News for Package coin

Changes in version 1.4-3 (2023-09-26)

Bug fixes

• Supplying case weights to tests for marginal homogeneity or symmetry hypotheses appeared to work, but returned incorrect test statistics and p-values; it now results in an error.

User-visible changes

• The shift algorithm is now computationally more efficient and allows for user interrupt.

• Documentation updates.

Other changes

• The Fligner-Killeen test, the Conover-Iman test and the Quade test performed transformations of the response variable prior to applying the influence function; these transformations are now done within the influence function.

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

Bug fixes

• Partial matching of argument teststat failed for formula methods.

User-visible changes

• Documentation updates.

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, i.e., stratified tests, 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 incorrect 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.

• Documentation updates.

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.

• Documentation updates.

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).

User-visible changes

• Asymptotic and exact p-values smaller than machine precision, i.e., .Machine$double.eps, or approximative (Monte Carlo) p-values smaller than resampling precision, i.e., 1 / nresample, are now reported as such in the printed output.

• Computations on the approximative (Monte Carlo) null distribution, e.g., adjusted p-values for maximum-type tests, are now more efficient.

• The Pearson chi-squared test is now computed more efficiently.

• Extracting the test statistic or the (global) p-value returned a named result under some circumstances; the results are now unnamed.

• The quantile function now returns a named vector if its p argument is named.

• Objects of class "ApproxNullDistribution" now has a slot nresample containing the number of Monte Carlo replicates.

• Classes "ExpectCovar" and "ExpectCovarInfluence" have been moved to the party package.

• The ‘coin_implementation’ vignette has been renamed to ‘Implementation’.

• Documentation updates.

Other changes

• The linear statistic, its conditional expectation and covariance, and permuted linear statistics are now computed by package libcoin.

• confint() is now an S4 method.

• R \ge3.4.0 and packages stats4 and matrixStats are now required.

Deprecated and defunct

• The B argument of approximate() and ApproxNullDistribution() is now deprecated and has been replaced by nresample (for consistency with the libcoin, party and partykit packages).

• Class "PValue" is now deprecated.

Changes in version 1.2-2 (2017-11-28)

Other changes

• The libcoin regression tests are now in libcoin 1.0-0.

Changes in version 1.2-1 (2017-07-16)

Bug fixes

• Precision issue in the quantile function of exact null distributions computed by the shift algorithm.

Changes in version 1.2-0 (2017-06-20)

New features

• The Gaugler-Kim-Liao class of tests for right-censored data is now available (see ?logrank_test and ?logrank_weight).

• The pvalue(), midpvalue() and pvalue_interval() methods for objects of class "NullDistribution" are now vectorized.

Bug fixes

• Precision issue in the density function of approximative (Monte Carlo) null distributions. This also impacts mid-p-values and p-value intervals.

• Precision issue in the support of approximative (Monte Carlo) null distributions.

• Precision issue in the symmetric median scores transformation.

• The weighted logrank transformation returned nonsense scores when supplied non-right-censored input; it now results in an error.

• The maximally selected statistics transformation for ordered factors returned the wrong labels under some circumstances.

User-visible changes

• The ties.method argument of logrank_trafo() no longer allows using "logrank" and "HL" to specify mid-ranks and the Hothorn-Lausen method, respectively.

• Documentation updates.

Deprecated and defunct

• Function surv_test() is now defunct.

• Option method = "discrete" in pvalue() is now defunct.

• The dperm(), pperm() and qperm() methods for objects of class "AsymptNullDistribution" are no longer needed and have been removed.

Changes in version 1.1-3 (2016-11-24)

Bug fixes

• Objects of class "AsIs" were handled incorrectly in some cases, leading to, e.g., misleading error messages or test statistics having the wrong sign.

• Supplying decreasing scores for ordered factors with two levels using the test functions' scores argument resulted in increasing normalized scores, leading to test statistics having the wrong sign.

• The transformation function for ordered factors did not return normalized scores in the two-level case when argument scores was used.

• Precision issues in confidence intervals for location and scale problems.

