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
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
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.
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".
