strip_mdpi_render = function(in_rmd = "doc/peakcharacterization_manuscript.Rmd",
   rmd_nostyle = rmd_notemplate[!has_style]
 
   cat(rmd_nostyle, file = out_rmd, sep = "\n")
-  rmarkdown::render(out_rmd, knit_root_dir = getwd(), quiet = TRUE)
+  rmarkdown::render(out_rmd,
+                    output_format = output_format,
+                    output_file = out_file,
+                    knit_root_dir = getwd(),
+                    quiet = TRUE)
   beepr::beep(4)
   out_rmd
 }

_targets.R

@@ -139,8 +139,17 @@ figures_tar = tar_plan(
              "doc/peakcharacterization_manuscript.Rmd"),
   tar_render(supplemental_materials,
              "doc/peakcharacterization_supplemental.Rmd"),
+  tar_render(supplemental_html,
+             "doc/peakcharacterization_supplemental.Rmd",
+             output_file = here::here("docs/scancentricpeakcharacterization_supplemental.html"),
+             output_format = "html_document"),
+             # output_format = "pdf_document"),
   tar_target(manuscript_nostyle,
              strip_mdpi_render(base_manuscript)),
+  tar_target(manuscript_html,
+             strip_mdpi_render(base_manuscript,
+                               out_file = here::here("docs/scancentricpeakcharacterization.html"),
+                               output_format = "html_document")),
   tar_target(manuscript_mdpi,
              strip_headers_render(base_manuscript))
 )

doc/peakcharacterization_manuscript.Rmd

@@ -24,6 +24,10 @@ output:
     pandoc_args:
       - '--lua-filter=scholarly-metadata.lua'
       - '--lua-filter=author-info-blocks.lua'
+  html_document:
+    pandoc_args:
+      - '--lua-filter=scholarly-metadata.lua'
+      - '--lua-filter=author-info-blocks.lua'
 bibliography: '`r here::here("doc/peakcharacterization.json")`'
 csl: plos-computational-biology.csl
 editor_options: 

doc/peakcharacterization_supplemental.Rmd

@@ -23,6 +23,14 @@ output:
     pandoc_args:
       - '--lua-filter=scholarly-metadata.lua'
       - '--lua-filter=author-info-blocks.lua'
+  html_document:
+    pandoc_args:
+      - '--lua-filter=scholarly-metadata.lua'
+      - '--lua-filter=author-info-blocks.lua'
+  pdf_document:
+    pandoc_args:
+      - '--lua-filter=scholarly-metadata.lua'
+      - '--lua-filter=author-info-blocks.lua'
 bibliography: '`r here::here("doc/peakcharacterization.json")`'
 csl: plos-computational-biology.csl
 editor_options: 

doc/scancentricpeakcharacterization.log

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