Merge pull request #22 from jhelvy/design-fixes

Design fixes

.Rbuildignore

@@ -4,13 +4,10 @@
 ^docs$
 ^pkgdown$
 ^\.github$
-vignettes
 ^README\.Rmd$
 ^LICENSE\.md$
-^cjTools\.Rproj$
 ^doc$
 ^Meta$
-^next_release\.md$
 ^build\.R$
 ^foo\.R$
 ^cran-comments\.md$

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 0.5.0
+Date: 2023-07-11 10:27:50 UTC
+SHA: a1ceb125c1d1f805dfa343c723227d8efe2565f5

DESCRIPTION

@@ -1,26 +1,29 @@
 Package: cbcTools
-Title: A Simulation-Based Workflow to Design and Evaluate Choice-Based Conjoint Survey Experiments
-Version: 0.4.0
+Title: Choice-Based Conjoint Experiment Design Generation and Power Evaluation in R
+Version: 0.5.0
 Maintainer: John Helveston <[email protected]>
 Authors@R: c(
     person(given   = "John",
            family  = "Helveston",
            role    = c("cre", "aut", "cph"),
            email   = "[email protected]",
            comment = c(ORCID = "0000-0002-2657-9191")))
-Description: A simulation-based workflow to design and evaluate choice-based conjoint survey experiments. Generate a variety of survey designs, including full factorial designs, orthogonal designs, and Bayesian D-efficient designs as well as designs with "no choice" options and "labeled" (also known as "alternative specific") designs. Full factorial and orthogonal designs are obtained using the 'DoE.base' package (Grömping, 2018) <doi:10.18637/jss.v085.i05>. Bayesian D-efficient designs are obtained using the 'idefix' package (Traets et al, 2020) <doi:10.18637/jss.v096.i03>. Conveniently inspect the design balance and overlap, and simulate choice data for a survey design either randomly or according to a multinomial or mixed logit utility model defined by user-provided prior parameters. Conduct a power analysis for a given survey design by estimating the same model on different subsets of the data to simulate different sample sizes. Choice simulation and model estimation in power analyses are handled using the 'logitr' package (Helveston, 2023) <doi:10.18637/jss.v105.i10>.
+Description: Design and evaluate choice-based conjoint survey experiments. Generate a variety of survey designs, including random designs, full factorial designs, orthogonal designs, D-optimal designs, and Bayesian D-efficient designs as well as designs with "no choice" options and "labeled" (also known as "alternative specific") designs. Conveniently inspect the design balance and overlap, and simulate choice data for a survey design either randomly or according to a multinomial or mixed logit utility model defined by user-provided prior parameters. Conduct a power analysis for a given survey design by estimating the same model on different subsets of the data to simulate different sample sizes. Full factorial and orthogonal designs are obtained using the 'DoE.base' package (Grömping, 2018) <doi:10.18637/jss.v085.i05>. D-optimal designs are obtained using the 'AlgDesign' package (Wheeler, 2022) <https://CRAN.R-project.org/package=AlgDesign>. Bayesian D-efficient designs are obtained using the 'idefix' package (Traets et al, 2020) <doi:10.18637/jss.v096.i03>. Choice simulation and model estimation in power analyses are handled using the 'logitr' package (Helveston, 2023) <doi:10.18637/jss.v105.i10>.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
+VignetteBuilder: knitr
 Depends:
     R (>= 3.5.0)
 Suggests:
     here,
+    knitr,
     testthat,
     tibble
 Imports:
+    AlgDesign,
     DoE.base,
     fastDummies,
     ggplot2,

NEWS.md

@@ -1,5 +1,11 @@
 # cbcTools (development version)
 
+# cbcTools 0.5.0
+
+- Further revisions to the `method` argument in the `cbc_design()` function.
+- Added the `"random"` and `"dopt"` methods.
+- Added restrictions so that orthogonal designs cannot use the `label` argument or restricted profile sets (as either of these would result in a non-orthogonal design).
+
 # cbcTools 0.4.0
 
 - Adjustments made to the `method` argument in the `cbc_design()` function in preparation for potentially adding new design methods.

R/input_checks.R

@@ -27,8 +27,22 @@ check_inputs_restrict <- function(profiles) {
 }
 
 check_design_method <- function(method, priors) {
+
+  # Check that an appropriate method is used
+
+  if (! method %in% c(
+    'random', 'full', 'orthogonal', 'dopt', 'CEA', 'Modfed'
+  )) {
+    stop(
+      'The "method" argument must be set to "random", "full", ',
+      '"orthogonal", "dopt", "CEA", or "Modfed"'
+    )
+  }
+
+  # Check that a Bayesian method is used if priors are used
+
   if (!is.null(priors)) {
-    if (! method_is_bayesian(method)) {
+    if (!method_is_bayesian(method)) {
       # Set method to 'CEA' if priors are specified and
       # user didn't specify an appropriate method.
       warning(
@@ -39,6 +53,7 @@ check_design_method <- function(method, priors) {
       method <- 'CEA'
     }
   }
+
   return(method)
 }
 
@@ -56,61 +71,73 @@ check_inputs_design <- function(
     priors,
     prior_no_choice,
     probs,
+    keep_d_eff,
     keep_db_error,
     max_iter,
-    parallel
+    parallel,
+    profiles_restricted
 ) {
 
+    # Checks on blocking
+
     if (n_blocks < 1) {
       stop('n_blocks must be greater than or equal to 1')
     }
 
     if (n_blocks > n_resp) {
-        stop("Maximum allowable number of blocks is one block per respondent")
+      stop("Maximum allowable number of blocks is one block per respondent")
     }
 
