r-cran-gnm 1.0-8-1 / usr / lib / R / site-library / gnm / NEWS

Changes in gnm 1.0-8
====================

Improvements
-------------

    o	now use lazy data loading.
    o	improvements to vignette (with thanks to Michael Friendly).
    o	copyright notices added to source files to clarify authorship, with
    	appropriate credit given to contributors in Rd and DESCRIPTION files.

Changes in behaviour
--------------------

    o   predict.gnm now includes eliminate term in predictions on new data.

Bug fixes
---------

    o	expandCategorical now works when there are no covariates in the data.
    o	better handling of single-column model matrices.
    o	predict.gnm now works with se.fit = TRUE for models with eliminated 
        terms; correctly handles new data without all levels of homogeneous 
	factors present, and respects contrasts settings.
    o	environment of formula preserved when using instances.

Changes in gnm 1.0-7
====================

Bug fixes
---------

    o	corrected use of anova.glmlist in anova.gnm.


Changes in gnm 1.0-6
====================

Bug fixes
---------

    o	added catch for when deviance becomes NaN.

Changes in gnm 1.0-5
====================

Improvements
------------

    o	eliminated coefficients now returned as named vector.
    o	step-quartering introduced to start-up iterations to avoid increasing 
    	deviance.

Changes in behaviour
--------------------

    o	gnm() no longer restarts if algorithm fails - better to provide 
    	improved starting values in this case. 

Bug fixes
---------

    o	fixed bug in the way 'etastart' is used to initialise the linear 
    	parameters when 'eliminate' is used as well. 


Changes in gnm 1.0-4
====================

Bug fixes
---------

    o	restarting mechanism now reinitialises correctly.
    o	removed call to external C function that is no longer available.
    o	gnm() now works with 'eliminate' argument when remaining linear part of 
        predictor only involves one parameter.

Changes in gnm 1.0-3
====================

Improvements
------------

    o	pickCoef() extended to allow fixed pattern matching and to optionally
    	return actual coefficients rather than their indices.
    o	gnm() now looks for exact match in coefficient names when a single 
    	character string is passed to the 'constrain' argument before treating 
	as regular expression.
    o	hatvalues.gnm() has been reimplemented to work more efficiently for large
    	model matrices.
    o	"nonlin" terms defined for homogeneous factors will now accept factors
    	specified as an interaction (using ':').

Bug fixes
---------

    o	results now returned in original order for models fitted with 'eliminate'
    	argument.
    o	bug introduced into residSVD reverted so that now correctly aggregates 
    	working residuals.
    o	anova.gnm() now works when model is a single "nonlin" term.


Changes in gnm 1.0-2
====================

Improvements
------------

    o	factors specified as homogenous in nonlin functions can now be 
    	specified as interactions of factors.

Bug fixes
---------

    o	fixed bug so that variables handled correctly in nonlinTerms.
    o	corrected rank calculation for constrained models.
    o	removed calls to Internal


Changes in gnm 1.0-1
====================

New Features
------------

    o	added meanResiduals() function
    o	'check' argument added to getContrasts.

Improvements
------------

    o	added example SVD calculation to wheat.Rd; also in vignette.

Bug fixes
---------

    o	added update.gnm() so that nonlinear terms were no ordered as linear, 
    	first order terms.


Changes in gnm 1.0-0
====================

Improvements
------------

    o	eliminated coefficients now treated entirely separately, in particular 
	the design matrix no longer has columns for these coefficients, making
	the algorithm far more efficient for models with many eliminated
	coefficients.

    o	more reliable calculation of rank

Changes in Behaviour
--------------------

    o	ofInterest and constrain now index non-eliminated coefficients only.

    o	eliminated coefficients now returned as attribute of returned 
	coefficient vector.

    o	"lsMethod" argument to gnm() removed as now the LAPACK routines are  
	always used to determine the least squares solution at the heart of 
	the fitting algorithm. Hence qrSolve() and cholInv() deprecated.

    o	the "eliminate", "onlyFirstCol" and "onlyNonElim" arguments to
	MPinv() have been removed as no longer used.

