# [R] Plotting Confidence Intervals into a density plot

Elysa Mitova elysa.mitova at gmail.com
Fri Dec 2 14:15:25 CET 2016

```Hi,

sadly it does not work either, because my index (x axis) is an atomic
vector.
Error Message: \$ operator is invalid for atomic vectors
I think I have to stick to displaying the confidence intervals with
straight lines (ablines) , instead of a shaded area (polygon)

Thank you so much for your help!

On Fri, Dec 2, 2016 at 11:45 AM, Jim Lemon <drjimlemon at gmail.com> wrote:

> Hang on, maybe you mean something like this:
>
> erupt_dens<-density(faithful\$eruptions)
> plot(erupt_dens,ylim=c(0,0.65))
> dispersion(erupt_dens\$x,erupt_dens\$y,ulim=erupt_dens\$y/5,
>  type="l",fill="lightgray",interval=TRUE)
> lines(erupt_dens)
>
> Jim
>
>
> On Fri, Dec 2, 2016 at 9:36 PM, Jim Lemon <drjimlemon at gmail.com> wrote:
> > In order to display a polygon, you need x/y pairs for each point. If
> > you just want a rectangle, you only need four x/y pairs, e.g.:
> >
> > plot(0,xlim=x(2.44,2.57),ylim=c(0,1),type="n")
> > polygon(c(2.44,2.57,2.57,2.44),c(0,0,1,1),col="lightgray")
> >
> > Now if you have a series of x values and want to display a band of
> > constant width around it:
> >
> > y_values<-runif(14)
> > plot(seq(2.44,2.57,by=0.01),y_values,ylim=c(-2,3))
> > dispersion(seq(2.44,2.57,by=0.01),y_values,ulim=rep(0.5,14),
> >  type="l",interval=TRUE,col="lightgray")
> > lines(seq(2.44,2.57,by=0.01),y_values)
> >
> > Jim
> >
> > On Fri, Dec 2, 2016 at 8:59 PM, Elysa Mitova <elysa.mitova at gmail.com>
> wrote:
> >> Thank you,
> >>
> >> this seems to work, but it is not exactly what I need (it indeed looks
> >> great, but a bit beyond my understanding)
> >>
> >> I just need a shaded area between  2.44 to 2.57 along the x-axis - a
> polygon
> >> inserted into my density plot (and not a confidence line along a scatter
> >> plot like your suggested solution)
> >>
> >> My x-axis is an index (a data frame), my y-axis is the automatically
> >> constructed density
> >>
> >> On Fri, Dec 2, 2016 at 10:01 AM, Jim Lemon <drjimlemon at gmail.com>
> wrote:
> >>>
> >>> Hi Elysa,
> >>> I think you are going a bit off course in your example. Try this and
> >>> see if it is close to what you want:
> >>>
> >>> data<-rnorm(100)+runif(100,0,15)
> >>> smu_data<-supsmu(1:100,data)
> >>> rollfun<-function(x,window=10,FUN=sd) {
> >>>  xlen<-length(x)
> >>>  xout<-NA
> >>>  forward<-window%/%2
> >>>  backward<-window-forward
> >>>  for(i in 1:xlen) {
> >>>   xstart<-i-backward
> >>>   if(xstart < 1) xstart<-1
> >>>   xend<-i+forward-1
> >>>   if(xend > xlen) xend<-xlen
> >>>   xout[i]<-do.call(FUN,list(x[xstart:xend],na.rm=TRUE))
> >>>  }
> >>>  return(xout)
> >>> }
> >>> plot(data,ylim=c(0,17))
> >>> library(plotrix)
> >>>  fill="lightgray")
> >>> lines(smu_data,lwd=2)
> >>> points(1:100,data)
> >>>
> >>> Jim
> >>>
> >>>
> >>> On Fri, Dec 2, 2016 at 7:18 PM, Elysa Mitova <elysa.mitova at gmail.com>
> >>> wrote:
> >>> > Hi, thank you!
> >>> >
> >>> > I've constructed the upper and lower bounds with
> >>> >
> >>> >  a <- 2.505766
> >>> >  s <- 0.7789832
> >>> >  n <- 607
> >>> >  error <- qnorm(0.975)*s/sqrt(n)
> >>> >  left <- a-error
> >>> >  right <- a+error
> >>> >  left
> >>> > right
> >>> >
> >>> > Now, I have the numbers I need, but I have no idea how to plot them.
