[CRAN MOD] optimize example runs and file specs

.Rbuildignore

@@ -9,3 +9,6 @@
 ^README\.Rmd$
 ^CODE_OF_CONDUCT\.md$
 ^logo\.png$
+^report.html$
+^LICENSE$
+^reports$

R/ctg_data_report.R

@@ -85,39 +85,13 @@
 #' \item The generated report is self-contained and can be easily shared or published on the web.
 #' }
 #'
-#' @examples
-#' \donttest{
-#' # Basic usage with default settings
-#' ctg_data_report(my_clinical_trial_data)
-#'
-#' # Customized report with specific settings
-#' ctg_data_report(
-#'   ctg_data = my_clinical_trial_data,
-#'   title = "Clinical Trials Analysis",
-#'   author = "Indra",
-#'   output_file = "reports/clinical_trials.html",
-#'   theme = "flatly",
-#'   color_palette = c("#4E79A7", "#F28E2B", "#E15759", "#76B7B2", "#59A14F", "#EDC948"),
-#'   include_data_quality = TRUE,
-#'   include_interactive_plots = TRUE,
-#'   custom_footer = "Proprietary report generated by SomeGreatOrg Inc."
-#' )
-#'
-#' # Generate a report with static plots and no data quality assessment
-#' ctg_data_report(
-#'   my_clinical_trial_data,
-#'   title = "Quick Clinical Trial Overview",
-#'   include_data_quality = FALSE,
-#'   include_interactive_plots = FALSE
-#' )
-#' }
-#'
 #' @seealso
 #' \url{https://www.indraneelchakraborty.com/clintrialx/} for more information about the ClinTrialX package.
 #' @importFrom grDevices colorRampPalette
 #' @importFrom utils install.packages installed.packages
 #' @importFrom rmarkdown render
 #' @export
+
 ctg_data_report <- function(ctg_data,
                             title = "Clinical Trial Data Report",
                             author = "Author Name",
@@ -127,49 +101,25 @@ ctg_data_report <- function(ctg_data,
                             include_data_quality = TRUE,
                             include_interactive_plots = TRUE,
                             custom_footer = NULL) {
+
   # List of required packages
   required_packages <- c("rmarkdown", "ggplot2", "plotly", "dplyr", "lubridate", "reactable", "scales", "RColorBrewer", "htmltools")
 
-  # Function to check if a package is installed
-  is_installed <- function(package) {
-    return(package %in% rownames(installed.packages()))
-  }
-
-  # Check which packages are missing
-  missing_packages <- required_packages[!sapply(required_packages, is_installed)]
+  # Check if required packages are available
+  missing_packages <- required_packages[!sapply(required_packages, requireNamespace, quietly = TRUE)]
 
-  # If there are missing packages, print a message and offer to install them
   if (length(missing_packages) > 0) {
-    cat("The following packages are required but not installed:\n")
-    cat(paste("-", missing_packages, collapse = "\n"), "\n\n")
-
-    install_choice <- readline(prompt = "Would you like to install these packages now? (yes/no): ")
-
-    if (tolower(install_choice) == "yes") {
-      install.packages(missing_packages)
-      cat("\nPackages installed successfully.\n")
-    } else {
-      cat("\nPlease install the missing packages before running the report generation function.\n")
-      return()
-    }
-  } else {
-    cat("All required packages are already installed.\n")
+    stop("The following required packages are not installed: ",
+         paste(missing_packages, collapse = ", "),
+         ". Please install these packages before running this function.")
   }
 
-  # Load all required packages
-  lapply(required_packages, library, character.only = TRUE)
-
-  cat("\nAll necessary packages are now loaded and ready to use.\n")
-
   # Available themes
   available_themes <- c("default", "cerulean", "journal", "flatly", "readable", "spacelab", "united", "cosmo", "lumen", "paper", "sandstone", "simplex", "yeti")
 
   # Check if the provided theme is valid
   if (!(theme %in% available_themes)) {
-    cat("Invalid theme selected. Available themes are:\n")
-    cat(paste("-", available_themes, collapse = "\n"), "\n\n")
-    theme_choice <- readline(prompt = "Please choose a valid theme: ")
-    theme <- match.arg(theme_choice, available_themes)
+    stop("Invalid theme selected. Available themes are: ", paste(available_themes, collapse = ", "))
   }
 
   # Create a temporary Rmd file
@@ -447,10 +397,10 @@ For any questions or further analysis requests, please contact the report author
 writeLines(rmd_content, temp_rmd)
 
 # Render the Rmd file to HTML
-render(temp_rmd, output_file = output_file, output_dir = dirname(output_file))
+rmarkdown::render(temp_rmd, output_file = output_file, output_dir = dirname(output_file))
 
 # Clean up the temporary file
 unlink(temp_rmd)
 
-cat("Report successfully generated at:", normalizePath(output_file), "\n")
+message("Report successfully generated at:", normalizePath(output_file), "\n")
 }

R/hello.R

@@ -1,13 +1,13 @@
 #' Print a Welcome Message
 #'
-#' This function prints a welcome message for ClinTrialX.
+#' This function returns a welcome message for ClinTrialX.
 #'
 #' @return A character string containing the welcome message.
 #' @export
 #' @examples
 #' hello()
 hello <- function() {
-  message <- "Welcome to ClinTrialX!"
-  Encoding(message) <- "UTF-8"
-  print(message)
+  msg <- "Welcome to ClinTrialX!"
+  Encoding(msg) <- "UTF-8"
+  return(msg)   # Return the message for further use
 }

README.Rmd

@@ -166,6 +166,14 @@ ctg_data_report(
   custom_footer = "Proprietary report generated by SomeGreatOrg Inc."
 )
 
+# Generate a report with static plots and no data quality assessment
+ctg_data_report(
+  ctg_data = my_clinical_trial_data,
+  title = "Quick Clinical Trial Overview",
+  include_data_quality = FALSE,
+  include_interactive_plots = FALSE
+)
+
 ```
 
 Check the path `reports/clinical_trials.html` on your local. It will

README.md

@@ -147,6 +147,14 @@ ctg_data_report(
   include_interactive_plots = TRUE,
   custom_footer = "Proprietary report generated by SomeGreatOrg Inc."
 )
+
+# Generate a report with static plots and no data quality assessment
+ctg_data_report(
+  ctg_data = my_clinical_trial_data,
+  title = "Quick Clinical Trial Overview",
+  include_data_quality = FALSE,
+  include_interactive_plots = FALSE
+)
 ```
 
 Check the path `reports/clinical_trials.html` on your local. It will