Nothing
interactionMeans <- function(model, factors=names(xlevels), slope=NULL, ...){
# Levels in existing factors
xlevels <- getXLevels(model)
dots <- list(...)
# Include within-subjects factors, if they are defined
if ("idata" %in% names(dots)) xlevels <- c(xlevels, lapply(dots$idata, levels))
# Check the factors specified in the arguments
specified.factors <- match(factors,names(xlevels))
if (any(is.na(specified.factors))) warning("Some factors are not in the model and will be ignored")
xlevels <- xlevels[sort(specified.factors)]
# Create diagonal matrices sized as the number of factor levels
nlev <- sapply(xlevels,length)
fdiags <- lapply(nlev,diag)
# Argument test.formula for testFactors
if (is.null(slope)){
terms.formula <- ~1
value.label <- "adjusted mean"
term.label <- "(Intercept)"
slope.term <- NULL
}else{
# Check predictors specified in the arguments
model.variables <- getPredictors(model)
numeric.predictors <- model.variables[!(model.variables %in% names(xlevels))]
specified.numeric <- match(slope,numeric.predictors)
if (any(is.na(specified.numeric))) warning("Some covariates are not in the model and will be ignored.")
slope <- numeric.predictors[sort(specified.numeric)]
slope.term <- term.label <- value.label <- paste(slope,collapse=":")
terms.formula <- as.formula(paste("~0 +",slope.term))
}
# Create data frame with values and standard errors
tf <- testFactors(model,fdiags,terms.formula=terms.formula,lht=FALSE,...)
interactions.table <- tf$terms[[1]]$adjusted.values
se.table <- tf$terms[[1]]$std.error
interactions.dataframe <- if (is.null(factors)) as.data.frame(matrix(,nrow=1,ncol=0)) else expand.grid(xlevels)
# Define what term is represented in the data frame
# (and redefine if it is the link function in a glm)
attr(interactions.dataframe,"term") <- term.label
se.label <- "std. error"
fam <- getFamily(model)
if (!is.null(fam)){
attr(interactions.dataframe,"family") <- fam
if (is.null(slope.term)){
if (attr(tf,"means")=="link"){
attr(interactions.dataframe,"term") <- "(Link)"
value.label <- "adjusted link"
}else se.label <- "SE of link"
}
}
# The calculated interactions are in just one variable (after possible response transformation)
nf <- length(xlevels)
if (length(interactions.table)==nrow(interactions.dataframe)){
interactions.dataframe[nf+1] <- as.numeric(interactions.table)
interactions.dataframe[nf+2] <- as.numeric(se.table)
names(interactions.dataframe)[nf+(1:2)] <- c(value.label, se.label)
}else{
# The calculated interactions are in several variables
if (nrow(interactions.table)==nrow(interactions.dataframe)){
rownames(interactions.table) <- NULL
if (!is.null(slope.term)) colnames(interactions.table) <- paste(value.label,colnames(interactions.table),sep=".")
rownames(se.table) <- NULL
colnames(se.table) <- paste("SE",colnames(se.table),sep=".")
