Changes for R-package relaimpo

Version 2.2-2 (Sep 11th, 2013)
  - adapted man files to new line length requirements for usage and example lines
  - adapted package to current startup policy
  - adapted to new namespace policy
  - adapted to new author coding
  - fixed improper documentation format for methods of calc.relimp and boot.relimp

Version 2.2-1 (July 18th, 2011, not published)
  - reduced number of observations required for running calc.relimp (used to be 
    larger than number of coefficients to be estimated + 2, 
    is now larger than number of coefficients to be estimated (i.e. at least 
    one error df)

Version 2.2 (Sep 15th, 2010)
  - added metrics genizi and car, prompted by a manuscript of Zuber and Strimmer (2010)
  - documentation adapted, with additional minor improvements
  
Version 2.1-4 (Oct 19th, 2009)
  Changes from previous versions
  - completed fix of slot information in documentation
  
Version 2.1-3 (Oct 19th, 2009)
  Changes from previous versions
  - re-included version footer into CITATION file
  - removed Umlauts from CITATION for removing MacOS warnings 
  - fixed slot information in documentation
  
Version 2.1-2 (May 15th, 2009)
  Changes from previous versions (globally licenced CRAN version without pmvd)
  - now really updated CITATION file to conform to standards
  
Version 2.1-1 (May 14th, 2009)
  Changes from previous versions (globally licenced CRAN version without pmvd)
  - updated CITATION file to conform to standards
  - made NEWS file text only to be viewable directly from CRAN
  - updated e-mail address in description (old one still works)
  - updated TFH Berlin to BHT Berlin (still the same place with a new name, 
    long version Beuth Hochschule fuer Technik Berlin)
  
Version 2.1 (August 12th, 2008)
  - Function calc.relimp now calculates averaged coefficients for each model size (slot 
    ave.coeffs of output object), whenever any of the metrics lmg or pmvd is used. These 
    are meant to enable users to gain some insight regarding the behavior of coefficients in 
    sub models, since the sub models form the basis of the variance contributions.
  - Calculation efficiency in the presence of interactions has been improved (omit calculation 
    for inadmissible sequences rather than removing them after calculation).
  
Version 2.0-2 (April 4th, 2008; applies to global version only)
  - Incomplete change from non-US version fixed
  
Version 2.0-1 (April 3rd, 2008)
  - Renamed ChangeLog.pdf to News.pdf for being closer to naming conventions - since this 
    log of changes is one of user-visible changes rather than one of programming details.
  - Replaced reference to included file COPYING by reference to licences on R-website in 
    file COPYRIGHT and renamed the file to LICENSE.
  - Removed German Umlauts from comments in order to eliminate problems with MAC OS
  - Removed function plot.R, which caused problems with methods / S4-class in R-devel
  - Updated URL to package website in manual and description, since old website will 
    become obsolete soon
  
