[Lme4-commits] r1601 - in pkg/lme4Eigen: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Feb 15 22:53:20 CET 2012
Author: dmbates
Date: 2012-02-15 22:53:19 +0100 (Wed, 15 Feb 2012)
New Revision: 1601
Modified:
pkg/lme4Eigen/R/AllClass.R
pkg/lme4Eigen/R/lmList.R
pkg/lme4Eigen/R/lmer.R
pkg/lme4Eigen/R/profile.R
pkg/lme4Eigen/R/utilities.R
pkg/lme4Eigen/man/Nelder_Mead.Rd
pkg/lme4Eigen/man/glmer.Rd
pkg/lme4Eigen/man/lmer.Rd
pkg/lme4Eigen/man/merMod-class.Rd
pkg/lme4Eigen/man/nlmer.Rd
pkg/lme4Eigen/man/simulate.merMod.Rd
Log:
Avoid partial matches of argument names to satisfy R-2.15.0 CMD check. Arrange aliases more effectively in documentation files.
Modified: pkg/lme4Eigen/R/AllClass.R
===================================================================
--- pkg/lme4Eigen/R/AllClass.R 2012-02-14 17:33:11 UTC (rev 1600)
+++ pkg/lme4Eigen/R/AllClass.R 2012-02-15 21:53:19 UTC (rev 1601)
@@ -849,11 +849,12 @@
##'
##' @name merMod-class
##' @aliases merMod-class lmerMod-class glmerMod-class nlmerMod-class
+##' show,merMod-method
##' anova.merMod coef.merMod deviance.merMod
##' fitted.merMod formula.merMod logLik.merMod
##' model.frame.merMod model.matrix.merMod print.merMod
-##' show.merMod simulate.merMod summary.merMod
-##' terms.merMod update.merMod VarCorr.merMod
+##' show.merMod summary.merMod
+##' terms.merMod update.merMod
##' vcov.merMod print.summary.mer show.summary.mer
##' summary.summary.mer vcov.summary.mer
##' @docType class
Modified: pkg/lme4Eigen/R/lmList.R
===================================================================
--- pkg/lme4Eigen/R/lmList.R 2012-02-14 17:33:11 UTC (rev 1600)
+++ pkg/lme4Eigen/R/lmList.R 2012-02-15 21:53:19 UTC (rev 1601)
@@ -212,8 +212,8 @@
ordered(rep(dn[[1]], dd[2] * dd[3]),
levels = levs),
intervals = as.vector(arr),
- what = gl(dd[3], dd[1] * dd[2], len = ll, lab = dn[[3]]),
- end = gl(dd[2], dd[1], len = ll))
+ what = gl(dd[3], dd[1] * dd[2], length = ll, labels = dn[[3]]),
+ end = gl(dd[2], dd[1], length = ll))
strip <- dots[["strip"]]
if (is.null(strip)) {
strip <- function(...) strip.default(..., style = 1)
Modified: pkg/lme4Eigen/R/lmer.R
===================================================================
--- pkg/lme4Eigen/R/lmer.R 2012-02-14 17:33:11 UTC (rev 1600)
+++ pkg/lme4Eigen/R/lmer.R 2012-02-15 21:53:19 UTC (rev 1601)
@@ -32,7 +32,7 @@
##' during the optimization. Default is \code{900}.}
##' \item{\code{tol}:}{a positive number specifying the
##' convergence tolerance, currently only for the PWRSS iterations
-##' in \code{glmer()}. Default is \code{0.000001}.}