• When the general symmetry and marginal homogeneity tests were applied to an object of class "table", the levels of the measurement conditions were not preserved (but reordered alphabetically).

User-visible changes

• Documentation updates.

Other changes

• Package mvtnorm \ge1.0-5 is now required.

Changes in version 1.1-2 (2015-11-13)

Bug fixes

• of_trafo() did not handle ordered factors of length one.

• Parallel operation (via approximate()) changed the random number generator state upon first invocation unless package parallel's namespace had already been loaded.

User-visible changes

• Documentation updates.

Changes in version 1.1-1 (2015-10-25)

Bug fixes

• Methods initialize() and show() were not imported from package methods.

User-visible changes

• Documentation and vignette updates.

Changes in version 1.1-0 (2015-08-14)

New features

• The Fisher-Yates correlation test (based on van der Waerden scores) is now available (see ?fisyat_test).

• The quadrant test is now available (see ?quadrant_test).

• The Koziol-Nemec test and its corresponding transformation function are now available (see ?koziol_test and ?koziol_trafo).

• The Savage test and its corresponding transformation function are now available (see ?savage_test and ?savage_trafo).

• The Taha test is now available (see ?taha_test).

• The Klotz test and its corresponding transformation function are now available (see ?klotz_test and ?klotz_trafo).

• The Mood test and its corresponding transformation function are now available (see ?mood_test and ?mood_trafo).

• The Conover-Iman test is now available (see ?conover_test).

• The weighted logrank test and its corresponding transformation function are now available, including weights for generalized Wilcoxon tests (Gehan-Breslow, Prentice, Prentice-Marek and Andersen-Borgan-Gill-Keiding), the Tarone-Ware class of tests, the Fleming-Harrington class of tests and the Self class of tests (see ?logrank_test, ?logrank_trafo and ?logrank_weight).

• The sign test for paired data is now available (see ?sign_test).

• The Quade test is now available (see ?quade_test).

• The Pearson chi-squared test, the generalized Cochran-Mantel-Haenszel test and the linear-by-linear association test now allow the alternative hypothesis to be specified in the doubly ordered case, i.e., when both the response variable and the explanatory variable are ordered factors (see ?chisq_test, ?cmh_test and ?lbl_test).

• The Kruskal-Wallis test, the van der Waerden test, the Brown-Mood median test, the logrank test and the Friedman test now allow the alternative hypothesis to be specified when the explanatory variable is an ordered factor (see ?kruskal_test, ?normal_test, ?median_test, ?logrank_test and ?friedman_test).

• The marginal homogeneity test now handles ordered responses and/or ordered measurement conditions and allows the alternative hypothesis to be specified in the doubly ordered case (see ?mh_test).

• The Brown-Mood median test and its corresponding transformation function now offer the choice of three different versions of the mid-score (see ?median_test and ?median_trafo).

• The van der Waerden test, the Brown-Mood median test and the Ansari-Bradley test now handle K-sample problems (see ?normal_test, ?median_test and ?ansari_test).

• The Fligner-Killeen test now handles two-sample problems (see ?fligner_test).

• Maximally selected statistics can now be computed for objects of class "table" (see ?maxstat_test).

• symmetry_test() has gained a new argument paired that is used to indicate if paired data have been transformed in such a way that the resulting unstandardized linear statistic is the sum of the absolute values of the positive differences between the paired observations (see ?symmetry_test).

• All transformation functions are now passing through missing values.

• New function for rank transformations (see ?rank_trafo).

• New function for maximally selected statistics transformation of ordered factors (see ?ofmaxstat_trafo).

• The Conover-Salsburg transformation function now allows the a constant to be set (see ?consal_trafo and ?neuropathy).

• The transformation function for ordered factors has gained a new argument scores that provides an alternative way of attaching scores to ordinal variables (see ?of_trafo).

• The approximative (Monte Carlo) null distribution can now be obtained by parallel operation using package parallel (see ?approximate).

• The exact null distribution of test statistics based on quadratic forms can now be obtained in the univariate two-sample case.

