Simplify code in examples

R/checkPairwise.R

@@ -37,8 +37,7 @@
 #' ### Example with realistic data
 #'
 #' x = avuncularPed() |>
-#'   setMarkers(locus = NorwegianFrequencies) |>
-#'   profileSim(N = 1, simplify1 = TRUE, seed = 1729)
+#'   profileSim(markers = NorwegianFrequencies, seed = 1729)
 #'
 #' checkPairwise(x)
 #'
@@ -53,7 +52,7 @@
 #' # Combined plot of pedigree and IBD estimates
 #' dev.new(height = 5, width = 8, noRStudioGD = TRUE)
 #' layout(rbind(1:2), widths = 2:3)
-#' plot(y, margins = c(4,2,4,2), title = "Sample swap 1 - 3")
+#' plot(y, margins = c(4,2,4,2), title = "Swapped 1 - 3")
 #' checkPairwise(y, labels = TRUE)
 #' }
 #'

R/findExclusions.R

@@ -10,15 +10,15 @@
 #'
 #' @examples
 #'
+#' db = NorwegianFrequencies[1:5]
+#'
 #' # Pedigree with 3 siblings; simulate data for first two
 #' x = nuclearPed(3) |>
-#'   setMarkers(locusAttributes = NorwegianFrequencies[1:5]) |>
-#'   profileSim(ids = 3:4, seed = 1)
+#'   profileSim(ids = 3:4, markers = db, seed = 1)
 #'
 #' # Simulate random person
 #' poi = singleton("POI") |>
-#'   setMarkers(locusAttributes = NorwegianFrequencies[1:5]) |>
-#'   profileSim(seed = 1)
+#'   profileSim(markers = db, seed = 1)
 #'
 #' # Identify incompatible markers
 #' findExclusions(x, id = 5, candidate = poi)   # D21S11

R/missingPersonLR.R

@@ -26,8 +26,7 @@
 #' db = NorwegianFrequencies[1:5]
 #'
 #' # Simulate reference data for grandmother and MP (5 STR markers)
-#' x = setMarkers(x, locusAttributes = db)
-#' x = profileSim(x, N = 1, ids = c(2, "MP"), seed = 2509)
+#' x = profileSim(x, markers = db, ids = c(2, "MP"), seed = 2509)
 #'
 #' # Compute LR
 #' lr = missingPersonLR(x, missing = "MP")

R/powerPlot.R

@@ -66,16 +66,16 @@
 #'
 #' ### Example 1: Comparing the power of 3 reference families ###
 #'
-#' # Helper function for simulating a single profile
-#' sim = function(x, id) {
-#'   y = setMarkers(x, locusAttributes = NorwegianFrequencies[1:3])
-#'   profileSim(y, N = 1, ids = id)
-#' }
+#' # Frequencies for 3 STR markers
+#' db = NorwegianFrequencies[1:3]
 #'
 #' # Define pedigrees and simulate data
-#' PAR = nuclearPed(1, child = "MP") |> sim(id = 1)
-#' SIB = nuclearPed(2) |> relabel(old = 4, new = "MP") |> sim(id = 3)
-#' GRA = linearPed(2) |> relabel(old = 5, new = "MP") |> sim(id = 1)
+#' PAR = nuclearPed(1, child = "MP") |>
+#'   profileSim(markers = db, ids = 1)
+#' SIB = nuclearPed(2) |> relabel(old = 4, new = "MP") |>
+#'   profileSim(markers = db, ids = 3)
+#' GRA = linearPed(2) |> relabel(old = 5, new = "MP") |>
+#'   profileSim(markers = db, ids = 1)
 #'
 #' # Collect in list and plot
 #' peds = list(PAR = PAR, SIB = SIB, GRA = GRA)
@@ -91,7 +91,6 @@
 #'
 #' # Plot
 #' powerPlot(ep, ip, size = 2)
-#' powerPlot(ep, ip, size = 2, jitter = TRUE)
 #'
 #' # Different plot type, not dependent of `threshold`
 #' powerPlot(ep, ip, size = 2, type = 3)