Bug fixes
---------

    o	etastart now works for models with no linear parameters.

    o	anova now ignores terms that are completely constrained.

Changes in gnm 0.10-0
=====================

Improvements
------------

    o	mustart/etastart now used to obtain starting values for linear and 
	nonlinear parameters separately, improving performance.

Changes in Behaviour
--------------------

    o	expandCategorical now groups together individuals with common covariate
	values, by default. New 'group' argument added to switch this behaviour.

Bug fixes
---------

    o	print.profile.gnm() now prints full result.

    o	data now read in correctly for Lee-Carter example in vignette.

Changes in gnm 0.9-9
====================

New Features
------------

    o	'etastart' and 'mustart' arguments added to gnm().


Changes in gnm 0.9-8
====================

Improvements
------------

    o	gnm() now returns 'data' argument as glm() does.


Changes in gnm 0.9-7
====================

Bug fixes
---------

    o	more minor corrections in documentation.


Changes in gnm 0.9-6
====================

Bug fixes
---------

    o	minor corrections in documentation.


Changes in gnm 0.9-5
====================	

Improvements
------------

    o	getContrasts() can now estimate _scaled_ contrasts with more flexibility in
	how the reference level is defined. 
    o	changed tolerance level in checkEstimable to 1e6 * .Machine$double.eps as
	previous tolerance too strict for some examples. 

Changes in Behaviour
--------------------

    o	getContrasts() now only handles one set of parameters at a time.
    o	use of Const() is now restricted to the symbolic predictors of "nonlin" 
	functions.
    o	Nonlin() - the wrapper function for plug-in functions - is now defunct. Use
	"nonlin" functions to specify custom nonlinear terms.

Bug fixes
---------

    o	plot.gnm now uses standardised Pearson residuals for plot 'which = 5' so 
	that the Cook's distance contours are correct


Changes in gnm 0.9-4
====================

New Features
------------

    o	predict() now implemented for "gnm" objects	   

Improvements
------------

    o	results formatted as contingency tables where appropriate by extractor 
	functions (fitted(), etc), rather than gnm()

Changes in Behaviour
--------------------

    o	default for `match' argument of nonlinTerms() now zero vector (i.e. no
	matching to arguments of `call' by default)

Bug fixes
---------

    o	termPredictors() now works on "gnm" objects fitted with glm.fit()
    o	intercept removed when `eliminate' argument of gnm() is non-NULL
    o	models with all parameters eliminated now summarised sensibly
    o	Diag() and Symm() now work for factors of length 1
    o	asGnm() now returns object with "gnm"-type terms component
    o	print method for "profile.gnm" objects now exported


Changes in gnm 0.9-3
====================

New Features
------------

    o	added DrefWeights() for computing the weights in a diagonal reference 
	term and the corresponding standard errors.
    

Improvements
------------

    o	"assign" attribute now attached to the parameter vector when passed to 
	start functions defined by "nonlin" functions, specifying the 
	correspondence between parameters and predictors in the nonlinear term.

Bug fixes
---------

    o	start function in Dref() now identifies weight parameters correctly.

    o   can now evaluate term predictors for "nonlin" terms that depend on 
	covariates.


Changes in gnm 0.9-2
====================    

Improvements
------------

    o	Calls to "nonlin" functions now evaluated in the same environment and 
	enclosure as call to create model frame, so "nonlin" functions should 
	be able to find variables in gnm calls - potentially useful for setting 
	starting values.

Bug fixes
---------

    o	gnm() algorithm now reinitiates correctly when restarting after 
	non-convergence.

    o	gnm() now works correctly when a model is specified with nonlinear terms 
	inbetween linear terms.


Changes in gnm 0.9-1
====================

New Features
------------

    o	introduction of functions of class "nonlin" for the unified specification 
	of nonlinear terms. Mult(), Exp(), Dref() and MultHomog() have all been
	converted to functions of this class.

    o	added Inv() to specify the reciprocal of a predictor.

    o	added Const() to specify a constant in a predictor.

    o	added instances() to specify multiple instances of a nonlinear term.
    

