Reorganised handling of tolerances.

   psp.R
   lengths.psp.Rd
	New argument 'squared'

   lineardisc.R
   spatstat-internal.Rd
	New internal function makeLinnetTolerance

   linnet.R
	reorganised/polished code for computing numerical tolerance threshold.

   chicago.rda
   dendrite.rda
   spiders.rda
   simplenet.rda
	Rebuilt datasets.

   circum.R -> boundingcircle.R [Renamed]
   circumradius.Rd -> boundingcircle.Rd [Renamed]
   spatstat-deprecated.Rd
	'circum*' functions renamed 'bounding*'
	eg boundingradius, boundingcircle
	Old names exist but are deprecated.

   edgeRipley.R
   Kest.R
   linearK.R
   linearpcf.R
   linearKmulti.R
   linearpcfmulti.R
   treebranches.R
	Replaced circum* by bounding*

   updates.Rnw
	updated to cover all the above.

   tests/lppstuff.R
	Added test of countends()

   DESCRIPTION
   NEWS
        Nickname changed to 'Pons Asinorum'
	Updated as version 1.46-1.008

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: spatstat
-Version: 1.46-1.007
-Nickname: Ultracrepidarian
-Date: 2016-07-15
+Version: 1.46-1.008
+Nickname: Pons Asinorum
+Date: 2016-07-16
 Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
 Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
 	Rolf Turner <r.turner@auckland.ac.nz> 

NAMESPACE

@@ -456,6 +456,16 @@ export("boundingbox.owin")
 export("boundingbox.ppp")
 export("boundingbox.solist")
 export("bounding.box.xy")
+export("boundingcentre")
+export("boundingcentre.owin")
+export("boundingcentre.ppp")
+export("boundingcircle")
+export("boundingcircle.owin")
+export("boundingcircle.ppp")
+export("boundingradius")
+export("boundingradius.linnet")
+export("boundingradius.owin")
+export("boundingradius.ppp")
 export("box3")
 export("boxx")
 export("branchlabelfun")
@@ -516,12 +526,6 @@ export("chop.tess")
 export("choptext")
 export("circdensity")
 export("circticks")
-export("circumcentre")
-export("circumcentre.owin")
-export("circumcentre.ppp")
-export("circumcircle")
-export("circumcircle.owin")
-export("circumcircle.ppp")
 export("circumradius")
 export("circumradius.linnet")
 export("circumradius.owin")
@@ -1393,6 +1397,7 @@ export("mad.test")
 export("majorminorversion")
 export("make.even.breaks")
 export("makefvlabel")
+export("makeLinnetTolerance")
 export("make.parseable")
 export("makeunits")
 export("mapSparseEntries")
@@ -2841,6 +2846,13 @@ S3method("boundingbox", "im")
 S3method("boundingbox", "owin")
 S3method("boundingbox", "ppp")
 S3method("boundingbox", "solist")
+S3method("boundingcentre", "owin")
+S3method("boundingcentre", "ppp")
+S3method("boundingcircle", "owin")
+S3method("boundingcircle", "ppp")
+S3method("boundingradius", "linnet")
+S3method("boundingradius", "owin")
+S3method("boundingradius", "ppp")
 S3method("by", "im")
  S3method("by", "ppp")
 S3method("cbind", "fv")
@@ -2852,10 +2864,6 @@ S3method("cdf.test", "mppm")
 S3method("cdf.test", "ppm")
 S3method("cdf.test", "ppp")
 S3method("cdf.test", "slrm")
-S3method("circumcentre", "owin")
-S3method("circumcentre", "ppp")
-S3method("circumcircle", "owin")
-S3method("circumcircle", "ppp")
 S3method("circumradius", "linnet")
 S3method("circumradius", "owin")
 S3method("circumradius", "ppp")

NEWS

@@ -1,21 +1,21 @@
 
-        CHANGES IN spatstat VERSION 1.46-1.007
+        CHANGES IN spatstat VERSION 1.46-1.008
 
 OVERVIEW
 
     o We thank Mehdi Moradi and Jorge Mateu for contributions.
 
-    o Circumcentre and circumcircle.
-
     o Non-Gaussian smoothing kernels.
 
     o Important bug fix in linearK, linearpcf
 
-    o Version nickname: 'Ultracrepidarian'
+    o Bounding circle of a spatial object.
+
+    o Version nickname: 'Pons Asinorum'
 
 NEW FUNCTIONS
 
-    o circumcircle, circumcentre
+    o boundingcircle, boundingcentre
     Find the smallest circle enclosing a window or point pattern.
 
