update forgets about offset() (PR#6656)

In R1.7 and above (including R 1.9 alpha), 'update.formula' forgets to copy any offset(...) term in the original '.' formula:

test> df <- data.frame( x=1:4, y=sqrt( 1:4), z=c(2:4,1))
test> fit1 <- glm( y~offset(x)+z, data=df)
test> fit1$call
glm(formula = y ~ offset(x) + z, data = df)

test> fit1u <- update( fit1, ~.)
test> fit1u$call
glm(formula = y ~ z, data = df)


The problem occurs when 'update.formula' calls 'terms.formula(..., simplify=TRUE)' which defines and calls a function 'fixFormulaObject'. The first line of 'fixFormulaObject' attempts to extract the contents of the RHS of the formula via 

tmp <- attr(terms(object), "term.labels")

but this omits any offsets. Replacing that line with the following,
which I think pulls in everything except the response, *seems* to fix
the problem without disrupting the guts of 'terms' itself:

tmp <- dimnames( attr(terms(object), "factors"))[[1]][ -attr( terms, 'response')]

The suggested line might be simpler than checking the 'offset' component
of 'terms(object)', which won't always exist.

Footnote: strange things happen when there is more than one offset (OK,
there probably shouldn't be, but I thought I'd experiment):

test> fit2 <- glm( y ~ offset( x) + offset( log( x)) + z, data=df)
test> fit2$call
glm(formula = y ~ offset(x) + offset(log(x)) + z, data = df)

test> fit2u <- update( fit2, ~.)
test> fit2u$call
glm(formula = y ~ offset(log(x)) + z, data = df)

Curiously, the 'term.labels' attribute of 'terms(object)' now includes the second offset, but  not the first.

On Tue, 9 Mar 2004 Mark.Bravington@csiro.au wrote:

In R1.7 and above (including R 1.9 alpha), 'update.formula' forgets to copy any offset(...) term in the original '.' formula:

test> df <- data.frame( x=1:4, y=sqrt( 1:4), z=c(2:4,1))
test> fit1 <- glm( y~offset(x)+z, data=df)
test> fit1$call
glm(formula = y ~ offset(x) + z, data = df)

test> fit1u <- update( fit1, ~.)
test> fit1u$call
glm(formula = y ~ z, data = df)


The problem occurs when 'update.formula' calls 'terms.formula(..., simplify=TRUE)' which defines and calls a function 'fixFormulaObject'. The first line of 'fixFormulaObject' attempts to extract the contents of the RHS of the formula via 

tmp <- attr(terms(object), "term.labels")

but this omits any offsets. Replacing that line with the following,
which I think pulls in everything except the response, *seems* to fix
the problem without disrupting the guts of 'terms' itself:

tmp <- dimnames( attr(terms(object), "factors"))[[1]][ -attr( terms, 'response')]

The suggested line might be simpler than checking the 'offset' component
of 'terms(object)', which won't always exist.

Sorry, but that is a common programming error.  The possible values of
attr(terms, "response") are 0 or 1 (although code should not rely on the 
non-existence of 2, 3, ...).  foo[-0] == foo[0] is a length-0 vector.

Also, in R please use rownames(): it is easier to read and safer.

Footnote: strange things happen when there is more than one offset (OK,
there probably shouldn't be, but I thought I'd experiment):

That is allowed, and works in general.

test> fit2 <- glm( y ~ offset( x) + offset( log( x)) + z, data=df)
test> fit2$call
glm(formula = y ~ offset(x) + offset(log(x)) + z, data = df)

test> fit2u <- update( fit2, ~.)
test> fit2u$call
glm(formula = y ~ offset(log(x)) + z, data = df)

Curiously, the 'term.labels' attribute of 'terms(object)' now includes the second offset, but  not the first.

The issue here is the code to remove offset terms fails if two successive 
terms are offsets, but not otherwise.