NEWS (original) (raw)

Changes inoptmatch Version 0.10.8

• Updates to internal C++ code.

Changes inoptmatch Version 0.10.7

• Hardened tests further against package unavailability
• Changed the name of default arguments for a version ofpredict. (#223)
• Several small documentation tweaks to pass CRAN checks on R-devel.
• Fix a bug introduced in version 0.10.6, involving discretization of distances. The fix avoids spurious errors for distance matrices with very large values, although you may still have to pass tol= arguments to pairmatch() and fullmatch() that are smaller than the desired tolerance.(#230)
• Disable passing of local variables from generic corresponding to change in R_USEMETHOD_FORWARD_LOCALS coming in the next major release. No user-facing change, except the @call slot of objects may look slighly different (but should function identically). (#234)

Changes inoptmatch Version 0.10.6

• Adjusted a check to avoid ambiguous failures when using LEMON vs RELAX-IV.
• Updated CITATION to use bibentry().
• Minor tweaks to address failing tests.

Changes inoptmatch Version 0.10.5

Minor revision to address a failing test.

Changes inoptmatch Version 0.10.4

• When including factor variables on the right hand side of the formula passed into match_on(), now more simply calculates the contrast to enable more intuitive results. (Thanks Noah Greifer, #220)
• dbind() will now properly support binding more than 26 unique matrices when renaming is necessary; in fact it supports up to 18,278 uniquely renamed matrices.
• A few tweaks in documentation, testing and vignettes to satisfy CRAN requirements and harden against loss of dependencies.

Changes inoptmatch Version 0.10.3

Interface changes

• The rank Mahalanobis distance being created inmatch_on() using the argumentmethod = "rank_mahalanobis" was accidentally returning the squared distance rather than the distance. This has been fixed. To recover results using the squared distance, square the results, e.g.:match_on(..., method = "rank_mahalanobis")^2. (Thanks Noah Greifer #218)
• New function as.list.BlockedInfinitySparseMatrix() to split a single BlockedInfinitySparseMatrix into alist of InfinitySparseMatrix based upon the separate blocks. (Called via as.list(b) when bis a BlockedInfinitySparseMatrix.)
• New function dbind() for binding several distance matrices into a single BlockedInfinitySparseMatrix. Valid inputs include any distance convertible into anInfinitySparseMatrix, orBlockedInfinitySparseMatrix, or lists of these. (#65)

Infrastructure changes

• Manually correcting License_is_FOSS andLicense_restricts_use flags after 0.10.0 transition to an open license.
• optmatch no longer depends ondigest, RItools, orsurvey, or imports from survival. This should harden us against unexpected downtime should any of these packages be removed from CRAN.
  • Implemented optmatch::strata to be used in place ofsurvival::strata. Loading survival and masking strata should not cause issues either.
  • Hashing of distance matrixes is now done internally.
  • RItools and survey are now only suggested with appropriate warnings if users attempt to utilize code with them without first installing the packages.
• Modernized some vignettes

(Note: 0.10.1 and 0.10.2 were functionally equivalent releases updated to address an issue with CRAN and theLicense_is_FOSS and License_restricts_useflags.)

Changes inoptmatch Version 0.10.0

Major changes

• optmatch no longer includes the RELAX-IV solver internally. That solver can be still be used by installing the newrrelaxiv package (which will not be hosted on CRAN). When rrelaxiv is not available,optmatch instead uses a min-cost flow solver provided by the LEMON project, https://lemon.cs.elte.hu/trac/lemon; bindings to these are provided by the rlemon package. The user interface remains the same, other than a new optional argument for specifying which solver to use. In very limited testing, we’ve seen similar matching results with the new solver.
• The rlemon package offers bindings to four LEMON solvers. See help(fullmatch) for a discussion on those, and the new argument to fullmatch(),solver =.
• To continue using the RELAX-IV solver, whether for back-compatibility or as a matter of preference, install therrelaxiv package, from https://errickson.net/rrelaxiv/. Ifrrelaxiv is installed, RELAX-IV will become the default solver automatically.

Minor changes

• Remove dependence on the digest package when generating hashes of distance matrices.
• RItools is moved to Suggests instead of Imports.