 SIGNIFICANT USER-VISIBLE CHANGES
@@ -26,13 +26,19 @@ SIGNIFICANT USER-VISIBLE CHANGES
     o rcellnumber
     New argument 'mu'.
 
+    o lengths.psp
+    New argument 'squared'.
+
     o density.ppp, Smooth.ppp
     Computation accelerated by about 15% 
     in the case where at='points' and kernel='gaussian'.
 
     o linearK, linearpcf
     Accelerated.
 
+    o circumradius
+    This function is now deprecated, in favour of 'boundingradius'
+
 BUG FIXES
 
     o linearK, linearpcf, and relatives:

R/Kest.R

@@ -1,7 +1,7 @@
 #
 #	Kest.R		Estimation of K function
 #
-#	$Revision: 5.118 $	$Date: 2016/04/01 05:55:30 $
+#	$Revision: 5.119 $	$Date: 2016/07/16 03:08:23 $
 #
 #
 # -------- functions ----------------------------------------
@@ -292,7 +292,7 @@ function(X, ..., r=NULL, rmax=NULL, breaks=NULL,
       wh <- whist(DIJ, breaks$val, edgewt)
       numKiso <- cumsum(wh)
       denKiso <- lambda2 * areaW
-      h <- circumradius(W)
+      h <- boundingradius(W)
       numKiso[r >= h] <- NA
       K <- bind.ratfv(K,
                       data.frame(iso=numKiso),

R/boundingcircle.R

@@ -0,0 +1,69 @@
+#'
+#'    boundingcircle.R
+#'
+#'  bounding circle and its centre
+#'
+#'  $Revision: 1.5 $ $Date: 2016/07/16 03:07:02 $
+#'
+
+circumradius <- function(x, ...) {
+  .Deprecated(boundingradius)
+  UseMethod("boundingradius")
+}
+circumradius.owin <- function(x, ...) {
+  .Deprecated(boundingradius.owin)
+  boundingradius.owin(x, ...)
+}
+circumradius.ppp <- function(x, ...) {
+  .Deprecated(boundingradius.ppp)
+  boundingradius.ppp(x, ...)
+}
+
+boundingradius <- function(x, ...) {
+  UseMethod("boundingradius")
+}
+
+boundingcentre <- function(x, ...) {
+  UseMethod("boundingcentre")
+}
+
+boundingcircle <- function(x, ...) {
+  UseMethod("boundingcircle")
+}
+
+#' owin
+
+boundingradius.owin <- function(x, ...) {
+  sqrt(min(fardist(x, ..., squared=TRUE)))
+}
+
+boundingcentre.owin <- function(x, ...) {
+  z <- where.min(fardist(x, ..., squared=TRUE))
+  Window(z) <- x
+  return(z)
+}
+
+boundingcircle.owin <- function(x, ...) {
+  d2 <- fardist(x, ..., squared=TRUE)
+  z <- where.min(d2)
+  r <- sqrt(min(d2))
+  w <- disc(centre=z, radius=r) 
+  return(w)
+}
+
+#' ppp
+
+boundingradius.ppp <- function(x, ...) {
+  boundingradius(convexhull(x), ...)
+}
+
+boundingcentre.ppp <- function(x, ...) {
+  z <- boundingcentre(convexhull(x), ...)
+  Window(z) <- Window(x)
+  return(z)
+}
+
+boundingcircle.ppp <- function(x, ...) {
+  boundingcircle(convexhull(x), ...)
+}
+

R/edgeRipley.R

@@ -1,7 +1,7 @@
 #
 #        edgeRipley.R
 #
-#    $Revision: 1.13 $    $Date: 2016/04/25 02:34:40 $
+#    $Revision: 1.15 $    $Date: 2016/07/16 03:11:15 $
 #
 #    Ripley isotropic edge correction weights
 #
@@ -173,11 +173,11 @@ edge.Ripley <- local({
 rmax.Ripley <- function(W) {
   W <- as.owin(W)
   if(is.rectangle(W))
-    return(circumradius(W))
+    return(boundingradius(W))
   if(is.polygonal(W) && length(W$bdry) == 1)
-    return(circumradius(W))
+    return(boundingradius(W))
   ## could have multiple connected components
   pieces <- tiles(tess(image=connected(W)))
-  answer <- sapply(pieces, circumradius)
+  answer <- sapply(pieces, boundingradius)
   return(as.numeric(answer))
 }

