Family objects provide a convenient way to specify the details of the
models used by functions such as `glm`

. See the
documentation for `glm`

for the details on how such model
fitting takes place.

`family(object, …)`binomial(link = "logit")
gaussian(link = "identity")
Gamma(link = "inverse")
inverse.gaussian(link = "1/mu^2")
poisson(link = "log")
quasi(link = "identity", variance = "constant")
quasibinomial(link = "logit")
quasipoisson(link = "log")

link

a specification for the model link function. This can be
a name/expression, a literal character string, a length-one character
vector, or an object of class
`"link-glm"`

(such as generated by
`make.link`

) provided it is not specified
*via* one of the standard names given next.

The `gaussian`

family accepts the links (as names)
`identity`

, `log`

and `inverse`

;
the `binomial`

family the links `logit`

,
`probit`

, `cauchit`

, (corresponding to logistic,
normal and Cauchy CDFs respectively) `log`

and
`cloglog`

(complementary log-log);
the `Gamma`

family the links `inverse`

, `identity`

and `log`

;
the `poisson`

family the links `log`

, `identity`

,
and `sqrt`

; and the `inverse.gaussian`

family the links
`1/mu^2`

, `inverse`

, `identity`

and `log`

.

The `quasi`

family accepts the links `logit`

, `probit`

,
`cloglog`

, `identity`

, `inverse`

,
`log`

, `1/mu^2`

and `sqrt`

, and
the function `power`

can be used to create a
power link function.

variance

for all families other than `quasi`

, the variance
function is determined by the family. The `quasi`

family will
accept the literal character string (or unquoted as a name/expression)
specifications `"constant"`

, `"mu(1-mu)"`

, `"mu"`

,
`"mu^2"`

and `"mu^3"`

, a length-one character vector
taking one of those values, or a list containing components
`varfun`

, `validmu`

, `dev.resids`

, `initialize`

and `name`

.

object

the function `family`

accesses the `family`

objects which are stored within objects created by modelling
functions (e.g., `glm`

).

…

further arguments passed to methods.

An object of class `"family"`

(which has a concise print method).
This is a list with elements

character: the family name.

character: the link name.

function: the link.

function: the inverse of the link function.

function: the variance as a function of the mean.

function giving the deviance for each observation
as a function of `(y, mu, wt)`

, used by the
`residuals`

method when computing
deviance residuals.

function giving the AIC value if appropriate (but `NA`

for the quasi- families). More precisely, this function
returns \(-2\ell + 2 s\), where \(\ell\) is the
log-likelihood and \(s\) is the number of estimated scale
parameters. Note that the penalty term for the location parameters
(typically the “regression coefficients”) is added elsewhere,
e.g., in `glm.fit()`

, or `AIC()`

, see the
AIC example in `glm`

.
See `logLik`

for the assumptions made about the
dispersion parameter.

function: derivative of the inverse-link function with respect to the linear predictor. If the inverse-link function is \(\mu = g^{-1}(\eta)\) where \(\eta\) is the value of the linear predictor, then this function returns \(d(g^{-1})/d\eta = d\mu/d\eta\).

expression. This needs to set up whatever data
objects are needed for the family as well as `n`

(needed for
AIC in the binomial family) and `mustart`

(see `glm`

).

logical function. Returns `TRUE`

if a mean
vector `mu`

is within the domain of `variance`

.

logical function. Returns `TRUE`

if a linear
predictor `eta`

is within the domain of `linkinv`

.

(optional) function `simulate(object, nsim)`

to be
called by the `"lm"`

method of `simulate`

. It will
normally return a matrix with `nsim`

columns and one row for
each fitted value, but it can also return a list of length
`nsim`

. Clearly this will be missing for ‘quasi-’ families.

`family`

is a generic function with methods for classes
`"glm"`

and `"lm"`

(the latter returning `gaussian()`

).

For the `binomial`

and `quasibinomial`

families the response
can be specified in one of three ways:

As a factor: ‘success’ is interpreted as the factor not having the first level (and hence usually of having the second level).

As a numerical vector with values between

`0`

and`1`

, interpreted as the proportion of successful cases (with the total number of cases given by the`weights`

).As a two-column integer matrix: the first column gives the number of successes and the second the number of failures.