-    # If using a Bayesian D-efficient design with a no choice option, user must
-    # specify a value for prior_no_choice
-    if (no_choice) {
-      if (!is.null(priors) & is.null(prior_no_choice)) {
+    if ((n_blocks > 1) & (method == 'random')) {
+      stop(
+        'The "random" method cannot use blocking. Either change the design ',
+        'method or set "n_blocks = 1"'
+      )
+      if ((method == 'full') & profiles_restricted) {
         stop(
-          'If "no_choice = TRUE", you must specify the prior utility ',
-          'value for the "no choice" option using prior_no_choice'
+          'The "full" method cannot use restricted profiles when blocking ',
+          'is used. Either set "n_blocks" to 1 or use an unrestricted ',
+          'set of profiles'
         )
       }
     }
 
-    # The labeled design isn't yet supported for Bayesian D-efficient designs
+    # Checks on labeled designs
 
-    if (!is.null(label) & method_is_bayesian(method)) {
-      stop(
-        'The use of the "label" argument is currently not compatible with ',
-        'Bayesian D-efficient designs'
-      )
+    if (!is.null(label)) {
+      if (!method %in% c('random', 'full')) {
+        stop(
+          'Labeled designs are currently only supported with the "random" or ',
+          '"full" method.'
+        )
+      }
     }
 
-    # Check that an appropriate method is used
+    # Check on restricted profile sets
 
-    if (! method %in% c('full', 'orthogonal', 'CEA', 'Modfed')) {
+    if (profiles_restricted) {
+      if (!method %in% c('random', 'full')) {
         stop(
-            'The "method" argument must be set to "full", "orthogonal", ',
-            '"Modfed", or "CEA"'
+          'Restricted profile sets can only be used with the "random", "full" ',
+          '"dopt", or "Modfed" methods'
         )
+      }
     }
 
     # Check that priors are appropriate if specified
 
     if (!is.null(priors)) {
 
-        # Check that user specified an appropriate method
-        # This should already be handled
-        if (! method_is_bayesian(method)) {
-            stop(
-                'Since "priors" are specified, the "method" argument must ',
-                'be either "Modfed" or "CEA" to obtain a Bayesian ',
-                'D-efficient design'
-            )
-        }
+      # If using a Bayesian D-efficient design with a no choice option,
+      # user must specify a value for prior_no_choice
+
+      if (no_choice & is.null(prior_no_choice)) {
+        stop(
+          'If "no_choice = TRUE" with the "CEA" or "Modfed" method, you must ',
+          'specify the prior utility for the "no choice" option using ',
+          '"prior_no_choice"'
+        )
+      }
 
         # Check that prior names aren't missing
         prior_names <- names(priors)

R/power.R

@@ -249,19 +249,20 @@ extract_errors <- function(models) {
 #' @importFrom rlang .data
 #' @export
 #' @examples
+#' \dontrun{
 #' library(cbcTools)
 #'
 #' # Generate all possible profiles
 #' profiles <- cbc_profiles(
-#'   price     = c(1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5),
+#'   price     = c(1, 1.5, 2, 2.5, 3),
 #'   type      = c("Fuji", "Gala", "Honeycrisp"),
 #'   freshness = c('Poor', 'Average', 'Excellent')
 #' )
 #'
 #' # Make designs to compare: full factorial vs bayesian d-efficient
-#' design_full <- cbc_design(
+#' design_random <- cbc_design(
 #'   profiles = profiles,
-#'   n_resp = 300, n_alts = 3, n_q = 6
+#'   n_resp = 100, n_alts = 3, n_q = 6
 #' )
 #' # Same priors will be used in bayesian design and simulated choices
 #' priors <- list(
@@ -271,26 +272,27 @@ extract_errors <- function(models) {
 #' )
 #' design_bayesian <- cbc_design(
 #'   profiles  = profiles,
-#'   n_resp = 300, n_alts = 3, n_q = 6, n_start = 1, method = "CEA",
+#'   n_resp = 100, n_alts = 3, n_q = 6, n_start = 1, method = "CEA",
 #'   priors = priors, parallel = FALSE
 #' )
 #'
 #' # Obtain power for each design by simulating choices
-#' power_full <- design_full |>
+#' power_random <- design_random |>
 #' cbc_choices(obsID = "obsID", priors = priors) |>
 #'   cbc_power(
 #'     pars = c("price", "type", "freshness"),
-#'     outcome = "choice", obsID = "obsID", nbreaks = 10, n_q = 6, n_cores = 2
+#'     outcome = "choice", obsID = "obsID", nbreaks = 5, n_q = 6, n_cores = 2
 #'   )
 #' power_bayesian <- design_bayesian |>
 #'   cbc_choices(obsID = "obsID", priors = priors) |>
 #'   cbc_power(
 #'     pars = c("price", "type", "freshness"),
-#'     outcome = "choice", obsID = "obsID", nbreaks = 10, n_q = 6, n_cores = 2
+#'     outcome = "choice", obsID = "obsID", nbreaks = 5, n_q = 6, n_cores = 2
 #'   )
 #'
 #' # Compare power of each design
-#' plot_compare_power(power_bayesian, power_full)
+#' plot_compare_power(power_bayesian, power_random)
+#' }
 plot_compare_power <- function(...) {
   power <- list(...)
   design_names <- unlist(lapply(as.list(match.call())[-1], deparse))