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Sam Albers

2010-Feb-20 00:22 UTC

[R] Error Bars in lattice- barcharts

Hello,

I am attempting to write a script that adds error bars to a barchart. I
basing my attempt heavily on the following thread:

http://tolstoy.newcastle.edu.au/R/e2/help/06/10/2791.html

I can't seem to get around the problem that was discussed in the thread. The
following example should illustrate my problem. Sorry about the messy
example but I am 1) trying to make it as close as possible to my actual work
and 2) my skill level is spotty at best. Can anyone suggest a way to do this
or even another way to make a grouped barchart with error bars? I'm not
married to this method although I prefer working with lattice. Thanks for
any help in advance!

Sam

#Generating the data
library(lattice)

temp <- abs(rnorm(81*5))
err <- as.data.frame(temp)
err$section=c("down","down","down","mid","mid","mid",
"up","up", "up")

err$depth=c("Surface","D50", "2xD50")

err$err.date=c("05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","28/08/2009",
"28/08/2009", "28/08/2009","28/08/2009",
"28/08/2009",
"28/08/2009","28/08/2009", "28/08/2009",
"28/08/2009")


err.split <-
     with(err,
          split(temp, list(depth,section, err.date)))

#I've tried to alter the panel function according to the thread to produce
vertical error bars in my barcharts

prepanel.ci <- function(x, y, ly, uy, subscripts, ...) {

        y <- as.numeric(y)
        ly <- as.numeric(ly[subscripts])
         uy <- as.numeric(uy[subscripts])
         list(ylim = range(y, uy, ly, finite = TRUE))
     }

panel.ci <- function(x, y, lx, ux, subscripts, pch = 16, ...) {
         x <- as.numeric(x)
         y <- as.numeric(y)
         lx <- as.numeric(lx[subscripts])
         ux <- as.numeric(ux[subscripts])

         panel.arrows(x, ly, x, uy, col = 'black',
                  length = 0.25, unit = "native",
                  angle = 90, code = 3)
         panel.barchart(x, y, pch = pch, ...)
     }

se <-function(x) sqrt(var(x)/length(x))



err.ucl <- sapply(err.split,
            function(x) {
                st <- boxplot.stats(x)
                c(mean(x), mean(x) + se(x), mean(x) -se(x))
            })



err.ucl <- as.data.frame(t(err.ucl))
names(err.ucl) <- c("mean", "upper.se",
"lower.se")
err.ucl$label <- factor(rownames(err.ucl),levels = rownames(err.ucl))

# add factor, grouping and by variables
err.ucl$section=c("down","down","down","mid","mid","mid",
"up","up", "up")
err.ucl$depth=c("Surface","D50", "2xD50")

#There has got to be a better way of doing this
err.ucl$err.date=c("05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","28/08/2009",
"28/08/2009", "28/08/2009","28/08/2009",
"28/08/2009",
"28/08/2009","28/08/2009", "28/08/2009",
"28/08/2009")

#This produces the figure I am looking for minus the error bars.

with(err.ucl, barchart(mean ~ err.date | section, group=depth,
        layout=c(1,3),
         horizontal=FALSE,
         scales=list(x=list(rot=45)),
        ))


# Deepayan's original example. I am unsure how to diagnose the packet error.
This is where I run into problems

with(err.ucl, barchart(mean ~ err.date | section, group=depth,
         layout=c(1,3),
         horizontal=FALSE,
         scales=list(x=list(rot=45)),
         ly=lower.se,
         uy=upper.se,
         prepanel=prepanel.ci,
         panel=panel.superpose,
         panel.groups=panel.ci
         ))





-- 
*****************************************************
Sam Albers
Geography Program
University of Northern British Columbia
3333 University Way
Prince George, British Columbia
Canada, V2N 4Z9
phone: 250 960-6777
*****************************************************

	[[alternative HTML version deleted]]

Ivan Gregoretti

2010-Apr-07 20:03 UTC

head link

[R] Error Bars in lattice- barcharts

Hi Sam and everybody,

Can you educate me a little bit on the use of barchart?

A command like this

barchart(~table(someProperty), data=A)

produces a barchart with horizontal bars.

I want to produce that graph but with VERTICAL bars.

clearly, horizontal=FALSE does not work.

