[R] Error Bar Issues
William Revelle
lists at revelle.net
Sun Jun 6 06:28:22 CEST 2010
Dear Beloitstudent;
Although Ben Bolker will have to give you the
definitive answer, the following will do what I
think you want to do.
library(plotrix) #for those of us who don't know where plotCI comes from
#give us the data:
Saline <- structure(list(Time = c(-20L, NA, 30L, 45L, 60L, 80L, 110L, 140L,
200L, 260L, 320L), Average = c(0, NA, 0, 3.227902, 5.066664,
6.107491, 6.968231, 7.325713, 7.875194, 6.513927, 4.204342),
SEM = c(0, NA, 0, 0.7462524, 1.1623944, 1.5027762, 1.3799637,
1.2282053, 1.1185175, 0.5386359, 0.6855906)), .Names = c("Time",
"Average", "SEM"), class = "data.frame", row.names = c("1", "2",
"3", "4", "5", "6", "7", "8", "9", "10", "11"))
# First draw the points
plotCI(x=Saline [,1],y=Saline [,2], uiw=Saline [,3], err="y",
pt.bg=par("bg"),pch=21, cex=1.5 ,gap=0, sfrac=0.005,
xlim=c(-20,340),xaxp=c(-20,320,17), xlab="Time (min)", ylim=c(0,12),
yaxp=c(0,12,12), ylab="Arterial Plasma Acetaminophen (µg/mL)", las=1,
font.lab=2) #draws the points
plotCI(x=Saline [,1],y=Saline [,2], uiw=Saline [,3], err="y",
pt.bg=par("bg"),pch=21, cex=1.5 ,gap=0, sfrac=0.005,
xlim=c(-20,340),xaxp=c(-20,320,17), ylim=c(0,12),
yaxp=c(0,12,12), las=1,
font.lab=2,add=TRUE,type="o") #puts the lines in and gives a message
You will get a warning message the type is
obsolete, but at least you have your graph.
Bill
At 3:51 PM -0700 6/5/10, beloitstudent wrote:
>Content-Type: text/plain
>Content-Disposition: inline
>Content-length: 4586
>
>
>Thanks for the suggestion...but R still doesn't like it. Now I have 3 error
>messages. It seems to dislike my *err=y* command. I'm going to continue
>trying. Thanks for your help! If you happen to spot anything else, please
>let me know!
>
>thanks!
>beloitstudent
>
>
>On Sat, Jun 5, 2010 at 5:16 PM, Joris FA Meys [via R] <
>ml-node+2244611-1554261936-278019 at n4.nabble.com<ml-node%2B2244611-1554261936-278019 at n4.nabble.com>
>> wrote:
>
>> you can't refer to an argument within a function call. Try
>>
>> uiw <- Saline[,3]
>>
>> plotCI(x=Saline [,1],y=Saline [,2], uiw=uiw, liw=uiw, err=y, pch=21,
>> pt.bg=par("bg"), cex=1.5, lty=1, type="o", gap=0, sfrac=0.005,
>> xlim=c(-21,340),xaxp=c(-20,320,11), xlab="Time (min)", ylim=c(0,12),
>> yaxp=c(0,12,11), ylab="Arterial Plasma Acetaminophen (Âµg/mL)", las=1,
>> font.lab=2, add=TRUE)
>>
>> Cheers
>> Joris
>>
>> On Sat, Jun 5, 2010 at 6:09 PM, beloitstudent
>><[hidden
>>email]<http://user/SendEmail.jtp?type=node&node=2244611&i=0>>
>> wrote:
>>
>> >
>> > Hello all,
>> >
>> > I am an undergraduate student who is having syntax issues trying to get
>> > error bars on my graph.
>> >
>> > This is the data, which I assigned the name "Saline" to.
>> > Time Average SEM
>> > 1 -20 0.000000 0.0000000
>> > 2
>> > 3 30 0.000000 0.0000000
>> > 4 45 3.227902 0.7462524
>> > 5 60 5.066664 1.1623944
>> > 6 80 6.107491 1.5027762
>> > 7 110 6.968231 1.3799637
>> > 8 140 7.325713 1.2282053
>> > 9 200 7.875194 1.1185175
>> > 10 260 6.513927 0.5386359
>> > 11 320 4.204342 0.6855906
>> >
>> > This is the command that I typed in to get my error bars.
>> >
>> > plotCI(x=Saline [,1],y=Saline [,2], uiw=Saline [,3], liw=uiw, err=y,
>> pch=21,
>> > pt.bg=par("bg"), cex=1.5, lty=1, type="o", gap=0, sfrac=0.005,
>> > xlim=c(-21,340),xaxp=c(-20,320,11), xlab="Time (min)", ylim=c(0,12),
>> > yaxp=c(0,12,11), ylab="Arterial Plasma Acetaminophen (Âµg/mL)", las=1,
>> > font.lab=2, add=TRUE)
>> >
>> > And this is the error message I keep getting
>> > Error in plotCI(x = Saline[, 1], y = Saline[, 2], uiw = Saline[, 3], liw
>> =
>> > uiw, :
>> > object 'uiw' not found
>> > In addition: Warning message:
>> > In if (err == "y") z <- y else z <- x :
>> > the condition has length > 1 and only the first element will be used
>> >
>> > Now, to me, the command seems correct.
>> > I want the error bars to show up where the points on my graph are...so
>> the x
>> > coordinates should be my time (aka Saline [1]) and the y coordinates
> > should
>> > be my Averages (aka Saline [2]) and my upper and lower limits to my
>> > confidence interval should be the SEM from Saline [3], but something is
>> > wrong with this and I cannot figure out what it is. If anyone has
>> > suggestions I would be very grateful. