R Error Bar
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Scatter Plot With Error Bars In R
Bars by Chris Wetherill on August 17, 2015 3 Comments Bar charts are error.bar function r a pretty common way to represent data visually, but constructing them isn't always the most intuitive thing in the world. One way that
Errbar R
we can construct these graphs is using R's default packages. Barplots using base R Let's start by viewing our dataframe: here we will be finding the mean miles per gallon by number of cylinders and number of error bars in r barplot gears. View(mtcars) We begin by aggregating our data by cylinders and gears and specify that we want to return the mean, standard deviation, and number of observations for each group: myData <- aggregate(mtcars$mpg, by = list(cyl = mtcars$cyl, gears = mtcars$gear), FUN = function(x) c(mean = mean(x), sd = sd(x), n = length(x))) After this, we'll need to do a little manipulation since the previous function returned matrices instead of vectors myData <- do.call(data.frame, myData) r summaryse And now let's compute the standard error for each group. We can then rename the columns just for ease of use. myData$se <- myData$x.sd / sqrt(myData$x.n) colnames(myData) <- c("cyl", "gears", "mean", "sd", "n", "se") myData$names <- c(paste(myData$cyl, "cyl /", myData$gears, " gear")) Now we're in good shape to start constructing our plot! Here, we'll start by widening the plot margins just a tad so that nothing runs off the edge of the figure (using the par() function). It's also a good habit to specify the upper bounds of your plot since the error bars are going to extend past the height of your bars. Beyond this, it's just any additional aesthetic styling that you want to tweak and you're good to go! The error bars are added in at the end using the segments() and arrows() functions. In this case, we are extending the error bars to ±2 standard errors about the mean. par(mar = c(5, 6, 4, 5) + 0.1) plotTop <- max(myData$mean) + myData[myData$mean == max(myData$mean), 6] * 3 barCenters <- barplot(height = myData$mean, names.arg = myData$names, beside = true, las = 2, ylim = c(0, plotTop), cex.names = 0.75, xaxt = "n", main = "Mileage by No. Cylinders and No. Gears", ylab = "Miles per Gallon", border = "black", axes = TRUE) # Specify the groupings. We use srt
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R Plot Standard Deviation
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Plot Mean And Standard Deviation In R
Sign up Add error bars to show standard deviation on a plot in R up vote 23 down vote favorite 10 For each X-value I calculated the average Y-value and the standard deviation (sd) of each Y-value x = 1:5 y http://datascienceplus.com/building-barplots-with-error-bars/ = c(1.1, 1.5, 2.9, 3.8, 5.2) sd = c(0.1, 0.3, 0.2, 0.2, 0.4) plot (x, y) How can I use the standard deviation to add error bars to each datapoint of my plot? r plot statistics standard-deviation share|improve this question edited Oct 16 '14 at 3:43 Craig Finch 11417 asked Feb 25 '13 at 8:59 John Garreth 4572413 also see plotrix::plotCI –Ben Bolker Feb 25 '13 at 15:13 add a comment| 5 Answers 5 active oldest votes up vote 16 http://stackoverflow.com/questions/15063287/add-error-bars-to-show-standard-deviation-on-a-plot-in-r down vote accepted A Problem with csgillespie solution appears, when You have an logarithmic X axis. The you will have a different length of the small bars on the right an the left side (the epsilon follows the x-values). You should better use the errbar function from the Hmisc package: d = data.frame( x = c(1:5) , y = c(1.1, 1.5, 2.9, 3.8, 5.2) , sd = c(0.2, 0.3, 0.2, 0.0, 0.4) ) ##install.packages("Hmisc", dependencies=T) library("Hmisc") # add error bars (without adjusting yrange) plot(d$x, d$y, type="n") with ( data = d , expr = errbar(x, y, y+sd, y-sd, add=T, pch=1, cap=.1) ) # new plot (adjusts Yrange automatically) with ( data = d , expr = errbar(x, y, y+sd, y-sd, add=F, pch=1, cap=.015, log="x") ) share|improve this answer answered Sep 6 '13 at 14:21 R_User 3,20984683 add a comment| up vote 19 down vote A solution with ggplot2 : qplot(x,y)+geom_errorbar(aes(x=x, ymin=y-sd, ymax=y+sd), width=0.25) share|improve this answer answered Feb 25 '13 at 9:06 juba 24.2k56081 add a comment| up vote 18 down vote You can use segments to add the bars in base graphics. Here epsilon controls the line across the top and bottom of the line. plot (x, y, ylim=c(0, 6)) epsilon = 0.02 for(i in 1:5) { up = y[i] + sd[i] low = y[i] - sd[i] segments(x[i],low , x[i], up) segments(x[i]-epsilon, up , x[i]+epsilon, up) segments(x[i]-epsilon, low , x[i]+epsilon, low) } As @thelatemail points out, I should really have used vectorised function calls: segment
|| is.character(x)) "" else as.character(substitute(y)), add=FALSE, lty=1, type='p', ylim=NULL, lwd=1, pch=16, Type=rep(1, length(y)), ...) Arguments x vector of numeric x-axis values (for vertical error bars) or a factor http://svitsrv25.epfl.ch/R-doc/library/Hmisc/html/errbar.html or character variable (for horizontal error bars, x representing the group labels) y vector of y-axis values. yplus vector of y-axis values: the tops of the error bars. yminus vector of y-axis values: the bottoms of the error bars. cap the width of the little lines at the tops and bottoms of the error bars in units of the width of the plot. error bar Defaults to 0.015. main a main title for the plot, see also title. sub a sub title for the plot. xlab optional x-axis labels if add=FALSE. ylab optional y-axis labels if add=FALSE. Defaults to blank for horizontal charts. add set to TRUE to add bars to an existing plot (available only for vertical error bars) lty type of line for error error bars in bars type type of point. Use type="b" to connect dots. ylim y-axis limits. Default is to use range of y, yminus, and yplus. For horizonal charts, ylim is really the x-axis range, excluding differences. lwd line width for line segments (not main line) pch character to use as the point. Type used for horizontal bars only. Is an integer vector with values 1 if corresponding values represent simple estimates, 2 if they represent differences. ... other parameters passed to all graphics functions. Details errbar adds vertical error bars to an existing plot or makes a new plot with error bars. It can also make a horizontal error bar plot that shows error bars for group differences as well as bars for groups. For the latter type of plot, the lower x-axis scale corresponds to group estimates and the upper scale corresponds to differences. The spacings of the two scales are identical but the scale for differences has its origin shifted so that zero may be included. If at least one of the confidence intervals includes zero, a vertical dotted reference line at zero is drawn. Author(s