Improvements
------------

    o	nonlinear terms can now be nested.

    o	Exp() can now be used outside of Mult() or to exponentiate part of a 
	constituent multiplier.

Changes in Behaviour
--------------------

    o	to accommodate the increased functionality introduced by "nonlin" 
	functions, new labelling conventions have been introduced. In 
	particular, most "nonlin" functions use argument-matched parameter 
	labels.

    o	in the new implementation of Dref() the 'formula' argument has been
	re-named 'delta' to provide more informative parameter labels under the
	new conventions.

Bug fixes
---------

    o	specifying 'ofInterest = "[?]"' in gnm() now works as documented.


Changes in gnm 0.8-5
====================

New Features
------------

    none in this release

Improvements
------------

    o	added a new `ridge' argument to gnm, to allow some control over
        the Levenberg-Marquardt regularization of the internal least squares
        calculation

    o	changed the default ridge constant to 1e-8 (from 1e-5), to increase
        speed of convergence (especially in cases where there are infinite
        parameter estimates)

    o	modified the "qr" method so that it no longer checks for rank deficiency
        (it was both unreliable, and not necessary since the matrix is regularized 
        prior to solving)

    o	substantial speed improvements in model fitting when there are large 
        numbers of eliminated parameters, achieved mainly via a new internal 
        function cholInv1().  Corresponding example timings changed in the 
        Overview document (vignette).

    o	speed improvements in vcov.gnm() when there are eliminated parameters; new
        logical argument `use.eliminate' gives control over this

    o	in getContrasts(), added new arguments `dispersion' and `use.eliminate', 
        both of which are passed on to vcov()

    o	implemented faster alternatives to ifelse in gnmFit()

    o	speed gains from use of tcrossprod().  Because of this the gnm
        package now requires R 2.3.0 or later.

Changes in Behaviour
--------------------

    o	in gnm(), changed the default value of argument x to TRUE (it was
        previously FALSE)

    o	in checkEstimable(), changed the name of the first argument from 
        `coefMatrix' to `combMatrix' (to reflect better that it is a matrix of 
        coefficient *combinations*); and changed the default tolerance value to 
        one which should give more reliable results.  Also, more fundamentally, 
        changed the check to be whether combinations are in the column span of 
        crossprod(X) instead of the row span of X; the results should be the same, 
        but the new version is much faster for large n.

    o	model.matrix.gnm() no longer passes extra arguments to gnm as it's unlikely 
        to be useful/sensible. For the same reasons it will not pass extra 
        arguments to model.frame(), unlike model.matrix.lm()

    o	getContrasts() now results in a list only when the `sets' argument itself
        is a list;  otherwise (ie, normally) the result is a single object 
        (rather than a list of objects) of class `qv'

Bug fixes
---------

    o	fixed a bug in internal function quick.glm.fit(), which greatly improves
        its performance.  Also changed the default value of the nIter argument
        from 3 to 2.

    o	fixed a small bug in demo(gnm)

    o	fixed a bug in vcov.gnm(), which previously gave an error when data were 
        of class "table")

    o	fixed summary.gnm() so that it now takes proper account of the dispersion
        argument

    o	in se(), added new arguments `Vcov' and `dispersion'; the latter fixes a 
        bug, while the former minimizes wasted computation in summary.gnm

    o	fixed bug in model.matrix.gnm() so that it can compute the model matrix 
        even when original data is not available - unless model frame has not been
        saved.  Original data still needed to update model frame - this is the 
        same as for glms, etc.

    o	fixed bug in gnm() so that reconstructing "table"-class data works for 
        models with weights/offsets 


Changes in gnm 0.8-4
====================

New Features
------------

    o	added "gnm" methods for profile() and confint(). Use of 'alpha' argument 
    	differs slightly from "glm" methods: see help files.

    o	'constrain' argument to gnm() now supplemented by 'constrainTo' 
	argument, allowing specification of values to which parameters should be 
	constrained.