  
Version 2.0 (November 22nd, 2007)
  - relaimpo now works on data frames, linear models and formulae which include factors 
    (treating all dummies for the factor as one group). 
  - relaimpo now allows interactions (currently second-order only), treating these as 
    hierarchically below main effects, i.e. excluding models with interactions included while 
    any of the main effects is not. This feature works with metric lmg only. Currently, it 
    cannot be combined with self-chosen groups (that have not been created by relaimpo 
    itself for accomodating factors).
  - relaimpo can now accommodate observation weights. Note that there are different 
    types of observation weights which can all be treated alike for calc.relimp (calculation of 
    metrics only) but have to be treated differently for confidence intervals. 
    a.  Weights that reflect different variances of the response values, e.g. if response 
        values are estimated coefficients from various studies with different variances, are 
        typically proportional to the inverse variance (the less uncertain the value, the 
        more weight it is given, as in the Aitken estimator for linear models). Such weights 
        can be specified with the new weights= option. They are used in calculating the 
        metrics, but each observation is given the same probability in resampling. 
        NOTE that it is inappropriate to use such data with the fixedox's bootstrap, since 
        the residuals cannot be assumed to be basically exchangeable. 
    b.  If the weights in a data frame represent the multiplicity of each observation (i.e. 
        there are several units with identical combination of values in the data, and the 
        weights represent the number of units with exactly this value pattern for each row 
        of the data frame), they can also be used in calc.relimp for calculating the metrics. 
        However, such frequency weights cannot be appropriately accomodated in 
        boot.relimp; instead, the data frame with frequencies has to be expanded to 
        include one row for each unit before using the resampling routine (e.g. using 
        function untable from package reshape or function expand.table from 
        package epitools; a future version of relaimpo may do that for you, currently 
        you have to do it yourself). 
    c.  If the weights in a data frame represent the number of units of the population that 
        this single observed unit represents, calc.relimp also works correctly, when simple 
        given these weights. However, for obtaining confidence intervals, the data have to 
        be treated as data from a complex survey (which they usually are anyway in such 
        a situation). You have to define the design yourself using package survey. Data 
        from complex surveys can now also be handled by relaimpo.
  - relaimpo now can accommodate data from complex sample surveys. Implementation 
    of this feature heavily relies on package survey. Consequently, relaimpo now requires 
    the package survey to be available. 
    The user needs to familiarize her/himself with the package survey in order to prepare a 
    design object or a linear model of class svyglm to be handed to the functions in package 
    relaimpo. 
    While calculation of metrics only uses the weights from the design object (which could 
    also be handed to relaimpo as a separate weights vector, cf. previous bullet point), 
    estimation of confidence intervals also makes use of the structure from the survey (e.g. 
    strata, clusters) by making the package survey determine the bootstrap weights. 
    so far, bootstrapping based on such data must be considered experimental in the 
    following sense: survey analysts typically use these bootstrap weights for calculating 
    variances only - whether they are under all circumstances usable for e.g. percentile 
    confidence intervals is not absolutely clear. It is considered likely that percentile intervals 
    are a safer option than more advanced intervals like bca intervals. 
    Note that bootstrapping survey data currently does not work in combination with factors or 
    interactions.
  - relaimpo has a new function mianalyze.relimp for relative importance 
    assessments based on multiply imputed data sets. 
    Note that mianalyze.relimp only works together with groups, factors, interactions or 
    x-variables calculated on the fly, if calculation of confidence intervals is suppressed 
    (no.CI=TRUE), so that the function is used as a convenience tool for aggregating 
    calculations from a list of multiply imputed data frames. Confidence intervals currently 
    cannot be obtained in the presence of groups, factors, interactions or calculated x-
    variables.
    Furthermore, note that mianalyze.relimp is experimental and approximate in the 
    following sense: 
  - It uses asymptotic todistributionobased confidence intervals based on Rubin's 
    degrees of freedom although the estimated percentages have not been derived als 
    maximum likelihood estimates
  - The intervals thus obtained are forced to be symmetric; since the distributions of 
    percentages are often far from symmetric, the intervals can be approximate only.
    Thus, confidence intervals should be used for rough indication only (even more so than 
    the other bootstrap confidence intervals in relaimpo, which have also been observed to 
    only approximately satisfy their nominal coverage probabilities.). 
  - Several users have asked for relaimpo to cover mixed models. While this issue has so 
    far not been worked on, note that clustered data (e.g. observation of two eyes for each 
    person, observation of several time points for each unit etc.) can be adequately addressed 
    by using the design= option for handing a clustered design (defined in package survey) 
    to package relaimpo. (Of course, this is not the same as fitting a mixed model.)
  - relaimpo now includes the call in all computational output objects for proper traceability 
    of what exactly has been done. 
  - The default for bootstrap confidence intervals has been changed from bca to perc, since 
    percentile intervals are much faster to compute and have not proven worse than BCa 
    intervals in simulations for this application. Sorry for any inconveniences this change may 
    cause.
  - Bug corrected: For booteval.relimp, numbers were truncated instead of rounded to four 
    digits.
  - Bug corrected: str() did not work on objects of class bootrelimpeval, because initialization 
    of the object was not formally correct. The functionality of the package was not affected 
    by this bug.
  
Version 1.2-2 (September 30th 2007)
  Changes from previous versions (globally licenced CRAN version without pmvd)
  - Corrected description text regarding licencing info, point readers to non-US version on 
    homepage again (was wrong since Version 1.2)
  
Version 1.2-1 (September 28th 2007)
  Changes from previous versions (globally licenced CRAN version without pmvd)
  - Eliminated warnings for R 2.6.0 regarding encoding of description file
  - Adapted to GPL notation standard
  
Version 1.2 (January 27th 2007)
  Changes from previous versions
  - Regressors can now be grouped, which 
  - allows to handle large numbers of regressors as long as they are combined into a 
    reasonably small number of groups
  - will in the future allow to handle factors via grouped dummy variables
  - Improvements to error messages
  
Version 1.1-1 (September 21st 2006)
  Changes from previous versions
  Package gave ERROR on R CMD check for R 2.4.0 alpha, presumably because of changed 
  behavior of automatic printing for S4 objects (error because of empty slots). This has been 
  fixed by creating S4 methods for show and print. 
  
Version 1.1 (June 29th 2006)
  Changes from previous versions
  Bug fix for the formula method for calc.relimp and boot.relimp: formulae with "." on the righto
  hand side did cause an error message. 
  
Version 1.0-1 (June 19th 2006)
  Changes from previous versions
  Global version on CRAN only: Correction to the description file, which for version 1.0 
  erroneously claimed that this were the non-US version of the package. 
  