R/linearK.R

@@ -1,7 +1,7 @@
 #
 # linearK
 #
-# $Revision: 1.37 $ $Date: 2016/07/15 12:09:15 $
+# $Revision: 1.38 $ $Date: 2016/07/16 03:08:23 $
 #
 # K function for point pattern on linear network
 #
@@ -122,7 +122,7 @@ linearKengine <- function(X, ..., r=NULL, reweight=NULL, denom=1,
   Y <- as.ppp(X)
   W <- Y$window
   # determine r values
-  rmaxdefault <- 0.98 * circumradius(L)
+  rmaxdefault <- 0.98 * boundingradius(L)
   breaks <- handle.r.b.args(r, NULL, W, rmaxdefault=rmaxdefault)
   r <- breaks$r
   rmax <- breaks$max

R/linearKmulti.R

@@ -1,7 +1,7 @@
 #
 # linearKmulti
 #
-# $Revision: 1.8 $ $Date: 2016/07/15 12:09:29 $
+# $Revision: 1.9 $ $Date: 2016/07/16 03:08:23 $
 #
 # K functions for multitype point pattern on linear network
 #
@@ -199,7 +199,7 @@ linearKmultiEngine <- function(X, I, J, ..., r=NULL, reweight=NULL, denom=1,
   XP <- as.ppp(X)
   W <- as.owin(XP)
   # determine r values
-  rmaxdefault <- 0.98 * circumradius(L)
+  rmaxdefault <- 0.98 * boundingradius(L)
   breaks <- handle.r.b.args(r, NULL, W, rmaxdefault=rmaxdefault)
   r <- breaks$r
   rmax <- breaks$max

R/lineardisc.R

@@ -209,10 +209,21 @@ countends <- function(L, x=locator(1), r, toler=NULL) {
 }
 
 default.linnet.tolerance <- function(L) {
+  # L could be a linnet or psp
   if(!is.null(toler <- L$toler)) return(toler)
-  lenfs <- lengths.psp(as.psp(L))
-  toler <- 0.001 * min(lenfs[lenfs > 0])
-  toler <- max(sqrt(.Machine$double.xmin),
-               toler[is.finite(toler)], na.rm=TRUE)
+  len2 <- lengths.psp(as.psp(L), squared=TRUE)
+  len2pos <- len2[len2 > 0]
+  toler <- if(length(len2pos) == 0) 0 else (0.001 * sqrt(min(len2pos)))
+  toler <- makeLinnetTolerance(toler)
   return(toler)
 }
+
+makeLinnetTolerance <- function(toler) {
+  max(sqrt(.Machine$double.xmin),
+      toler[is.finite(toler)], na.rm=TRUE)
+}
+
+
+
+
+

R/linearpcf.R

@@ -1,7 +1,7 @@
 #
 # linearpcf.R
 #
-# $Revision: 1.15 $ $Date: 2016/07/15 12:08:39 $
+# $Revision: 1.16 $ $Date: 2016/07/16 03:08:23 $
 #
 # pair correlation function for point pattern on linear network
 #
@@ -91,7 +91,7 @@ linearpcfengine <- function(X, ..., r=NULL,
   Y <- as.ppp(X)
   W <- Y$window
   # determine r values
-  rmaxdefault <- 0.98 * circumradius(L)
+  rmaxdefault <- 0.98 * boundingradius(L)
   breaks <- handle.r.b.args(r, NULL, W, rmaxdefault=rmaxdefault)
   r <- breaks$r
   rmax <- breaks$max

R/linearpcfmulti.R

@@ -1,7 +1,7 @@
 #
 # linearpcfmulti.R
 #
-# $Revision: 1.7 $ $Date: 2016/07/15 12:08:51 $
+# $Revision: 1.8 $ $Date: 2016/07/16 03:08:23 $
 #
 # pair correlation functions for multitype point pattern on linear network
 #
@@ -198,7 +198,7 @@ linearPCFmultiEngine <- function(X, I, J, ..., r=NULL, reweight=NULL, denom=1,
   XP <- as.ppp(X)
   W <- as.owin(XP)
   # determine r values
-  rmaxdefault <- 0.98 * circumradius(L)
+  rmaxdefault <- 0.98 * boundingradius(L)
   breaks <- handle.r.b.args(r, NULL, W, rmaxdefault=rmaxdefault)
   r <- breaks$r
   rmax <- breaks$max