CVS commit: pkgsrc/math/R-lme4

["Wen Heping" <wen%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wen
Date:           Fri Dec 21 12:53:49 UTC 2018

Modified Files:
        pkgsrc/math/R-lme4: Makefile distinfo

Log Message:
Update to 1.1.19

Upstream changes:
CHANGES IN VERSION 1.1-19
NEW FEATURES

    influence measure code from car rolled in (see ?influence.merMod)

    mkReTrm gets new arguments reorder.terms, reorder.vars to control arrangement of RE terms and individual effects with RE terms within model structures

    adding material from the RePsychLing package (on GitHub; see Bates et al 2015 arXiv:1506.04967) to show orthogonal variance components.

USER-VISIBLE CHANGES

    as.data.frame.merMod finds conditional variance information stored either as attr(.,"postVar") or attr(.,"condVar") (for glmmTMB compatibility)

    change to defaults of [g]lmerControl to print a message when fits are singular

    new utility isSingular() function for detecting singular fits; by default a message is printed for singular fits

    allFit function/methods have been moved to the main package, rather than being included in an auxiliary source file

    post-fitting convergence checks based on estimated gradient and Hessian (see troubleshooting) are no longer performed for (nearly-)singular fits (see isSingular)

CHANGES IN VERSION 1.1-18-1 (2018-08-17)

    This is a minor release; the only change is to roll back (unexport) the influence.merMod method, pending resolution of conflicts with the car package

CHANGES IN VERSION 1.1-18 ((2018-08-16)
USER-VISIBLE CHANGES

    ranef(.,condVar=TRUE) now works when there are multiple random effects terms per factor

NEW FEATURES

    rstudent and influence methods are available for merMod objects

    devfun2 function (for generating a deviance function that works on the standard deviation/correlation scale) is now exported

BUG FIXES

    lmList now obeys its pool argument (instead of always using what currently is the default, GH #476)

CHANGES IN VERSION 1.1-17 (2018-04-03)

    This is a maintenance release only (fixes CRAN problems with cross-platform tests and examples)

CHANGES IN VERSION 1.1-16 (2018-03-28)
BUG FIXES

    lmList no longer ignores the subset argument (John Fox)

    fixed several minor issues with predicting when (1) grouping variables have different levels from original model (e.g. missing levels/factor levels not explicitly specified in newdata) or (2) 
re.form is a subset of the original RE formula and some (unused) grouping variables are omitted from newdata (GH #452, #457)

USER-VISIBLE CHANGES

    lmList tries harder to collect errors and pass them on as warnings

    documented as.function method (given a merMod object, returns a function that computes the deviance/REML criterion for specified parameters)

    print method for summary.merMod objects no longer collapses small values of the t-statistic to zero


To generate a diff of this commit:
cvs rdiff -u -r1.3 -r1.4 pkgsrc/math/R-lme4/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/math/R-lme4/distinfo

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

Modified files:

Index: pkgsrc/math/R-lme4/Makefile
diff -u pkgsrc/math/R-lme4/Makefile:1.3 pkgsrc/math/R-lme4/Makefile:1.4
--- pkgsrc/math/R-lme4/Makefile:1.3     Sat Jul 28 14:40:49 2018
+++ pkgsrc/math/R-lme4/Makefile Fri Dec 21 12:53:49 2018
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.3 2018/07/28 14:40:49 brook Exp $
+# $NetBSD: Makefile,v 1.4 2018/12/21 12:53:49 wen Exp $
 #
 
 CATEGORIES=    math
@@ -9,7 +9,7 @@ COMMENT=        Linear mixed-effects models usi
 LICENSE=       gnu-gpl-v2
 
 R_PKGNAME=     lme4
-R_PKGVER=      1.1-15
+R_PKGVER=      1.1-19
 
 USE_LANGUAGES= c c++
 

Index: pkgsrc/math/R-lme4/distinfo
diff -u pkgsrc/math/R-lme4/distinfo:1.1 pkgsrc/math/R-lme4/distinfo:1.2
--- pkgsrc/math/R-lme4/distinfo:1.1     Mon Jan 22 03:16:11 2018
+++ pkgsrc/math/R-lme4/distinfo Fri Dec 21 12:53:49 2018
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.1 2018/01/22 03:16:11 wen Exp $
+$NetBSD: distinfo,v 1.2 2018/12/21 12:53:49 wen Exp $
 
-SHA1 (R/lme4_1.1-15.tar.gz) = 6e32d8f42a4372d01e6b684f0b630b5d38120e92
-RMD160 (R/lme4_1.1-15.tar.gz) = f14c00b40d1a72495b388503c91bd8e1300a959b
-SHA512 (R/lme4_1.1-15.tar.gz) = c3e58e9cb2ec04ae21a767e3d344d8215fd267952a06dab9c8a3de1f0aa888b024548605725cd783457a13c2b01b7e7552ddbc90bd091161fcd4915b3349ad24
-Size (R/lme4_1.1-15.tar.gz) = 3610706 bytes
+SHA1 (R/lme4_1.1-19.tar.gz) = 2b7f7060e970dd58fce1138d8e7aa70c4f1a9197
+RMD160 (R/lme4_1.1-19.tar.gz) = ca3ef68788a45cac5d8a2a99a3a6706c30b6b713
+SHA512 (R/lme4_1.1-19.tar.gz) = 4e27ab14b91b6349a0923a80d5ee1a0e2549a6ec7f133cfafb45fb28921c6f4249af8fc97bd4d80e841d5da586af3d4ebe15bb764f8a4ce6b52eb71c67e310c7
+Size (R/lme4_1.1-19.tar.gz) = 4120276 bytes