Version 1.0 (June 16th 2006)
  Changes from previous versions
  
  Several improvements have been made:
  - It is now possible to designate some regressors as adjustment regressors that are adjusted 
    out before assessing relative importance of the remaining regressors (option always for 
    functions calc.relimp and boot.relimp). 
  - Function calc.relimp has been made generic with methods for formula and linear model 
    objects. The default method has also been enhanced to accept more different types of 
    input.  
    Overall, the first object handed over to calc.relimp can now be any of the following:  
    a covariance matrix (former parameter covg), 
    a data matrix or data frame the first column of which needs to be the response variable 
    (like in function lm), 
    a response vector (if a regressor matrix x is also provided), 
    a linear model formula, 
    or a linear model object (class lm). 
    Note, however, that relaimpo does not accept factors as regressors.
  - Function boot.relimp has been made generic with methods for formula and linear model 
    objects. The default method has also been enhanced to accept more different types of 
    input. Except for a covariance matrix that is not sufficient for the bootstrapping routine, 
    boot.relimp accepts the same objects as calc.relimp.
  - Besides a bootstrapping routine for random regressors, a bootstrapping routine for fixed 
    regressors is now also available (option fixed=TRUE in boot.relimp).
  - If data vectors, matrices or frames include missing values,  
    relaimpo uses complete cases only (based on function complete.cases from package 
    stats) and prints a warning message.  
    Options regarding na.action are in effect only if the formula specification of the model is 
    used.  
    Previously, a missing value in the data for boot.relimp would have caused an error. 
    (Naturally, a covariance matrix given to calc.relimp must not have any missing values.)
  - The plots are annotated in a more useful way (overall title, better axis labels, annotation 
    indicating what options were chosen in the calculations).
  - Annotation of printed output has been enhanced in line with annotation of plots.
  - two bugs regarding output of booteval.relimp have been fixed: 
  - For rank=TRUE and norank=FALSE: If shares or confidence bounds were very 
    small, the printed numbers were far to- large (all calculations were correct, but a 
    formatting issue showed cutooff scientific notation).
  - For rank=FALSE or norank=TRUE: the empty line between several metrics 
    showed 0.0000 instead of blanks.
  
  The following changes have been made to settings and defaults (apologies to any pioneering 
  users wh- may be inconvenienced by one of these)
  - relaimpo no longer works for R-versions before 2.2.1  
    (calculations do work from 2.0.1, but number printout can be wrong!) 
  - The default for option rela has been changed from TRUE to FALSE - sorry for 
    any inconvenience this may cause to pioneering users.
  - The default number of bootstrap resamples has been reduced from b=1500 to 
    b=1000.
  
  
Version 0.5-1 (April 13th 2006)
  This change applies to the non-US version only: PMVD gave an error message, if 
  after leaving out regressors with coefficients estimated as 0 there were less than two 
  remaining regressors. This issue has been fixed. 
  
Version 0.5 (February 3rd 2006)
  Change from previous versions
  The files $.relimplm.R and $.relimplmbooteval.R have been renamed to dollar.relimplm.R and 
  dollar.relimplmbooteval.R respectively in order to eliminate warnings in checks of R 
  development version. 
  
Version 0.4 (January 21st 2006)
  Change from previous versions
  Bootstrapping and evaluation of bootstrap results now also works for two regressors only.  
  Previously, this did not work due to three bugs: 
  - The internal function nchoosek produced a "subscript out of bounds" error (on this 
    occasion, reference to the original package vsn within the function was also corrected; 
    previously, erroneously referenced e1071).
  - The internal function last.calc had a bug for two regressors only.
  - The function booteval.relimp did not like to receive a numeric value instead of a 1x1 
    matrix.
  
Version 0.3 (January 12th 2006)
  Change from version 0.2
  correction to column labelling of outputs from function calc.relimp: 
  In version 0.2, column labels of calculated metrics were in the order the metrics were 
  requested and did not fit the calculated metrics, which were in the standard order of the 
  metrics (lmg, pmvd, last, first, betasq, pratt).
  
Version 0.2 (December 16th 2005)
  Changes from version 0.1
  1. correction to coerce method for relimplm (as.relimplm.R) and its documentation: 
  coerce method coerces the full object to list, including the nononumeric components
  2. R-code tidied, and comments improved/corrected in many files
  3. percentages and ranks metrics output by relimplm are named
  4. placing of column names for differences output is improved
  5. vignette and change log added to documentation 
  
Original version: Version 0.1 (December 1st 2005)
  
  
  Ulrike Grömping
  Beuth University of Applied Sciences Berlin
  http://prof.beuth-hochschule.de/groemping/
