[R] Plotting Confidence Intervals into a density plot

Elysa Mitova
Fri, 02 Dec 2016 08:18:44 -0000

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]]