• The exact null distribution can now be obtained for tests specified with case weights, implying that exact p-values can be computed for 2 \times 2 tables or K \times 2 tables with K ordered categories.

• Evaluation of the null distribution can now be suppressed for all test procedures by setting distribution = "none".

• The mid-p-value can now be computed and is accompanied by a 99 % mid-p confidence interval when resampling has been used to obtain the null distribution (see ?midpvalue).

• The p-value interval can now be computed (see ?pvalue_interval).

• Step-down adjusted p-values based on the joint distribution of the test statistics can now be obtained when the asymptotic null distribution is used.

• Adjusted p-values based on the marginal distributions of the test statistics can now be obtained when the asymptotic null distribution is used.

• Adjusted p-values based on the marginal distributions of the test statistics now use a max-T procedure, instead of a min-P (which is now deprecated), incorporating discrete distributional characteristics when the approximative (Monte Carlo) null distribution is used (see ?pvalue).

• Single-step or step-down adjusted p-values based on the marginal distributions of the test statistics can now be obtained using the Bonferroni or the Šidák method (see ?pvalue).

• Unadjusted p-values can now be obtained (see ?pvalue).

• Random numbers can now be generated from the permutation distribution (see ?rperm).

• New data sets on gastric cancer, congenital sex organ malformation and unaided distance vision have been added (see ?GTSG, ?malformations and ?vision).

Bug fixes

• The standardized linear statistic of the Pearson chi-squared test was off by a factor \sqrt{n / (n - 1)}.

• The Pearson chi-squared test ignored user-specified transformations.

• Partial matching of the scores argument did not work for Pearson's chi-squared test and the marginal homogeneity test.

• The Fisher-Pitman permutation test, the Wilcoxon-Mann-Whitney test, the Kruskal-Wallis test, the van der Waerden test, the Brown-Mood median test, the Ansari-Bradley test, the Fligner-Killeen test, the Wilcoxon signed-rank test, the Friedman test and the Page test did not return an error message when supplied with a censored response variable.

• The Brown-Mood median test p-value computation used the wrong tail of the null distribution in the one-sided case.

• The test statistic of the Wilcoxon signed-rank test had the wrong sign under some circumstances, due to being based on the sum of the absolute values of the negative differences, instead of the positive, between the paired measurements.

• The Friedman test did not warn when case weights were supplied.

• Maximally selected statistics did not handle user-specified scores for ordinal variables correctly.

• Two-sample problems were not identified as such if the grouping variable had unused factor levels, causing problems if, e.g., trying to use the subset argument of formula methods.

• Stratified tests were not allowed if block had unused factor levels, causing problems, e.g., if trying to use the subset argument of the formula methods.

• Transformations involving ordered factors or survival data failed under some circumstances when performed within blocks.

• The maximally selected statistics transformation for factors dropped its column names under some circumstances.

• The maximally selected statistics transformation for factors retained unused levels.

• Approximative (Monte Carlo) p-values for stratified tests were wrong when the data were not ordered with respect to the blocks.

• Exact p-values for stratified tests were wrong when each block contained precisely two observations.

• Exact p-values for tests with an ordinal grouping variable were wrong.

• The smallest single-step and step-down adjusted p-values differed from the global p-value under some circumstances.

• Single-step adjusted p-values were too small when the support of the null distribution contained values equal to the observed test statistics.

• Monotonicity of step-down adjusted p-values was not enforced when using the approximative (Monte Carlo) null distribution.

• The density function of asymptotic permutation distributions for maximum-type tests returned nonsense; it now reports NA.

• The density function of approximative (Monte Carlo) permutation distributions returned nonzero probabilities for values not included in the support.

• The density function of exact permutation distributions returned a zero-length vector for values not included in the support; the probability of such values are now reported as ‘⁠0⁠’.

• The distribution and quantile functions of asymptotic permutation distributions for maximum-type tests were not handling vector arguments correctly.

• The quantile function of exact permutation distributions reported NA when the 100 % quantile was requested under some circumstances.

• The support of exact permutation distributions for stratified tests was not guaranteed to be distinct and ordered, which in turn caused failure when trying to obtain values from the density and quantile functions.

