CVS commit: pkgsrc/geography/R-spatstat.core

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Mon Sep 20 10:38:59 UTC 2021

Added Files:
        pkgsrc/geography/R-spatstat.core: DESCR Makefile distinfo

Log Message:
(geography/R-spatstat.core) import R-spatstat.core-2.3.0

Functionality for data analysis and modelling of spatial data, mainly
spatial point patterns, in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network, which is
covered by the separate package 'spatstat.linnet'.) Exploratory
methods include quadrat counts, K-functions and their simulation
envelopes, nearest neighbour distance and empty space statistics, Fry
plots, pair correlation function, kernel smoothed intensity, relative
risk estimation with cross-validated bandwidth selection, mark
correlation functions, segregation indices, mark dependence
diagnostics, and kernel estimates of covariate effects. Formal
hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov,
Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte
Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson,
Kolmogorov-Smirnov, ANOVA) are also supported. Parametric models can
be fitted to point pattern data using the functions ppm(), kppm(),
slrm(), dppm() similar to glm(). Types of models include Poisson,
Gibbs and Cox point processes, Neyman-Scott cluster processes, and
determinantal point processes. Models may involve dependence on
covariates, inter-point interaction, cluster formation and dependence
on marks. Models are fitted by maximum likelihood, logistic
regression, minimum contrast, and composite likelihood methods. A
model can be fitted to a list of point patterns (replicated point
pattern data) using the function mppm(). The model can include random
effects and fixed effects depending on the experimental design, in
addition to all the features listed above. Fitted point process models
can be simulated, automatically. Formal hypothesis tests of a fitted
model are supported (likelihood ratio test, analysis of deviance,
Monte Carlo tests) along with basic tools for model selection
(stepwise(), AIC()) and variable selection (sdr). Tools for validating
the fitted model include simulation envelopes, residuals, residual
plots and Q-Q plots, leverage and influence diagnostics, partial
residuals, and added variable plots.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/geography/R-spatstat.core/DESCR \
    pkgsrc/geography/R-spatstat.core/Makefile \
    pkgsrc/geography/R-spatstat.core/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Added files:

Index: pkgsrc/geography/R-spatstat.core/DESCR
diff -u /dev/null pkgsrc/geography/R-spatstat.core/DESCR:1.1
--- /dev/null   Mon Sep 20 10:38:59 2021
+++ pkgsrc/geography/R-spatstat.core/DESCR      Mon Sep 20 10:38:59 2021
@@ -0,0 +1,32 @@
+Functionality for data analysis and modelling of spatial data, mainly
+spatial point patterns, in the 'spatstat' family of packages.
+(Excludes analysis of spatial data on a linear network, which is
+covered by the separate package 'spatstat.linnet'.) Exploratory
+methods include quadrat counts, K-functions and their simulation
+envelopes, nearest neighbour distance and empty space statistics, Fry
+plots, pair correlation function, kernel smoothed intensity, relative
+risk estimation with cross-validated bandwidth selection, mark
+correlation functions, segregation indices, mark dependence
+diagnostics, and kernel estimates of covariate effects. Formal
+hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov,
+Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte
+Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson,
+Kolmogorov-Smirnov, ANOVA) are also supported. Parametric models can
+be fitted to point pattern data using the functions ppm(), kppm(),
+slrm(), dppm() similar to glm(). Types of models include Poisson,
+Gibbs and Cox point processes, Neyman-Scott cluster processes, and
+determinantal point processes. Models may involve dependence on
+covariates, inter-point interaction, cluster formation and dependence
+on marks. Models are fitted by maximum likelihood, logistic
+regression, minimum contrast, and composite likelihood methods. A
+model can be fitted to a list of point patterns (replicated point
+pattern data) using the function mppm(). The model can include random
+effects and fixed effects depending on the experimental design, in
+addition to all the features listed above. Fitted point process models
+can be simulated, automatically. Formal hypothesis tests of a fitted
+model are supported (likelihood ratio test, analysis of deviance,
+Monte Carlo tests) along with basic tools for model selection
+(stepwise(), AIC()) and variable selection (sdr). Tools for validating
+the fitted model include simulation envelopes, residuals, residual
+plots and Q-Q plots, leverage and influence diagnostics, partial
+residuals, and added variable plots.
Index: pkgsrc/geography/R-spatstat.core/Makefile
diff -u /dev/null pkgsrc/geography/R-spatstat.core/Makefile:1.1
--- /dev/null   Mon Sep 20 10:38:59 2021
+++ pkgsrc/geography/R-spatstat.core/Makefile   Mon Sep 20 10:38:59 2021
@@ -0,0 +1,28 @@
+# $NetBSD: Makefile,v 1.1 2021/09/20 10:38:59 mef Exp $
+
+R_PKGNAME=     spatstat.core
+R_PKGVER=      2.3-0
+CATEGORIES=    geography
+
+MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
+COMMENT=       Core Functionality of the 'spatstat' Family
+LICENSE=       gnu-gpl-v2 OR gnu-gpl-v3
+
+# ERROR: dependencies 'spatstat.data', 'spatstat.geom', 'spatstat.utils', 'spatstat.sparse', 'abind', 'tensor', 'goftest' are not available for package 'spatst
+DEPENDS+=      R-spatstat.data>=2.1.0:../../geography/R-spatstat.data
+DEPENDS+=      R-spatstat.geom>=2.1.0:../../geography/R-spatstat.geom
+DEPENDS+=      R-spatstat.utils>=2.2.0:../../geography/R-spatstat.utils
+DEPENDS+=      R-spatstat.sparse>=2.0.0:../../geography/R-spatstat.sparse
+DEPENDS+=      R-abind>=1.4.5:../../math/R-abind
+DEPENDS+=      R-goftest>=1.2.2:../../math/R-goftest
+DEPENDS+=      R-tensor>=1.5:../../math/R-tensor
+
+# Packages suggested but not available:
+#   'sm', 'maptools', 'gsl', 'locfit', 'RandomFields',
+#   'RandomFieldsUtils', 'fftwtools', 'nleqslv', 'spatstat.linnet',
+#   'spatstat'
+
+USE_LANGUAGES= c c++
+
+.include "../../math/R/Makefile.extension"
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/geography/R-spatstat.core/distinfo
diff -u /dev/null pkgsrc/geography/R-spatstat.core/distinfo:1.1
--- /dev/null   Mon Sep 20 10:38:59 2021
+++ pkgsrc/geography/R-spatstat.core/distinfo   Mon Sep 20 10:38:59 2021
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1 2021/09/20 10:38:59 mef Exp $
+
+SHA1 (R/spatstat.core_2.3-0.tar.gz) = 8191b916506528cde74ce0bef24639a0bb7b1ae1
+RMD160 (R/spatstat.core_2.3-0.tar.gz) = 3c0ff9af514c3f078652469544605e992eba5e4f
+SHA512 (R/spatstat.core_2.3-0.tar.gz) = c98ec6c63bb4a44a0f8f2d441418cf8f91a2a2d1b041b41b182a7ae5126307902d459444e0dec0ca2aed0c335091c42f6db88b281b9a3a2fecaacb2f1b602849
+Size (R/spatstat.core_2.3-0.tar.gz) = 1556158 bytes