NEWS R Documentation

News for Package coin

Changes in version 1.4-2 (2021-10-07)

Bug fixes

• Partial matching of the teststat argument name failed for formula methods.

• Fix problem reported by rchk,

Other changes

• Package libcoin \ge1.0-9 is now required.

Changes in version 1.4-1 (2021-02-08)

Bug fixes

• Fix LaTeX problem.

Changes in version 1.4-0 (2021-01-15)

New features

• The Peto-Peto test for right-censored data is now available (see ?logrank_test and ?logrank_weight).

• The Moore-Penrose inverse of the conditional covariance matrix can now be extracted (see ?covariance).

• For tests of conditional independence within blocks, the partial linear statistic for each block and its conditional expectation and variance as well as its conditional covariance and corresponding Moore-Penrose inverse can now be extracted (see ?statistic, ?expectation, ?variance and ?covariance).

Bug fixes

• Exact multivariate two-sample tests with quadratic test statistics appeared to work but returned nonsense p-values; it now results in an error.

• Extraction of the standardized linear statistic from objects of class "IndependenceLinearStatistic" resulted in an error.

User-visible changes

• Extraction of the conditional expectation or variance now returns a matrix instead of a vector (for consistency with linear statistics and p-values).

• The test size is now computed more efficiently.

Other changes

• The internal storage of the linear statistic and its conditional expectation and covariance, i.e., slots linearstatistic, expectation and covariance in classes inheriting from "IndependenceLinearStatistic", as well as the Moore-Penrose inverse of the conditional covariance, i.e., slot covarianceplus in classes inheriting from "QuadTypeIndependenceTestStatistic", has been changed. In particular, the conditional covariance and its Moore-Penrose inverse now use a memory-efficient packed format.

• R \ge3.6.0 and package libcoin \ge1.0-5 are now required.

Deprecated and defunct

• Classes "Variance", "CovarianceMatrix" and "VarCovar" are now deprecated.

Changes in version 1.3-1 (2019-08-22)

Bug fixes

• Precision issues in point and interval estimates associated with location and scale problems.

User-visible changes

• The density, distribution and quantile functions now propagate any attributes of the x, q and p arguments, respectively, to the results.

Changes in version 1.3-0 (2019-03-04)

New features

• Ordered factors can now be transformed to a finite collection of order-restricted scores (see ?zheng_trafo); this can be used to formulate score-independent tests for ordered categorical data (see ?malformations, ?jobsatisfaction and ?vision).

• The test size, i.e., the actual significance level, of approximative (Monte Carlo) and exact tests can now be computed (see ?size).

• The centered linear statistic can now be extracted (see ?statistic).

• P-values can now be extracted from objects of class "PValue" using pvalue().

Bug fixes

• Adjusted p-values based on the approximative (Monte Carlo) marginal null distributions were incorrect under some circumstances.

• The point and/or interval estimate of the ratio of scales parameter (for tests against scale alternatives) were incorrect when using the asymptotic null distribution.

• Exact distributions of symmetry tests for paired data, e.g., the exact sign and Wilcoxon signed-rank tests, used the Streitberg-Röhmel algorithm for independent samples instead of the more efficient version for dependent samples.

• The class definition of "PValue" erroneously included the midpvalue and pvalueinterval slots; these slots are now part of the "NullDistribution" subclass (as they should have been originally).

Changes in version 1.0-7 (2009-09-29)

• dperm(), pperm() and qperm() are vectorized also for exact and approximative null distributions.

Changes in version 1.0-6 (2009-09-08)

• Exact distribution for independent two-sample problems with only two observations was wrong, spotted by Fritz Scholz fscholz@u.washington.edu.

Changes in version 1.0-4 (2009-05-11)

• Evaluate all formulae in xxx_test()'s parent.frame.

Changes in version 1.0-3 (2009-04-01)

• Add alternative ties handling to wilcoxsign_test() feature request by Fritz Scholz fscholz@u.washington.edu.

• Vignette update.

Changes in version 1.0-1 (2009-01-09)

• Add average scores for logrank test.

• Fix Rd problems.

Changes in version 1.0-0 (2008-11-06)

• JSS paper doi:10.18637/jss.v028.i08 documents version 1.0-0.

• Set default for <IndependenceTest>@method to ‘⁠General Independence Test⁠’.

• covariance() always returns a covariance matrix.

• Add show() method for "IndependenceTest" objects.

• Functions supplied via distribution does not need to have a class.

• Export all classes.