    o	gnm() now has 'ofInterest' argument to specify a subset of coefficients 
	which are of interest - returned in 'ofInterest' component of "gnm" 
	object as named numeric vector. print() summaries of model object/its 
	components extracted by accessor functions only print coefficients of 
	interest and (where appropriate) methods for "gnm" objects select 
	coefficients of interest by default.

    o	added ofInterest() and ofInterest<-() to extract/replace 'ofInterest'
  	component of "gnm" object.

    o	added parameters() to which returns coefficient vector with constrained
	parameters replaced by their constrained value.

    o	added pickCoef() function to aid selection of coefficients - returns 
	numeric indices of coefficients selected by Tk dialog or regular 
	expression matching.

Improvements
------------

    o	'constrain' argument to gnm() now accepts a regular expression to match 
	against coefficient names.


Changes in Behaviour
--------------------

    o	'constrain' component of "gnm" objects is now a numeric, rather than 
	logical, vector of indices.

    o	all "gnm" methods for which a subset of the coefficients may be 
	specified by numeric indices now interpret those indices as 
	referencing the full coefficient vector (not just non-eliminated
	parameters).

    o	gnm() now preserves order of terms rather than moving all linear 
	terms to the start (this fixes bug in anova.gnm()).

    o	the "pick" option for the 'constrain' argument to gnm() and the 
	'estimate' argument to se() has been replaced by "[?]" to avoid
	possible conflict with coefficient names/regular expressions.

Bug Fixes
---------

    o	fixed bug in se() so will now work for single parameter.

    o	fixed bug in summary.gnm() so will now work for models with one 
	parameter.

    o	fixed bug in anova() so that rows of returned table are correct for 
	models with eliminated terms.

    o	fixed bug in eliminate() so that it now accepts interactions.

    o   fixed bug in MPInv() so that it works for models in which all parameters 
	are eliminated.


Changes in gnm 0.8-3
====================

Improvements
------------

    o	improved use of functions from other packages

Bug Fixes
---------

    o	fixed bug in asGnm.lm() where object not fully identified

    o	corrected maintainer address in DESCRIPTION!


Changes in gnm 0.8-2
====================

New Features
------------

    o	added demonstration script to run using demo()

    o	added package help file, opened by package?gnm

Improvements
------------

    o	improved existing documentation


Changes in gnm 0.8-1
====================

New Features
------------

    o	added the `method' argument to MPinv(), to allow the method of 
	calculation to be specified.  Permitted values are "svd" to
	compute the pseudo-inverse by singular value decomposition, 
	and "chol" to use the Cholseky decomposition instead.  The latter
	is valid only for symmetric matrices, but is usually faster
    	and more accurate.

    o	added the `lsMethod' argument to gnm(), to allow specification of 
	the numerical method used for least-squares calculations in the
	core of the iterative algorithm.  Permitted options are "chol" and 
        "qr".

    o	added new function qrSolve(), which behaves like base::qr.coef but 
        in the non-full-rank case gives the minimum-length solution rather
        than an arbitrary solution determined by pivoting.

    o	added .onUnload() so that compiled code is unloaded when namespace of 
	package is unloaded using unloadNamespace().

    o	added 'coef' argument to model.matrix.gnm() so that the model matrix 
        can be evaluated at any specified value of the parameter vector. 

    o	added asGnm() generic to coerce linear model objects to gnm objects.

    o	added exitInfo() for printing numerical details of last iteration on 
	non-convergence of gnm().

    o	added new dataset, friend, to illustrate a workaround to fit a
	homogeneous RC(2) using gnm() - documented in help file for MultHomog().

Improvements
------------

    o	gnm() now takes less time per (main) iteration, due to improvements 
        made internally in the iterative algorithm.  These include 
        pre-scaling of the local design matrix, and Levenberg-Marquardt 
        adjustment of the least-squares solvers so that rank determination
        is no longer necessary.  

    o	the default convergence tolerance has been tightened (from 1e-4 to 1e-6)

    o	modified model.matrix.gnm() so it can be used when only the namespace 
        of gnm is loaded.