The `quasibinomial`

and `quasipoisson`

families differ from
the `binomial`

and `poisson`

families only in that the
dispersion parameter is not fixed at one, so they can model
over-dispersion. For the binomial case see McCullagh and Nelder
(1989, pp.124--8). Although they show that there is (under some
restrictions) a model with
variance proportional to mean as in the quasi-binomial model, note
that `glm`

does not compute maximum-likelihood estimates in that
model. The behaviour of S is closer to the quasi- variants.

McCullagh P. and Nelder, J. A. (1989)
*Generalized Linear Models.*
London: Chapman and Hall.

Dobson, A. J. (1983)
*An Introduction to Statistical Modelling.*
London: Chapman and Hall.

Cox, D. R. and Snell, E. J. (1981).
*Applied Statistics; Principles and Examples.*
London: Chapman and Hall.

Hastie, T. J. and Pregibon, D. (1992)
*Generalized linear models.*
Chapter 6 of *Statistical Models in S*
eds J. M. Chambers and T. J. Hastie, Wadsworth & Brooks/Cole.

For binomial *coefficients*, `choose`

;
the binomial and negative binomial *distributions*,
`Binomial`

, and `NegBinomial`

.

# NOT RUN { require(utils) # for str nf <- gaussian() # Normal family nf str(nf) gf <- Gamma() gf str(gf) gf$linkinv gf$variance(-3:4) #- == (.)^2 ## Binomial with default 'logit' link: Check some properties visually: bi <- binomial() et <- seq(-10,10, by=1/8) plot(et, bi$mu.eta(et), type="l") ## show that mu.eta() is derivative of linkinv() : lines((et[-1]+et[-length(et)])/2, col=adjustcolor("red", 1/4), diff(bi$linkinv(et))/diff(et), type="l", lwd=4) ## which here is the logistic density: lines(et, dlogis(et), lwd=3, col=adjustcolor("blue", 1/4)) stopifnot(exprs = { all.equal(bi$ mu.eta(et), dlogis(et)) all.equal(bi$linkinv(et), plogis(et) -> m) all.equal(bi$linkfun(m ), qlogis(m)) # logit(.) == qlogis(.) ! }) ## Data from example(glm) : d.AD <- data.frame(treatment = gl(3,3), outcome = gl(3,1,9), counts = c(18,17,15, 20,10,20, 25,13,12)) glm.D93 <- glm(counts ~ outcome + treatment, d.AD, family = poisson()) ## Quasipoisson: compare with above / example(glm) : glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = quasipoisson()) # } # NOT RUN { glm.qD93 anova (glm.qD93, test = "F") summary(glm.qD93) ## for Poisson results (same as from 'glm.D93' !) use anova (glm.qD93, dispersion = 1, test = "Chisq") summary(glm.qD93, dispersion = 1) # } # NOT RUN { ## Example of user-specified link, a logit model for p^days ## See Shaffer, T. 2004. Auk 121(2): 526-540. logexp <- function(days = 1) { linkfun <- function(mu) qlogis(mu^(1/days)) linkinv <- function(eta) plogis(eta)^days mu.eta <- function(eta) days * plogis(eta)^(days-1) * binomial()$mu.eta(eta) valideta <- function(eta) TRUE link <- paste0("logexp(", days, ")") structure(list(linkfun = linkfun, linkinv = linkinv, mu.eta = mu.eta, valideta = valideta, name = link), class = "link-glm") } (bil3 <- binomial(logexp(3))) # } # NOT RUN { ## in practice this would be used with a vector of 'days', in ## which case use an offset of 0 in the corresponding formula ## to get the null deviance right. ## Binomial with identity link: often not a good idea, as both ## computationally and conceptually difficult: binomial(link = "identity") ## is exactly the same as binomial(link = make.link("identity")) ## tests of quasi x <- rnorm(100) y <- rpois(100, exp(1+x)) glm(y ~ x, family = quasi(variance = "mu", link = "log")) # which is the same as glm(y ~ x, family = poisson) glm(y ~ x, family = quasi(variance = "mu^2", link = "log")) # } # NOT RUN { glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails # } # NOT RUN { y <- rbinom(100, 1, plogis(x)) # need to set a starting value for the next fit glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit"), start = c(0,1)) # }

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