Changes inoptmatch Version 0.9-17

• Fix to FORTRAN to conform with Writing R Extensions §6.6.2.
• Observations with NAs in a blocking variable are now retained, although marked as unmatchable (#206). And similarly for observations with NAs in a scalar matching variable (#189).
• Minor bug fix(es) incl. #211, #204

Changes inoptmatch Version 0.9-16

• Bug fix: integer overflow issue arising with large problems (#209)
• Minor refinement of support for glms fromsurvey::svyglm() (#194)

Changes inoptmatch Version 0.9-15

• Small bug fix related to survey::mad andsurvey::med interface

Changes inoptmatch Version 0.9-14

• Bug fix: within= arguments to match_on(), or functions calling match_on() such aspairmatch() or fullmatch(), were sometimes ignored (#181).
• Binary operations on sparse matching distances now compare dimnames of the two before proceeding (#190).
• Bug fix: when fullmatch() or pairmatch()found it infeasible to create matches within an exact matching category, under some circumstances all members of that category were being placed into a single category labeled 1.NA, or 2.NAetc. Instead, all members of that category are now NA(#203).
• Fixed a bug causing match_on(), scores()to misinterpret propensity or other scores fitted withsurvey::svyglm() (#194).
• boxplot() gains a method for svyglmobjects, e.g. propensity score models fitted with case weights viasurvey::svyglm() (#194).
• The meaning of one of match_on.glm()’s arguments has changed slightly: to circumvent scale standardization when matching on a propensity score or other index, you should now passstandardization.scale = 1, notstandardization.scale = NULL (#194).

Changes inoptmatch Version 0.9-12

• Fixed a bug causing summary.optmatch() to fail b/c of NAs in the treatment variable (#155).
• Fixed bug with using custom distance functions (#180) and updated documentation related to custom distance functions.
• Fixed minor compatibility error in R-devel for math operations on sparse distance matrices (#179).

Changes inoptmatch Version 0.9-11

• Added exclude argument to match_on()mirroring the exclude argument forcaliper().
• Optmatch objects now support an update()function, update.Optmatch(). (#54)
• Optmatch objects can be combined via a c()function, c.Optmatch(). (#68)
• Added support for labelled treatment vectors which often arise when importing from Stata or SPSS. (#159)
• Introduced more informative error messages in a few situations. (#149, #104)
• Better handling of NA’s in variables involved in matching/calipering/exactMatching. (#147)
• Fixed a bug with incorrect results in matchfailed(). (#175)

Changes inoptmatch Version 0.9-10

• Minor release to fix warnings during CRAN checks.

Changes inoptmatch Version 0.9-9

• Fixed a bug that caused the effective sample size to be rounded too aggresively in summary.optmatch().
• Improved several error messages and warnings. (#138, #149, #142)
• Fixed use of if(vectorOfThings) usage that will give an error in upcoming R release.

Changes inoptmatch Version 0.9-8

• If pairmatch is asked to match within a stratum with fewer eligible controls than controls times the number of treatments, it now attempts to match in that stratum by leaving out some of the treatment units. (#116)
• The treatment indicator must be either numeric 0/1 (1 for treatment, 0 for control) or logical (TRUE for treatment, FALSE for control).
• Support for any other type of treatment vector (factors, character, other numerical values) has been deprecated. You can easily update treatment vectors using conditional statements, e.g. if you have a character “T” and “C”,treatment_new = treatment == "T".
• The treatment indicator can now include NA’s. Any observations with NA treatment status will be excluded from distances matrices and will never match. WARNING: if the data argument is excluded fromfullmatch() or pairmatch() andnum_NA > 0 entries in the treatment status vector are NA, then the length of the vector produced by fullmatch()or pairmatch() won’t match the length of the treatment status vector, having num_NA fewer observations. Don’t forget to pass a data argument!
• Fixed bug affecting rank Mahalanobis matching in combination with calipers and/or exact matching constraints (#128)
• Addressed an issue affecting certain problems with both exact matching and caliper restrictions, wheremin.controls/mean.controls/max.controlsdirectives would have been mistakenly applied to the wrong subclasses, resulting in strange warnings and, potentially, spurious match failures or unintended structural restrictions in some subclasses (#129).
• Structural restrictions allowing only many-one matches no longer cause fullmatch() to automatically fail. I.e. we’ve restored the behaviour of the software prior to version 0.8. (#132)

Changes inoptmatch Version 0.9-7

• Added support for CBPS created objects (#121).
• Improvments to documentation for several functions.
• Several small bugfixes.

