High-Performance Open-Source Archive
New testthat predicate,
skip_if_not_checking(), that skips the test if it’s not
part of an R CMD check, e.g., if run by
testthat::test_local().
New function, enlist() to wrap an object into a
singleton list if it’s not already a list, for various definitions of
“list”.
New function, which_top_n(), to return the indices
of top or bottom n elements of a vector, with several
methods for resolving ties.
New function, split_len() to split a split()-able
object by lengths.
term_list objects now have envir(),
envir<-(), sign(), and
sign<-() methods to better encapsulate their environment
and sign information.
ERRVL*() functions if not given any non-erroring
expressions now throw the last error rather than a generic
message.
New matrix functions: qrssolve() to solve linear
systems via QR decomposition after scaling, and qrsolve()
to do the same without scaling, along with
sandwich_qrsolve(), sandwich_qrssolve(),
sandwich_ginv(), and
sandwich_sginv().
New function, match_names() to replace
vector.namesmatch() with more flexible behavior and error
checking.
New functions, ERRVL2() and ERRVL3()
that, unlike ERRVL(), do not require the expressions to be
wrapped in try().
New function, replace(), a more pipe-friendly
drop-in replacement for base::replace() for which
replacement indices and values can be specified as functions evaluated
on the input vector. replace()<- is also implemented,
allowing the list to be modified in place.
New pair of functions, arr_to_coo() and
arr_from_coo(), to translate between an array and its list
of non-default values.
New function, set_diag() to set a diagonal of a
matrix to specified values and return (as opposed to modifying it in
place).
statnetStartupMessage() now prints
Remote: information if the package was installed from a
remote.
Matrices returned by the lweighted.*() family of
functions now inherit dimensional names.
xTAx_eigen() (and therefore
xTAx_seigen()) now handle matrix-valued x correctly and
check that x is in the span of A.
Scaling version of matrix operations now use
.Machine$double.xmax/(1 + .Machine$double.eps) as the
inverse of the zero diagonal.
all_identical() can now use a custom comparison
predicate (e.g., all.equal()), and the use any of the
elements in the list as the reference. (Thanks to Michał Bojanowski
@mbojan.)
New function, modify_in_place(), that attempts to
modify the argument of its caller in place. A function can call it to
modify its own arguments in place.
New function, log1mexp(x) to compute
log(1-exp(-x)) minimizing the loss of precision. R provides
a C macro log1mexp(x) but not the corresponding R
wrapper.
trim_env() has changed: if no variables
are to be copied in, the environment is set directly to
baseenv().New linear algebra utilities: ginv_eigen(), which
performs generalised inverse via eigendecomposition rather than SVD, to
be used by sginv() if snnd=TRUE; and
xTAx_eigen() and xTAx_seigen() to evaluate the
inverse quadratic form using eigendecomposition.
A new function var.mcmc.list() “method” to evaluate
the covariance matrix for an mcmc.list without constructing
a large matrix.
colMeans.mcmc.list() “method” no longer constructs a
large matrix when calculating.
lweighted.var() and lweighted.cov() now
take an additional argument onerow= to specify what they
should return (NA, 0, or something else) if the input
matrix has one row.
as.cntrol.list.list() and hence
snctrl() no longer clobbers nested controls, e.g.,
control.ergm(SAN=control.san(...),...).
To facilitate support for earlier versions of R, avoid using the
built-in pipe (|>) for now.
A new function,lweighted.cov(), to compute weighted
covariance between two matrices or vectors.
New linear algebra utilities, is.SPD(),
sandwich_solve(), sandwich_ssolve(),
sginv(), snearPD(), srcond(),
ssolve(), xAxT(), xTAx(),
xTAx_qrsolve(), xTAx_qrssolve(),
xTAx_solve(), and xTAx_ssolve() moved from
ergm and documented.
handle.controls(), arguments that are
match.arg()-ed are now evaluated in the correct frame.unused_dots_warning() is exported
that works with rlang::check_dots_used() to print an
informative message.term_list for storing terms extracted from
a formula, by list_rhs.formula() and others, containing
information about each term’s sign and environment. Concatenation,
indexing, and print methods are implemented.list_rhs.formula() can now handle NULL
terms on the RHS.Welford
that implements method update() and maintains elements
$n, $means, $SSDs, and
$vars.snctrl() was issuing a warning twice when called
with a misspelled argument.
deInf() now handles NULL
input.
in locate_function() a subtle bug has been fixed in
handling of visible as opposed to invisible objects.
ergm’s term locator functions
(locate_function() and
locate_prefixed_function()) have been moved from
ergm.
A new function, default_options(), a wrapper around
options() that drops options already set.
A new function, as.control.list() generic and
methods which take an R list and call an appropriate
control.*() function on it.
check.control.class() now first runs the control
argument through as.control.list() and overwrites, so
control= arguments to many functions can be plain
lists.
A new function, simplify_simple(), which takes a
list and returns an atomic vector if the elements of the list are atomic
and of length 1, with particular handling for NULL and
empty (0-length) elements.