• The printed output of the Pearson chi-squared test and the generalized Cochran-Mantel-Haenszel test claimed that a ‘⁠Linear-by-Linear Association Test⁠’ had been carried out even in the singly ordered case, i.e., when either the response variable or the explanatory variable is an ordered factor; these are now reported as ‘⁠Generalized Pearson Chi-squared Test⁠’ and ‘⁠Generalized Cochran-Mantel-Haenszel Test⁠’, respectively.

• The printed output of the Fisher-Pitman permutation test reported the parameter tested in the two-sample case when the explanatory variable was an ordered factor.

• The printed output of the one-sided Ansari-Bradley test reported the opposite direction of the specified alternative (but performed the test in the specified direction and thus reported the correct p-value).

• The printed output of the logrank test did not report whether a two- or K-sample test had been carried out.

• The printed output of the logrank test did not report the tested parameter in the two-sample case.

• The printed output of maximum-type tests did not include the alternative hypothesis.

• The printed output of the general symmetry test claimed that a ‘⁠General Independence Test⁠’ had been carried out; it is now reported as ‘⁠General Symmetry Test⁠’.

• Objects of class "SymmetryProblem" were not checked for validity.

User-visible changes

• The Pearson chi-squared test, the generalized Cochran-Mantel-Haenszel test, the linear-by-linear association test and the marginal homogeneity test now use a scalar test statistic in the doubly ordered case.

• The Fisher-Pitman permutation test, the Kruskal-Wallis test, the logrank test and the Friedman test now use a scalar test statistic in case the explanatory variable is an ordered factor.

• The Fisher-Pitman permutation test no longer allows the test statistic to be specified; a quadratic form is now used in the K-sample case.

• The Pearson chi-squared test, the generalized Cochran-Mantel-Haenszel test, the Kruskal-Wallis test, the Friedman test, the Fligner-Killeen test and the marginal homogeneity test no longer features the distribution argument (but still allow the type of null distribution to be specified).

• The Ansari-Bradley test no longer features the alternative argument (but still allows the alternative hypothesis to be specified).

• When the general symmetry test or the marginal homogeneity test is applied to a table, the variable indicating the measurement conditions has been renamed to ‘⁠conditions⁠’ (from ‘⁠groups⁠’).

• The teststat argument no longer allows the use of maximum-type statistics and quadratic forms to be specified using "maxtype" and "quadtype", respectively.

• The median and logrank transformations are now increasing functions.

• The default number of Monte Carlo replicates used to approximate the exact conditional distribution has been increased to 10000.

• The exact distribution of stratified test statistics is now obtained more efficiently, and especially so for large numbers of strata.

• exact() has algorithm = "auto" as its new default, preserving the behavior of algorithm = "shift" in previous versions of the package.

• The shift algorithm (exact(algorithm = "shift")) no longer silently switches to the split-up algorithm when non-integer scores are detected; it now fails with an error message.

• Single-step adjusted p-values based on the joint distribution of the test statistics are now computed slightly faster due to using only the unique realizations of the test statistics.

• The support of an asymptotic null distribution is now reported as NA.

• Small changes in the printed output of the Pearson chi-squared test, the Fisher-Pitman permutation test, the Wilcoxon-Mann-Whitney test, the van der Waerden test, the Brown-Mood median test, the marginal homogeneity test, the Wilcoxon signed-rank test, and generalized maximally selected statistics.

• The printed output of the Fisher-Pitman permutation test now reports that a ‘⁠Linear-by-Linear Association Test⁠’ is carried out when the explanatory variable is an ordered factor.

• In the printed output of the Ansari-Bradley test and the Spearman test the tested parameter has been renamed to ‘⁠ratio of scales⁠’ and ‘⁠rho⁠’, respectively.

• wilcoxsign_test.IndependenceProblem() has been replaced by wilcoxsign_test.SymmetryProblem().

• The "IndependenceTestStatistic" class is now virtual.

• Objects of class "IndependenceProblem" drop unused factor levels.

