Bug fix in lppm; add warnings about scaled distances

spatstat · Jan 18, 2025 · 718d397 · 718d397
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: spatstat.linnet
-Version: 3.2-3
-Date: 2024-11-19
+Version: 3.2-3.001
+Date: 2025-01-18
 Title: Linear Networks Functionality of the 'spatstat' Family
 Authors@R: c(person("Adrian", "Baddeley", 
                     role = c("aut", "cre", "cph"),
@@ -25,8 +25,8 @@ Authors@R: c(person("Adrian", "Baddeley",
 	     person("Ottmar", "Cronie",
 	            role = "ctb"))
 Maintainer: Adrian Baddeley <[email protected]>
-Depends: R (>= 3.5.0), stats, graphics, grDevices, methods, utils, spatstat.data (>= 3.1-4), spatstat.univar (>= 3.1-1), spatstat.geom (>= 3.3-4), spatstat.random (>= 3.3-2), spatstat.explore (>= 3.3-3), spatstat.model (>= 3.3-2)
-Imports: Matrix, spatstat.utils (>= 3.1-1), spatstat.sparse (>= 3.1-0)
+Depends: R (>= 3.5.0), stats, graphics, grDevices, methods, utils, spatstat.data (>= 3.1-4), spatstat.univar (>= 3.1-1), spatstat.geom (>= 3.3-4), spatstat.random (>= 3.3-2), spatstat.explore (>= 3.3-3), spatstat.model (>= 3.3-3.002)
+Imports: Matrix, spatstat.utils (>= 3.1-2), spatstat.sparse (>= 3.1-0)
 Suggests: goftest, locfit, spatstat (>= 3.0)
 Description: Defines types of spatial data on a linear network
 	     and provides functionality for geometrical operations,

diff --git a/NEWS b/NEWS
@@ -1,4 +1,20 @@
 
+        CHANGES IN spatstat.linnet VERSION 3.2-3.001
+
+OVERVIEW
+
+    o Bug fix in lppm.
+
+BUG FIXES
+
+    o lppm
+    For models involving covariates of class 'lintess', the internal
+    structure of the fitted model was corrupted, leading to errors in
+    calculating properties of the fitted model, such as predict.lppm.
+    [Spotted by Andrea Gilardi.]
+    [Bug fix requires spatstat.model 3.3-3.002]
+    Fixed.
+
         CHANGES IN spatstat.linnet VERSION 3.2-3
 
 OVERVIEW

diff --git a/inst/doc/packagesizes.txt b/inst/doc/packagesizes.txt
@@ -33,4 +33,6 @@ date version nhelpfiles nobjects ndatasets Rlines srclines
 "2024-02-04" "3.1-4" 148 312 0 12340 3270
 "2024-03-24" "3.1-5" 148 312 0 12343 3270
 "2024-07-09" "3.2-1" 148 324 0 12882 3270
+"2024-09-18" "3.2-2" 148 324 0 12882 3270
 "2024-11-19" "3.2-3" 148 324 0 12980 3270
+"2025-01-18" "3.2-3.001" 148 324 0 12980 3270
diff --git a/inst/info/packagesizes.txt b/inst/info/packagesizes.txt
@@ -33,4 +33,6 @@ date version nhelpfiles nobjects ndatasets Rlines srclines
 "2024-02-04" "3.1-4" 148 312 0 12340 3270
 "2024-03-24" "3.1-5" 148 312 0 12343 3270
 "2024-07-09" "3.2-1" 148 324 0 12882 3270
+"2024-09-18" "3.2-2" 148 324 0 12882 3270
 "2024-11-19" "3.2-3" 148 324 0 12980 3270
+"2025-01-18" "3.2-3.001" 148 324 0 12980 3270
diff --git a/man/distfun.lpp.Rd b/man/distfun.lpp.Rd
@@ -60,6 +60,18 @@
   It also belongs to the class \code{"linfun"} which has methods
   for \code{plot}, \code{print} etc.
 }
+\section{Distance values}{
+  The values returned by the distance function
+  \code{f <- distfun(X)} are distances,
+  expressed as multiples of the unit of length of the spatial
+  coordinates in \code{X}.
+  The unit of length is given by \code{\link{unitname}(X)}.
+
+  Note that, if the unit of length in \code{X} is
+  a composite expression such as \sQuote{2 microns},
+  then the values of \code{f} are expressed as multiples
+  of 2 microns, rather than being expressed in microns.
+}
 \seealso{
   \code{\link{linfun}},
   \code{\link{methods.linfun}}.

