Nothing
ANOM <- function(mc, xlabel=NULL, ylabel=NULL, printn=TRUE, printp=TRUE,
stdep=NULL, stind=NULL, pst=NULL, pbin=NULL, bg="white",
bgrid=TRUE, axlsize=18, axtsize=25, npsize=5, psize=5,
lwidth=1, dlstyle="dashed", fillcol="darkgray"){
if(!(class(mc)[1] %in% c("glht", "SimCi", "mctp", "binomRDci"))){
stop("Please insert an object of class 'glht', 'SimCi', 'mctp', or 'binomRDci' for mc!")
}
if(class(mc)[1]=="glht"){
if(mc$type!="GrandMean"){
stop("For ANOM you need a 'GrandMean' contrast matrix!")
}
modclass <- attr(mc$model, "class")[1]
if(modclass=="aov" | modclass=="lm" | modclass=="glm"){
dd <- attr(attr(mc$model$terms, "factors"), "dimnames")[[1]][1]
ii <- attr(attr(mc$model$terms, "factors"), "dimnames")[[1]][2]
dep <- mc$model$model[dd][, 1]
ind <- mc$model$model[ii][, 1]
}
if(modclass=="lme"){
dd <- attr(attr(mc$model$terms, "factors"), "dimnames")[[1]][1]
ii <- attr(attr(mc$model$terms, "factors"), "dimnames")[[1]][2]
dep <- mc$model$data[, dd]
ind <- mc$model$data[, ii]
}
if(modclass=="lmerMod"){
dd <- rownames(attr(attr(mc$model@frame, "terms"), "factors"))[1]
ii <- rownames(attr(attr(mc$model@frame, "terms"), "factors"))[2]
dep <- mc$model@frame[, dd]
ind <- mc$model@frame[, ii]
}
ss <- as.vector(tapply(ind, ind, length))
ci <- confint(mc)
if(modclass!="glm"){
means <- as.vector(tapply(dep, ind, mean))
mea <- mean(dep)
}
if(modclass=="glm"){
if(mc$model$family$family=="poisson"){
cit <- apply(ci$confint, 2, poisson()$linkinv)
m <- mean(poisson()$linkinv(predict(mc$model)))
}
if(mc$model$family$family=="binomial"){
cit <- apply(ci$confint, 2, binomial()$linkinv)
m <- mean(binomial()$linkinv(predict(mc$model)))
}
}
if(is.null(xlabel)==TRUE){
xlabel <- ii
}else{
xlabel <- xlabel
}
if(is.null(ylabel)==TRUE){
ylabel <- dd
}else{
ylabel <- ylabel
}
if(printp==TRUE){
pvals <- summary(mc)$test$pvalues[1:length(ss)]
}else{
pvals <- NULL
}
bg <- match.arg(bg, choices=c("gray", "grey", "white"))
if(modclass!="glm"){
if(modclass=="lmerMod"){
ANOMgen(mu=means, n=ss, lo=ci$confint[, "lwr"], up=ci$confint[, "upr"],
names=levels(mc$model@frame[, ii]), alternative=mc$alternative,
xlabel=xlabel, ylabel=ylabel, printn=printn, p=pvals, bg=bg,
bgrid=bgrid, axlsize=axlsize, axtsize=axtsize, npsize=npsize,
psize=psize, lwidth=lwidth, dlstyle=dlstyle, fillcol=fillcol)
}else{
ANOMgen(mu=means, n=ss, lo=ci$confint[, "lwr"], up=ci$confint[, "upr"],
names=mc$model$xlevels[[1]], alternative=mc$alternative,
xlabel=xlabel, ylabel=ylabel, printn=printn, p=pvals, bg=bg,
bgrid=bgrid, axlsize=axlsize, axtsize=axtsize, npsize=npsize,
psize=psize, lwidth=lwidth, dlstyle=dlstyle, fillcol=fillcol)
}
}
if(modclass=="glm"){
if(mc$model$family$family=="poisson"){
if(mc$alternative=="two.sided"){
ANOMintern(mu=m*cit[, 1], n=ss, gm=m, lo=m*cit[, 2]-m, up=m*cit[, 3]-m,
names=mc$model$xlevels[[1]], alternative=mc$alternative,
xlabel=xlabel, ylabel=ylabel, printn=printn, p=pvals, bg=bg,