A new function, snctrl() (StatNet ConTRoL), designed
so that argument completion will complete all available control
functions. Looking up its help (?snctrl) produces a dynamic
list of all control parameters and their packages and control functions
that is updated as packages are loaded and unloaded.
A new function, handle.controls(), that performs the
most normal functions in a control.*() function.
Two trivial helper functions, base_env() and
empty_env(), to replace an object’s environment with
baseenv() and emptyenv(),
respectively.
A new function, fixed.pval() that wraps
base::format.pval() with better default arguments.
A reimplementation of attr() is exported, which
disables partial matching by default.
statnetStartupMessage() now first looks for a
comment=(affil=...) for the contributor’s affiliation,
before using e-mail.
Improved output formatting for
.Deprecate_once().
append_rhs.formula() now accepts NULL as the first
argument, in which case it creates a new formula, and takes an additonal
argument env=, which is used as this new formula’s
environment.
rle utilities are no longer reexported.
statnet.common no longer depends on
purrr.
statnetStartupMessage() has been
simplified.
rle
utilities have been moved to a separate package, rlesplit() methods for matrices and arrays, to split
them along a margin.
trim_env(), a generic that will replace an
environment (possibly attached to another object) with a sub-environment
containing only objects whose names are specified.
A diff() method for control lists and a
print() method for the resulting differences.
deInf(), to replace .deinf() in package
ergm.
A compress() generic, a compress()
method for RLEs, and a doNotCompress argument to
rep.rle(). Both compact.rle() and the
doNotCompact argument to rep.rle() are now
deprecated.
Various optimizations have been made to RLEs.
nonsimp_update.formula() now handles both one and
two sided formulas; it also now copies all names except ...
when from.new = TRUE.
str.rle() now works despite the overridden
length() method.EVL(), a family of functions like
NVL(), that treat any object of length 0 as
NULL.
once(), a purrr-style adverb that wraps
a function to only evaluate the first time it’s called with a given
configuration of arguments.
persistEval() and persistEvalQ() to
retry evaluating a given expression a specified number of
times.
forkTimeout(), don’t collect a process twice. Thanks
to Tomas Kalibera for suggesting the fix..Deprecate_once() calls .Deprecated(),
passing all its arguments through, but only the first time it’s
called.
.Deprecate_method() calls
.Deprecated(), but only if a method has been called by
name, i.e., METHOD.CLASS.
forkTimeout() evaluates an R expression with a hard
time limit (except on Windows) by forking a process. Unlike
setTimeLimit(), it enforces the limit even on native
code.
ult() is a convenience function that extracts or
replaces elements of a list indexed from the end.
statnet.common now depends on R >= 3.5 due to
what appears to be a method dispatching bug in earlier
versions.
The package no longer Enhances coda.
despace() removes whitespace from a string.
Pseudo-methods colMeans.mcmc.list(),
sweep.mcmc.list(), and lapply.mcmc.list()
(migrated from the ergm package).
filter_rhs.formula() selectively deletes terms in on
the RHS of a formula.
eval_lhs.formula() extracts the LHS of the formula
and evaluates it in the specified environment.
NVL2() and NVL3() for flexible
substitution of null values.
message_print() formats its arguments as if for
print() or show() methods, but then prints to
stderr like message().
paste.and() now takes an additional
con= argument, allowing a conjunction other than “and” to
be used.
ERRVL() now uses lazy evaluation and lets the user
dot-substitute the previous argument’s try-error into the next
argument.
Printing for control lists now works for function arguments.
A number of improvements to rle methods.
term.list.formula() →
list_rhs.formula()append.rhs.formula() →
append_rhs.formula()nonsimp.update.formula() →
nonsimp_update.formula()The package now uses Roxygen for
documentation.
term.list.formula() output format has been changed,
since support of attributes on symbols is being deprecated.
A library of methods has been added for the base rle
class, implementing concatenation, compaction, and a number of binary
operations.
all_same() has been moved from ergm and renamed to
all_identical().
A new assignment method NVL()<- overwrites a
variable if its value is NULL.
A set of classes and functions for manipulating and efficiently performing calculations on dense matrices or vectors with weighted rows or elements (possibly on the log scale) has been added.
New control parameter helper function, control.remap() has been
added. Autodetection of function names by
set.control.class() and check.control.class()
has been deprecated and now results in a warning.
Improvements to the compressed data frame code, including an order() generic.
Miscellaneous robustifications added.
Native routine registration has been added.
append.rhs.formula(),
vectors.namesmatch(), term.list.formula(), and
ergm.update.formula() (renamed to
nosimp.update.formula()) moved from
ergm.
Skye Bender-deMoll has been added as a contributor.
ERRVL() moved from ergm.
Some NAMESPACE and other fixes to pass CRAN
checks.
Updated e-mail address
Some improvements to opttest.
set.control.class(), check.control.class(),
print.control.list()); startup message framework;
NVL(); sort.data.frame();
compress.data.frame(); paste.and(); citation
utilities framework; and opttest() framework.
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