ix <- (1:ncol(interactions.table))
ix <- rbind(ix,ix+length(ix))
interactions.table <- cbind(interactions.table,se.table)[,ix]
interactions.dataframe <- cbind(interactions.dataframe,interactions.table)
}else stop("Incompatible dimensions of the intra-subjects design")
}
# Assign more attributes and class for further methods on this object
attr(interactions.dataframe,"factors") <- names(interactions.dataframe)[1:nf]
attr(interactions.dataframe,"values") <- names(interactions.dataframe)[seq(nf+1,ncol(interactions.dataframe),by=2)]
attr(interactions.dataframe,"se") <- names(interactions.dataframe)[seq(nf+2,ncol(interactions.dataframe),by=2)]
# Create a list of covariance matrices for each variable
mix <- matrix(1L:length(se.table), nrow=nrow(interactions.dataframe), dimnames=list(NULL,attr(interactions.dataframe,"values")))
covmatlist <- lapply(as.data.frame(mix), function(ix) as.matrix(tf$terms[[1]]$covmat[ix,ix]))
attr(interactions.dataframe,"covmat") <- covmatlist
class(interactions.dataframe) <- c("interactionMeans","data.frame")
return(interactions.dataframe)
}
# Auxiliar function to get pooled standard errors from covariance matrices
# x: interactionMeans object
# y: outcome variable of x
# f: 1 or 2 factor names of x
poolse <- function(x,y,f){
vcf <- split.data.frame(attr(x,"covmat")[[y]], x[f])
vcf <- sapply(vcf, function(M) split.data.frame(t(M), x[f]))
se <- sqrt(sapply(diag(vcf), mean))
nlev <- sapply(x[f], nlevels)
levnames <- lapply(x[f], levels)
array(se, dim=nlev, dimnames=levnames)
}
matploterrorbars <- function(lower, upper, barwidth=0.25,...){
# upper and lower are matrice of the same size
nr <- nrow(lower)
nc <- ncol(lower)
nr3 <- nr*3L
xlow <- xup <- xcross <- ylow <- yup <- ycross <- matrix(nrow=nr3,ncol=nc)
xlow[seq(1,nr3,by=3),] <- xup[seq(1,nr3,by=3),] <- (1:nr)-barwidth/2
xlow[seq(2,nr3,by=3),] <- xup[seq(2,nr3,by=3),] <- (1:nr)+barwidth/2
xcross[seq(1,nr3,by=3),] <- xcross[seq(2,nr3,by=3),] <- (1:nr)
ylow[seq(1,nr3,by=3),] <- ylow[seq(2,nr3,by=3),] <- ycross[seq(1,nr3,by=3),] <- lower
yup[seq(1,nr3,by=3),] <- yup[seq(2,nr3,by=3),] <- ycross[seq(2,nr3,by=3),] <- upper
# Force solid line type and overplot
dots <- list(...)
dots$type <- "l"
dots$lty <- "solid"
dots$add <- TRUE
do.call(matplot,c(list(xlow,ylow),dots))
do.call(matplot,c(list(xup,yup),dots))
do.call(matplot,c(list(xcross,ycross),dots))
}
cimse <- function(m,se,ci){
q <- qnorm((1-ci)/2)
list(m+q*se, m-q*se)
}
plot.interactionMeans <- function(x, atx=attr(x,"factors"), traces=atx, xlab=atx, ylab="", main=NULL, multiple=TRUE, y.equal=FALSE, legend=TRUE, legend.margin=0.2, cex.legend=1, abbrev.levels=FALSE, type="b", pch=0:6, errorbar,...){
# Define function for limits of the errorbars
if (missing(errorbar)) errorbar <- function(m,se) list(m-se,m+se)
ferrbar <- if(is.null(errorbar)) function(m,se) list(m,m) else errorbar
if (is.character(ferrbar)){
if (grepl("[0-9]{1,2}", ci <- sub("^ci","",ferrbar))){
ci <- 0.01*as.numeric(ci)
ferrbar <- function(m,se) cimse(m,se,ci)
}else stop("Invalid errorbar definition")
}
# Check consistency between x and atx, traces
if (!("interactionMeans" %in% class(x))) stop("The first argument must be an interactionMeans object.")
valid.atx <- (atx %in% attr(x,"factors"))
if (!all(valid.atx)){
warning("Some values of atx are not factors of x and will be ignored.")
atx <- atx[valid.atx]
}
valid.traces <- (traces %in% attr(x,"factors"))
if (!all(valid.traces)){
warning("Some values of traces are not factors of x and will be ignored.")