Changes inoptmatch Version 0.9-6

• New material in vignettes, on general use of the package and on import/export of matching results and material between R and SAS or Stata (Josh Errickson).
• New summary() methods forInfinitySparseMatrix(summary.InfinitySparseMatrix()),BlockedInfinitySparseMatrix, (summary.BlockedInfinitySparseMatrix()) andDenseMatrix (summary.DenseMatrix()). I.e., you can call summary() on the result of a call tomatch_on() or caliper(). The information this returns may be useful for selecting caliper widths, and for managing computational burdens with large matching problems.
• Streamlined combinations of exact and propensity score matching. If you include “+ strata(fac)” on the right hand side of a propensity scoring model formula, then pass the fitted model topairmatch(), fullmatch() ormatch_on(), then the factor “fac” will both serve as an independent variable for the propensity model and an exact matching variable (#101). See the examples on the help documentation forfullmatch().
• pairmatch() and fullmatch() no longer generate “matched.distances” attributes for their results. To get this information, use matched.distances().
• (Internal) methods for sorting of InfinitySparseMatrix’s
• Deprecated: support passing the results of fill.NAs()directly to glm() or similar. Use the traditional formula and data argument version. See help documentation forfill.NAs() for examples.
• Fixed: Rcpp incompatibilities for some OSX users (4bbcaca);boxplot() method for fitted propensities ignoring varwidth argument (#113); various minor issues affecting package development and deployment (#110,…).

Changes inoptmatch Version 0.9-5

• Documentation adjustments.
• Explicit print method for output from explicit calls tostratumStructure().

Changes inoptmatch Version 0.9-4

• Significant speed up of math operations for sparse distance objects (by Josh Buckner).
• Introducing contr.match_on(), a new default contrasts function for making Mahalanobis and Euclidean distances. Previously we used R defaults, which (a) generated different answers for the same factor depending on the ordering of the levels and (b) led to different distances for {0,1}-valued numeric variables and two level factors. (#80)
• match_on now takes strata as element of formula. Now users can write: match_on(z ~ x1 + x2 + strata(exactMatchVar)) Instead of match_on(z ~ x1 + x2, within = exactMatch(z ~ exactMatchVar))
• Fixed bug giving spurious infeasibility warnings, sample size reductions when using fullmatch() with feasible combinations of min.controls,mean.controls/max.controls andmax.controls (#92)
• Various small bug fixes and documentation improvements.

Changes inoptmatch Version 0.9-3

• Fixed memory issues, potential segfaults in solver code. (Thank you, Peter Solenberger).
• Fixed bug in dropping cases with extraneous NAs when usingfullmatch() or pairmatch() to create distance specifications directly.
• Fixed bug (#83) in glm() method formatch_on() that caused observations with fixable NAs to be dropped too often.
• New function distUnion() allows combining arbitrary distance specifications.
• New function antiExactMatch() provides for matches that may only occur between treated and control units with _different_values on a factor variable. This is the opposite ofexactMatch(), which ensures matches occur within factor levels.
• Can now infer data argument in more cases when using the summary() method when the RItoolspackage is present.
• Additional warnings and clarifications.

Changes inoptmatch Version 0.9-2

• Fixed issue #74 by properly setting the omit.fractionargument when there are unmatched controls.
• Improvements to the minExactMatch() function.
• Added optmatch_verbose_message option to provide additional warnings.
• Fixed crash when all NULL or NA vectors passed as arguments tofullmatch().
• Added argument to caliper() function that allows returning values that fit the caliper instead of just indicators of which entries fit the caliper width.
• Calipers widths can be given per-treated unit, instead of globally.
• Additional binary operators for sparse matrix representations.
• Added new ranked Mahalanobis method for the formula method ofmatch_on().

Changes inoptmatch Version 0.9-1

• Subsetting of Optmatch objects now preserves (and subsets) the subproblem attribute.
• Performance improvements for match_on applied to glm’s.
• The solver update of version 0.9-0 had a bug that in some circumstances caused hangups or malloc’s [Issue #70]. We believe this is now fixed – but please notify maintainer if you continue to experience the problem. (If you do, we’ll reward you with an easy workaround.)