• Compute linear statistics, expectations and (co)variances when constructing <IndependenceLinearStatistic> instead of <IndependenceTestStatistic> and define methods for this class.

• maxstat_test() with integer weights gave NA or wrong cutpoints.

Changes in version 0.6-7 (2007-10-09)

• Remove non_function entries from Rd files.

• Disable Biobase example in vignette.

Changes in version 0.6-6 (2007-08-13)

• Fix precision issues with exact p-values (spotted by Michael Fay mfay@niaid.nih.gov.

Changes in version 0.6-5 (2007-07-23)

• Add new vignette on technical details.

• Update to new mvtnorm 0.8-0.

• Check for overflow errors in ‘StreitbergRoehmel.c’ (thanks for Michael Fay mfay@niaid.nih.gov for spotting this).

Changes in version 0.6-4 (2007-06-28)

• Add new argument ordered_trafo to trafo() and deal with ordered factors in a more transparent way (via a new function of_trafo()).

Changes in version 0.6-3 (2007-06-21)

• New vignette ‘MAXtest’.

Changes in version 0.6-2 (2007-05-13)

• Print name of x variable and levels when x is a factor.

• New class "IndependenceLinearStatistic".

Changes in version 0.6-1 (2007-04-25)

• LazyLoad: yes.

Changes in version 0.6-0 (2007-03-01)

• Rename some C source files & update doxygen documentation.

• Simplify some methods and the class structure.

• Clean up code and simplify wrapper functions.

• Deal with factors containing only one level.

• Do not compute design matrices in ModelEnvFormula.

• Expand weights if distribution = approximate().

• Assign names to user-specified transformation in case they are missing.

• The distribution argument may now be a function with one argument allowing for user-specified distributions.

• surv_test() ignored the alternative argument.

Changes in version 0.5-2 (2006-11-03)

• maxstat_trafo did not always choose the correct maximal cutpoint.

• Formula evaluation without data argument was partially broken (thanks to Achim Zeileis for spotting this).

Changes in version 0.5-1 (2006-10-27)

• Improve formula interface for wilcoxsign_test().

Changes in version 0.5-0 (2006-10-17)

• Implement exact distribution for symmetry problems (especially wilcoxsign_test()).

• Add more checks on StatXact examples.

Changes in version 0.4-14 (2006-09-18)

• Fix problems reported by valgrind.

Changes in version 0.4-13 (2006-09-13)

• coin-Ex.R’ generated by R 2.4.0.

• Enhances: Biobase.

Changes in version 0.4-12 (2006-09-07)

• Add \$(FLIBS) to ‘Makevars’.

• Include doxygen documentation for C functions.

Changes in version 0.4-10 (2006-08-25)

• maxstat_test(y ~ x) is now able to deal with unordered x variables.

• maxstat_test() returns estimates of both the selected variable and the cutpoint in multivariate situations (as a list).

• More checks for maxstat_test().

• Add codetools checks to tests.

Changes in version 0.4-9 (2006-07-24)

• Fix typo: Homegeneity.

Changes in version 0.4-8 (2006-06-23)

• Clarify that the Stuart-Maxwell test is computed by mh_test() and add a further example (thanks to Henric Nilsson henric.nilsson@phadia.com for pointing this out!).

Changes in version 0.4-7 (2006-05-16)

• Improve maxstat_trafo(): some potential cutpoints could have been overlooked in case of ties equal to the maxprob and minprob sample quantiles.

• Reproduce two examples from Hothorn and Lausen (2003) in ?maxstat_test (and added hohnloser data set).

• Add more regression tests on maxstat_test().

Changes in version 0.4-6 (2006-04-24)

• Updated ‘LegoCondInf’ vignette.

• Printed names of test statistics are now ‘⁠chi-squared⁠’, ‘⁠maxT⁠’, or ‘⁠Z⁠’ instead of ‘⁠T⁠’.

Changes in version 0.4-5 (2006-04-12)

• User-supplied transformations can return a vector which is coerced to matrix(..., ncol = 1) internally.

• ytrafo and xtrafo may take functions like rank() directly. However, the use of trafo() is recommended.

• Argument teststat may take values "max", "quad" or "scalar".

• Internal reimplementation of score handling for ordered factors.

• Handling of multiple ordered factors / ordered factors in multivariate situations implemented.

• f_trafo() returns a design matrix with NA rows in case missing values were present.

Changes in version 0.4-4 (2006-02-03)

• Make R CMD check happy and move ‘src/README’ to ‘inst/README’.

Changes in version 0.4-3 (2006-01-12)

• isequal() must not check equality of attributes.