Bug Fixes
---------

    o	fixed bug in gnm() so that 'subset' now works with table data.

    o	fixed bug in model.matrix.gnm() so can construct model matrix from "gnm" 
	object even when original call not made in .GlobalEnv.

    o	fixed bug in the examples on help page for House2001 data.

    o	fixed bug so that 'formula' in gnm() now accepts '.' in formulae 
        even when 'eliminate = NULL'.

    o	fixed bug in getContrasts(), so that the first two columns
        of the qvframe component of each element of the result list
        are correctly named as "estimate" and "SE", as required for
        objects of class "qv".


Changes in gnm 0.8-0
=======================

New Features
------------

    o	added "model.matrix" option for 'method' argument of gnm() so that 
	model matrix can be obtained much faster. The new method is used in 
	model.matrix.gnm() and vcov.gnm().

    o	added new utility function residSVD(), to facilitate the calculation
        of good starting values for parameters in certain Mult() terms.

    o	added new dataset House2001, to illustrate the use of gnm in 
        Rasch-type scaling of legislator votes.

    o	added new utility function expandCategorical() for expanding data frame
	on the basis of a categorical variable.

    o	added formula.gnm() method - returns formula from "gnm" object excluding
	the 'eliminate'd factor where necessary.

Improvements
------------

    o	gnm() now takes less time to run due to improvements made in internal 
	functions.

    o   the fitting algorithm used by gnm() now copes better with zero-valued 
        residuals.

    o	output given by gnm() when 'trace' = TRUE or 'verbose' = TRUE is now 
	displayed as it is generated on console-based versions of R. 

    o	plot.gnm() now includes option 'which' = 5 as in plot.lm() in 
   	R >= 2.2.0. Now has separate help page.	

    o	the 'constrain' argument to gnm() now accepts the names of parameters.

    o	the 'formula' argument to gnm() now accepts '.' as described in 
	?terms.formula, ignoring eliminated factor if in 'data'.

    o	interface for se() extended - can now use to find standard errors for 
	all parameters or (a selection of) individual parameters in a gnm model.

    o	made it possible to use gnm() with alternative fitting function.

    o	".Environment" attribute now attached to "gnm" objects so that gnm package
	loaded when workspace containing "gnm" objects is loaded.	

	
Changes in Behaviour
--------------------

    o	start-up iterations now only update column of design matrix required in 
	next iteration. Therefore plug-in functions using the default start-up 
	procedure for nonlinear parameters need a localDesignFunction() with the 
	argument 'ind' specifying the column that should be returned.

    o	modified output given by gnm() when 'trace' = TRUE: now prints initial
	deviance and the deviance at the end of each iteration.

    o	modified updates of linear parameters in starting procedure: now offset 
	contribution of fully specified terms only.

    o	results of summary.gnm(), vcov.gnm() and coef.gnm() now include any 
	eliminated parameters. Print methods have been added for vcov.gnm and 
	coef.gnm objects so that any eliminated parameters are not shown.

    o	Mult() terms are no longer split into components by anova.gnm(),
  	termPredictors.gnm(), labels.gnm() or the "assign" attribute of the 
	model matrix - consistent with terms() output. 

    o	the 'eliminate' argument to gnm() must now be an expression that 
	evaluates to a factor - this reverts the extension of 0.7-2.	

    o	when using gnm() with 'constrain' = "pick", the name(s) of the chosen 
	parameter(s) will replace "pick" in the reurned model call.

    o	getContrasts() now uses first level of a factor as the reference level
	(by default).

    o	gnmControl() replaced by arguments to gnm().

    o	gnm() now uses glm.fit() for linear models (with control parameters at 
	the gnm() defaults).unless 'eliminate'is non-NULL.

    o	vcov.gnm() and summary.gnm() now return variance-covariance matrices 
	including any aliased parameters.

    o	summary.gnm() now returns standard errors with test statistics etc, 
	where estimated parameters are identified.

