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# $Id: HTMLlme.R 47 2008-05-23 17:29:31Z mentus $
# R2HTML.lme.r
# Formattted HTML printout of lme/nlme results
# Remove R2HTML::: when in namespace
# Dieter Menne, (Dr. Menne Biomed Software Tuebingen)
# dieter.menne@menne-biomed.de
#
# Revision 0.9, 15.2.2005 # first version forwarded to Eric
#% rm(list=ls(all=TRUE)) # test code, make sure we start fresh
#% library(nlme)
#% library(R2HTML)
# Assumes the following entry in R2HTML.CSS
#TD.cellinsideLeft {
# padding: 5 5;
# background: #FFFFFF;
# text-align:left
#}
# In addition, for easier reading I use
# p {text-align:left}
# which overrides the default align=center.
#
# -------------------- HTML.summary.lme --------------------------------
# After print.summary.lme
HTML.summary.lme = function (x, file=HTMLGetFile(),
digits = max(3,getOption("digits")-3),
use.cormat = TRUE, # no symbolic.cor used when true
symbolic.cor = p>4,
signif.stars = getOption("show.signif.stars"),
append=TRUE,verbose = FALSE, ...)
{
verbose <- verbose || attr(x, "verbose")
method <- x$method
header = as.character()
if (inherits(x, "nlme")) {
header["Model"] <- "<font class='call'>Nonlinear</font>"
}
else {
header["Model"] <- "<font class='call'>Linear</font>"
}
header["Method"]=ifelse(method == "REML", "REML","Max likelihood")
header["Data"]= deparse(x$call$data)
if (!is.null(x$call$subset)) {
header["Subset"] <-
deparse(asOneSidedFormula(x$call$subset)[[2]])
}
header["Observations"] <- x$dims[["N"]]
f <- "Number of Groups: "
dd <- x$dims
Ngrps <- dd$ngrps[1:dd$Q]
if ((lNgrps <- length(Ngrps)) == 1) {
header["Groups"] <- Ngrps
}
else {
sNgrps <- 1:lNgrps
aux <- rep(names(Ngrps), sNgrps)
aux <- split(aux, array(rep(sNgrps, lNgrps), c(lNgrps,
lNgrps))[!lower.tri(diag(lNgrps))])
names(Ngrps) <- unlist(lapply(aux, paste, collapse = " in "))
header <- c(header,t(Ngrps)[1,])
}
if (verbose && !is.null(x$numItr)) {
header["Iterations"] <- x$numIter
}
HTML(as.matrix(header),classcellinside="cellinsideLeft",file=file)
HTML(data.frame(AIC = x$AIC, BIC = x$BIC, logLik = c(x$logLik),
row.names = " "),file=file)
# Random effects
lapply(summary(x$modelStruct),HTML.reStruct, sigma = x$sigma,
reEstimates = x$coef$random, verbose = verbose,file=file,
digits=digits,use.cormat=use.cormat)
# Fixed effects
HTML(as.title("Fixed effects"),HR=3,file=file)
fixF <- x$call$fixed
if (inherits(fixF, "formula") || is.call(fixF)) {
f <- deparse(x$call$fixed)
}
else {
f <- deparse(lapply(fixF, function(el) as.name(deparse(el))))
}
HTMLli(paste("Formula:",f),file=file)
xtTab <- as.data.frame(x$tTable)
# Note: lme has a "DF" column, which should be printed as an int
# According to Eric, this will be corrected for in a later
# version, when individual formatting is possible
# We force has.Pvalue to TRUE, because the column name is p-value, not Pr(..
# If this should lead to problems, I could also rename the column
HTML.coefmat(xtTab,signif.stars=TRUE,file=file,digits=digits,
has.Pvalue=TRUE,...)
if (nrow(x$tTable) > 1) {
corr <- x$corFixed
p <- NCOL(corr)
if (p > 1) {
HTMLli("Correlation of Coefficients:\n", file = file,append = TRUE, ...)
# use of cormat has priority over symbolic
if (use.cormat) {
HTML.cormat(corr, file = file, ...)
} else # conventional display
if (symbolic.cor)
HTML(symnum(corr)[-1, -p], file = file,...)
else {
HTML(corr[-1, -p, drop = FALSE], file = file, ...)