• Objects of classes "ScalarIndependenceTestStatistic" or "QuadTypeIndependenceTestStatistic" now have a paired slot.

• Objects of class "ScalarIndependenceTest" now has a parameter slot.

• Objects of classes "ApproxNullDistribution" or "AsymptNullDistribution" now have a slot seed containing the state of the random number generator.

• The package manual has been completely revised.

• The memory consumption during computations has been reduced.

Other changes

• Henric Winell, a long-time collaborator who donated almost all changes in coin 1.1-0, is now listed as author. Welcome on board, Henric!

Deprecated and defunct

• surv_test() is now deprecated and has been replaced by logrank_test().

• method = "discrete" in pvalue() is now deprecated.

• The Wilcoxon signed-rank test no longer features the defunct ties.method argument.

Changes in version 1.0-24 (2014-09-17)

• as.integer(round(x)) is safer than as.integer(x) due to truncation in the latter.

Changes in version 1.0-23 (2013-09-03)

• Fix ‘DESCRIPTION’ and ‘NAMESPACE’ issues.

Changes in version 1.0-22 (2013-04-16)

• Documentation updates.

• Test update (for Sparc Solaris).

Changes in version 1.0-21 (2012-03-08)

• Move ‘inst/doc/vignettes/*’ to ‘vignettes/*’.

• New CWD data.

Changes in version 1.0-20 (2011-10-04)

• Report a warning for rank tests with case weights.

Changes in version 1.0-19 (2011-08-17)

• No require() in .onLoad().

Changes in version 1.0-18 (2010-12-21)

• exact() can not work for symmetry_test(); spotted by LE PAPE Gilles lepape.gilles@neuf.fr.

Changes in version 1.0-17 (2010-09-13

• Add dependencies required for ‘tests/*’.

Changes in version 1.0-16 (2010-08-23)

• Change ties.method = c("HollanderWolfe", "Pratt") to zero.method = c("Pratt", "Wilcoxon") in wilcoxsign_test() following a suggestion by Fritz Scholz. A warning is fired to avoid misleading and nonreproducible results.

• Use quantile(..., type = 1) for computing approximate quantiles (suggested by Fritz Scholz).

Changes in version 1.0-14 (2010-08-10

• Documentation Biobase::expressionSet.

• Further checks and better error messages for nonsense data in (paired) two-sample tests.

Changes in version 1.0-12 (2010-07-03)

• Better error message for wilcoxsign_test(c(1, 1, 1) ~ c(1, 1, 1)).

Changes in version 1.0-11 (2010-04-13)

• Bugfix in discrete MTP adjustment.

Changes in version 1.0-10 (2010-01-27)

• Improve upon qperm() for van de Wiel algorithm again.

Changes in version 1.0-9 (2009-12-30)

• Again precision issues in van de Wiel algorithm: qperm() suffered from too large tolerances of the inverted probability function.

Changes in version 1.0-8 (2009-10-30)

• Precision issues in van de Wiel algorithm fixed. In rare cases, P(T < t) was returned as p-value instead of P(T \le t). Two statistics are now considered equal (in all computations) when the difference is smaller than sqrt(.Machine$double.eps).

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 1.0-5 (2009-06-04)

• Documentation updates.

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 1.0-2 (2009-03-16)

• Fix location confidence interval problem spotted by Fritz Scholz fscholz@u.washington.edu.

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" objects instead of "IndependenceTestStatistic" and define methods for this class.

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

Changes in version 0.6-9 (2008-05-05)

• any() was misused in one place, spotted by Kasper Daniel Hansen khansen@stat.Berkeley.EDU.

• Code cosmetics by Johannes Huesing johannes@huesing.name.

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 to 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.

• Documentation updates.

• Deal with factors containing only one level.

• Do not compute design matrices in ModelEnvFormula.

• Expand case 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.

• Documentation updates.

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.

• Add ASA copyright to ‘LegoCondInf’ vignette.

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 for 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)

• Documentation updates.

• 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().

• Documentation updates.

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.

• Documentation updates.

• 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’ \rightarrow ‘⁠asymptotic⁠’ 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.