Received: by mail.netbsd.org (Postfix, from userid 605) id 98FE684F6A; Sun, 14 Jan 2024 02:44:44 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id CA44F84EF8 for ; Sun, 14 Jan 2024 02:44:43 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([IPv6:::1]) by localhost (mail.netbsd.org [IPv6:::1]) (amavisd-new, port 10025) with ESMTP id E-0bmUH8DHyM for ; Sun, 14 Jan 2024 02:44:42 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.netbsd.org [199.233.217.197]) by mail.netbsd.org (Postfix) with ESMTP id 8884384E5A for ; Sun, 14 Jan 2024 02:44:42 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id 7F28AFA42; Sun, 14 Jan 2024 02:44:42 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1705200282294170" MIME-Version: 1.0 Date: Sun, 14 Jan 2024 02:44:42 +0000 From: "Makoto Fujiwara" Subject: CVS commit: pkgsrc/geography/R-spatstat.linnet To: pkgsrc-changes@NetBSD.org Reply-To: mef@netbsd.org X-Mailer: log_accum Message-Id: <20240114024442.7F28AFA42@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_1705200282294170 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: mef Date: Sun Jan 14 02:44:42 UTC 2024 Modified Files: pkgsrc/geography/R-spatstat.linnet: Makefile distinfo Log Message: (geography/R-spatstat.linnet) Updated 2.3.0 to 3.1.3 CHANGES IN spatstat.linnet VERSION 3.1-3 OVERVIEW o Minor corrections to help files. CHANGES IN spatstat.linnet VERSION 3.1-2 OVERVIEW o Minor improvements to help files. CHANGES IN spatstat.linnet VERSION 3.1-1 OVERVIEW o Minor improvements SIGNIFICANT USER-VISIBLE CHANGES o rhohat.lpp, rhohat.lppm New argument 'rule.eps' passed to 'as.mask'. o as.linim.default, as.linim.linfun New argument 'rule.eps' passed to 'as.mask'. CHANGES IN spatstat.linnet VERSION 3.1-0 OVERVIEW o Inhomogeneous K and pcf using automatic estimation of intensity. o density.lpp accepts bandwidth selection rules. o density.lpp accepts sigma=NULL and has a simple default. o Updated package documentation. SIGNIFICANT USER-VISIBLE CHANGES o linearKinhom, linearpcfinhom, linearKEuclidInhom, linearpcfEuclidInhom Argument 'lambda=NULL' is now interpreted to mean that the intensity should be estimated by kernel smoothing. A warning is issued that this is different from the previous behaviour. o linearKdot.inhom, linearpcfdot.inhom Argument 'lambdaI=NULL' or 'lambdadot=NULL' is now interpreted to mean that the intensity should be estimated by kernel smoothing. o linearKcross.inhom, linearpcfcross.inhom Argument 'lambdaI=NULL' or 'lambdaJ=NULL' is now interpreted to mean that the intensity should be estimated by kernel smoothing. o density.lpp Argument 'sigma' can now be a function in the R language, assumed to provide a bandwidth selection rule. This function will be applied to the point pattern x to compute the bandwidth. o density.lpp Argument 'sigma=NULL' is now accepted. The default value is one-eighth of the length of the shortest side of the bounding box of x. o densityQuick.lpp Argument 'X' changed to 'x' for consistency. o linearpcfinhom New arguments 'adjust.sigma', 'bw' and 'adjust.bw'. o linearpcfdot.inhom, linearpcfcross.inhom New arguments 'adjust.sigma', 'bw' and 'adjust.bw'. o linearpcfEuclidInhom New arguments 'adjust.sigma', 'bw' and 'adjust.bw'. CHANGES IN spatstat.linnet VERSION 3.0-6 OVERVIEW o Internal improvements and bug fixes. CHANGES IN spatstat.linnet VERSION 3.0-5 OVERVIEW o Improvements and bug fixes in 'lppm' class. o Minor extension to random generators. SIGNIFICANT USER-VISIBLE CHANGES o runiflpp, rpoislpp The simulation parameters can be determined from an example point pattern, given as the argument 'ex'. o print.lppm, summary.lppm The name of the original point pattern dataset (to which the model was fitted) is now printed. o print.lppm, summary.lppm Improved output. o update.lppm Internal improvements. CHANGES IN spatstat.linnet VERSION 3.0-4 OVERVIEW o quantile function on a network. o Minor enhancements and bug fixes. NEW FUNCTIONS o quantilefun.linim Quantile function, returned as a function. Method for 'quantilefun' for images on a network. BUG FIXES o relrisk.lpp Crashed if allow.infinite=FALSE. Fixed. CHANGES IN spatstat.linnet VERSION 3.0-3 OVERVIEW o We thank Brian Ripley for contributions. o Internal bug fix. BUG FIXES o pairdist.lpp Results could have been completely