#!/usr/bin/env Rscript # ============================================================================== # scripts/render_rmd.R # # Automatically renders R Markdown (*.Rmd) documents across R/ sub-folders into # self-contained GitHub Pages Markdown (*.md) files with base64 Data URIs for plots. # # Key Features: # 1. Zero External Files: Sets knitr upload.fun to image_uri so all plots # (ggplot2, base R, igraph, lattice) are base64-inlined into the .md file. # 2. Just-the-Docs Integration: Automatically adds Jekyll YAML frontmatter # (title, parent, grand_parent, nav_order) matching site hierarchy. # 3. Interactive Widget Support: Compiles network_visNetwork.Rmd to self-contained # HTML (with interactive visNetwork JS) and generates a matching .md page. # 4. Clean Artifact Hygiene: Removes any temporary figure/ folders after knitting. # # Usage: # Rscript scripts/render_rmd.R # Render all 26 Rmd documents # Rscript scripts/render_rmd.R --file path # Render a single document # ============================================================================== suppressPackageStartupMessages({ library(knitr) library(rmarkdown) }) # Manifest of all Rmd files with their Just-the-docs navigation metadata rmd_manifest <- list( # --- R/curate/ (Parent: "Curate R Data", grand_parent: "R Language") --- list(path = "R/curate/data_tables.Rmd", title = "Working with Data in R", parent = "Curate R Data", grand_parent = "R Language", nav_order = 1), list(path = "R/curate/applyExample.Rmd", title = "Examples Using for and apply", parent = "Curate R Data", grand_parent = "R Language", nav_order = 2), list(path = "R/curate/intro_dplyr.Rmd", title = "Intro to R Adapted to dplyr", parent = "Curate R Data", grand_parent = "R Language", nav_order = 3), list(path = "R/curate/tidyverse.Rmd", title = "Tidyverse Split-Apply-Combine Example", parent = "Curate R Data", grand_parent = "R Language", nav_order = 4), list(path = "R/curate/purrr.Rmd", title = "purrr Package Example", parent = "Curate R Data", grand_parent = "R Language", nav_order = 5), list(path = "R/curate/species.Rmd", title = "Species Analysis with dplyr and purrr", parent = "Curate R Data", grand_parent = "R Language", nav_order = 6), list(path = "R/curate/string.Rmd", title = "Characters and Strings", parent = "Curate R Data", grand_parent = "R Language", nav_order = 7), list(path = "R/curate/regex.Rmd", title = "Regular Expressions (regex)", parent = "Curate R Data", grand_parent = "R Language", nav_order = 8), list(path = "R/curate/file.Rmd", title = "Reading and Writing Files", parent = "Curate R Data", grand_parent = "R Language", nav_order = 9), # --- R/analyze/ (Parent: "Analyze Data", grand_parent: "R Language") --- list(path = "R/analyze/correlate.Rmd", title = "Correlation Analysis", parent = "Analyze Data", grand_parent = "R Language", nav_order = 1), list(path = "R/analyze/covary.Rmd", title = "Covariation Analysis", parent = "Analyze Data", grand_parent = "R Language", nav_order = 2), list(path = "R/analyze/linear_model.Rmd", title = "Linear Models", parent = "Analyze Data", grand_parent = "R Language", nav_order = 3), list(path = "R/analyze/Formulas.Rmd", title = "Formulas for Linear Models", parent = "Analyze Data", grand_parent = "R Language", nav_order = 4), # --- R/organize/ (Parent: "Organize Data & Docs", grand_parent: "R Language") --- list(path = "R/organize/RmarkdownExample.Rmd", title = "R Markdown Example", parent = "Organize Data & Docs", grand_parent = "R Language", nav_order = 1), list(path = "R/organize/function.Rmd", title = "R Functions", parent = "Organize Data & Docs", grand_parent = "R Language", nav_order = 2), list(path = "R/organize/SQLiteDplyr.Rmd", title = "SQLite and dplyr", parent = "Organize Data & Docs", grand_parent = "R Language", nav_order = 3), list(path = "R/organize/package.Rmd", title = "R Packages", parent = "Organize Data & Docs", grand_parent = "R Language", nav_order = 4), # --- R/profile/ (Parent: "Profile & Simulate", grand_parent: "R Language") --- list(path = "R/profile/profile.Rmd", title = "Profiling R Code", parent = "Profile & Simulate", grand_parent = "R Language", nav_order = 1), list(path = "R/profile/lineprof.Rmd", title = "Memory Profiling with lineprof", parent = "Profile & Simulate", grand_parent = "R Language", nav_order = 2), list(path = "R/profile/simulate.Rmd", title = "Simulation Studies in R", parent = "Profile & Simulate", grand_parent = "R Language", nav_order = 3), # --- R/visualize/ (Parent: "Visualize Data with R", grand_parent: "R Language") --- list(path = "R/visualize/ggplot2.Rmd", title = "ggplot2 Visualization", parent = "Visualize Data with R", grand_parent = "R Language", nav_order = 1), list(path = "R/visualize/shiny.Rmd", title = "Shiny Web Applications", parent = "Visualize Data with R", grand_parent = "R Language", nav_order = 2), # --- R/visualize/network/ (Parent: "Network Observatins in Connected Graphs") --- list(path = "R/visualize/network/network_data.Rmd", title = "Network Data Preparation", parent = "Network Observatins in Connected Graphs", grand_parent = "Visualize Data with R", nav_order = 1), list(path = "R/visualize/network/network_igraph.Rmd", title = "igraph Network Visualization (Dataset 1)", parent = "Network Observatins in Connected Graphs", grand_parent = "Visualize Data with R", nav_order = 2), list(path = "R/visualize/network/network2_igraph.Rmd", title = "igraph Network Visualization (Dataset 2)", parent = "Network Observatins in Connected Graphs", grand_parent = "Visualize Data with R", nav_order = 3), list(path = "R/visualize/network/network_visNetwork.Rmd", title = "visNetwork Interactive Visualization", parent = "Network Observatins in Connected Graphs", grand_parent = "Visualize Data with R", nav_order = 4) ) # Parse command line args args <- commandArgs(trailingOnly = TRUE) target_filter <- NULL if (length(args) > 0) { if (args[1] == "--file" && length(args) >= 2) { target_filter <- args[2] } else if (!startsWith(args[1], "-")) { target_filter <- args[1] } } if (!is.null(target_filter)) { rmd_manifest <- Filter(function(item) grepl(target_filter, item$path, fixed = TRUE), rmd_manifest) if (length(rmd_manifest) == 0) { stop(sprintf("No matching file found for pattern: %s", target_filter)) } } root_dir <- getwd() cat(sprintf("Starting render for %d Rmd file(s)...\n\n", length(rmd_manifest))) render_file <- function(item, root_dir) { rel_path <- item$path base_name <- basename(rel_path) sub_dir <- dirname(rel_path) out_md_name <- sub("\\.Rmd$", ".md", base_name) out_md_path <- file.path(sub_dir, out_md_name) cat(sprintf("[Rendering] %s -> %s ... ", rel_path, out_md_path)) # Special handling for visNetwork interactive HTML widget is_visnetwork <- grepl("network_visNetwork\\.Rmd$", rel_path) result <- tryCatch({ setwd(file.path(root_dir, sub_dir)) # Configure knitr to base64 encode all figures directly into markdown opts_knit$set(upload.fun = image_uri) opts_chunk$set( echo = TRUE, warning = FALSE, message = FALSE, fig.width = 7, fig.height = 5 ) tmp_out <- tempfile(fileext = ".md") # Knit Rmd to markdown knit(base_name, tmp_out, quiet = TRUE) # Clean up temporary figure/ directory left by knitr if (dir.exists("figure")) { unlink("figure", recursive = TRUE) } # If interactive visNetwork, also render standalone self-contained HTML if (is_visnetwork) { suppressMessages(rmarkdown::render( base_name, output_format = "html_document", output_file = "network_visNetwork.html", output_options = list(self_contained = TRUE), quiet = TRUE )) } # Read knitted content lines <- readLines(tmp_out, warn = FALSE) # Strip existing YAML frontmatter if present if (length(lines) > 0 && lines[1] == "---") { end_yaml <- which(lines[-1] == "---") if (length(end_yaml) > 0) { lines <- lines[-(1:(end_yaml[1] + 1))] } } # Trim leading empty lines while (length(lines) > 0 && grepl("^\\s*$", lines[1])) { lines <- lines[-1] } # Construct clean Just-the-Docs YAML frontmatter yaml_header <- c( "---", sprintf('title: "%s"', item$title), sprintf('parent: "%s"', item$parent), sprintf('grand_parent: "%s"', item$grand_parent), sprintf('nav_order: %d', item$nav_order), "---", "" ) # Ensure there is an # H1 Title tag at top of body has_h1 <- any(grepl("^#\\s+", lines[1:min(length(lines), 5)])) body_header <- if (!has_h1) { c(sprintf("# %s", item$title), "") } else { character(0) } # For interactive visNetwork, add banner link to the standalone interactive HTML vis_banner <- if (is_visnetwork) { c( "> **Interactive Widget**: An interactive version of this network visualization is available at [Open Interactive Visualization](network_visNetwork.html).", "" ) } else { character(0) } final_content <- c(yaml_header, body_header, vis_banner, lines) writeLines(final_content, out_md_name) plots_count <- sum(grepl("data:image", final_content)) file_bytes <- file.size(out_md_name) cat(sprintf("DONE (%d plots, %s)\n", plots_count, format(file_bytes, big.mark = ","))) list( file = rel_path, out = out_md_path, status = "SUCCESS", plots = plots_count, bytes = file_bytes ) }, error = function(e) { cat(sprintf("ERROR: %s\n", conditionMessage(e))) list( file = rel_path, out = out_md_path, status = "ERROR", plots = 0, bytes = 0, msg = conditionMessage(e) ) }, finally = { setwd(root_dir) }) return(result) } results <- lapply(rmd_manifest, render_file, root_dir = root_dir) cat("\n======================================================================\n") cat("RENDERING SUMMARY\n") cat("======================================================================\n") cat(sprintf("%-42s | %-8s | %-6s | %-10s\n", "Output File", "Status", "Plots", "Size")) cat(paste(rep("-", 72), collapse = ""), "\n") for (i in seq_along(results)) { res <- results[[i]] cat(sprintf("%-42s | %-8s | %-6d | %-10s\n", res$out, res$status, res$plots, format(res$bytes, big.mark = ","))) } cat("======================================================================\n")