`Symm()`

now works for > 2 factors, fixes #16.- Character strings passed from C to Fortran now handled correctly, fixes #17.

`confint.profile.gnm()`

now works for a single parameter`gnm()`

now works when`eliminate`

is specified as`NULL`

- allow
`set`

argument of`getContrasts()`

to be numeric, as documented - convert old tests to unit tests.

- generalize
`Diag`

and`Symm`

to work with factors with levels that are not in alphabetical order. Factor levels are now only sorted by`Diag`

if the input factors have different sets of levels. - make
`se()`

generic to allow methods to be added (e.g. as in**logmult**package).

- C routines now registered to avoid accidental clashes with other packages.
- use of
`R_forceSymbols`

routine requires R >= 3.0.0.

- use of
- use jss.bst vs chicago.bst in vignette.
- update imports to include recommended packages.
- avoid warnings regarding recycling a length 1 array.
- avoid using
`print`

or`cat`

outside print methods, so print output always optional (e.g. by setting`verbose`

argument or using`suppressMessages`

).

- environment of formula preserved when using
`gnm()`

with`eliminate`

argument. - allow factor response in binomial gnms.
- allow matrix response in quasibinomial gnms.
- make
`x = FALSE`

also work when using`gnm()`

with`eliminate`

argument. - allow response in formula to be specified as an expression (e.g.
`D/E`

) when formula uses`instances`

.

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

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

`expandCategorical`

now works when there are no covariates in the data.- better handling of single-column model matrices.
`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.- environment of formula preserved when using instances.

- corrected use of
`anova.glmlist`

in`anova.gnm`

.

- added catch for when deviance becomes
`NaN`

.

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

`gnm`

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

- fixed bug in the way
`etastart`

is used to initialise the linear parameters when`eliminate`

is used as well.

- restarting mechanism now reinitialises correctly.
- removed call to external C function that is no longer available.
`gnm`

now works with`eliminate`

argument when remaining linear part of predictor only involves one parameter.

`pickCoef`

extended to allow fixed pattern matching and to optionally return actual coefficients rather than their indices.`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.`hatvalues.gnm`

has been reimplemented to work more efficiently for large model matrices.`"nonlin"`

terms defined for homogeneous factors will now accept factors specified as an interaction (using`:`

).

- results now returned in original order for models fitted with
`eliminate`

argument. - bug introduced into
`residSVD`

reverted so that now correctly aggregates working residuals. `anova.gnm`

now works when model is a single`"nonlin"`

term.

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

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

- added
`meanResiduals`

function `check`

argument added to getContrasts.

- added example SVD calculation to
`?wheat`

; also in vignette.

- added
`update.gnm`

so that nonlinear terms were no ordered as linear, first order terms.

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.

more reliable calculation of rank

`ofInterest`

and`constrain`

now index non-eliminated coefficients only.eliminated coefficients now returned as attribute of returned coefficient vector.

`"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.the

`"eliminate"`

,`"onlyFirstCol"`

and`"onlyNonElim"`

arguments to`MPinv`

have been removed as no longer used.

`etastart`

now works for models with no linear parameters.`anova`

now ignores terms that are completely constrained.

`mustart`

/`etastart`

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

`expandCategorical`

now groups together individuals with common covariate values, by default. New`group`

argument added to switch this behaviour.

`print.profile.gnm`

now prints full result.data now read in correctly for Lee-Carter example in vignette.

`etastart`

and`mustart`

arguments added to`gnm`

.

`gnm`

now returns`data`

argument as`glm`

does.

- more minor corrections in documentation.

- minor corrections in documentation.

`getContrasts`

can now estimate*scaled*contrasts with more flexibility in how the reference level is defined.- changed tolerance level in checkEstimable to
`1e6 * .Machine$double.eps`

as previous tolerance too strict for some examples.

`getContrasts`

now only handles one set of parameters at a time.- use of
`Const`

is now restricted to the symbolic predictors of`"nonlin"`

functions. `Nonlin`

- the wrapper function for plug-in functions - is now defunct. Use`"nonlin"`

functions to specify custom nonlinear terms.

`plot.gnm`

now uses standardised Pearson residuals for plot`which = 5`

so that the Cook’s distance contours are correct

`predict`

now implemented for`"gnm"`

objects

- results formatted as contingency tables where appropriate by extractor functions (
`fitted`

, etc), rather than`gnm`

- default for
`match`

argument of`nonlinTerms`

now zero vector (i.e. no matching to arguments of`call`

by default)

`termPredictors`

now works on`"gnm"`

objects fitted with`glm.fit`

- intercept removed when
`eliminate`

argument of`gnm`

is non-`NULL`

- models with all parameters eliminated now summarised sensibly
`Diag`

and`Symm`

now work for factors of length 1- as
`gnm`

now returns object with`"gnm"`

-type terms component - print method for
`"profile.gnm"`

objects now exported

- added
`DrefWeights`

for computing the weights in a diagonal reference term and the corresponding standard errors.