Thank you,

Ivan

> sessionInfo()R version 2.10.0 (2009-10-26)
x86_64-redhat-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] lattice_0.18-3

loaded via a namespace (and not attached):
[1] grid_2.10.0



Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1592
Fax: 1-301-496-9878



On Fri, Feb 19, 2010 at 7:22 PM, Sam Albers <tonightsthenight at
gmail.com> wrote:> Hello,
>
> I am attempting to write a script that adds error bars to a barchart. I
> basing my attempt heavily on the following thread:
>
> http://tolstoy.newcastle.edu.au/R/e2/help/06/10/2791.html
>
> I can't seem to get around the problem that was discussed in the
thread. The
> following example should illustrate my problem. Sorry about the messy
> example but I am 1) trying to make it as close as possible to my actual
work
> and 2) my skill level is spotty at best. Can anyone suggest a way to do
this
> or even another way to make a grouped barchart with error bars? I'm not
> married to this method although I prefer working with lattice. Thanks for
> any help in advance!
>
> Sam
>
> #Generating the data
> library(lattice)
>
> temp <- abs(rnorm(81*5))
> err <- as.data.frame(temp)
>
err$section=c("down","down","down","mid","mid","mid",
"up","up", "up")
>
> err$depth=c("Surface","D50", "2xD50")
>
>
err$err.date=c("05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","28/08/2009",
> "28/08/2009", "28/08/2009","28/08/2009",
"28/08/2009",
> "28/08/2009","28/08/2009", "28/08/2009",
"28/08/2009")
>
>
> err.split <-
> ? ? with(err,
> ? ? ? ? ?split(temp, list(depth,section, err.date)))
>
> #I've tried to alter the panel function according to the thread to
produce
> vertical error bars in my barcharts
>
> prepanel.ci <- function(x, y, ly, uy, subscripts, ...) {
>
> ? ? ? ?y <- as.numeric(y)
> ? ? ? ?ly <- as.numeric(ly[subscripts])
> ? ? ? ? uy <- as.numeric(uy[subscripts])
> ? ? ? ? list(ylim = range(y, uy, ly, finite = TRUE))
> ? ? }
>
> panel.ci <- function(x, y, lx, ux, subscripts, pch = 16, ...) {
> ? ? ? ? x <- as.numeric(x)
> ? ? ? ? y <- as.numeric(y)
> ? ? ? ? lx <- as.numeric(lx[subscripts])
> ? ? ? ? ux <- as.numeric(ux[subscripts])
>
> ? ? ? ? panel.arrows(x, ly, x, uy, col = 'black',
> ? ? ? ? ? ? ? ? ?length = 0.25, unit = "native",
> ? ? ? ? ? ? ? ? ?angle = 90, code = 3)
> ? ? ? ? panel.barchart(x, y, pch = pch, ...)
> ? ? }
>
> se <-function(x) sqrt(var(x)/length(x))
>
>
>
> err.ucl <- sapply(err.split,
> ? ? ? ? ? ?function(x) {
> ? ? ? ? ? ? ? ?st <- boxplot.stats(x)
> ? ? ? ? ? ? ? ?c(mean(x), mean(x) + se(x), mean(x) -se(x))
> ? ? ? ? ? ?})
>
>
>
> err.ucl <- as.data.frame(t(err.ucl))
> names(err.ucl) <- c("mean", "upper.se",
"lower.se")
> err.ucl$label <- factor(rownames(err.ucl),levels = rownames(err.ucl))
>
> # add factor, grouping and by variables
>
err.ucl$section=c("down","down","down","mid","mid","mid",
"up","up", "up")
> err.ucl$depth=c("Surface","D50", "2xD50")
>
> #There has got to be a better way of doing this
>
err.ucl$err.date=c("05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/09/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","05/10/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","12/09/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","13/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","19/10/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","21/09/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","26/10/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","27/09/2009","28/08/2009",
> "28/08/2009", "28/08/2009","28/08/2009",
"28/08/2009",
> "28/08/2009","28/08/2009", "28/08/2009",
"28/08/2009")
>
> #This produces the figure I am looking for minus the error bars.
>
> with(err.ucl, barchart(mean ~ err.date | section, group=depth,
> ? ? ? ?layout=c(1,3),
> ? ? ? ? horizontal=FALSE,
> ? ? ? ? scales=list(x=list(rot=45)),
> ? ? ? ?))
>
>
> # Deepayan's original example. I am unsure how to diagnose the packet
error.
> This is where I run into problems
>
> with(err.ucl, barchart(mean ~ err.date | section, group=depth,
> ? ? ? ? layout=c(1,3),
> ? ? ? ? horizontal=FALSE,
> ? ? ? ? scales=list(x=list(rot=45)),
> ? ? ? ? ly=lower.se,
> ? ? ? ? uy=upper.se,
> ? ? ? ? prepanel=prepanel.ci,
> ? ? ? ? panel=panel.superpose,
> ? ? ? ? panel.groups=panel.ci
> ? ? ? ? ))
>
>
>
>
>
> --
> *****************************************************
> Sam Albers
> Geography Program
> University of Northern British Columbia
> 3333 University Way
> Prince George, British Columbia
> Canada, V2N 4Z9
> phone: 250 960-6777
> *****************************************************
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.
>