+##' in \code{\link{glmer}}. Default is \code{0.000001}.}
##' }
##' @param start a named list of starting values for the parameters in the
##' model. For \code{lmer} this can be a numeric vector or a list with one
@@ -714,7 +714,7 @@
## just for the "boot" result -- TODOmaybe drop
mle <- list(beta = beta, theta = theta0, sigma = sigm.x)
- t.star <- matrix(t0, nr = length(t0), nc = nsim)
+ t.star <- matrix(t0, nrow = length(t0), ncol = nsim)
## resp <- x at resp
for(i in 1:nsim) {
y <- {
@@ -765,8 +765,8 @@
## Anova for merMod objects
##
-## @title anova() for both "lmerenv" and "lmer" fitted models
-## @param object an "lmerenv", "lmer" or "lmerMod" - fitted model
+## @title anova() for merMod objects
+## @param a merMod object
## @param ... further such objects
## @return an "anova" data frame; the traditional (S3) result of anova()
anovaLmer <- function(object, ...) {
@@ -810,7 +810,7 @@
deviance = -2*llk,
Chisq = chisq,
"Chi Df" = dfChisq,
- "Pr(>Chisq)" = pchisq(chisq, dfChisq, lower = FALSE),
+ "Pr(>Chisq)" = pchisq(chisq, dfChisq, lower.tail = FALSE),
row.names = names(mods), check.names = FALSE)
class(val) <- c("anova", class(val))
attr(val, "heading") <-
@@ -1126,7 +1126,7 @@
nbseq <- rep.int(seq_along(nb), nb)
ml <- split(ans, nbseq)
for (i in seq_along(ml))
- ml[[i]] <- matrix(ml[[i]], nc = nc[i], byrow = TRUE,
+ ml[[i]] <- matrix(ml[[i]], ncol = nc[i], byrow = TRUE,
dimnames = list(NULL, cnms[[i]]))
## create a list of data frames corresponding to factors
ans <- lapply(seq_along(fl),
@@ -1277,7 +1277,7 @@
##' @param object a fitted model object
##' @param nsim positive integer scalar - the number of responses to simulate
##' @param seed an optional seed to be used in \code{set.seed} immediately
-##' before the simulation so as to to generate a reproducible sample.
+##' before the simulation so as to generate a reproducible sample.
##' @param use.u (logical) generate new random-effects values (FALSE) or
##' generate a simulation condition on the current random-effects estimates (TRUE)?
##' @param ... optional additional arguments, none are used at present
@@ -1316,13 +1316,13 @@
} else {
U <- getME(object, "Z") %*% getME(object, "Lambda")
q <- ncol(U)
- as(U %*% matrix(rnorm(q * nsim), nc = nsim), "matrix")
+ as(U %*% matrix(rnorm(q * nsim), ncol = nsim), "matrix")
}
if (is(object at resp,"lmerResp")) {
## result will be matrix n x nsim :
val <- etasim.fix + sigma * (etasim.reff +
## residual contribution:
- matrix(rnorm(n * nsim), nc = nsim))
+ matrix(rnorm(n * nsim), ncol = nsim))