> I
> >>> > was
> >>> > thinking of using a polygon, but somehow it doesn't work out,
> because my
> >>> > y-axis shows only density and is in itself not a variable?
> >>> >
> >>> > xx <- data
> >>> >
> >>> > fit1 <- density(data,na.rm=TRUE)
> >>> >
> >>> > fit2 <- replicate(10000, { x <- sample(xx, replace=TRUE);
> >>> >         density(x, na.rm=TRUE, from=min(fit1\$x), to=max(fit1\$x))\$y }
> )
> >>> >
> >>> > fit3 <- apply(fit2, 1, quantile, c(0.025,0.975) )  - Probably herein
> >>> > lies the problem?
> >>> >
> >>> > plot(fit1, ylim=range(fit3))
> >>> > polygon( c(fit1\$x, rev(fit1\$x)), c(fit3[1,], rev(fit3[2,])),
> >>> > col='grey', border=F)
> >>> > lines(fit1)
> >>> >
> >>> > I tried working with this solution I found on the internet, but
> >>> > somehow now the lines the shaded areas sporadically everywhere around
> >>> > my density plot? I just want a polygon spreading from  2.44 to 2.57
> >>> > along the x-axis.
> >>> >
> >>> >
> >>> > Any tipps?
> >>> >
> >>> >
> >>> >
> >>> >
> >>> > On Fri, Dec 2, 2016 at 1:24 AM, David Winsemius <
> dwinsemius at comcast.net>
> >>> > wrote:
> >>> >
> >>> >>
> >>> >> > On Dec 1, 2016, at 12:10 PM, Elysa Mitova <elysa.mitova at gmail.com
> >
> >>> >> wrote:
> >>> >> >
> >>> >> > Hi,
> >>> >> >
> >>> >> > I am desperately looking for a way to plot confidence intervals
> into
> >>> >> > a
> >>> >> > density plot of only one variable (not a scatter plot etc.)
> >>> >> >
> >>> >> > Have you any advice how to do this?
> >>> >> >
> >>> >> > I've only found manual ways to do with "abline", but this is a
> rather
> >>> >> > bothersome method and only works with ggplot (and not ggplot2).
> >>> >>
> >>> >> This makes it appear that you expect this to be done in ggplot2
> >>> >> automagically. I suspect you must instead first find the right
> approach
> >>> >> to
> >>> >> construction of those upper and lower bounds before plotting. It's
> not
> >>> >> clear what methods you expect to be needed. Your desperation is not
> a
> >>> >> guide. Perhaps trying a bit of searching?
> >>> >>
> >>> >> install.packages("sos")
> >>> >> library(sos)
> >>> >> findFn("confidence intervals density estimates")
> >>> >>
> >>> >>
> >>> >> Delivers quite a few results. Then searching on the text within that
> >>> >> webpage you find
> >>> >>
> >>> >>
> >>> >> 208     2       27      54      nprobust        kdrobust
> >>> >> 2016-11-14
> >>> >> 16:41:50     27      Kernel Density Estimation with Robust
> Confidence
> >>> >> Intervals
> >>> >> 209     2       27      54      nprobust        lprobust
> >>> >> 2016-11-14
> >>> >> 16:41:50     27      Local-Polynomial Estimation with Robust
> Confidence
> >>> >> Intervals
> >>> >>
> >>> >> Is that what you seek?
> >>> >>
> >>> >> >
> >>> >> > Thank you!
> >>> >> >
> >>> >> >       [[alternative HTML version deleted]]
> >>> >> I know you just subscribed, so now is the time to read the Posing
> >>> >> Guide.
> >>> >>
> >>> >> ==
> >>> >>
> >>> >> David Winsemius
> >>> >> Alameda, CA, USA
> >>> >>
> >>> >>
> >>> >
> >>> >         [[alternative HTML version deleted]]
> >>> >
> >>> > ______________________________________________
> >>> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >>> > https://stat.ethz.ch/mailman/listinfo/r-help
> >>> > PLEASE do read the posting guide
> >>> > http://www.R-project.org/posting-guide.html
> >>> > and provide commented, minimal, self-contained, reproducible code.
> >>
> >>
>

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