Normalize beta parameter string aliases before calling downstream functions (#111)

* Initial plan

* Normalize beta parameter string aliases to TRUE/FALSE before calling downstream functions

Co-authored-by: smasongarrison <6001608+smasongarrison@users.noreply.github.com>

* Fix inconsistencies in beta parameter validation and add support for all string aliases

Co-authored-by: smasongarrison <6001608+smasongarrison@users.noreply.github.com>

* Fix test for original alias to use proper seed and add test for index alias

Co-authored-by: smasongarrison <6001608+smasongarrison@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: smasongarrison <6001608+smasongarrison@users.noreply.github.com>

Author: Copilot

R/simulatePedigree.R

@@ -27,7 +27,20 @@ buildBetweenGenerations <- function(df_Fam, Ngen, sizeGens, verbose = FALSE, mar
                                     momID = "momID",
                                     dadID = "dadID",
                                     code_male = "M", code_female = "F", beta = FALSE) {
-  if (beta == TRUE || beta %in% c("optimized", "index", "indexed")) {
+  # Normalize string aliases to logical values for downstream functions
+  use_optimized <- FALSE
+  
+  if (beta %in% c("index", "indexed")) {
+    stop("The 'index' or 'indexed' option for parameter 'beta' is not yet implemented.")
+  } else if (isTRUE(beta) || identical(beta, "optimized")) {
+    use_optimized <- TRUE
+  } else if (isFALSE(beta) || beta %in% c("base", "original") || is.null(beta)) {
+    use_optimized <- FALSE
+  } else {
+    stop("Invalid value for parameter 'beta'. Accepted values are TRUE, FALSE, 'optimized', 'base', 'original', or 'index'/'indexed'.")
+  }
+  
+  if (use_optimized) {
     df_Fam <- buildBetweenGenerations_optimized(
       df_Fam = df_Fam,
       Ngen = Ngen,
@@ -42,9 +55,9 @@ buildBetweenGenerations <- function(df_Fam, Ngen, sizeGens, verbose = FALSE, mar
       dadID = dadID,
       code_male = code_male,
       code_female = code_female,
-      beta = beta
+      beta = TRUE
     )
-  } else if (beta == FALSE || beta %in% c("base", "original") || is.null(beta)) {
+  } else {
     df_Fam <- buildBetweenGenerations_base(
       df_Fam = df_Fam,
       Ngen = Ngen,
@@ -59,10 +72,8 @@ buildBetweenGenerations <- function(df_Fam, Ngen, sizeGens, verbose = FALSE, mar
       dadID = dadID,
       code_male = code_male,
       code_female = code_female,
-      beta = beta
+      beta = FALSE
     )
-  } else {
-    stop("Invalid value for beta parameter. Use TRUE/'optimized' or FALSE/'base'.")
   }
   return(df_Fam)
 }

R/simulatePedigree_within.R

@@ -17,7 +17,20 @@ buildWithinGenerations <- function(
   code_female = "F",
   fam_shift = 1L
 ) {
-  if (beta == TRUE || beta == "optimized") {
+  # Normalize string aliases to logical values for downstream functions
+  use_optimized <- FALSE
+  
+  if (beta %in% c("index", "indexed")) {
+    stop("The 'index' or 'indexed' option for parameter 'beta' is not yet implemented.")
+  } else if (isTRUE(beta) || identical(beta, "optimized")) {
+    use_optimized <- TRUE
+  } else if (isFALSE(beta) || beta %in% c("base", "original") || is.null(beta)) {
+    use_optimized <- FALSE
+  } else {
+    stop("Invalid value for parameter 'beta'. Accepted values are TRUE, FALSE, 'optimized', 'base', 'original', or 'index'/'indexed'.")
+  }
+  
+  if (use_optimized) {
     df_Fam <- buildWithinGenerations_optimized(
       sizeGens = sizeGens,
       marR = marR,
@@ -30,11 +43,9 @@ buildWithinGenerations <- function(
       code_male = code_male,
       code_female = code_female,
       fam_shift = fam_shift,
-      beta = beta
+      beta = TRUE
     )
-  } else if (beta %in% c("index", "indexed")) {
-    stop("The 'index' or 'indexed' option for parameter 'beta' is not yet implemented.")
-  } else if (beta == FALSE || is.null(beta)) {
+  } else {
     df_Fam <- buildWithinGenerations_base(
       sizeGens = sizeGens,
       marR = marR,
@@ -47,10 +58,8 @@ buildWithinGenerations <- function(
       code_male = code_male,
       code_female = code_female,
       fam_shift = fam_shift,
-      beta = beta
+      beta = FALSE
     )
-  } else {
-    stop("Invalid value for parameter 'beta'. Accepted values are TRUE, FALSE, 'optimized', or 'index'.")
   }
   return(df_Fam)
 }

tests/testthat/test-simulatePedigree.R

@@ -165,3 +165,61 @@ test_that("simulatePedigree verbose prints updates", {
     message("Beta option Ending: ", beta)
   }
 })
+
+test_that("simulatePedigree accepts string aliases for beta parameter", {
+  seed <- 5
+  Ngen <- 4
+  kpc <- 4
+  sexR <- .50
+  marR <- .7
+  
+  # Test that "optimized" string alias works
+  set.seed(seed)
+  result_true <- simulatePedigree(kpc = kpc, Ngen = Ngen, sexR = sexR, marR = marR, beta = TRUE)
+  
+  set.seed(seed)
+  result_optimized <- simulatePedigree(kpc = kpc, Ngen = Ngen, sexR = sexR, marR = marR, beta = "optimized")
+  
+  # Results should be identical when using TRUE vs "optimized"
+  expect_equal(nrow(result_true), nrow(result_optimized))
+  expect_equal(ncol(result_true), ncol(result_optimized))
+  expect_equal(result_true$ID, result_optimized$ID)
+  
+  # Test that "base" string alias works
+  set.seed(seed)
+  result_false <- simulatePedigree(kpc = kpc, Ngen = Ngen, sexR = sexR, marR = marR, beta = FALSE)
+  
+  set.seed(seed)
+  result_base <- simulatePedigree(kpc = kpc, Ngen = Ngen, sexR = sexR, marR = marR, beta = "base")
+  
+  # Results should be identical when using FALSE vs "base"
+  expect_equal(nrow(result_false), nrow(result_base))
+  expect_equal(ncol(result_false), ncol(result_base))
+  expect_equal(result_false$ID, result_base$ID)
+  
+  # Test that "original" string alias works
+  set.seed(seed)
+  result_original <- simulatePedigree(kpc = kpc, Ngen = Ngen, sexR = sexR, marR = marR, beta = "original")
+  
+  # Results should be identical when using FALSE vs "original"
+  expect_equal(nrow(result_false), nrow(result_original))
+  expect_equal(ncol(result_false), ncol(result_original))
+  expect_equal(result_false$ID, result_original$ID)
+  
+  # Test that invalid beta values throw errors
+  expect_error(
+    simulatePedigree(kpc = kpc, Ngen = Ngen, sexR = sexR, marR = marR, beta = "invalid"),
+    "Invalid value for parameter"
+  )
+  
+  # Test that "index" and "indexed" both throw appropriate error
+  expect_error(
+    simulatePedigree(kpc = kpc, Ngen = Ngen, sexR = sexR, marR = marR, beta = "index"),
+    "not yet implemented"
+  )
+  
+  expect_error(
+    simulatePedigree(kpc = kpc, Ngen = Ngen, sexR = sexR, marR = marR, beta = "indexed"),
+    "not yet implemented"
+  )
+})