Bug Fixes
---------

    o	fixed bug in summary.gnm(), anova.gnm(), termPredictors.gnm() and 
	model.matrix.gnm() where search for model variables was incorrect. 

    o	fixed bug preventing estimation of weight parameters in Dref() terms and 
	changed default starting values so that these parameters no longer sum 
	to one or appear to be estimable. 

    o	corrected options for 'method' argument in gnm() help file: replaced 
	'method' = "coef" with 'method' = "coefNames".

    o	fixed bug in gnm() so that it can handle tables with missing values when
  	formatting components of fit.

    o	hatvalues.gnm() now works for objects produced from table data.

    o	residuals.gnm() now returns table not matrix when 'type' = "deviance" 
	for "gnm" objects produced from table data.

    o	hatvalues.gnm(), cooks.distance.gnm() and plot.gnm() now handle cases 
	which are fitted exactly (giving a hat value of 1).

    o	example fitting proportional odds model in backPain help file now works.

    o	fixed bug in Mult() terms so that an offset can be added to a constituent
  	multiplier without an unspecified intercept being added also.

    o	gnm() argument 'constrain' = "pick" now allows selection of more than 
	one constraint and is compatible with use of 'eliminate'.

    o	gnm() can now fit models which only have the term specified by 'eliminate'.


Changes in gnm 0.7-2
=======================

Improvements
------------

    o	Extended use of the 'eliminate' argument of gnm() to allow crossed 
	factors - this also fixes bug which occurred when interactions were 
	eliminated in the presence of lower order terms involving other factors 

Changes in Behaviour
--------------------

    o	'vcov' returned by gnm() now has no rank attribute (as before, the
	rank is returned as the separate component 'rank').

Bug Fixes
---------

    o	Changed the calculation of 'df.residual' returned by gnm() to 
	correctly take account of zero-weighted observations (as in glm()).

    o	When gnm() is called with arguments 'x' = TRUE or 'VCOV' = TRUE, the 
	returned matrices now include columns of zeros for constrained 
	parameters.

    o	Corrected evaluation of model frame in gnm() so that if data is missing, 
	variables are taken from environment(formula), as documented. Modified 
	evaluation of plug-in functions to be consistent with this, i.e. 
	objects are taken from environment(formula) if not in model frame.

    o	MPinv() now checks that the diagonal elements of an 'eliminate'd 
	submatrix are all non-zero and reports an error otherwise.



Changes in gnm 0.7-1
=======================

New Features
------------

    o	Topo() introduced for creating topological interaction factors.

    o	anova() implemented for objects of class c("gnm", "glm").


Improvements
------------

    o	Diagnostic messages given by gnm() have been improved.

    o	Step-halving introduced in main iterations of gnm() to ensure deviance 
	is reduced at every iteration.

    o	getContrasts() now (additionally) reports quasi standard errors, when
	available.

    o	Calls to gnm() plug-in functions are now evaluated in the environment 
	of the model frame and the enclosing environment of the parent frame 
	of the call to gnm(). This means that variables can be found in a 
	more standard fashion.


Changes in Behaviour
--------------------

    o	The 'data' argument of Nonlin() is defunct: Nonlin() now identifies 
	variables to be added to the model frame as those passed to unspecified
	arguments of the plug-in function or those identified by a companion 
	function to the plug-in, which is of a specified format.

    o	The (optional) 'start' object returned by a plug-in function can no 
	longer be a function, only a vector. However it may now include NA 
	values, to indicate parameters which may be treated as linear for the 
	purpose of finding starting values, given the non-NA values.


Bug Fixes
---------

    o	The 'eliminate' argument of gnm() now handles functions of variables in 
	the given formula e.g. ~ strata(A, B), ~ as.factor(A):as.factor(B), etc. 

    o	gnm() was giving an error for models with either no linear parameters, 
	or none specified by the 'start' argument, this is now fixed.

    o	Long calls to plug-in functions caused problems in parsing the model 
	formula: now fixed.

    o	gnm() now only restarts after failing if there are unspecified nonlinear
	parameters.

    o	gnm() now returns NULL if model fails.

    o	Bug fixed in calculation of starting values for gnm() that occurred when some
	parameters were constrained.