traces <- traces[valid.traces]
}
# Abbreviate factors, if required
if (abbrev.levels){
specified.factors <- unique(c(atx,traces))
if (is.logical(abbrev.levels)){
x[specified.factors] <- lapply(specified.factors, function(f) as.factor(abbreviate(x[[f]])))
}else x[specified.factors] <- lapply(specified.factors, function(f) as.factor(abbreviate(x[[f]],minlength=abbrev.levels)))
}
# Get values of link function if specified (for glm)
fam <- NULL
if (transform <- (!is.null(fam <- attr(x,"family")) && attr(x,"term")=="(Intercept)")){
yy <- attr(x,"values")
x[[yy]] <- fam$linkfun(x[[yy]])
}
# Calculate and apply margin-plot regions ratio
marginRatio <- function(n,prop) n*prop/(1-prop)
xax.margin <- 0.25
# Loop over the numeric columns
for (y in attr(x,"values")){
maintitle <- if(is.null(main)) y else main
# List of data values for plots,
# setting legend to FALSE if there are no traces
if (is.null(traces)){
legend <- FALSE
nr <- 1
nc <- length(atx)
atx.pattern <- atx
plotdata <- lapply(atx, function(margin) tapply(x[,y],x[margin],mean))
sedata <- lapply(atx, function(margin) poolse(x,y,margin))
}else{
nr <- length(traces)
nc <- length(atx)
atx.pattern <- rep(atx,nr)
traces.pattern <- rep(traces,each=nc)
if (all(atx.pattern==traces.pattern)) legend <- FALSE
plotdata <- mapply(
function(xf,lf){
margins <- unique(c(xf,lf))
tapply(x[,y],x[margins],mean)
},
atx.pattern,traces.pattern,USE.NAMES=FALSE,SIMPLIFY=FALSE)
sedata <- mapply(function(xf,lf){
margins <- unique(c(xf,lf))
poolse(x,y,margins)
},atx.pattern, traces.pattern,USE.NAMES=FALSE,SIMPLIFY=FALSE)
}
# Data of the errorbars (first row, lower limit; second row, upper limit)
errbardata <- mapply(ferrbar, plotdata, sedata)
# Re-transform data if suitable (glm)
# if (transform) plotdata <- lapply(plotdata,fam$linkinv)
# Define figures
dots <- list(...)
# Parameters for legend
defpar <- formals(matplot)
col <- if ("col" %in% names(dots)) dots$col else eval(defpar$col)
lty <- if ("lty" %in% names(dots)) dots$lty else eval(defpar$lty)
lwd <- if ("lwd" %in% names(dots)) dots$lwd else eval(defpar$lwd)
if (multiple){
# Create device with multiple figures
if (length(y)>1L) dev.new()
# Reserve extra column if there is y axis label
leftcol <- if (nchar(ylab)) 1 else 0
ylab.mar <- 0.25*leftcol
columnwidths <- if(leftcol) c(ylab.mar, rep(1,nc)) else rep(1,nc)
if (leftcol){
par(oma=c(1,1,4,2),mar=rep(0,4))
}else{
par(oma=c(1,4,4,2),mar=rep(0,4))
}
# Parameters for x label and title
cex.lab <- if("cex.lab" %in% names(dots)) dots$cex.lab else 1
col.lab <- if("col.lab" %in% names(dots)) dots$cex.lab else par("col")
font.lab <- if("font.lab" %in% names(dots)) dots$font.lab else par("font")
cex.main <- if("cex.main" %in% names(dots)) dots$cex.lab else 1
col.main <- if("col.main" %in% names(dots)) dots$cex.lab else par("col")
font.main <- if("font.main" %in% names(dots)) dots$font.lab else par("font")
if (legend){
layout(matrix(1:((nr+1)*(nc+1+leftcol)),nrow=nr+1,byrow=TRUE),
c(columnwidths,marginRatio(nc,legend.margin)),
c(rep(1,nr),xax.margin))
}else{
layout(matrix(1:((nr+1)*(nc+leftcol)),nrow=nr+1,byrow=TRUE),
columnwidths,
c(rep(1,nr),xax.margin))
}
# Get y limits to set common values
# ylim.all <- sapply(plotdata,range)
ylim.all <- rbind(sapply(errbardata[1,],min), sapply(errbardata[2,], max))
f <- 0L
# Start plotting by rows
for (row in 1:nr){
# y limits for the row
ylim <- if (y.equal) range(ylim.all) else range(ylim.all[,f+(1:nc)])
# Redefine the labels of y-axes if suitable (glm)
if (transform){
ylabels <- pretty(fam$linkinv(ylim))
at <- fam$linkfun(ylabels)
yaxis <- list(at=at,labels=as.character(ylabels))
}else yaxis <- list(at=pretty(ylim),labels=TRUE)
# do not draw legend until a figure with traces is found in the row
legend.labels <- NULL
# column for y label if it exists
if (leftcol){
plot.new()
text(0.1,0.5,ylab,adj=0.5,srt=90,cex=cex.lab,col=col.lab,font=font.lab)
}
for(column in 1:nc){
# Increase plot counter, get and plot data without axes
f <- f+1
means <- plotdata[[f]]
if (is.matrix(means)) legend.labels <- colnames(means) else means <- as.matrix(means)
lower <- as.matrix(errbardata[[1,f]])
upper <- as.matrix(errbardata[[2,f]])
matplot(means,type=type,pch=pch,
axes=FALSE,xlab="",ylab="",main=NULL,
xlim=c(0.5,nrow(means)+0.5),ylim=ylim,...)
