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lme4 (version 1.1-11)

prt-utilities: Print and Summary Method Utilities for Mixed Effects

Description

The print, summary methods (including the print for the summary() result) in lme4 are modular, using about ten small utility functions. Other packages, building on lme4 can use the same utilities for ease of programming and consistency of output.

Notably see the Examples.

llikAIC() extracts the log likelihood, AIC, and related statics from a Fitted LMM.

formatVC() format()s the VarCorr matrix of the random effects -- for print()ing and show()ing; it is also the workhorse of .prt.VC(), and returns a character matrix.

.prt.*() all use cat and print to produce output.

Usage

llikAIC(object, devianceFUN = devCrit, chkREML = TRUE,
        devcomp = object@devcomp)
methTitle(dims)
.prt.methTit(mtit, class)
.prt.family (famL)
.prt.resids (resids, digits, title = "Scaled residuals:", ...)
.prt.call   (call, long = TRUE)
.prt.aictab (aictab, digits = 1)
.prt.grps   (ngrps, nobs)
.prt.warn   (optinfo, summary = FALSE, ...)
.prt.VC (varcor, digits, comp, formatter = format, ...)
formatVC(varcor, digits = max(3, getOption("digits") - 2),
         comp = "Std.Dev.", formatter = format,
         useScale = attr(varcor, "useSc"), ...)

Arguments

object
a LMM model fit
devianceFUN
the function to be used for computing the deviance; should not be changed for lme4 created objects.
chkREML
optional logical indicating if object maybe a REML fit.
devcomp
for lme4 always the equivalent of object@devcomp; here a list
dims
for lme4 always the equivalent of object@devcomp$dims, a named vector or list with components "GLMM", "NLMM", "REML", and "nAGQ" of which the first two are
mtit
the result of methTitle(object)
class
typically class(object).
famL
a list with components family and link, each a character string; note that standard Rfa
resids
numeric vector of model residuals.
digits
non-negative integer of (significant) digits to print minimally.
title
character string.
...
optional arguments passed on, e.g., to residuals().
call
the call of the model fit; e.g., available via (generic) function getCall().
long
logical indicating if the output may be long, e.g., printing the control part of the call if there is one.
aictab
typically the AICtab component of the result of llikAIC().
varcor
typically the result of VarCorr().
comp
optional ...
formatter
a function used for formatting the numbers.
ngrps
integer (vector), typically the result of ngrps(object).
nobs
integer; the number of observations, e.g., the result of nobs.
optinfo
typically object @ optinfo, the optimization infos, including warnings if there were.
summary
logical
useScale
(logical) whether the parent model estimates a scale parameter

Value

Examples

Run this code
## Create a few "lme4 standard" models ------------------------------
fm1 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
fmM <- update(fm1, REML=FALSE) # -> Maximum Likelihood

gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
             data = cbpp, family = binomial)
gmA <- update(gm1, nAGQ = 5)


(lA1 <- llikAIC(fm1))
(lAM <- llikAIC(fmM))
(lAg <- llikAIC(gmA))

(m1 <- methTitle(fm1 @ devcomp $ dims))
(mM <- methTitle(fmM @ devcomp $ dims))
(mG <- methTitle(gm1 @ devcomp $ dims))
(mA <- methTitle(gmA @ devcomp $ dims))

.prt.methTit(m1, class(fm1))
.prt.methTit(mA, class(gmA))

.prt.family(gaussian())
.prt.family(binomial())
.prt.family( poisson())

.prt.resids(residuals(fm1), digits = 4)
.prt.resids(residuals(fmM), digits = 2)

.prt.call(getCall(fm1))
.prt.call(getCall(gm1))

.prt.aictab ( lA1 $ AICtab ) # REML
.prt.aictab ( lAM $ AICtab ) # ML --> AIC, BIC, ...

V1 <- VarCorr(fm1)
m <- formatVC(V1)
stopifnot(is.matrix(m), is.character(m), ncol(m) == 4)
print(m, quote = FALSE) ## prints all but the first line of .prt.VC() below:
.prt.VC( V1, digits = 4, formatter = format)
## Random effects:
##  Groups   Name        Std.Dev. Corr
##  Subject  (Intercept) 24.740
##           Days         5.922   0.07
##  Residual             25.592

p1 <- capture.output(V1)
p2 <- capture.output( print(m, quote=FALSE) )
pX <- capture.output( .prt.VC(V1, digits = max(3, getOption("digits")-2)) )
stopifnot(identical(p1, p2),
          identical(p1, pX[-1])) # [-1] : dropping 1st line

.prt.grps(ngrps = ngrps(fm1),
          nobs  = nobs (fm1))
## --> Number of obs: 180, groups:  Subject, 18

.prt.warn(fm1 @ optinfo) # nothing .. had no warnings

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