incorrect, due to an internal bug, if the linear network data was in the non-sparse representation. CHANGES IN spatstat.linnet VERSION 3.0-2 OVERVIEW o Internal tweaks to satisfy package checker. CHANGES IN spatstat.linnet VERSION 3.0-1 OVERVIEW o Internal improvements. CHANGES IN spatstat.linnet VERSION 3.0-0 OVERVIEW o We thank Greg McSwiggan, Fernando Milesi, Mehdi Moradi, Gopalan Nair and James Pope for contributions. o spatstat.linnet now depends on the new packages 'spatstat.explore' and 'spatstat.model' rather than the old 'spatstat.core'. o Kernel smoothing on a linear network. o K function and pair correlation function based on Euclidean distance. o Inhomogeneous J function on a network. o Terminal vertices of a network. o Points along a network can be drawn as cross-ticks. o Marks attached to vertices and segments of a network. o Important change to K function and pair correlation function when 'ratio=TRUE'. o U-shaped curves in 'rhohat'. o Faster computation of the length of the disc in the shortest path metric. o Minor improvements and bug fixes. o Improvements to internal code. o Minor internal changes to package information. NEW FUNCTIONS o lineardisclength Compute the length of the disc in the shortest-path metric. o marks.linnet, marks<-.linnet Marks attached to the vertices and segments of a linear network. o Smooth.lpp Kernel smoothing (Nadaraya-Watson) on a linear network. o distmap.lpp Distance map for a point pattern on a network. o linearKEuclid, linearpcfEuclid, linearKEuclidInhom, linearpcfEuclidInhom K function and pair correlation function based on Euclidean distances. o linearJinhom Inhomogeneous J function on a linear network. o terminalvertices Extract the terminal vertices of a linear network. o bw.relrisk.lpp This function replaces 'bw.relrisklpp' and is a method for the generic 'bw.relrisk'. o rThomaslpp Simulate Thomas cluster process on a network. SIGNIFICANT USER-VISIBLE CHANGES o Package dependence 'spatstat.linnet' now depends on the new packages 'spatstat.explore' and 'spatstat.model' rather than the old 'spatstat.core'. o plot.lpp If 'shape="crossticks"', the points will be drawn as short line segments perpendicular to the network. o linearK, linearpcf, linearKdot, linearKcross, linearpcfcross, linearpcfdot When 'ratio=TRUE', the denominator is now equal to the number of ordered pairs of data points considered. This does not affect the summary function, but it changes the calculation of pooled estimates. o densityQuick.lpp If 'sigma' is a function for selecting a bandwidth, additional arguments '...' of densityQuick.lpp will be passed to 'sigma', provided they match the name of a formal argument of 'sigma'. o bw.relrisklpp This function is now deprecated, and is replaced by 'bw.relrisk.lpp', a method for the generic 'bw.relrisk'. o bw.relrisk.lpp When 'method="likelihood"', the cross-validation criterion is now defined as the *negative* likelihood. This is consistent with 'bw.relrisk.ppp', and ensures that the optimum bandwidth is always found by minimising the cross-validation criterion. o integral.linim, integral.linfun New argument 'weight' specifies a weight function for the integration. o rhohat.lpp, rhohat.lppm New options 'smoother="mountain"' and 'smoother="valley"' for estimating a unimodal function (U-shaped curve). o rhohat.lpp, rhohat.lppm If the covariate is a 'distfun' on a network, the unit of length will be saved, and will be displayed on the plot. o rhohat.lpp, rhohat.lppm New arguments 'jitter', 'jitterfactor', 'interpolate' allow greater control over the calculation. o plot.linnet Optionally displays the marks of the segments or marks of the vertices. Changed argument list. o print.linnet, summary.linnet These functions print information about marks of the segments or vertices. o predict.lppm Can now compute standard errors. o predict.lppm New formal arguments 'covariates' and 'se'. o rhohat.lpp, rhohat.lppm New argument 'do.CI' specifies whether to calculate confidence bands. BUG FIXES o density.lpp If 'weights' were given, the results were completely incorrect when leaveoneout=TRUE (the default) and at="points". o spatstat.model::effectfun Results were sometimes incorrect for 'lppm' objects. [Spotted by Fernando A. Milesi] Fixed. o predict.lppm Ignored argument 