`"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.

start function in

`Dref`

now identifies weight parameters correctly.can now evaluate term predictors for

`"nonlin"`

terms that depend on covariates.

- 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.

`gnm`

algorithm now reinitiates correctly when restarting after non-convergence.`gnm`

now works correctly when a model is specified with nonlinear terms in between linear terms.

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.added

`Inv`

to specify the reciprocal of a predictor.added

`Const`

to specify a constant in a predictor.added

`instances`

to specify multiple instances of a nonlinear term.

nonlinear terms can now be nested.

`Exp`

can now be used outside of`Mult`

or to exponentiate part of a constituent multiplier.

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.in the new implementation of

`Dref`

the`formula`

argument has been re-named`delta`

to provide more informative parameter labels under the new conventions.

- specifying
`ofInterest = "[?]"`

in`gnm`

now works as documented.

`none in this release`

added a new

`ridge`

argument to gnm, to allow some control over the Levenberg-Marquardt regularization of the internal least squares calculationchanged the default ridge constant to 1e-8 (from 1e-5), to increase speed of convergence (especially in cases where there are infinite parameter estimates)

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)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).speed improvements in

`vcov.gnm`

when there are eliminated parameters; new logical argument`use.eliminate`

gives control over thisin

`getContrasts`

, added new arguments`dispersion`

and`use.eliminate`

, both of which are passed on to`vcov`

implemented faster alternatives to

`ifelse`

in`gnmFit`

speed gains from use of

`tcrossprod`

. Because of this the gnm package now requires R 2.3.0 or later.

in

`gnm`

, changed the default value of argument x to`TRUE`

(it was previously`FALSE`

)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.`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`

`getContrasts`

now results in a list only when the`sets`

argument itself is a list; otherwise (i.e., normally) the result is a single object (rather than a list of objects) of class`qv`

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.fixed a small bug in

`demo(gnm)`

fixed a bug in

`vcov.gnm`

, which previously gave an error when data were of class`"table"`

)fixed

`summary.gnm`

so that it now takes proper account of the dispersion argumentin

`se`

, added new arguments`Vcov`

and`dispersion`

; the latter fixes a bug, while the former minimizes wasted computation in`summary.gnm`

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.fixed bug in

`gnm`

so that reconstructing`"table"`

-class data works for models with weights/offsets

added

`"gnm"`

methods for`profile`

and`confint`

. Use of`alpha`

argument differs slightly from`"glm"`

methods: see help files.`constrain`

argument to`gnm`

now supplemented by`constrainTo`

argument, allowing specification of values to which parameters should be constrained.`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.added

`ofInterest`

and`ofInterest<-`

to extract/replace`ofInterest`

component of`"gnm"`

object.added

`parameters`

which returns coefficient vector with constrained parameters replaced by their constrained value.added

`pickCoef`

function to aid selection of coefficients - returns numeric indices of coefficients selected by Tk dialog or regular expression matching.

`constrain`

argument to`gnm`

now accepts a regular expression to match against coefficient names.

`constrain`

component of`"gnm"`

objects is now a numeric, rather than logical, vector of indices.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).`gnm`

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

).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.

fixed bug in

`se`

so will now work for single parameter.fixed bug in

`summary.gnm`

so will now work for models with one parameter.fixed bug in

`anova`

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

`eliminate`

so that it now accepts interactions.fixed bug in

`MPinv`

so that it works for models in which all parameters are eliminated.

- improved use of functions from other packages

fixed bug in

`asGnm.lm`

where object not fully identifiedcorrected maintainer address in DESCRIPTION!

added demonstration script to run using

`demo`

added package help file, opened by package?gnm

- improved existing documentation

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 Cholesky decomposition instead. The latter is valid only for symmetric matrices, but is usually faster and more accurate.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"`

.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.added

`.onUnload`

so that compiled code is unloaded when namespace of package is unloaded using`unloadNamespace`

.added

`coef`

argument to`model.matrix.gnm`

so that the model matrix can be evaluated at any specified value of the parameter vector.added as

`gnm`

generic to coerce linear model objects to gnm objects.added

`exitInfo`

for printing numerical details of last iteration on non-convergence of`gnm`

.added new dataset, friend, to illustrate a workaround to fit a homogeneous RC(2) using

`gnm`

- documented in help file for`MultHomog`

.

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

modified

`model.matrix.gnm`

so it can be used when only the namespace of gnm is loaded.

fixed bug in

`gnm`

so that`subset`

now works with table data.fixed bug in

`model.matrix.gnm`

so can construct model matrix from`"gnm"`

object even when original call not made in`.GlobalEnv`

.fixed bug in the examples on help page for

`House2001`

data.fixed bug so that

`formula`

in`gnm`

now accepts`.`

in formulae even when`eliminate = NULL`

.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”.