} else if (is(object at resp,"glmResp")) {
## GLMM
## n.b. DON'T scale random-effects (???)
@@ -1459,7 +1459,7 @@
p <- ncol(corF)
if (p > 1) {
rn <- rownames(so$coefficients)
- rns <- abbreviate(rn, minlen=11)
+ rns <- abbreviate(rn, minlength=11)
cat("\nCorrelation of Fixed Effects:\n")
if (is.logical(symbolic.cor) && symbolic.cor) {
corf <- as(corF, "matrix")
@@ -1469,8 +1469,8 @@
}
else {
corf <- matrix(format(round(corF at x, 3), nsmall = 3),
- nc = p,
- dimnames = list(rns, abbreviate(rn, minlen=6)))
+ ncol = p,
+ dimnames = list(rns, abbreviate(rn, minlength=6)))
corf[!lower.tri(corf)] <- ""
print(corf[-1, -p, drop=FALSE], quote = FALSE)
}
@@ -1781,7 +1781,7 @@
cbind(cc, matrix("", nr, maxlen-nr))
}))[, -maxlen, drop = FALSE]
if (nrow(corr) < nrow(reMat))
- corr <- rbind(corr, matrix("", nr = nrow(reMat) - nrow(corr), nc = ncol(corr)))
+ corr <- rbind(corr, matrix("", nrow = nrow(reMat) - nrow(corr), ncol = ncol(corr)))
colnames(corr) <- rep.int("", ncol(corr))
colnames(corr)[1] <- "Corr"
cbind(reMat, corr)
Modified: pkg/lme4Eigen/R/profile.R
===================================================================
--- pkg/lme4Eigen/R/profile.R 2012-02-14 17:33:11 UTC (rev 1600)
+++ pkg/lme4Eigen/R/profile.R 2012-02-15 21:53:19 UTC (rev 1601)
@@ -50,7 +50,7 @@
nvp <- nptot - p # number of variance-covariance pars
fe.orig <- opt[-seq_len(nvp)]
res <- c(.zeta = 0, opt)
- res <- matrix(res, nr = maxpts, nc = length(res),
+ res <- matrix(res, nrow = maxpts, ncol = length(res),
dimnames = list(NULL, names(res)), byrow = TRUE)
cutoff <- sqrt(qchisq(1 - alphamax, nptot))
@@ -518,7 +518,7 @@
panel.axis(side = side,
at = at,
labels = format(at, trim = TRUE),
- tick = TRUE,
+ ticks = TRUE,
check.overlap = TRUE,
half = side == "top" && j > 1,
@@ -541,7 +541,7 @@
which.half <- ifelse(j == 1, "lower", "upper")
at <- pretty(lims)
panel.axis(side = side, at = at, labels = format(at, trim = TRUE),
- tick = TRUE, half = TRUE, which.half = which.half,
+ ticks = TRUE, half = TRUE, which.half = which.half,
tck = 1, rot = 0,
text.col = axis.text.col,
Modified: pkg/lme4Eigen/R/utilities.R
===================================================================
--- pkg/lme4Eigen/R/utilities.R 2012-02-14 17:33:11 UTC (rev 1600)
+++ pkg/lme4Eigen/R/utilities.R 2012-02-15 21:53:19 UTC (rev 1601)
@@ -49,7 +49,7 @@
## grouping factor are adjacent.
if (nc > 1)
sm <- sm[as.vector(matrix(seq_len(nc * nl),
- nc = nl, byrow = TRUE)),]
+ ncol = nl, byrow = TRUE)),]
list(ff = ff, sm = sm, nl = nl, cnms = colnames(mm))
}
blist <- lapply(bars, mkBlist)
@@ -81,7 +81,7 @@
do.call(rBind,
lapply(seq_along(blist), function(i)
{
- mm <- matrix(seq_len(nb[i]), nc = nc[i],
+ mm <- matrix(seq_len(nb[i]), ncol = nc[i],
byrow = TRUE)
dd <- diag(nc[i])
ltri <- lower.tri(dd, diag = TRUE)
Modified: pkg/lme4Eigen/man/Nelder_Mead.Rd
===================================================================
--- pkg/lme4Eigen/man/Nelder_Mead.Rd 2012-02-14 17:33:11 UTC (rev 1600)
+++ pkg/lme4Eigen/man/Nelder_Mead.Rd 2012-02-15 21:53:19 UTC (rev 1601)
@@ -41,7 +41,7 @@
a list with 4 components \item{fval}{numeric scalar - the
minimum function value achieved} \item{par}{numeric
vector - the value of \code{x} providing the minimum}
- \item{ierr}{integer scalar - error code}
+ \item{ierr}{integer scalar - error code (see below)}
\item{control}{list - the list of control settings after
substituting for defaults}
