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76 lines
2.5 KiB
R
76 lines
2.5 KiB
R
#' Forrest plot from ordinal logistic regression, version2.
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#'
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#' Heavily inspired by https://www.r-bloggers.com/plotting-odds-ratios-aka-a-forrestplot-with-ggplot2/
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#' @param meas outcome meassure variable name or response in data-data.frame as a string. Should be factor, preferably ordered.
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#' @param vars variables to compare against. As vector of columnnames.
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#' @param data dataframe of data.
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#' @param title plot title
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#' @param dec decimals for labels
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#' @param lbls labels for variable names. Carefull, as the right order is not checked automatically!
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#' @param hori labels the horizontal axis (this i the y axis as the plot is rotated)
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#' @param vert labels the horizontal axis (this i the x axis as the plot is rotated)
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#' @param short flag to half number of ticks on horizontal axis.
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#' @param analysis can be either "biv", or "multi", for creation of forest plot from either bivariate (unadjusted) or multivariate (adjusted) ordinal logistic regression.
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#' @keywords forestplot
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#' @export
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plot_ord_odds2<-function(meas,vars,data, title = NULL,dec=3,lbls=NULL,hori="OR (95 % CI)",vert="Variables",short=FALSE,analysis=c("biv","multi")){
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require(ggplot2)
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d <- data
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x <- data.frame(d[, c(ad)])
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y <- d[, c(meas)]
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if (analysis=="biv"){
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dt <- cbind(y, x)
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odds<-c(matrix(ncol = 3))
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nms<-c("or","lo","hi")
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for (i in 1:ncol(x)) {
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dat <- data.frame(y = y, x[, i])
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m <- polr(y ~ ., data = dat, Hess = TRUE)
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mat<-suppressMessages(matrix(c(exp(coef(m)), exp(confint(m))),ncol=3,byrow=FALSE))
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colnames(mat)<-nms
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odd <- data.frame(mat)
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odds<-rbind(odds,odd)
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}
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}
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if (analysis=="multi"){
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m<-polr(y~.,data = dta2,Hess = TRUE)
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odds<-data.frame(cbind(exp(coef(m)), exp(confint(m))))
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}
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names(odds)<-c("or", "lo", "up")
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rodds<-round(odds,digits = dec)
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if (!is.null(lbls)){
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odds$vars<-paste0(lbls," \n",paste0(rodds$or," [",rodds$lo,":",rodds$up,"]"))
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}
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else {
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odds$vars<-paste0(row.names(odds)," \n",paste0(rodds$or," [",rodds$lo,":",rodds$up,"]"))
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}
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ticks<-c(seq(0, 1, by =.1), seq(1, 10, by =1), seq(10, 100, by =10))
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if (short==TRUE){
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ticks<-ticks[seq(1, length(ticks), 2)]
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}
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else {ticks<-ticks}
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odds$ord<-c(nrow(odds):1)
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ggplot(odds, aes(y= or, x = reorder(vars,ord))) +
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geom_point() +
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geom_errorbar(aes(ymin=lo, ymax=up), width=.2) +
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scale_y_log10(breaks=ticks, labels = ticks) +
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geom_hline(yintercept = 1, linetype=2) +
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coord_flip() +
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labs(title = title, x = vert, y = hori) +
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theme_bw()
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}
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