Changes in version 0.4-2 (2005-12-21)

• New data set alpha.

• Data set alzheimer is now a "data.frame", not a "table".

• New vignette with more applications.

Changes in version 0.4-1 (2005-12-02)

• Remove unused setAs definitions.

• expectation(), variance() and covariance() return named vectors or matrices. Names for objects returned by statistic() have been partially improved.

• All observations with NAs are removed now.

• Some internal improvements (removed unused code, avoid duplicated code chunks etc.).

• More checks on NAs, blocks and multiple ordinal variables (one univariate problems are currently allowed to have ordinal variables).

Changes in version 0.3-8 (2005-11-29)

• Export independence_test.table().

• Add conf.level attribute for "MCp" objects when quasi-randomized Monte Carlo procedures (from mvtnorm) have been used.

• Add new var_trafo argument to trafo().

Changes in version 0.3-7 (2005-11-23)

• statistic() now returns correct linear and standardized statistics when scores are in play.

• alzheimer data added.

• photocar data added.

• support() and dperm() methods have been improved for asymptotic and approximative null distributions.

Changes in version 0.3-6 (2005-11-17)

• Internal C function R_MonteCarloIndependenceTest returns a pq \times B matrix instead of a list with B elements (the linear statistic for each random permutation of the data).

• Various simplifications for the computations of adjusted p-values.

• I() in formulae could still cause trouble with class "AsIs", now fixed.

• Logical variables are now allowed in formulae (and are treated like factors).

• Fix print method for marginal homogeneity tests (‘⁠...stratified by block...⁠’).

• R_kronecker in C now available.

• C versions of nrow() and ncol() return 1 or length for vectors.

• Some internal optimisation.

• C functions nrow(x) and ncol(x) return LENGTH(x) or 1 when x has no dim attribute.

• New R interface function R_kronecker to C_kronecker (which returns a _vector_!).

• Speedup of variance computations in internal functions.

Changes in version 0.3-3 (2005-09-07)

• Fix more problems reported by new codetools. Try to work around the terms(y ~ ., data = data.frame(1:10)) problem in R 2.2.0.

Changes in version 0.3-2 (2005-08-31)

• Fix some problems reported by codetools.

Changes in version 0.3-1 (2005-08-20)

• alternative = "less" and alternative = "greater" are now defined for "maxtype" statistics as well.

• One- and two-sided single-step and step-down max-T p-value adjustments are now available from the appropriate pvalue() method. (NOTE: those procedures have not been tested carefully, yet.)

In addition, the Bonferroni-adjustment by Westfall & Wolfinger (1997) is available now. Note that the interface to pvalue() changed slightly, adjustment = TRUE was replaced by method = "single-step".

• More examples added to the vignette.

Changes in version 0.2-14 (2005-07-14)

• distribution = "approximate" for "maxtype" statistics was wrong in case both xtrafo and ytrafo were multivariate (the conditional expectation was computed incorrectly).

Changes in version 0.2-13 (2005-07-11)

• I() in formulae returns objects of class "AsIs" which caused troubles in trafo().

Changes in version 0.2-12 (2005-06-15)

• Functionality for formula parsing and evaluation is now imported from package modeltools.

• show() returns objects (of class "htest", for example) invisibly, really.

• maxstat_trafo() is much faster now and returns a matrix with both row- and column names set appropriately.

Changes in version 0.2-11 (2005-06-02)

• The distribution argument now takes the return values of functions exact(), approximate() or asymptotic() as well. Those functions can be used to specify parameters, such as the number of Monte Carlo replications via ..., distribution = approximate(B = 9999), ....

• show() returns objects (of class "htest", for example) invisibly.

• expectation() returns a vector, not a matrix.

• New generic variance() for extracting the variance(s) of linear statistics.

• Only variances (instead of the whole covariance matrix) is computed when the distribution of maximum-type test statistics is to be approximated.

• data may be an object of class "exprSet" (-> Biobase), the vignette has an example.

• logrank_trafo() (and surv_test()) now have a ties.method argument, see ?surv_test for more information.

Changes in version 0.2-10 (2005-05-04)

• ⁠asymptotical⁠\rightarrow⁠asymptotic⁠’ in print methods.

• mercuryfish example added.

• <x,y>trafo now can return matrices with number of columns different from the lhs and rhs of formula.

Changes in version 0.2-9 (2005-03-15)

• mergesort is already defined in ‘/usr/include/stdlib.h’:270 on some platforms.

• delay is deprecated in R 2.1.0.