update constructors and add documentation

- update Parameter and LogisticSelectivity constructors
- add R/generate_man_pages to document constructors

R/generate_man_pages.R

@@ -0,0 +1,125 @@
+#' Format RD Block Content for .Rd Files
+#'
+#' This function takes an RD block extracted from a C++ or a header file, parses its 
+#' components, and formats it into a string suitable for inclusion in an .Rd
+#' documentation file.
+#'
+#' @param rd_block A string containing the raw RD block extracted from a C++ or a header file.
+#'
+#' @return A formatted string representing the content of the .Rd file, 
+#' including sections such as title, description, param, return, 
+#' and examples.
+format_rd_content <- function(rd_block) {
+  rd_content <- ""
+
+  # Extract different components
+  title <- stringr::str_extract(rd_block, "(?<=@title ).*")
+  description <- stringr::str_extract(rd_block, "(?<=@description ).*")
+  params <- stringr::str_extract_all(rd_block, "(?<=@param )[^@]+")[[1]]
+  return_val <- stringr::str_extract(rd_block, "(?<=@return ).*")
+  examples <- stringr::str_extract(rd_block, "(?<=@examples).*")
+
+  # Construct the Rd content
+  if (!is.na(title)) {
+    rd_content <- paste0(rd_content, "\\name{", title, "}\n")
+    rd_content <- paste0(rd_content, "\\title{", title, "}\n")
+  }
+
+  if (!is.na(description)) {
+    rd_content <- paste0(rd_content, "\\description{\n", description, "\n}\n")
+  }
+
+  if (length(params) > 0) {
+    rd_content <- paste0(rd_content, "\\arguments{\n")
+    for (param in params) {
+      param_name <- stringr::str_extract(param, "\\S+")
+      param_desc <- stringr::str_trim(stringr::str_replace(param, param_name, ""))
+      rd_content <- paste0(rd_content, "\\item{", param_name, "}{", param_desc, "}\n")
+    }
+    rd_content <- paste0(rd_content, "}\n")
+  }
+
+  if (!is.na(return_val)) {
+    rd_content <- paste0(rd_content, "\\value{\n", return_val, "\n}\n")
+  }
+
+  if (!is.na(examples)) {
+    examples <- stringr::str_replace_all(examples, "^\\s*//[']", "")
+    examples <- stringr::str_replace_all(examples, "^\\s*//", "")
+    examples <- stringr::str_trim(examples)
+    rd_content <- paste0(rd_content, "\\examples{\n", examples, "\n}\n")
+  }
+
+  return(rd_content)
+}
+
+#' Process a C++ File to Extract RD Blocks
+#'
+#' This function reads a specified C++ file, searches for RD blocks
+#' (documentation comments) within the file, and writes the extracted
+#' and formatted RD content to an .Rd file in the man/ directory.
+#'
+#' @param file_path A string specifying the path to the C++ file to be processed.
+process_cpp_file <- function(file_path) {
+  cpp_content <- readr::read_lines(file_path)
+  cpp_content <- paste(cpp_content, collapse = "\n")
+
+  # Regular expressions to match RD blocks
+  block_rd_blocks <- stringr::str_extract_all(cpp_content, "(?s)/\\*\\*\\s*@rd.*?\\*/")[[1]]
+  line_rd_blocks <- stringr::str_extract_all(cpp_content, "(?m)//\\s*@rd.*?$(\n.*//\\s*@[a-zA-Z0-9]+.*?$)*")[[1]]
+  line_squote_rd_blocks <- stringr::str_extract_all(cpp_content, "(?m)//'\\s*@rd.*?$(\n.*//'\\s*@[a-zA-Z0-9]+.*?$)*")[[1]]
+
+  # Combine all found blocks
+  rd_blocks <- c(block_rd_blocks, line_rd_blocks, line_squote_rd_blocks)
+
+  if (length(rd_blocks) == 0) {
+    message("No RD tags found in ", file_path)
+    return()
+  }
+
+  for (block in rd_blocks) {
+    function_name <- stringr::str_extract(block, "(?<=@name )\\w+")
+    rd_block_clean <- stringr::str_replace_all(block, "(^/\\*\\*\\s*@rd|^//\\s*@rd|^//'\\s*@rd|\\*/$)", "")
+    rd_block_clean <- stringr::str_replace_all(rd_block_clean, "^//\\s*", "")
+    rd_block_clean <- stringr::str_replace_all(rd_block_clean, "^//'\\s*", "")
+    rd_block_clean <- stringr::str_trim(rd_block_clean)
+
+    rd_content <- format_rd_content(rd_block_clean)
+
+    if (!is.na(function_name)) {
+      output_file <- paste0("man/",paste0(function_name, ".Rd"))
+      readr::write_lines(rd_content, output_file)
+      message("Created: ", output_file)
+    } else {
+      warning("Could not extract function name from block in ", file_path)
+    }
+  }
+}
+
+#' Process C++ and Header Files in a Directory
+#'
+#' This function processes all `.cpp` and `.hpp` files within a specified
+#' directory, including subdirectories, by applying the `process_cpp_file`
+#' function to each file. It searches for RD blocks in the files and generates
+#' corresponding `.Rd` files.
+#'
+#' @param dir_path A string specifying the path to the directory containing C++ 
+#' and header files.
+process_directory <- function(dir_path) {
+  cpp_files <- fs::dir_ls(dir_path, recurse = TRUE, glob = "*.cpp")
+
+  for (cpp_file in cpp_files) {
+    message("Processing file: ", cpp_file)
+    process_cpp_file(cpp_file)
+  }
+
+   hpp_files <- fs::dir_ls(dir_path, recurse = TRUE, glob = "*.hpp")
+
+  for (hpp_file in hpp_files) {
+    message("Processing file: ", hpp_file)
+    process_cpp_file(hpp_file)
+  }
+}
+
+
+# process_directory("inst/include/interface/rcpp")