bgrid=bgrid, axlsize=axlsize, axtsize=axtsize, npsize=npsize,
psize=psize, lwidth=lwidth, dlstyle=dlstyle, fillcol=fillcol,
whichone="glm")
}
if(mc$alternative=="greater"){
ANOMintern(mu=m*cit[, 1], n=ss, gm=m, lo=m*cit[, 2]-m, up=Inf,
names=mc$model$xlevels[[1]], alternative=mc$alternative,
xlabel=xlabel, ylabel=ylabel, printn=printn, p=pvals, bg=bg,
bgrid=bgrid, axlsize=axlsize, axtsize=axtsize, npsize=npsize,
psize=psize, lwidth=lwidth, dlstyle=dlstyle, fillcol=fillcol,
whichone="glm")
}
if(mc$alternative=="less"){
ANOMintern(mu=m*cit[, 1], n=ss, gm=m, lo=-Inf, up=m*cit[, 3]-m,
names=mc$model$xlevels[[1]], alternative=mc$alternative,
xlabel=xlabel, ylabel=ylabel, printn=printn, p=pvals, bg=bg,
bgrid=bgrid, axlsize=axlsize, axtsize=axtsize, npsize=npsize,
psize=psize, lwidth=lwidth, dlstyle=dlstyle, fillcol=fillcol,
whichone="glm")
}
}
if(mc$model$family$family=="binomial"){
if(mc$alternative=="two.sided"){
ANOMintern(mu=cit[, 1], n=ss, gm=m, lo=cit[ ,2]-m, up=cit[ ,3]-m,
names=mc$model$xlevels[[1]], alternative=mc$alternative,
xlabel=xlabel, ylabel=ylabel, printn=printn, p=pvals, bg=bg,
bgrid=bgrid, axlsize=axlsize, axtsize=axtsize, npsize=npsize,
psize=psize, lwidth=lwidth, dlstyle=dlstyle, fillcol=fillcol,
whichone="glm")
}
if(mc$alternative=="less"){
ANOMintern(mu=cit[, 1], n=ss, gm=m, lo=-Inf, up=cit[ ,3]-m,
names=mc$model$xlevels[[1]], alternative=mc$alternative,
xlabel=xlabel, ylabel=ylabel, printn=printn, p=pvals, bg=bg,
bgrid=bgrid, axlsize=axlsize, axtsize=axtsize, npsize=npsize,
psize=psize, lwidth=lwidth, dlstyle=dlstyle, fillcol=fillcol,
whichone="glm")
}
if(mc$alternative=="greater"){
ANOMintern(mu=cit[, 1], n=ss, gm=m, lo=cit[ ,2]-m, up=Inf,
names=mc$model$xlevels[[1]], alternative=mc$alternative,
xlabel=xlabel, ylabel=ylabel, printn=printn, p=pvals, bg=bg,
bgrid=bgrid, axlsize=axlsize, axtsize=axtsize, npsize=npsize,
psize=psize, lwidth=lwidth, dlstyle=dlstyle, fillcol=fillcol,
whichone="glm")
}
}
}
}
if(class(mc)[1]=="SimCi"){
if(mc$type!="GrandMean"){
stop("For ANOM you need a 'GrandMean' contrast matrix!")
}
if(is.null(stdep)==TRUE){
stop("Please insert a vector giving the values\n
of the dependent variable for stdep!")
}
if(is.null(stind)==TRUE){
stop("Please insert a numeric vector giving the values\n
of the independent variable for stind!")
}
if(is.numeric(stdep)==FALSE){stop("The dependent variable must be numeric.")}
if((length(stdep)==length(stind))==FALSE){
stop("Dependent and independent variable must be vectors of equal length.")
}
stind <- as.factor(stind)
ss <- as.vector(tapply(stdep, stind, length))
if(mc$test.class=="ratios"){
grame <- 100
}else{
grame <- mean(stdep)
}
if(is.null(xlabel)==TRUE){
xlabel <- "group"
}else{
xlabel <- xlabel
}
if(is.null(ylabel)==TRUE){
ylabel <- mc$resp
}else{
ylabel <- ylabel
}
if(printp==TRUE){
if(class(pst)!="SimTest"){
stop("Please insert an object of class 'SimTest' for pst,\n
or set printp to 'FALSE'.")