'covariates'. Fixed. o rhohat.lpp, rhohat.lppm The argument 'subset' was not handled correctly in the internal data. The estimated function 'rho' was correct but the results of 'predict.rhohat' may have been incorrect and were computed only on the 'subset'. Fixed. o plot.lpp Did not display the main title in some cases. Fixed. o "[.lpp", "[.linnet" Ignored marks attached to the network segments. Fixed. o "[.lpp", "[.linnet" Crashed if the network vertices had marks, when 'snip=TRUE'. Fixed. o densityQuick.lpp Crashed sometimes with a message about unequal lengths of vectors. Fixed. CHANGES IN spatstat.linnet VERSION 2.3-2 OVERVIEW o 'spatstat.linnet' now depends on 'spatstat.random'. SIGNIFICANT USER-VISIBLE CHANGES o package dependence 'spatstat.linnet' now depends on the new package 'spatstat.random'. CHANGES IN spatstat.linnet VERSION 2.3-1 OVERVIEW o More control over resolution of 'linim' objects. o Improved documentation. o Minor improvements and bug fixes. SIGNIFICANT USER-VISIBLE CHANGES o as.linim.default, as.linim.linfun New argument 'nd' o integral.linfun New argument 'nd' o rjitterlpp, rjitter.lpp The function 'rjitterlpp' has been renamed 'rjitter.lpp' and is now a method for the generic 'rjitter'. o rjitterlpp This function still exists, but is now deprecated in favour of 'rjitter.lpp'. BUG FIXES o rjitterlpp The argument 'radius' was interpreted as a fraction of segment length rather than an absolute distance. Fixed. To generate a diff of this commit: cvs rdiff -u -r1.1 -r1.2 pkgsrc/geography/R-spatstat.linnet/Makefile cvs rdiff -u -r1.3 -r1.4 pkgsrc/geography/R-spatstat.linnet/distinfo Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_1705200282294170 Content-Disposition: inline Content-Length: 2521 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/geography/R-spatstat.linnet/Makefile diff -u pkgsrc/geography/R-spatstat.linnet/Makefile:1.1 pkgsrc/geography/R-spatstat.linnet/Makefile:1.2 --- pkgsrc/geography/R-spatstat.linnet/Makefile:1.1 Mon Sep 20 10:45:32 2021 +++ pkgsrc/geography/R-spatstat.linnet/Makefile Sun Jan 14 02:44:42 2024 @@ -1,18 +1,21 @@ -# $NetBSD: Makefile,v 1.1 2021/09/20 10:45:32 mef Exp $ +# $NetBSD: Makefile,v 1.2 2024/01/14 02:44:42 mef Exp $ R_PKGNAME= spatstat.linnet -R_PKGVER= 2.3-0 +R_PKGVER= 3.1-3 CATEGORIES= geography MAINTAINER= pkgsrc-users@NetBSD.org COMMENT= Linear Networks Functionality of the 'spatstat' Family LICENSE= gnu-gpl-v2 OR gnu-gpl-v3 -DEPENDS+= R-spatstat.core>=2.3.0:../../geography/R-spatstat.core -DEPENDS+= R-spatstat.data>=2.1.0:../../geography/R-spatstat.data -DEPENDS+= R-spatstat.geom>=2.2.2:../../geography/R-spatstat.geom +DEPENDS+= R-spatstat.data>=3.0:../../geography/R-spatstat.data +DEPENDS+= R-spatstat.explore>=3.2.5:../../geography/R-spatstat.explore +DEPENDS+= R-spatstat.geom>=3.2.7:../../geography/R-spatstat.geom +DEPENDS+= R-spatstat.model>=3.2.8:../../geography/R-spatstat.model +DEPENDS+= R-spatstat.random>=3.2.1:../../geography/R-spatstat.random DEPENDS+= R-spatstat.utils>=2.2.0:../../geography/R-spatstat.utils +USE_LANGUAGES= c # Packages suggested but not available: 'locfit', 'spatstat' .include "../../math/R/Makefile.extension" Index: pkgsrc/geography/R-spatstat.linnet/distinfo diff -u pkgsrc/geography/R-spatstat.linnet/distinfo:1.3 pkgsrc/geography/R-spatstat.linnet/distinfo:1.4 --- pkgsrc/geography/R-spatstat.linnet/distinfo:1.3 Tue Oct 26 10:45:07 2021 +++ pkgsrc/geography/R-spatstat.linnet/distinfo Sun Jan 14 02:44:42 2024 @@ -1,5 +1,5 @@ -$NetBSD: distinfo,v 1.3 2021/10/26 10:45:07 nia Exp $ +$NetBSD: distinfo,v 1.4 2024/01/14 02:44:42 mef Exp $ -BLAKE2s (R/spatstat.linnet_2.3-0.tar.gz) = dc7e0359618794651123bda1fc98bceabe16e0031bfafeede273265c6cffd354 -SHA512 (R/spatstat.linnet_2.3-0.tar.gz) = d5b3d1d393b10e06f2d5adfba264a15d72cc24a044a088fc3c109881964b85657e985fcbf707d8edbfc60cbdb1f93debf5ee17bc233a17dd9c8fc7f4e5303e0f -Size (R/spatstat.linnet_2.3-0.tar.gz) = 245724 bytes +BLAKE2s (R/spatstat.linnet_3.1-3.tar.gz) = 91edca5e753f81f3a45b0a0aa3e8f8242293b2c3b854fa0635d03b4aa02c42eb +SHA512 (R/spatstat.linnet_3.1-3.tar.gz) = c3700d7d172366edfa136de1229c114f3175d74831b9b358598129afbdeccb6b4435a6c077aacf69ae8790452c7587ec29e84518112666ffc0c053a2b96bc477 +Size (R/spatstat.linnet_3.1-3.tar.gz) = 274881 bytes --_----------=_1705200282294170--