diff --git a/DESCRIPTION b/DESCRIPTION index f1302f2..e9c1e9b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: spatstat.geom -Version: 3.3-4.010 -Date: 2025-01-07 +Version: 3.3-4.011 +Date: 2025-01-17 Title: Geometrical Functionality of the 'spatstat' Family Authors@R: c(person("Adrian", "Baddeley", role = c("aut", "cre", "cph"), @@ -25,7 +25,7 @@ Authors@R: c(person("Adrian", "Baddeley", person("Rasmus", "Waagepetersen", role = "ctb")) Maintainer: Adrian Baddeley Depends: R (>= 3.5.0), spatstat.data (>= 3.1), spatstat.univar (>= 3.1-0), stats, graphics, grDevices, utils, methods -Imports: spatstat.utils (>= 3.1-1.001), deldir (>= 1.0-2), polyclip (>= 1.10-0) +Imports: spatstat.utils (>= 3.1-2), deldir (>= 1.0-2), polyclip (>= 1.10-0) Suggests: spatstat.random (>= 3.3), spatstat.explore (>= 3.3), spatstat.model (>= 3.3), spatstat.linnet (>= 3.2), spatial, fftwtools (>= 0.9-8), spatstat (>= 3.2) Description: Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), diff --git a/NEWS b/NEWS index 55511dc..4f06b18 100644 --- a/NEWS +++ b/NEWS @@ -1,4 +1,4 @@ - CHANGES IN spatstat.geom VERSION 3.3-4.010 + CHANGES IN spatstat.geom VERSION 3.3-4.011 OVERVIEW diff --git a/inst/doc/packagesizes.txt b/inst/doc/packagesizes.txt index b910b81..b8d71dd 100755 --- a/inst/doc/packagesizes.txt +++ b/inst/doc/packagesizes.txt @@ -30,4 +30,4 @@ date version nhelpfiles nobjects ndatasets Rlines srclines "2024-07-09" "3.3-2" 442 1186 0 35638 15596 "2024-09-18" "3.3-3" 443 1187 0 35818 15596 "2024-11-18" "3.3-4" 444 1190 0 35978 15596 -"2025-01-07" "3.3-4.010" 445 1191 0 36158 15596 +"2025-01-17" "3.3-4.011" 445 1191 0 36158 15596 diff --git a/inst/info/packagesizes.txt b/inst/info/packagesizes.txt index b910b81..b8d71dd 100755 --- a/inst/info/packagesizes.txt +++ b/inst/info/packagesizes.txt @@ -30,4 +30,4 @@ date version nhelpfiles nobjects ndatasets Rlines srclines "2024-07-09" "3.3-2" 442 1186 0 35638 15596 "2024-09-18" "3.3-3" 443 1187 0 35818 15596 "2024-11-18" "3.3-4" 444 1190 0 35978 15596 -"2025-01-07" "3.3-4.010" 445 1191 0 36158 15596 +"2025-01-17" "3.3-4.011" 445 1191 0 36158 15596 diff --git a/man/distfun.Rd b/man/distfun.Rd index ad03417..2cf3a3a 100644 --- a/man/distfun.Rd +++ b/man/distfun.Rd @@ -85,6 +85,18 @@ It also belongs to the class \code{"funxy"} which has methods for \code{plot}, \code{contour} and \code{persp}. } +\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{distmap}}, \code{\link{summary.distfun}}, diff --git a/man/distmap.Rd b/man/distmap.Rd index f112922..efd44b0 100644 --- a/man/distmap.Rd +++ b/man/distmap.Rd @@ -35,7 +35,18 @@ This is generic. Methods are provided for point patterns (\code{\link{distmap.ppp}}), line segment patterns (\code{\link{distmap.psp}}) - and windows (\code{\link{distmap.owin}}). + and windows (\code{\link{distmap.owin}}) as well as other classes. +} +\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{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{ \code{\link{distmap.ppp}}, diff --git a/man/distmap.owin.Rd b/man/distmap.owin.Rd index 82b4f35..1ff22a0 100644 --- a/man/distmap.owin.Rd +++ b/man/distmap.owin.Rd @@ -75,6 +75,17 @@ This function is a method for the generic \code{\link{distmap}}. } +\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{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{ \code{\link{distmap}}, \code{\link{distmap.ppp}}, diff --git a/man/distmap.ppp.Rd b/man/distmap.ppp.Rd index 64b486d..634d2ef 100644 --- a/man/distmap.ppp.Rd +++ b/man/distmap.ppp.Rd @@ -62,6 +62,17 @@ to the nearest data point in \code{X}, use \code{\link{distfun}} or \code{\link{nncross}}. } +\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{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{distmap}} and other methods \code{\link{distmap.psp}}, @@ -69,7 +80,10 @@ Generic function \code{\link{distfun}}. - Nearest neighbour distance \code{\link{nncross}} + Nearest neighbour distance \code{\link{nncross}}. + + \code{\link{unitname}} and \code{\link{rescale}} to control the unit + of length. } \examples{ U <- distmap(cells) diff --git a/man/distmap.psp.Rd b/man/distmap.psp.Rd index ef186db..1e9032a 100644 --- a/man/distmap.psp.Rd +++ b/man/distmap.psp.Rd @@ -74,6 +74,17 @@ low-level functions \code{\link{nncross}} or \code{\link{project2segment}}. } +\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{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{ \code{\link{distmap}}, \code{\link{distmap.owin}}, diff --git a/man/nndist.Rd b/man/nndist.Rd index 6be0017..7a359a4 100644 --- a/man/nndist.Rd +++ b/man/nndist.Rd @@ -157,6 +157,17 @@ distance is not defined (e.g. if there is only one point in the point pattern). } +\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. +} \seealso{ \code{\link{nndist.psp}}, \code{\link{nndist.pp3}}, diff --git a/man/nndist.pp3.Rd b/man/nndist.pp3.Rd index 4de98ec..78e6901 100644 --- a/man/nndist.pp3.Rd +++ b/man/nndist.pp3.Rd @@ -82,6 +82,17 @@ To find the nearest neighbour distances from one point pattern to another point pattern, use \code{\link{nncross}}. } +\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. +} \section{Warnings}{ An infinite or \code{NA} value is returned if the distance is not defined (e.g. if there is only one point diff --git a/man/nndist.ppx.Rd b/man/nndist.ppx.Rd index ac29077..1a3ded9 100644 --- a/man/nndist.ppx.Rd +++ b/man/nndist.ppx.Rd @@ -83,6 +83,17 @@ To obtain the spatial distance between points in a space-time point pattern, set \code{temporal=FALSE}. } +\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. +} \section{Warnings}{ An infinite or \code{NA} value is returned if the distance is not defined (e.g. if there is only one point diff --git a/man/nndist.psp.Rd b/man/nndist.psp.Rd index c10e07a..35bbdfb 100644 --- a/man/nndist.psp.Rd +++ b/man/nndist.psp.Rd @@ -71,6 +71,17 @@ (the default) then compiled \code{C} code is used. The \code{C} code is somewhat faster. } +\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. +} \seealso{ \code{\link{nndist}}, \code{\link{nndist.ppp}} diff --git a/man/pairdist.Rd b/man/pairdist.Rd index e71200d..c9614c4 100644 --- a/man/pairdist.Rd +++ b/man/pairdist.Rd @@ -36,6 +36,17 @@ for \code{\link{pairdist.ppp}}, \code{\link{pairdist.psp}} or \code{\link{pairdist.default}} for details. } +\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. +} \seealso{ \code{\link{pairdist.ppp}}, \code{\link{pairdist.psp}}, diff --git a/man/pairdist.pp3.Rd b/man/pairdist.pp3.Rd index 6b682b5..6952da1 100644 --- a/man/pairdist.pp3.Rd +++ b/man/pairdist.pp3.Rd @@ -36,8 +36,8 @@ points in \code{X}, and returns the matrix of distances. Alternatively if \code{periodic=TRUE} and the window containing \code{X} is a - box, then the distances will be computed in the `periodic' - sense (also known as `torus' distance): opposite faces of the + box, then the distances will be computed in the \sQuote{periodic} + sense (also known as \sQuote{torus} distance): opposite faces of the box are regarded as equivalent. This is meaningless if the window is not a box. @@ -46,6 +46,17 @@ The squared distances are faster to calculate, and are sufficient for many purposes (such as finding the nearest neighbour of a point). } +\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. +} \seealso{ \code{\link{pairdist}}, \code{\link{crossdist}}, diff --git a/man/pairdist.ppp.Rd b/man/pairdist.ppp.Rd index 91f80b0..e84a7bf 100644 --- a/man/pairdist.ppp.Rd +++ b/man/pairdist.ppp.Rd @@ -61,6 +61,17 @@ computed using interpreted R code only. If \code{method="C"} (the default) then C code is used. The C code is somewhat faster. } +\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. +} \seealso{ \code{\link{pairdist}}, \code{\link{pairdist.default}}, diff --git a/man/pairdist.ppx.Rd b/man/pairdist.ppx.Rd index ce842c8..9bc5d15 100644 --- a/man/pairdist.ppx.Rd +++ b/man/pairdist.ppx.Rd @@ -33,6 +33,18 @@ To obtain the spatial distance between points in a space-time point pattern, set \code{temporal=FALSE}. } +\section{Distance values}{ + The values returned by \code{pairdist(X, temporal=FALSE)} 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, temporal=FALSE)} + are expressed as multiples + of 2 microns, rather than being expressed in microns. +} \seealso{ \code{\link{pairdist}}, \code{\link{crossdist}}, @@ -45,8 +57,6 @@ } \author{ \adrian - - } \keyword{spatial} \keyword{math} diff --git a/man/pairdist.psp.Rd b/man/pairdist.psp.Rd index 079f9f7..dfdefc7 100644 --- a/man/pairdist.psp.Rd +++ b/man/pairdist.psp.Rd @@ -56,6 +56,17 @@ (the default) then compiled \code{C} code is used, which is somewhat faster. } +\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. +} \seealso{ \code{\link{crossdist}}, \code{\link{nndist}}, @@ -68,10 +79,7 @@ } \author{ \adrian - - and \rolf - } \keyword{spatial} \keyword{math}