R Under development (unstable) (2026-07-17 r90265 ucrt) -- "Unsuffered Consequences"
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> # Regression tests for audit item 12: documentation / API-surface polish.
> #
> # Covered here:
> #   - binarize() emits a message (not a warning) when splitting continuous
> #     data into binary form.
> #   - differenceTest() on an undirected (pcor) bootstrap still resolves edge
> #     endpoints via the "--" separator (guards the undirected path after the
> #     "--"/"->" both-separator change).
> #   - estimateNetwork(default = "Borsboom") now errors via match.arg()
> #     instead of returning the removed easter-egg value 42.
> #   - Building a case-drop area plot no longer opens a graphics device as a
> #     side effect (previously par("pin") created an Rplots.pdf in scripts).
> 
> library(bootnet)
Loading required package: ggplot2
This is bootnet 1.9.1
For questions and issues, please see github.com/SachaEpskamp/bootnet.
> 
> set.seed(1)
> 
> ## ---------------------------------------------------------------------------
> ## (a) binarize(): median split emits a message, not a warning.
> ## ---------------------------------------------------------------------------
> contData <- as.data.frame(matrix(rnorm(40 * 4), ncol = 4))
> colnames(contData) <- paste0("V", 1:4)
> 
> msgs <- character(0)
> warns <- character(0)
> res <- withCallingHandlers(
+     bootnet:::binarize(contData, verbose = TRUE),
+     message = function(m) {
+         msgs <<- c(msgs, conditionMessage(m))
+         invokeRestart("muffleMessage")
+     },
+     warning = function(w) {
+         warns <<- c(warns, conditionMessage(w))
+         invokeRestart("muffleWarning")
+     }
+ )
> stopifnot(any(grepl("Splitting data by", msgs, fixed = TRUE)))
> # The splitting notice must no longer be a warning:
> stopifnot(!any(grepl("Splitting data by", warns, fixed = TRUE)))
> # Result is 0/1 binary:
> stopifnot(all(unlist(res) %in% c(0, 1)))
> 
> ## Constant-column guard: a column that is constant after a median split
> ## should now trigger a real warning.
> constData <- data.frame(
+     A = c(1, 2, 3, 4, 5, 6),   # normal, splits into 0/1
+     B = c(5, 5, 5, 5, 5, 5)    # constant -> constant after any split
+ )
> warns2 <- character(0)
> invisible(withCallingHandlers(
+     bootnet:::binarize(constData, verbose = FALSE),
+     warning = function(w) {
+         warns2 <<- c(warns2, conditionMessage(w))
+         invokeRestart("muffleWarning")
+     }
+ ))
> stopifnot(any(grepl("constant", warns2, ignore.case = TRUE)))
> 
> ## ---------------------------------------------------------------------------
> ## (b) differenceTest() on an undirected pcor bootstrap ("--" IDs).
> ## ---------------------------------------------------------------------------
> set.seed(2)
> gdata <- as.data.frame(matrix(rnorm(60 * 4), ncol = 4))
> colnames(gdata) <- paste0("V", 1:4)
> 
> boot <- bootnet(gdata, default = "pcor", nBoots = 8, verbose = FALSE,
+                 statistics = c("edge", "strength"))
Note: bootnet will store only the following statistics:  edge, strength
> 
> # Strength difference test (node IDs, no separator involved):
> dtStrength <- differenceTest(boot, x = "V1", y = "V2",
+                              measure = "strength", verbose = FALSE)
> stopifnot(is.data.frame(dtStrength))
> stopifnot(nrow(dtStrength) >= 1)
> 
> # Edge difference test using x2/y2 endpoints -> exercises the "--" branch of
> # the both-separator resolution added in item 12.
> dtEdge <- differenceTest(boot, x = "V1", x2 = "V2", y = "V3", y2 = "V4",
+                          measure = "edge", verbose = FALSE)
> stopifnot(is.data.frame(dtEdge))
> stopifnot(nrow(dtEdge) >= 1)
> # Directed "->" path is not exercised here: the cheap defaults (pcor) produce
> # undirected networks only; directed defaults (e.g. relimp) are heavy, so the
> # directed separator is left to the code path guarded by "--" symmetry.
> 
> ## ---------------------------------------------------------------------------
> ## (c) estimateNetwork(default = "Borsboom") now errors (no easter egg).
> ## ---------------------------------------------------------------------------
> borsboom <- tryCatch(
+     estimateNetwork(gdata, default = "Borsboom", verbose = FALSE),
+     error = function(e) e
+ )
> stopifnot(inherits(borsboom, "error"))
> stopifnot(!identical(borsboom, 42))
> 
> ## ---------------------------------------------------------------------------
> ## (d) No-device safety: building a case-drop area plot must not create an
> ##     Rplots.pdf via par("pin").
> ## ---------------------------------------------------------------------------
> owd <- setwd(tempdir())
> on.exit(setwd(owd), add = TRUE)
> 
> # Make sure we start clean and that no device is currently open.
> if (file.exists("Rplots.pdf")) file.remove("Rplots.pdf")
> while (!is.null(grDevices::dev.list())) grDevices::dev.off()
> 
> set.seed(3)
> bootPerson <- bootnet(gdata, default = "pcor", type = "case",
+                       nBoots = 8, caseN = 3, verbose = FALSE,
+                       statistics = "strength")
Note: bootnet will store only the following statistics:  strength
> 
> # Default plot for a case-drop bootstrap is the "area" branch that used
> # par("pin"). ggplot_build forces construction without opening a device.
> g <- plot(bootPerson, statistics = "strength")
> invisible(ggplot2::ggplot_build(g))
> 
> stopifnot(!file.exists("Rplots.pdf"))
> 
> setwd(owd)
> 
> cat("item12-polish: OK\n")
item12-polish: OK
> 
> proc.time()
   user  system elapsed 
   5.78    0.92    6.70