NEWS.md

statnet.common 4.13.0

New utilities

• 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.

Enhancements to existing utilities

• 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.

statnet.common 4.12.0

New utilities

• 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).

Enhancements to existing utilities

• 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.)

statnet.common 4.11.0

New utilities

• 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.

Enhancements to existing utilities

• The behavior of trim_env() has changed: if no variables are to be copied in, the environment is set directly to baseenv().

statnet.common 4.10.0

New utilities

• 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.

Enhancements to existing utilities

• 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.

Bug fixes

• 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.

statnet.common 4.9.0

New utilities

• 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.

Bug fixes

• In handle.controls(), arguments that are match.arg()-ed are now evaluated in the correct frame.

statnet.common 4.8.0

New utilities

• A helper function unused_dots_warning() is exported that works with rlang::check_dots_used() to print an informative message.

statnet.common 4.7.0

New utilities

• An S3 class 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.

Bug fixes

• list_rhs.formula() can now handle NULL terms on the RHS.

statnet.common 4.6.0

New utilities

• An implementation of Welford's online algorithm for calculating sample mean and variance has been added as a class Welford that implements method update() and maintains elements $n, $means, $SSDs, and $vars.

Bug fixes

• 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.

statnet.common 4.5.0

New utilities

• 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.

Enhancements to existing utilities

• 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.

Miscellaneous changes

• rle utilities are no longer reexported.

• statnet.common no longer depends on purrr.

• statnetStartupMessage() has been simplified.

statnet.common 4.4.0

rle utilities have been moved to a separate package, rle

• Major methods are reexported, for now.

New utilities

• split() 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.

Enhancements to existing utilities

• 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.

Bug fixes

• str.rle() now works despite the overridden length() method.

statnet.common 4.3.0

New utilities

• 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.

Bug fixes

• In forkTimeout(), don't collect a process twice. Thanks to Tomas Kalibera for suggesting the fix.

statnet.common 4.2.0

New utilities

• .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.

Miscellaneous

• 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.

statnet.common 4.1.4

New utilities

• 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().

Enhancements to existing utilities

• 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.

Bug fixes

• Printing for control lists now works for function arguments.

• A number of improvements to rle methods.

Miscellaneous

• A number of functions have been renamed for consistency:

  • term.list.formula() → list_rhs.formula()
  • append.rhs.formula() → append_rhs.formula()
  • nonsimp.update.formula() → nonsimp_update.formula()

• Citation utilities have been deprecated, since CRAN's structure makes them unusable.

statnet.common 4.0.0

• 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.

statnet.common 3.3.0

• 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.

statnet.common 3.2.3

• ERRVL() moved from ergm.

• Some NAMESPACE and other fixes to pass CRAN checks.

statnet.common 3.2.2

• control class improvements and bug fixes.

statnet.common 3.1.1

• Updated e-mail address

• Some improvements to opttest.

statnet.common 3.1.0

• Initial release, incorporating the control class framework (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.