if (!is.null(errorbar)) matploterrorbars(lower,upper,...)
box()
# Draw x axis, with labels if it is the last row
axis(1,at=1:nrow(means),labels=if (row==nr) rownames(means) else FALSE,...)
# Draw y axis, with labels if it is the first column
axis(2,at=yaxis$at,labels=if (column==1) yaxis$labels else FALSE,...)
}
# If there are legends, jump to the last column and add it (if required)
if (legend){
plot.new()
if (!is.null(legend.labels)) legend("right",legend.labels,title=traces[row],
pch=pch,cex=cex.legend,col=col,lty=lty,lwd=lwd)
}
}
# Add x labels in the regions of the last row
if (leftcol) plot.new()
for (column in 1:nc){
plot.new()
text(0.5,0.1,xlab[column],pos=3,cex=cex.lab,col=col.lab,font=font.lab)
}
mtext(maintitle,outer=TRUE,line=1,cex=cex.main,col=col.main,font=font.main)
}else{
for (f in 1:length(plotdata)){
means <- plotdata[[f]]
lower <- as.matrix(errbardata[[1,f]])
upper <- as.matrix(errbardata[[2,f]])
if (f > 1L) dev.new()
ylim <- if (y.equal) range(ylim.all) else range(means)
if (transform){
ylabels <- pretty(fam$linkinv(ylim))
at <- fam$linkfun(ylabels)
yaxis <- list(at=at,labels=as.character(ylabels))
}else yaxis <- list(at=pretty(ylim),labels=TRUE)
# Draw with legend if there are multiple traces
if (legend && is.matrix(means)){
margins <- par("mar")
oma <- mar <- rep(0,4)
oma[c(2,4)] <- margins[c(2,4)]
mar[c(1,3)] <- margins[c(1,3)]
par(oma=oma,mar=mar)
layout(matrix(1:2,1),c(1,marginRatio(1,legend.margin)),1)
matplot(means,type=type,pch=pch,
xaxt="n",yaxt="n",xlab=xlab[(f-1)%%nc + 1],ylab=ylab,
xlim=c(0.5,nrow(means)+0.5),ylim=ylim,main=maintitle,...)
if (!is.null(errorbar)) matploterrorbars(lower,upper,...)
axis(1,at=1:nrow(means),labels=rownames(means),...)
axis(2,at=yaxis$at,labels=yaxis$labels,...)
plot.new()
legend("right",colnames(means),title=traces.pattern[f],
pch=pch,cex=cex.legend,col=col,lty=lty,lwd=lwd)
}else{
means <- as.matrix(means)
matplot(means,type=type,pch=pch,
xaxt="n",yaxt="n",xlab=xlab[(f-1)%%nc + 1],ylab=ylab,
xlim=c(0.5,nrow(means)+0.5),ylim=ylim,main=maintitle,...)
if (!is.null(errorbar)) matploterrorbars(lower,upper,...)
axis(1,at=1:nrow(means),labels=rownames(means),...)
axis(2,at=yaxis$at,labels=yaxis$labels,...)
}
}
}
}
}
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