Felix Andrews

2010-Apr-08 04:54 UTC

head link

[R] Error Bars in lattice- barcharts

On 8 April 2010 06:03, Ivan Gregoretti <ivangreg at gmail.com>
wrote:> Hi Sam and everybody,
>
> Can you educate me a little bit on the use of barchart?
>
> A command like this
>
> barchart(~table(someProperty), data=A)
>
> produces a barchart with horizontal bars.

That should be
barchart(table(someProperty), data=A)
     (the method for objects of class "table")

> I want to produce that graph but with VERTICAL bars.
>
> clearly, horizontal=FALSE does not work.
and you will find that horizontal = FALSE does work.






-- 
Felix Andrews / ???
Postdoctoral Fellow
Integrated Catchment Assessment and Management (iCAM) Centre
Fenner School of Environment and Society [Bldg 48a]
The Australian National University
Canberra ACT 0200 Australia
M: +61 410 400 963
T: + 61 2 6125 4670
E: felix.andrews at anu.edu.au
CRICOS Provider No. 00120C
-- 
http://www.neurofractal.org/felix/

Felix Andrews

2010-Apr-08 05:03 UTC

head link

[R] Error Bars in lattice- barcharts

On 20 February 2010 11:22, Sam Albers <tonightsthenight at gmail.com>
wrote:
> #I've tried to alter the panel function according to the thread to
produce
> vertical error bars in my barcharts
>
> prepanel.ci <- function(x, y, ly, uy, subscripts, ...) {
>
> ? ? ? ?y <- as.numeric(y)
> ? ? ? ?ly <- as.numeric(ly[subscripts])
> ? ? ? ? uy <- as.numeric(uy[subscripts])
> ? ? ? ? list(ylim = range(y, uy, ly, finite = TRUE))
> ? ? }
>
> panel.ci <- function(x, y, lx, ux, subscripts, pch = 16, ...) {
> ? ? ? ? x <- as.numeric(x)
> ? ? ? ? y <- as.numeric(y)
> ? ? ? ? lx <- as.numeric(lx[subscripts])
> ? ? ? ? ux <- as.numeric(ux[subscripts])
>
> ? ? ? ? panel.arrows(x, ly, x, uy, col = 'black',
> ? ? ? ? ? ? ? ? ?length = 0.25, unit = "native",
> ? ? ? ? ? ? ? ? ?angle = 90, code = 3)
> ? ? ? ? panel.barchart(x, y, pch = pch, ...)
> ? ? }
>

> # Deepayan's original example. I am unsure how to diagnose the packet
error.
> This is where I run into problems

Well, when the error message says "argument 'lx' is missing, with
no
default", it really means that argument 'lx' is missing, with no
default. Your panel function has an argument 'lx', which you forgot to
change to 'ly' as you did with the prepanel function.

Hope that helps...

> with(err.ucl, barchart(mean ~ err.date | section, group=depth,
> ? ? ? ? layout=c(1,3),
> ? ? ? ? horizontal=FALSE,
> ? ? ? ? scales=list(x=list(rot=45)),
> ? ? ? ? ly=lower.se,
> ? ? ? ? uy=upper.se,
> ? ? ? ? prepanel=prepanel.ci,
> ? ? ? ? panel=panel.superpose,
> ? ? ? ? panel.groups=panel.ci
> ? ? ? ? ))
>


-- 
Felix Andrews / ???
Postdoctoral Fellow
Integrated Catchment Assessment and Management (iCAM) Centre
Fenner School of Environment and Society [Bldg 48a]
The Australian National University
Canberra ACT 0200 Australia
M: +61 410 400 963
T: + 61 2 6125 4670
E: felix.andrews at anu.edu.au
CRICOS Provider No. 00120C
-- 
http://www.neurofractal.org/felix/

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