| NEWS | R Documentation |
as.integer(round(x)) is safer than as.integer(x) = trunc(x)
fix ‘DESCRIPTION’ and ‘NAMESPACE’ issues
documentation updates
test update (for Sparc Solaris)
move ‘inst/doc/vignettes/*’ to ‘vignettes/*’
new CWD data
report a warning for rank tests with weights
no require() in .onLoad()
exact() can not work for symmetry_test(); spotted by LE
PAPE Gilles lepape.gilles@neuf.fr
add dependencies required for ‘tests/*’
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)
documentation Biobase::expressionSet
further checks and better error messages for nonsense data in (paired) two-sample tests
better error message for
wilcoxsign_test(c(1, 1, 1) ~ c(1, 1, 1))
bugfix in discrete MTP adjustment
improve upon qperm() for van de Wiel algorithm again
again precision problems in van de Wiel algorithm: qperm()
suffered from too large tolerances of the inverted probability function.
precision problems in van de Wiel algorithm fixed. In rare cases,
P(T < t) was returned as p-value instead of P(T ≤ t).
Two statistics are now considered equal (in all computations) when the
difference is smaller than sqrt(.Machine$double.eps)
dperm(), pperm() and qperm() are vectorized also
for exact and approximate null distributions
exact distribution for independent two-sample problems with only two observations was wrong, spotted by Fritz Scholz fscholz@u.washington.edu
documentation updates
evaluate all formulae in xxx_test()'s
parent.frame
add alternative ties handling to wilcoxsign_test() feature
request by Fritz Scholz fscholz@u.washington.edu
vignette update
fix location confidence interval problem spotted by Fritz Scholz fscholz@u.washington.edu
add average scores for logrank test
fix Rd problems
JSS paper http://www.jstatsoft.org/v28/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
any() was misused in one place, spotted by Kasper Daniel Hansen
khansen@stat.Berkeley.EDU
code cosmetics by Johannes Huesing johannes@huesing.name
remove non_function entries from Rd files
disable Biobase example in vignette
fix precision problems with exact p-values (spotted by Michael Fay mfay@niaid.nih.gov
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)
add new argument ordered_trafo to trafo() and deal with
ordered factors in a more transparent way (via a new function
of_trafo())
new vignette ‘MAXtest’
print name of x variable and levels when x is a factor
new class "IndependenceLinearStatistic"
LazyLoad: yes
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 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
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)
improve formula interface for wilcoxsign_test()
implement exact distribution for symmetry problems (especially
wilcoxsign_test())
add more checks on StatXact examples
fix problems reported by valgrind
‘coin-Ex.R’ generated by R 2.4.0
Enhances: Biobase
add $(FLIBS) to ‘Makevars’
include doxygen documentation for C functions
documentation updates
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
fix typo: Homegeneity
add ASA copyright to ‘LegoCondInf’ vignette
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!)
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()
updated ‘LegoCondInf’ vignette
printed names of test statistics are now chi-squared, maxT, or Z instead of T
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
make R CMD check happy and move ‘src/README’ to ‘inst/README’
isequal() must not check equality of attributes
new data set alpha
data set alzheimer is now a "data.frame", not a
"table"
new vignette with more applications
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)
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
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 approximate null distributions
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
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.
fix some problems reported by codetools
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.
distribution = "approximate" for "maxtype" statistics
was wrong in case both xtrafo and ytrafo were
multivariate (the conditional expectation was computed incorrectly)
I() in formulae returns objects of class AsIs
which caused troubles in trafo()
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
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
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
mergesort is already defined in
‘/usr/include/stdlib.h’:270 on some platforms
delay is deprecated in R 2.1.0