}
@@ -49,4 +49,11 @@
Nelder-Mead optimization of parameters that may be
subject to box constraints
}
+\note{
+ Return codes: \describe{ \item{-4}{\code{nm_evals}:
+ maximum evaluations reached} \item{-3}{\code{nm_forced}:
+ ?} \item{-2}{\code{nm_nofeasible}: cannot generate a
+ feasible simplex} \item{-1}{\code{nm_x0notfeasible}:
+ initial x is not feasible (?)} }
+}
Modified: pkg/lme4Eigen/man/glmer.Rd
===================================================================
--- pkg/lme4Eigen/man/glmer.Rd 2012-02-14 17:33:11 UTC (rev 1600)
+++ pkg/lme4Eigen/man/glmer.Rd 2012-02-15 21:53:19 UTC (rev 1601)
@@ -93,7 +93,7 @@
allowed during the optimization. Default is \code{900}.}
\item{\code{tol}:}{a positive number specifying the
convergence tolerance, currently only for the PWRSS
- iterations in \code{glmer()}. Default is
+ iterations in \code{\link{glmer}}. Default is
\code{0.000001}.} }}
\item{verbose}{integer scalar. If \code{> 0} verbose
Modified: pkg/lme4Eigen/man/lmer.Rd
===================================================================
--- pkg/lme4Eigen/man/lmer.Rd 2012-02-14 17:33:11 UTC (rev 1600)
+++ pkg/lme4Eigen/man/lmer.Rd 2012-02-15 21:53:19 UTC (rev 1601)
@@ -44,7 +44,7 @@
allowed during the optimization. Default is \code{900}.}
\item{\code{tol}:}{a positive number specifying the
convergence tolerance, currently only for the PWRSS
- iterations in \code{glmer()}. Default is
+ iterations in \code{\link{glmer}}. Default is
\code{0.000001}.} }}
\item{start}{a named list of starting values for the
Modified: pkg/lme4Eigen/man/merMod-class.Rd
===================================================================
--- pkg/lme4Eigen/man/merMod-class.Rd 2012-02-14 17:33:11 UTC (rev 1600)
+++ pkg/lme4Eigen/man/merMod-class.Rd 2012-02-15 21:53:19 UTC (rev 1601)
@@ -15,13 +15,12 @@
\alias{print.merMod}
\alias{print.summary.mer}
\alias{show.merMod}
+\alias{show,merMod-method}
\alias{show.summary.mer}
-\alias{simulate.merMod}
\alias{summary.merMod}
\alias{summary.summary.mer}
\alias{terms.merMod}
\alias{update.merMod}
-\alias{VarCorr.merMod}
\alias{vcov.merMod}
\alias{vcov.summary.mer}
\title{Class "merMod" of Fitted Mixed-Effect Models}
Modified: pkg/lme4Eigen/man/nlmer.Rd
===================================================================
--- pkg/lme4Eigen/man/nlmer.Rd 2012-02-14 17:33:11 UTC (rev 1600)
+++ pkg/lme4Eigen/man/nlmer.Rd 2012-02-15 21:53:19 UTC (rev 1601)
@@ -45,7 +45,7 @@
allowed during the optimization. Default is \code{900}.}
\item{\code{tol}:}{a positive number specifying the
convergence tolerance, currently only for the PWRSS
- iterations in \code{glmer()}. Default is
+ iterations in \code{\link{glmer}}. Default is
\code{0.000001}.} }}
\item{verbose}{integer scalar. If \code{> 0} verbose
Modified: pkg/lme4Eigen/man/simulate.merMod.Rd
===================================================================
--- pkg/lme4Eigen/man/simulate.merMod.Rd 2012-02-14 17:33:11 UTC (rev 1600)
+++ pkg/lme4Eigen/man/simulate.merMod.Rd 2012-02-15 21:53:19 UTC (rev 1601)
@@ -13,7 +13,7 @@
\item{seed}{an optional seed to be used in
\code{set.seed} immediately before the simulation so as
- to to generate a reproducible sample.}
+ to generate a reproducible sample.}
\item{use.u}{(logical) generate new random-effects values
(FALSE) or generate a simulation condition on the current
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