Changes inoptmatch Version 0.9-0

NEW FEATURES

• Solver limits now depend on machine limits, not arbitrary constants defined by the optmatch maintainers. For large problems, users will see a warning, but the solver will attempt to solve.
• fullmatch() and pairmatch() can now take distance generating arguments directly, instead of having to first call match_on(). See the documentation for these two functions for more details.
• Infeasibility recovery in fullmatch(). When passing a combination of constraints (e.g. max.controls) that would make the matching infeasible, fullmatch() will now attempt to find a feasible match that respects those constraints, which will likely result in omitting some controls units.
• An additional argument to fullmatch(),mean.controls, is an alternative to the previousomit.fraction. (Only one of the two arguments can be presented.) The match will attempt to average mean.controls number of controls per treatment.
• Each Optmatch object now carries with it the constraints used to generate it (e.g. max.controls) as well as a hashed version of the distance it matched up, to help with some debugging/error checking but avoiding having to carry the entire distance matrix around.
• Creating a distance matrix prior to matching is now optional.fullmatch() now accepts arguments from whichmatch_on() would create a distance, and create the match behind the scenes.
• Performance enhancements for distance calculations.
• Several new utility functions, including subdim(),optmatch_restrictions(),optmatch_same_distance(),num_eligible_matches(). See their help documentation for additional details.
• Arithmetic operations between InfinitySparseMatrices and vectors are supported. The operation is carried out as column by vector steps.
• scores() function allows including model predictions (such as propensity scores) in formulas directly (such as combining multiple propensity scores). The scores() function is preferred to predict() as it makes several smart choices to avoid dropping observations due to partial missingness and other useful preparations for matching.

BUG FIXES

• match_on() is now a S3 generic function, which solves several bugs using propensity models from other packages.
• summary() method was giving overly pessimistic warnings about failures.
• fixed bug in how Optmatch objects were printing.

DEPRECATED AND DEFUNCT

• mdist() is now deprecated, in favor ofmatch_on().

Changes inoptmatch Version 0.8-3

• Changes to make examples compatible with PDF manual

Changes inoptmatch Version 0.8-2

• full() and pair() are now aliases tofullmatch() and pairmatch()
• All match_on() methods take caliperarguments (formerly just the numeric method and derived methods had this argument).
• boxplot methods for fitted propensity score methods (glm() and bigglm())
• fill.NAs() now takes contrasts.argargument to mimic model.matrix()
• Several bug fixes in examples, documentation
• The methods pscore.dist() andmahal.dist() are now deprecated, with useful error messages pointing users to replacements.
• Significant performance improvements for sparse matching problems.
• Functions umatched() and matched() were backwards. Corrected.

Changes inoptmatch Version 0.8-1

• Several small bug fixes

Changes inoptmatch Version 0.8-0

NEW FEATURES

• More efficient data structure for sparse matching problems, those with relatively few allowed (finite) distances between units. Sparse problems often arise when calipers are employed. The new data structure (InfinitySparseMatrix) behaves like a simple matrix, allowing cbind(), rbind(), andsubset() operations, making it easier to work with the older optmatch.dlist data structure.
• match_on(): A series of methods to generate matching problems using the new data structure when appropriate, or using a standard matrix when the problem is dense. This function is being deployed along side the mdist() function to provide complete backward compatibility. New development will focus on this function for distance creation, and users are encouraged to use it right away. One difference for mdist() users is thewithin argument. This argument takes an existing distance specification and limits the new comparisons to only those pairs that have finite distances in the within argument. See thematch_on(), exactMatch(), andcaliper() documentation for more details.
• exactMatch(): A new function to create stratified matching problems (in which cross strata matches are forbidden). Users can specify the strata using either a factor vector or a convenient formula interface. The results can be used in callsmatch_on() to limit distance calculations to only with-in strata treatment-control pairs.
• New data argument to fullmatch() andpairmatch(): This argument will set the order of the match to that of the row.names, names, or contents of the passed data.frame or vector. This avoids potential bugs caused when the optmatch objects were in a different order than users’ data.
• Test suite expanded and now uses the testthatlibrary.
• fill.NAs() allows (optionally) filling in all columns (previously, the first column was assumed to be an outcome or treatment indicator and was not filled in).
• New tools to find minimum feasible constraints: Large matching problems could exceed the upper limit for a matching problem. The functions minExactmatch() and maxCaliper()find the smallest interaction of potential factors for stratified matchings or the largest (most generous) caliper, respectively, that make the problem small enough to fit under the maximum problem size limit. See the help pages for these functions for more information.