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`

.added new utility function

`residSVD`

, to facilitate the calculation of good starting values for parameters in certain`Mult`

terms.added new dataset

`House2001`

, to illustrate the use of`gnm`

in Rasch-type scaling of legislator votes.added new utility function

`expandCategorical`

for expanding data frame on the basis of a categorical variable.added

`formula.gnm`

method - returns formula from`"gnm"`

object excluding the`eliminate`

d factor where necessary.

`gnm`

now takes less time to run due to improvements made in internal functions.the fitting algorithm used by

`gnm`

now copes better with zero-valued residuals.output given by

`gnm`

when`trace = TRUE`

or`verbose = TRUE`

is now displayed as it is generated on console-based versions of R.`plot.gnm`

now includes option`which = 5`

as in`plot.lm`

in R >= 2.2.0. Now has separate help page.the

`constrain`

argument to`gnm`

now accepts the names of parameters.the

`formula`

argument to`gnm`

now accepts`.`

as described in`?terms.formula`

, ignoring eliminated factor if in`data`

.interface for

`se`

extended - can now use to find standard errors for all parameters or (a selection of) individual parameters in a gnm model.made it possible to use

`gnm`

with alternative fitting function.`".Environment"`

attribute now attached to`"gnm"`

objects so that gnm package loaded when workspace containing`"gnm"`

objects is loaded.

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.modified output given by

`gnm`

when`trace = TRUE`

: now prints initial deviance and the deviance at the end of each iteration.modified updates of linear parameters in starting procedure: now offset contribution of fully specified terms only.

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.`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.the

`eliminate`

argument to`gnm`

must now be an expression that evaluates to a factor - this reverts the extension of 0.7-2.when using

`gnm`

with`constrain = "pick"`

, the name(s) of the chosen parameter(s) will replace`"pick"`

in the returned model call.`getContrasts`

now uses first level of a factor as the reference level (by default).`gnmControl`

replaced by arguments to`gnm`

.`gnm`

now uses`glm.fit`

for linear models (with control parameters at the`gnm`

defaults) unless`eliminate`

is non-`NULL`

.`vcov.gnm`

and`summary.gnm`

now return variance-covariance matrices including any aliased parameters.`summary.gnm`

now returns standard errors with test statistics etc, where estimated parameters are identified.

fixed bug in

`summary.gnm`

,`anova.gnm`

,`termPredictors.gnm`

and`model.matrix.gnm`

where search for model variables was incorrect.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.corrected options for

`method`

argument in`gnm`

help file: replaced`method = "coef"`

with`method = "coefNames"`

.fixed bug in

`gnm`

so that it can handle tables with missing values when formatting components of fit.`hatvalues.gnm`

now works for objects produced from table data.`residuals.gnm`

now returns table not matrix when`type = "deviance"`

for`"gnm"`

objects produced from table data.`hatvalues.gnm`

,`cooks.distance.gnm`

and`plot.gnm`

now handle cases which are fitted exactly (giving a hat value of 1).example fitting proportional odds model in

`backPain`

help file now works.fixed bug in

`Mult`

terms so that an offset can be added to a constituent multiplier without an unspecified intercept being added also.`gnm`

argument`constrain = "pick"`

now allows selection of more than one constraint and is compatible with use of`eliminate`

.`gnm`

can now fit models which only have the term specified by`eliminate`

.

- 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

`vcov`

returned by`gnm`

now has no rank attribute (as before, the rank is returned as the separate component`rank`

).

Changed the calculation of

`df.residual`

returned by`gnm`

to correctly take account of zero-weighted observations (as in`glm`

).When

`gnm`

is called with arguments`x = TRUE`

or`VCOV = TRUE`

, the returned matrices now include columns of zeros for constrained parameters.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.`MPinv`

now checks that the diagonal elements of an`eliminate`

d submatrix are all non-zero and reports an error otherwise.

`Topo`

introduced for creating topological interaction factors.`anova`

implemented for objects of class`c("gnm", "glm")`

.

Diagnostic messages given by

`gnm`

have been improved.Step-halving introduced in main iterations of

`gnm`

to ensure deviance is reduced at every iteration.`getContrasts`

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

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.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.

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.`gnm`

was giving an error for models with either no linear parameters, or none specified by the`start`

argument, this is now fixed.Long calls to plug-in functions caused problems in parsing the model formula: now fixed.

`gnm`

now only restarts after failing if there are unspecified nonlinear parameters.`gnm`

now returns`NULL`

if model fails.Bug fixed in calculation of starting values for

`gnm`

that occurred when some parameters were constrained.