}
}
}
HTML(as.title("Standardized Within-Group Residuals"),HR=3,file=file)
HTML(x$residuals,file=file)
}
# -------------------- HTML.reStruct ----------------------------------
# Modelled after print.reStruct in nlme
# This function used internally
HTML.reStruct = function (x, sigma = 1, reEstimates, verbose = FALSE,
file=HTMLGetFile(),digits=max(3,getOption("digits")-3),use.cormat=FALSE,...)
{
if (nlme::isInitialized(x)) {
nobj <- length(x)
if (is.null(namx <- names(x)))
names(x) <- nobj:1
aux <- t(array(rep(names(x), nobj), c(nobj, nobj)))
aux[lower.tri(aux)] <- ""
x[] <- rev(x)
names(x) <- rev(apply(aux, 1, function(x) paste(x[x !=
""], collapse = " %in% ")))
HTML(as.title("Random effects"),HR=3,file=file)
for (i in seq(along = x)) {
sm <-summary(x[[i]])
p <- NCOL(sm)
Level <- names(x)[i]
resid <- p==length(x)
HTML.summary.pdDiag(sm,sigma,Level=Level,resid=resid,file=file)
if (p > 1) { # for p==1 we let HTML.summary.pdDiag do the job
# use of cormat has priority over symbolic
if (use.cormat) {
HTML.cormat(sm, file = file, ...)
} else # conventional display
HTML.matrix(sm, file = file, ...)
}
if (verbose) {
HTMLli("Random effects estimates",file=file)
HTML(reEstimates[[i]],file=file,digits=digits)
}
HTML("\n",file=file)
}
}
else {
HTMLli("Uninitialized random effects structure",file=file)
}
}
# -------------------- HTML.summary.pdDiag ---------------------------------
# Modelled after print.summary.pdDiag in nlme
HTML.summary.pdDiag <-
function (x, sigma = 1, rdig = 3, Level = NULL, resid = FALSE, ...)
{
if (!(is.null(form <- attr(x, "formula")))) {
f <- "Formula: "
if (inherits(form, "formula")) {
f <- paste(f,deparse(form))
if (!is.null(Level)) {
f <- paste(f," |", Level)
}
}
else {
if (length(form) == 1) {
paste(f,deparse(form[[1]]))
if (!is.null(Level)) {
f <- paste(f," |", Level)
}
}
else {
f <- paste(f,deparse(lapply(form, function(el) as.name(deparse(el)))))
f <- paste(f,"\n Level:", Level)
}
}
HTMLli(f)
}
if (ncol(x) == 1) {
if (resid) {
HTML(array(sigma * c(attr(x, "stdDev"), 1),
c(1, 2), list("StdDev:", c(names(attr(x, "stdDev")),
"Residual"))), ...)
}
else {
HTML(array(sigma * attr(x, "stdDev"), c(1, 1),
list("StdDev:", names(attr(x, "stdDev")))),...)
}
}
else {
HTMLli(paste(" Structure: ", attr(x, "structName"),"\n", sep = ""))
if (attr(x, "noCorrelation") | (1 >= (p <- dim(x)[2]))) {
if (resid) {
HTML(array(sigma * c(attr(x, "stdDev"), 1),
c(1, p + 1), list("StdDev:", c(names(attr(x,
"stdDev")), "Residual"))), ...)
}
else {
HTML(array(sigma * attr(x, "stdDev"), c(1,p),
list("StdDev:", names(attr(x, "stdDev")))),...)
}
}
else {
ll <- lower.tri(x)
stdDev <- attr(x, "stdDev")
x[ll] <- format(round(x[ll], digits = rdig),...)
x[!ll] <- ""
xx <- array("", dim(x), list(names(attr(x, "stdDev")),
c("StdDev", "Corr", rep("", p - 2))))
xx[, 1] <- format(sigma * attr(x, "stdDev"))
xx[-1, -1] <- x[-1, -p]
if (!is.null(colnames(x))) {
xx[1, -1] <- abbreviate(colnames(x)[-p], minlength = rdig + 3)
}
if (resid) {
x <- array("", dim(xx) + c(1, 0), list(c(rownames(xx),
"Residual"), colnames(xx)))
x[1:p, ] <- xx
x[, 1] <- format(sigma * c(stdDev, 1))
xx <- x
}
HTML(xx, ..., quote = FALSE)
}
}
invisible(x)
}
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