diff --git a/man/distmap.lpp.Rd b/man/distmap.lpp.Rd
@@ -35,6 +35,17 @@
   nearest point of the pattern \code{X} (or the \eqn{k}-th nearest point
   of \code{X}).
 }
+\section{Distance values}{
+  The pixel values in the image \code{distmap(X)} are distances,
+  expressed as multiples of the unit of length of the spatial
+  coordinates in \code{X}.
+  The unit of length is given by \code{\link[spatstat.geom]{unitname}(X)}.
+
+  Note that, if the unit of length in \code{X} is a composite
+  expression such as \sQuote{2 microns},
+  then the values in \code{distmap(X)} are expressed as multiples
+  of 2 microns, rather than being expressed in microns.
+}
 \seealso{
   Generic function \code{\link[spatstat.geom]{distmap}} and methods.
 }

diff --git a/man/nndist.lpp.Rd b/man/nndist.lpp.Rd
@@ -61,6 +61,17 @@
   for each entry of \code{k}. Entries are nonnegative numbers or
   infinity (\code{Inf}).
 }
+\section{Distance values}{
+  The values returned by \code{nndist(X)} are distances,
+  expressed as multiples of the unit of length of the spatial
+  coordinates in \code{X}.
+  The unit of length is given by \code{\link{unitname}(X)}.
+
+  Note that, if the unit of length in \code{X} is a composite
+  expression such as \sQuote{2 microns},
+  then the values of \code{nndist(X)} are expressed as multiples
+  of 2 microns, rather than being expressed in microns.
+}
 \author{
   \adrian
 }

diff --git a/man/pairdist.lpp.Rd b/man/pairdist.lpp.Rd
@@ -50,6 +50,17 @@
   the argument \code{method} has no effect, and the distances are
   computed using an efficient C algorithm.
 }
+\section{Distance values}{
+  The values returned by \code{pairdist(X)} are distances,
+  expressed as multiples of the unit of length of the spatial
+  coordinates in \code{X}.
+  The unit of length is given by \code{\link{unitname}(X)}.
+
+  Note that, if the unit of length in \code{X} is a composite
+  expression such as \sQuote{2 microns},
+  then the values of \code{pairdist(X)} are expressed as multiples
+  of 2 microns, rather than being expressed in microns.
+}
 \value{
   A symmetric matrix, whose values are nonnegative numbers or infinity
   (\code{Inf}).

diff --git a/tests/testsL.R b/tests/testsL.R
@@ -17,7 +17,7 @@ cat(paste("--------- Executing",
 #
 # Tests for lpp code
 #
-#  $Revision: 1.72 $  $Date: 2024/06/05 09:11:58 $
+#  $Revision: 1.74 $  $Date: 2025/01/18 03:44:09 $
 
 
 local({
@@ -376,7 +376,7 @@ local({
     df <- data.frame(seg=1:ns, t0=0, t1=1, tile=letters[1:ns])
     M <- data.frame(len=lengths_psp(S), ang=angles.psp(S))
     V <- lintess(simplenet, df, marks=M)
-
+    
     ## methods for class lintess
     U <- unmark(V)
     U <- unstack(V)
@@ -413,6 +413,7 @@ local({
     Zmm <- intersect.lintess(X,Y)
     Zum <- intersect.lintess(unmark(X),Y)
     Zmu <- intersect.lintess(X,unmark(Y))
+
   }
 
   if(FULLTEST) {
@@ -710,7 +711,7 @@ reset.spatstat.options()
 #'
 #'   Tests of lppm and class support
 #' 
-#'   $Revision: 1.2 $ $Date: 2020/06/12 00:24:09 $
+#'   $Revision: 1.3 $ $Date: 2025/01/18 03:43:52 $
 #'
 
 
@@ -767,6 +768,15 @@ local({
     fit3e <- emend(fit3)
   }
 
+  if(FULLTEST) {
+    #' handling of lintess covariates
+    df <- data.frame(seg=1:10, t0=0, t1=1, tile=rep(c("A", "B"), 5))
+    V <- lintess(simplenet, df)
+    X <- runiflpp(20, simplenet)
+    mod <- lppm(X ~ V)
+    Lam <- predict(mod)
+  }
+
   #' fundamental utilities:
   #' spatialCovariateEvidence (was: evalCovar)
   ycoord <- function(x,y) { y }