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CVS log for pkgsrc/math/R-lme4/Makefile

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Default branch: MAIN


Revision 1.6 / (download) - annotate - [select for diffs], Thu Aug 8 19:53:50 2019 UTC (6 weeks, 1 day ago) by brook
Branch: MAIN
CVS Tags: HEAD
Changes since 1.5: +4 -6 lines
Diff to previous 1.5 (colored)

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

Revision 1.5 / (download) - annotate - [selected], Wed Jul 31 19:49:55 2019 UTC (7 weeks, 2 days ago) by brook
Branch: MAIN
Changes since 1.4: +6 -7 lines
Diff to previous 1.4 (colored)

R-lme4: update to version 1.1.21.

Update to the canonical form of an R package and fix the LICENSE
field.

Revision 1.4 / (download) - annotate - [select for diffs], Fri Dec 21 12:53:49 2018 UTC (8 months, 4 weeks ago) by wen
Branch: MAIN
CVS Tags: pkgsrc-2019Q2-base, pkgsrc-2019Q2, pkgsrc-2019Q1-base, pkgsrc-2019Q1, pkgsrc-2018Q4-base, pkgsrc-2018Q4
Changes since 1.3: +2 -2 lines
Diff to previous 1.3 (colored) to selected 1.5 (colored)

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

Revision 1.3 / (download) - annotate - [select for diffs], Sat Jul 28 14:40:49 2018 UTC (13 months, 3 weeks ago) by brook
Branch: MAIN
CVS Tags: pkgsrc-2018Q3-base, pkgsrc-2018Q3
Changes since 1.2: +1 -2 lines
Diff to previous 1.2 (colored) to selected 1.5 (colored)

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.

Revision 1.2 / (download) - annotate - [select for diffs], Mon Jan 22 03:27:45 2018 UTC (19 months, 4 weeks ago) by wen
Branch: MAIN
CVS Tags: pkgsrc-2018Q2-base, pkgsrc-2018Q2, pkgsrc-2018Q1-base, pkgsrc-2018Q1
Changes since 1.1: +1 -2 lines
Diff to previous 1.1 (colored) to selected 1.5 (colored)

Remove an unneeded line

Revision 1.1 / (download) - annotate - [select for diffs], Mon Jan 22 03:16:11 2018 UTC (19 months, 4 weeks ago) by wen
Branch: MAIN
Diff to selected 1.5 (colored)

Import lme4-1.1.15 as math/R-lme4.

Fit linear and generalized linear mixed-effects models. The models
and their components are represented using S4 classes and methods.
The core computational algorithms are implemented using the Eigen
C++ library for numerical linear algebra and RcppEigen "glue".

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