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locks; strict; comment @# @; 1.19 date 2023.06.02.13.55.59; author mef; state Exp; branches; next 1.18; commitid D0wguvMhk3r9vnrE; 1.18 date 2021.09.18.12.31.31; author mef; state Exp; branches; next 1.17; commitid IyUi4IVpDGhS1r9D; 1.17 date 2019.08.08.19.53.54; author brook; state Exp; branches; next 1.16; commitid K2VPfA0XCw7xfgyB; 1.16 date 2019.07.31.20.33.59; author brook; state Exp; branches; next 1.15; commitid Jeu9477sGrBRLexB; 1.15 date 2018.07.28.14.40.51; author brook; state Exp; branches; next 1.14; commitid hIRYb3oU4xMfBULA; 1.14 date 2017.12.02.12.00.34; author wen; state Exp; branches; next 1.13; commitid Aa2yPjsolp7lpjhA; 1.13 date 2016.11.06.02.54.08; author wen; state Exp; branches; next 1.12; commitid DpJQw0ZRXFQ6X0tz; 1.12 date 2016.04.09.08.36.34; author wen; state Exp; branches; next 1.11; commitid efZ2REpy1Nh3DV1z; 1.11 date 2015.05.30.10.50.34; author wen; state Exp; branches; next 1.10; commitid xgNPMvTwCnsQusny; 1.10 date 2014.07.13.12.47.38; author wen; state Exp; branches; next 1.9; commitid 0lYuw57br8UBsdIx; 1.9 date 2014.03.09.14.28.57; author wen; state Exp; branches; next 1.8; commitid 37AuDLddydEl42sx; 1.8 date 2013.07.07.11.07.18; author wen; state Exp; branches; next 1.7; commitid xN2gUpZ6ahsBPwWw; 1.7 date 2012.11.30.13.55.48; author wen; state Exp; branches; next 1.6; 1.6 date 2012.04.15.15.45.16; author brook; state Exp; branches; next 1.5; 1.5 date 2009.12.11.19.43.07; author adam; state Exp; branches; next 1.4; 1.4 date 2008.10.13.19.28.48; author markd; state Exp; branches; next 1.3; 1.3 date 2007.02.22.19.26.47; author wiz; state Exp; branches; next 1.2; 1.2 date 2006.02.05.23.10.01; author joerg; state Exp; branches; next 1.1; 1.1 date 2005.11.04.08.19.17; author rillig; state Exp; branches 1.1.1.1; next ; 1.1.1.1 date 2005.11.04.08.19.17; author rillig; state Exp; branches; next ; desc @@ 1.19 log @(math/R-statmod) Updated 1.4.36 to 1.5.0 28 Dec 2022: statmod 1.5.0 - New function expectedDeviance() to compute expected values and variances of unit deviances for linear exponential families, using C code written by Lizhong Chen. Add Lizhong Chen as package author. - Replace NAMESPACE exportPattern() with export(). - New argument `n0` for compareGrowthCurves() and CompareTwoGrownCurves() to avoid permutation p-values exactly zero. - Add link to Phipson & Smyth postprint on arXiv in help references for permp() and compareGrowthCurves(). 12 Aug 2022: statmod 1.4.37 - Fix mathematic equations in remlscor.Rd. - Explain simulation method of power.fisher.test() in power.Rd. - Update http to https URLs in elda.Rd, gauss.quad.Rd and gauss.quad.prob.Rd. - Change url to doi for reference in elda.Rd. - Add doi for reference in fitNBP.Rd. @ text @# $NetBSD: Makefile,v 1.18 2021/09/18 12:31:31 mef Exp $ R_PKGNAME= statmod R_PKGVER= 1.5.0 MAINTAINER= pkgsrc-users@@NetBSD.org COMMENT= Statistical modeling LICENSE= gnu-gpl-v2 OR gnu-gpl-v3 #TEST_DEPENDS+= R-tweedie-[0-9]*:../.. USE_LANGUAGES+= c fortran .include "../../math/R/Makefile.extension" .include "../../mk/bsd.pkg.mk" @ 1.18 log @(math/R-statmod) Updated 1.4.32 to 1.4.36 25 Aug 2020: Statmod 1.4.35 - Fix Bug in tweedie(link.power=0) so that the resulting functions $linkinv() and $mu.eta() preserve the attributes of their arguments. 16 Feb 2020: statmod 1.4.34 - Improve the model description provided in the remlscoregamma() help page. - tweedie() now checks whether `var.power` or `link.power` are character strings instead of numeric. If `var.power` is one of the standard family names ("gaussian", "poisson", "gamma" or "inverse.gaussian") or `link.power` is one of the standard link functions ("identity","log","inverse") then the argument is reset to the corresponding numerical value with a message, otherwise an informative error message is given. - Cleaning up of internal code to avoid partial matching of function arguments, attributes or list component names. The automatic package tests are now run with the warnPartialMatchArgs, warnPartialMatchAttr and warnPartialMatchDollar options all set to TRUE. 4 Jan 2020: statmod 1.4.33 - The components returned by mixedModel2Fit() relating to fixed coefficients are now documented explicitly. The help page has been corrected to refer to the argument `only.varcomp` instead of `fixed.estimates`. The vector of `reml.residuals` is no longer part of the output. - The test file has been slightly revised using zapsmall() so ensure that the test output file remains correct for R with ATLAS BLAS. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.17 2019/08/08 19:53:54 brook Exp $ d4 1 a4 1 R_PKGVER= 1.4.36 @ 1.17 log @Update all R packages to canonical form. The canonical form [1] of an R package Makefile includes the following: - The first stanza includes R_PKGNAME, R_PKGVER, PKGREVISION (as needed), and CATEGORIES. - HOMEPAGE is not present but defined in math/R/Makefile.extension to refer to the CRAN web page describing the package. Other relevant web pages are often linked from there via the URL field. This updates all current R packages to this form, which will make regular updates _much_ easier, especially using pkgtools/R2pkg. [1] http://mail-index.netbsd.org/tech-pkg/2019/08/02/msg021711.html @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.16 2019/07/31 20:33:59 brook Exp $ d4 1 a4 2 R_PKGVER= 1.4.32 CATEGORIES= math d10 2 @ 1.16 log @R-statmod: update to version 1.4.32. Update to the canonical form of an R package and fix the LICENSE field. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.15 2018/07/28 14:40:51 brook Exp $ d3 3 a5 1 CATEGORIES= math R a7 1 HOMEPAGE= ${R_HOMEPAGE_BASE}/statmod/ a10 3 R_PKGNAME= statmod R_PKGVER= 1.4.32 @ 1.15 log @Remove MASTER_SITES= from individual R package Makefiles. Each R package should include ../../math/R/Makefile.extension, which also defines MASTER_SITES. Consequently, it is redundant for the individual packages to do the same. Package-specific definitions also prevent redefining MASTER_SITES in a single common place. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.14 2017/12/02 12:00:34 wen Exp $ d3 1 a3 1 CATEGORIES= math d7 2 a8 2 COMMENT= Miscellaneous biostatistical modeling functions LICENSE= gnu-lgpl-v2 OR gnu-lgpl-v3 d11 1 a11 1 R_PKGVER= 1.4.30 @ 1.14 log @Update to 1.4.30 Upstream changes: 16 June 2017: statmod 1.4.30 - Bug fix to qinvgauss(). In some case the gamma approximation used for small right tail probabilities was taking the initial value outside the domain of convergence. 27 February 2017: statmod 1.4.29 - rinvgauss() now accurately handles large or infinite values for the mean or dispersion. 26 February 2017: statmod 1.4.28 - R_registerRoutines is now used to register the Fortran subroutine gaussq2. - pinvgauss() and qinvgauss() now use a gamma approximation when the coefficient of variation is very small. 17 December 2016: statmod 1.4.27 - qinvgauss() now supports mean=Inf. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.13 2016/11/06 02:54:08 wen Exp $ a3 1 MASTER_SITES= ${MASTER_SITE_R_CRAN:=contrib/} @ 1.13 log @Update to 1.4.26 Upstream changes: 28 August 2016: statmod 1.4.26 - Fortran function gaussq2 updated to Fortran 77. 5 August 2016: statmod 1.4.25 - Add CITATION file. - pinvgauss() now uses an asymptotic approximation to compute right tail probabilities for extreme large quantiles. This allows it to give correct right tail probabilities for virtually any quantile. - Fix to qinvgauss() to avoid NA values when computing extreme tail quantiles where the inverse Gaussian density is subject to floating underflow. - Bug fix to qresiduals() and qresid.invgauss() for the inverse Guassian distribution. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.12 2016/04/09 08:36:34 wen Exp $ d12 1 a12 1 R_PKGVER= 1.4.26 @ 1.12 log @Update to 1.4.24 Upstream changes: 2 February 2016: statmod 1.4.24 - speedup for rinvgauss() by replacing rchisq() with rnorm() and rbinom() with runif(). - speedup for qinvgauss() by using qgamma as starting approximation for very small right tail probabilities, and inverse chisq as starting approximation for very small left tail probabilities. - qinvgauss() now computes Newton step using log probabilities and a Taylor series expansion for small steps. This improves accuracy in extreme cases. The stopping criterion for the Newton iteration has been revised. - Bug fix to dinvgauss(), pinvgauss() and qinvgauss() which were not preserving attributes of the first argument. 30 December 2015: statmod 1.4.23 - qinvgauss() has been improved to return best achievable machine accuracy. It now checks for backtracking of the Newton iteration. - dinvgauss() and pinvgauss() now check for a wider range of special cases. This allows them to give valid results in some cases for infinite or missing parameter values and for x outside the support of the distribution. 26 October 2015: statmod 1.4.22 - Functions needed from the stats and graphics packages are now explicitly imported into the package NAMESPACE. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.11 2015/05/30 10:50:34 wen Exp $ d12 1 a12 1 R_PKGVER= 1.4.24 @ 1.11 log @Update to 1.4.21 Upstream changes: 30 March 2015: statmod 1.4.21 - qinvgauss() now treats input arguments of different lengths or NA parameter values more carefully. - elda() now gracefully removes structural zeros, i.e., rows where the number of cells or the number of assays is zero. - S3 print and plot methods for "limdil" class now registered. - Use of require("tweedie") in the qres.tweedie() code replaced by requireNameSpace("tweedie"). @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.10 2014/07/13 12:47:38 wen Exp $ d12 1 a12 1 R_PKGVER= 1.4.21 @ 1.10 log @Update to 1.4.20 Update LICENSE Upstream changes: 30 May 2014: statmod 1.4.20 - Considerable work on the inverse Gaussian functions dinvgauss(), pinvgauss(), qinvgauss() and rinvgauss(). The parameter arguments are changed to mean, shape and dispersion instead of mu and lambda. The functions now include arguments lower.tail and log.p, meaning that right-tailed probabilities can be used and probabilities can be specified on the log-scale. Good numerical precision is maintained in these case. The functions now respect attributes, so that a matrix argument for example will produce a matrix result. Checking is now done for missing values and invalid parameter values on an element-wise basis. A technical report has been written to describe the methodology behind qinvgauss(). - This file has been renamed to NEWS instead of changelog.txt. - The introductory help page previously called 1.Introduction is now named statmod-package. 13 April 2014: statmod 1.4.19 - qinvgauss() now uses a globally convergent Newton iteration, which produces accurate values for a greater range of parameter values. - glmnb.fit() now supports weights. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.9 2014/03/09 14:28:57 wen Exp $ d12 1 a12 1 R_PKGVER= 1.4.20 @ 1.9 log @Update to 1.4.18 Upstream changes: 27 September 2013: statmod 1.4.18 - Update reference for permp(). - bug fix to elda() so that it returns NA for the tests instead of giving an error when the Fisher information for the slope isNA. - Exact roles of authors specified in DESCRIPTION file. - All usage lines in help files wrapped at 90 characters to ensure that code is not truncated in pdf manual. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.8 2013/07/07 11:07:18 wen Exp $ d9 1 a9 1 LICENSE= gnu-lgpl-v2 d12 1 a12 1 R_PKGVER= 1.4.18 @ 1.8 log @Update to 1.4.17 (No upstream changelog) @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.7 2012/11/30 13:55:48 wen Exp $ d12 1 a12 1 R_PKGVER= 1.4.17 @ 1.7 log @Update to 1.4.16 @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.6 2012/04/15 15:45:16 brook Exp $ d12 1 a12 1 R_PKGVER= 1.4.16 @ 1.6 log @Update to statmod v1.4.14, add LICENSE and regularize package files. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.5 2009/12/11 19:43:07 adam Exp $ d12 3 a14 1 R_PKGVER= 1.4.14 @ 1.5 log @Update to the latest version of the module along with R update @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.4 2008/10/13 19:28:48 markd Exp $ d6 1 a6 1 MAINTAINER= mchittur@@cs.nmsu.edu d9 1 d12 1 a12 1 R_PKGVER= 1.4.1 @ 1.4 log @Update R-statmod to 1.3.6 Changes unknown @ text @d1 1 a1 2 # $NetBSD: Makefile,v 1.3 2007/02/22 19:26:47 wiz Exp $ # d3 2 a4 2 CATEGORIES= math MASTER_SITES= ${MASTER_SITE_R_CRAN:=contrib/} d6 3 a8 3 MAINTAINER= mchittur@@cs.nmsu.edu HOMEPAGE= ${R_HOMEPAGE_BASE}/statmod/ COMMENT= Miscellaneous biostatistical modeling functions d10 2 a11 2 R_PKGNAME= statmod R_PKGVER= 1.3.6 @ 1.3 log @Whitespace cleanup, courtesy of pkglint. Patch provided by Sergey Svishchev in private mail. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.2 2006/02/05 23:10:01 joerg Exp $ a3 1 PKGREVISION= 1 d8 1 a8 1 HOMEPAGE= ${R_HOMEPAGE_BASE}/statmod.html d12 1 a12 1 R_PKGVER= 1.0.6 @ 1.2 log @Recursive revision bump / recommended bump for gettext ABI change. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.1.1.1 2005/11/04 08:19:17 rillig Exp $ d5 2 a6 2 CATEGORIES= math MASTER_SITES= ${MASTER_SITE_R_CRAN:=contrib/} d8 2 a9 2 MAINTAINER= mchittur@@cs.nmsu.edu HOMEPAGE= ${R_HOMEPAGE_BASE}/statmod.html d13 1 a13 1 R_PKGVER= 1.0.6 @ 1.1 log @Initial revision @ text @d1 1 a1 1 # $NetBSD$ d4 1 @ 1.1.1.1 log @Imported R-statmod from pkgsrc-wip. Miscellaneous biostatistical modeling functions. @ text @@