BUG FIXES

• Unmatched units are always NA (instead of being labeled1.NA or similar). This avoids some obscure bugs when feeding the results of fullmatch() to other functions.

FOR A DETAILED CHANGELOG, SEE https://github.com/markmfredrickson/optmatch

Changes inoptmatch Version 0.7-1

NEW FEATURES

• pairmatch() has a new option,remove.unmatchables, that may be useful in conjunction with caliper matching. With remove.unmatchables = TRUE, prior to matching any units with no counterparts within caliper distance are removed. Pair matching can still fail, if for example for two distinct treatment units only a single control, the same one, is available for matching to them; but remove.unmatchables eliminates one simple and common reason for pair matching to fail.
• Applying summary() to an optmatch object now creates a summary.optmatch containing the summary information, in addition to reporting it to the console (via asummary.optmatch() method forprint()).
• mdist.formula() no longer requires an explicit data argument. I.e., you can get away with a call likemdist(Treat~X1+X2|S) if the variables Treat,X1, X2 and S are available in the environment you’re working from (or in one of its parent environments). Previously you would have had to domdist(Treat~X1+X2|S, data=mydata). (The latter formulation is still to be preferred, however, in part because with itmdist() gets to use data’s row names, whereas otherwise it would have to make up row names.)

Changes inoptmatch Version 0.7

NEW FEATURES

• New function fill.NAs() replaces missing observations (ie. NA values) with minimally informative values (ie. the mean of observed columns). fill.NAs() handles functions in formulas intelligently and provides missing indicators for each variable. See the help documentation for more information and examples.

BUG FIXES

• mdist.function() method now properly returns anoptmatch.dlist object for use insummary.optmatch(), etc.
• mdist.function() maintains label on grouping factor.

Changes inoptmatch Version 0.6-1

NEW FEATURES

• New mdist() method to extract propensity scores from models fitted using bigglm() in packagebiglm.
• mdist()’s formula method now understands grouping factors indicated with a pipe (|)
• informative error message for mdist() called on numeric vectors
• updated mdist() documentation

Changes inoptmatch Version 0.6

NEW FEATURES

• There is a new generic function, mdist(), for creating matching distances. It accepts: fitted glm’s, which it uses to extract propensity distances; formulas, which it uses to construct squared Mahalanobis distances; and functions, with which a user can construct his or her own type of distance. The function method is more intuitive to work with than the older makedist()function.
• A new function, caliper(), builds on themdist() structure to provide a convenient way to add calipers to a distance. In contrast to earlier ways of adding calipers,caliper() has an optional argument specify observations to be excluded from the caliper requirement — this permits one to relax it for just a few observations, for instance.
• summary.optmatch() now removes strata in which matching failed (b/c the matching problem was found to be infeasible) before summarizing. It also indicates when such strata are present, and how many observations fall in them.
• Demo has been updated to reflect changes as of version 0.4, 0.5, 0.6.

DEPRECATED & DEFUNCT

• The vignette is sufficiently out of date that it’s been removed.

BUG FIXES

• subsetting of objects of class Optmatch now preserves matched.distances attribute.
• fixed bug inmaxControlsCap()/minControlsCap() whereby they behaved unreliably on subclasses within which some subjects had no permissible matches.
• Removed unnecessary panic in fullmatch() when it was given a min.controls argument with attributes other than names (as when it is created by tapply()).
• fixed bug wherein summary.optmatch() fails to retrieve balance tests if given a propensity model that had function calls in its formula.
• Documentation pages for fullmatch(),pairmatch() filled out a bit.

Changes inoptmatch Version 0.5

NEW FEATURES:

• summary.optmatch() completely revised. It now reports information about the configuration of the matched sets and about matched distances. In addition, if given a fitted propensity model as a second argument it summarizes covariate balance.