Add foodwebr article demonstrating package function dependencies

.gitignore

@@ -30,3 +30,4 @@ _quarto/*
 !_quarto/_freeze/
 *.docx
 *.knit.md
+tests/testthat/_snaps/

DESCRIPTION

@@ -15,9 +15,11 @@ Language: en-US
 Depends: 
     R (>= 4.1.0)
 Imports: 
+    cli,
     stats
 Suggests: 
     altdoc,
+    foodwebr,
     knitr,
     rmarkdown,
     spelling,

NAMESPACE

@@ -1,3 +1,4 @@
 # Generated by roxygen2: do not edit by hand
 
+export(calculate_summary)
 export(example_function)

NEWS.md

@@ -1,5 +1,9 @@
 # rpt (development version)
 
+* Added package structure visualization article using foodwebr to demonstrate function dependencies and call graphs
+* Created layered helper function architecture for realistic foodwebr demonstrations
+* Added `calculate_summary()` function for computing summary statistics
+
 * Switched from pkgdown to altdoc for documentation generation. Now using Quarto Website for documentation with native math equation support via MathJax.
 * Removed pkgdown-specific configurations and workflows.
 * Retained RevealJS multi-format support for Quarto vignettes and articles.

R/calculate_statistic.R

@@ -0,0 +1,13 @@
+#' Calculate Statistic
+#'
+#' Internal helper function to calculate a statistical measure on cleaned data.
+#'
+#' @param x A numeric vector
+#'
+#' @return The median value
+#' @keywords internal
+#' @noRd
+calculate_statistic <- function(x) {
+  x_clean <- clean_data(x)
+  stats::median(x_clean)
+}

R/calculate_summary.R

@@ -0,0 +1,21 @@
+#' Calculate Summary Statistics
+#'
+#' Calculate multiple summary statistics for a numeric vector.
+#'
+#' @param x A numeric vector
+#'
+#' @return A named list with mean, median, and standard deviation
+#' @export
+#'
+#' @examples
+#' calculate_summary(c(1, 2, 3, 4, 5))
+#' calculate_summary(c(1, NA, 3, 4, 5))
+calculate_summary <- function(x) {
+  x_clean <- clean_data(x)
+
+  list(
+    mean = format_result(mean(x_clean)),
+    median = example_function(x),
+    sd = format_result(stats::sd(x_clean))
+  )
+}

R/clean_data.R

@@ -0,0 +1,14 @@
+#' Clean Data
+#'
+#' Internal helper function to clean data by removing NA values and preparing
+#' for analysis.
+#'
+#' @param x A numeric vector
+#'
+#' @return A cleaned numeric vector with NA values removed
+#' @keywords internal
+#' @noRd
+clean_data <- function(x) {
+  validate_input(x)
+  x[!is.na(x)]
+}

R/example_function.R

@@ -1,14 +1,17 @@
 #' Example Function
 #'
 #' This is an example function that demonstrates basic functionality.
+#' It validates, cleans, calculates statistics, and formats the result.
 #'
 #' @param x A numeric vector
 #'
-#' @return The median of the input vector
+#' @return The median of the input vector, rounded to 2 decimal places
 #' @export
 #'
 #' @examples
 #' example_function(c(1, 2, 3, 4, 5))
+#' example_function(c(1, NA, 3, 4, 5))
 example_function <- function(x) {
-  stats::median(x)
+  result <- calculate_statistic(x)
+  format_result(result)
 }

R/format_result.R

@@ -0,0 +1,12 @@
+#' Format Result
+#'
+#' Internal helper function to format the result for output.
+#'
+#' @param result A numeric value
+#'
+#' @return A formatted numeric value (rounded to 2 decimal places)
+#' @keywords internal
+#' @noRd
+format_result <- function(result) {
+  round(result, digits = 2)
+}

R/validate_input.R

@@ -0,0 +1,21 @@
+#' Validate Input Data
+#'
+#' Internal helper function to validate input data for statistical calculations.
+#'
+#' @param x A numeric vector
+#'
+#' @return TRUE if valid, throws error otherwise
+#' @keywords internal
+#' @noRd
+validate_input <- function(x) {
+  if (!is.numeric(x)) {
+    cli::cli_abort("Input must be numeric", call = NULL)
+  }
+  if (length(x) == 0) {
+    cli::cli_abort("Input must have at least one element", call = NULL)
+  }
+  if (all(is.na(x))) {
+    cli::cli_abort("Input cannot be all NA values", call = NULL)
+  }
+  TRUE
+}

altdoc/quarto_website.yml

@@ -34,6 +34,8 @@ website:
             file: vignettes/quarto_vignette.qmd
           - text: "Advanced"
             file: vignettes/articles/quarto_article.qmd
+          - text: "Package Structure"
+            file: vignettes/articles/package-structure.qmd
   sidebar:
     collapse-level: 1
     contents:
@@ -48,6 +50,7 @@ website:
           - section: Advanced
             contents:
               - vignettes/articles/quarto_article.qmd
+              - vignettes/articles/package-structure.qmd
       - section: $ALTDOC_MAN_BLOCK
         style: floating
       - text: News

inst/WORDLIST

@@ -2,9 +2,11 @@ CMD
 Callouts
 CodeFactor
 Codecov
+DiagrammeR
 DOCX
 Lifecycle
 MathJax
+README
 RevealJS
 Shortcode
 Slidebreak
@@ -14,9 +16,14 @@ altdoc
 callout
 callouts
 cdot
+codebases
 emplate
 foldable
+foodweb
+foodwebr
+formatter
 frac
+graphviz
 frontmatter
 linter
 lintr
@@ -26,3 +33,4 @@ serodynamics
 shortcode
 slidebreak
 tabset
+tidygraph

tests/testthat/test-calculate_summary.R

@@ -0,0 +1,27 @@
+test_that("calculate_summary works", {
+  result <- calculate_summary(c(1, 2, 3, 4, 5))
+  expect_type(result, "list")
+  expect_named(result, c("mean", "median", "sd"))
+  expect_equal(result$mean, 3)
+  expect_equal(result$median, 3)
+  expect_equal(result$sd, 1.58)
+})
+
+test_that("calculate_summary handles NA values", {
+  result <- calculate_summary(c(1, NA, 3, 4, 5))
+  expect_type(result, "list")
+  expect_equal(result$median, 3.5)
+  expect_equal(result$mean, 3.25)
+})
+
+test_that("calculate_summary handles errors", {
+  expect_error(calculate_summary(character()), "Input must be numeric")
+  expect_error(
+    calculate_summary(numeric()),
+    "Input must have at least one element"
+  )
+  expect_error(
+    calculate_summary(c(NA_real_, NA_real_, NA_real_)),
+    "Input cannot be all NA values"
+  )
+})

tests/testthat/test-example_function.R

@@ -1,4 +1,18 @@
 test_that("example_function works", {
   expect_equal(example_function(c(1, 2, 3)), 2)
   expect_equal(example_function(c(1, 2, 3, 4, 5)), 3)
+  expect_equal(example_function(c(1, NA, 3, 4, 5)), 3.5)
+  expect_equal(example_function(c(1.111, 2.222, 3.333)), 2.22)
+})
+
+test_that("example_function handles errors", {
+  expect_error(example_function(character()), "Input must be numeric")
+  expect_error(
+    example_function(numeric()),
+    "Input must have at least one element"
+  )
+  expect_error(
+    example_function(c(NA_real_, NA_real_, NA_real_)),
+    "Input cannot be all NA values"
+  )
 })