}
ppp <- pst$p.val.adj[1:length(ss)]
}else{
ppp <- NULL
}
if(mc$test.class=="ratios"){
ANOMintern(mu=100*as.vector(mc$estimate), n=ss, lo=100*as.vector(mc$lower),
up=100*as.vector(mc$upper), alternative=mc$alternative,
xlabel=xlabel, ylabel=ylabel, printn=printn, p=ppp, bg=bg,
bgrid=bgrid, axlsize=axlsize, axtsize=axtsize, npsize=npsize,
psize=psize, lwidth=lwidth, dlstyle=dlstyle, fillcol=fillcol,
whichone="ratio")
}else{
ANOMgen(mu=as.vector(mc$estimate)+grame, n=ss, lo=as.vector(mc$lower),
up=as.vector(mc$upper), alternative=mc$alternative,
xlabel=xlabel, ylabel=ylabel, printn=printn, p=ppp, bg=bg,
bgrid=bgrid, axlsize=axlsize, axtsize=axtsize, npsize=npsize,
psize=psize, lwidth=lwidth, dlstyle=dlstyle, fillcol=fillcol)
}
}
if(class(mc)[1]=="mctp"){
if(mc$input$type!="UserDefined"){
stop("For ANOM you need a 'UserDefined' grand-mean-type contrast matrix!")
}
if(is.null(mc$Correlation)==TRUE){
stop("Set the argument 'correlation' in function 'mctp()' to 'TRUE'.")
}
if(is.null(xlabel)==TRUE){
xlabel <- as.character(mc$input$formula[3])
}else{
xlabel <- xlabel
}
if(is.null(ylabel)==TRUE){
ylabel <- as.character(mc$input$formula[2])
}else{
ylabel <- ylabel
}
if(printp==TRUE){
pvals <- mc$Analysis$p.Value
}
if(mc$input$alternative=="two.sided"){
ANOMgen(mu=mc$Data.Info$Effect, n=mc$Data.Info$Size,
lo=mc$Analysis$Lower, #abs(mc$Analysis$Estimator - mc$Analysis$Lower),
up=mc$Analysis$Upper, #abs(mc$Analysis$Estimator - mc$Analysis$Upper),
names=colnames(mc$Contrast), alternative=mc$input$alternative,
xlabel=xlabel, ylabel=ylabel,
printn=printn, p=pvals, bg=bg, bgrid=bgrid,
axlsize=axlsize, axtsize=axtsize, npsize=npsize, psize=psize, lwidth=lwidth,
dlstyle=dlstyle, fillcol=fillcol)
}
if(mc$input$alternative=="greater"){
ANOMgen(mu=mc$Data.Info$Effect, n=mc$Data.Info$Size,
lo=mc$Analysis$Lower, #abs(mc$Analysis$Estimator - mc$Analysis$Lower),
up=Inf,
names=colnames(mc$Contrast), alternative=mc$input$alternative,
xlabel=xlabel, ylabel=ylabel,
printn=printn, p=pvals, bg=bg, bgrid=bgrid,
axlsize=axlsize, axtsize=axtsize, npsize=npsize, psize=psize, lwidth=lwidth,
dlstyle=dlstyle, fillcol=fillcol)
}
if(mc$input$alternative=="less"){
ANOMgen(mu=mc$Data.Info$Effect, n=mc$Data.Info$Size,
lo=Inf,
up=mc$Analysis$Upper, #abs(mc$Analysis$Estimator - mc$Analysis$Upper),
names=colnames(mc$Contrast), alternative=mc$input$alternative,
xlabel=xlabel, ylabel=ylabel,
printn=printn, p=pvals, bg=bg, bgrid=bgrid,
axlsize=axlsize, axtsize=axtsize, npsize=npsize, psize=psize, lwidth=lwidth,
dlstyle=dlstyle, fillcol=fillcol)
}
}
if(class(mc)[1]=="binomRDci"){
if(attr(mc$cmat, "type")!="GrandMean"){
stop("For ANOM you need a 'GrandMean' contrast matrix!")
}
if(is.null(xlabel)==TRUE){
xlabel <- "group"
}else{
xlabel <- xlabel
}
if(is.null(ylabel)==TRUE){
ylabel <- "probability of success"
}else{
ylabel <- ylabel
}
if(printp==TRUE){
if(class(pbin)!="binomRDtest"){
stop("Please insert an object of class 'binomRDtest' for pbin,\n
or set printp to 'FALSE'.")
}
ppp <- pbin$p.val.adj
}else{
ppp <- NULL
}
ANOMgen(mu=mc$p, n=mc$n, lo=mc$conf.int[, "lower"],
up=mc$conf.int[, "upper"], names=mc$names,
alternative=mc$alternative, xlabel=xlabel, ylabel=ylabel,
printn=printn, p=ppp, bg=bg, bgrid=bgrid,
axlsize=axlsize, axtsize=axtsize, npsize=npsize, psize=psize, lwidth=lwidth,
dlstyle=dlstyle, fillcol=fillcol)
}
}
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