fixes #49 and rsbivand/classInt#1

Author: rsbivand

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: classInt
 Version: 0.4-11
-Date: 2024-11-26
+Date: 2025-01-06
 Title: Choose Univariate Class Intervals
 Authors@R: c(
   person("Roger", "Bivand", role=c("aut", "cre"), email="[email protected]", comment=c(ORCID="0000-0003-2392-6140")),

NEWS.md

@@ -1,6 +1,6 @@
 ## Version 0.4-11
 
-- #49 permit use of `"quantile"` `style` `probs=` argument; should really use `n=`, as `probs` is set internally to `seq(0, 1, 1/n)`. For other vectors, the use of `"fixed"` `style` is preferable.
+- #49 explicitly forbid use of `"quantile"` style `probs=` argument; should really use `n=`, as `probs` is set internally to `seq(0, 1, 1/n)`. Similarly, forbid `centers=` argument in `"kmeans"` and `"bclust"` styles as it is set internally to `n`.
 
 ## Version 0.4-10
 

R/classInt.R

@@ -191,40 +191,19 @@ classIntervals <- function(var, n, style="quantile", rtimes=3, ..., intervalClos
       brks <- c(pretty(x=var, n=n, ...))
     } else if (style =="quantile") {
 # stats
-      dots <- list(...)
       probs <- seq(0, 1, 1/n)
+      dots <- list(...)
       if (!is.null(dots$probs)) {
-        if (n_missing) {
-          probs <- dots$probs
-        } else {
-          if (length(dots$probs)-1 != n) {
-            stop("both n and probs given, but length(probs)-1 != ", n)
-          } else probs <- dots$probs
-        }
-        r_probs <- range(probs)
-        if (r_probs[1] < 0 || r_probs[2] > 1)
-          stop("given probs range exceeds the unit interval: [",
-            paste(r_probs, collapse=", "), "]")
-        if (r_probs[1] != 0 || r_probs[2] != 1) {
-          warning("given probs range does not span the unit interval: [",
-            paste(r_probs, collapse=", "), "]")
-        }
-        if (length(unique(round(diff(probs), digits=14))) != 1L)
-           warning("given probs do not have equal steps")
+            stop("probs is set internally to seq(0, 1, 1/n) for style quantile\nit must not be passed in ...")
       }
-      na.rm <- FALSE
-      if (!is.null(dots$na.rm)) na.rm <- dots$na.rm
-      names <- FALSE
-      if (!is.null(dots$names)) names <- dots$names
-      type <- 7
-      if (!is.null(dots$type)) type <- dots$type
-      digits <- 7
-      if (!is.null(dots$digits)) digits <- dots$digits
-      brks <- c(quantile(x=var, probs=probs, na.rm=na.rm, names=names,
-        type=type, digits=digits))
+      brks <- c(quantile(x=var, probs=probs, ...))
       names(brks) <- NULL
     } else if (style =="kmeans") {
 # stats
+      dots <- list(...)
+      if (!is.null(dots$centers)) {
+            stop("centers is set internally to n for style kmeans\nit must not be passed in ...")
+      }
       pars <- try(kmeans(x=var, centers=n, ...))
       if (inherits(pars, "try-error")) {
         warning("jittering in kmeans")
@@ -252,6 +231,10 @@ classIntervals <- function(var, n, style="quantile", rtimes=3, ..., intervalClos
       brks <- .rbrks(rbrks)
     } else if (style =="bclust") {
 # e1071, class
+      dots <- list(...)
+      if (!is.null(dots$centers)) {
+            stop("centers is set internally to n for style bclust\nit must not be passed in ...")
+      }
       pars <- try(bclust(x=var, centers=n, ...))
       if (inherits(pars, "try-error")) {
         warning("jittering in bclust")

inst/tinytest/test_quantile_probs.R

@@ -2,17 +2,6 @@ library(classInt)
 # issue #1
 set.seed(101)
 data_censored <- c(rep(0,10), rnorm(100, mean=20,sd=1),rep(26,10))
-expect_silent(classInt::classIntervals(data_censored, style = "quantile", 
-  probs = seq(0, 1, 0.25)))
-expect_error(classInt::classIntervals(data_censored, style = "quantile", 
-  n = 5, probs = seq(0, 1, 0.25)))
-expect_silent(classInt::classIntervals(data_censored, style = "quantile", 
-  n = 4, probs = seq(0, 1, 0.25)))
 expect_error(classInt::classIntervals(data_censored, style = "quantile", 
-  probs = seq(-0.25, 1.25, 0.25)))
-expect_warning(classInt::classIntervals(data_censored, style = "quantile", 
-  probs = seq(0.25, 0.75, 0.25)))
-expect_error(classInt::classIntervals(data_censored, style = "quantile", 
-  probs = seq(0, 1, 0.25)-0.25))
-expect_warning(classInt::classIntervals(data_censored, style = "quantile", 
-  probs = c(0, 0.15804, 0.36603, 0.63975, 1))) # log sequence (bigsnpr::seq_log(1, 3, 5)-1)/2
+  probs = seq(0, 1, 0.25)))
+

man/classIntervals.Rd

@@ -53,7 +53,7 @@ classIntervals2shingle(x)
 
   The "pretty" style chooses a number of breaks not necessarily equal to n using \code{pretty}, but likely to be legible; arguments to \code{pretty} may be passed through \code{\dots}.
 
-  The "quantile" style provides quantile breaks; arguments to \code{quantile} may be passed through \code{\dots}. Rather than giving \code{probs}, use the \code{n} argument as by default \code{probs = seq(0, 1, 1/n)}. If \code{probs} is given, it should span the unit interval [0, 1]. If given \code{probs} values do not have equal steps, consider using \code{style = "fixed"} and giving \code{"fixedBreaks"} directly.
+  The "quantile" style provides quantile breaks; arguments to \code{quantile} may be passed through \code{\dots}. \code{probs} is never permitted, as it is set using the \code{n} argument to \code{probs = seq(0, 1, 1/n)}.
 
   The "kmeans" style uses \code{kmeans} to generate the breaks; it may be anchored using \code{set.seed}; the \code{pars} attribute returns the kmeans object generated; if \code{kmeans} fails, a jittered input vector containing \code{rtimes} replications of \code{var} is tried --- with few unique values in \code{var}, this can prove necessary; arguments to \code{kmeans} may be passed through \code{\dots}.