addressing #49

Author: rsbivand

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: classInt
-Version: 0.4-10
-Date: 2023-08-24
+Version: 0.4-11
+Date: 2024-11-26
 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")),

R/classInt.R

@@ -107,7 +107,11 @@ classIntervals <- function(var, n, style="quantile", rtimes=3, ..., intervalClos
   # Fix 22: Diego Hernangómez
   needn <- !(style %in% c("dpih", "headtails", "box"))
 
-  if (missing(n)) n <- nclass.Sturges(var)
+  n_missing <- FALSE
+  if (missing(n)) {
+    n <- nclass.Sturges(var)
+    n_missing <- TRUE
+  }
   if (n < 2 & needn) stop("n less than 2")
   n <- as.integer(n)
   pars <- NULL
@@ -187,7 +191,27 @@ classIntervals <- function(var, n, style="quantile", rtimes=3, ..., intervalClos
       brks <- c(pretty(x=var, n=n, ...))
     } else if (style =="quantile") {
 # stats
-      brks <- c(quantile(x=var, probs=seq(0,1,1/n), ...))
+      dots <- list(...)
+      probs <- seq(0,1,1/n)
+      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
+        }
+      }
+      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))
       names(brks) <- NULL
     } else if (style =="kmeans") {
 # stats

inst/tinytest/test_quantile_probs.R

@@ -0,0 +1,11 @@
+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)))
+

man/classIntervals.Rd

@@ -96,7 +96,7 @@ Dent, B. D., 1999, Cartography: thematic map design. McGraw-Hill, Boston, 417 pp
 
 Slocum TA, McMaster RB, Kessler FC, Howard HH 2005 Thematic Cartography and Geographic Visualization, Prentice Hall, Upper Saddle River NJ.;
 
-Fisher, W. D. 1958 "On grouping for maximum homogeneity", Journal of the American Statistical Association, 53, pp. 789--798 (\url{http://lib.stat.cmu.edu/cmlib/src/cluster/fish.f})
+Fisher, W. D. 1958 "On grouping for maximum homogeneity", Journal of the American Statistical Association, 53, pp. 789--798 (\url{https://lib.stat.cmu.edu/cmlib/src/cluster/fish.f})
 
 Wand, M. P. 1995. Data-based choice of histogram binwidth. The American Statistician, 51, 59-64.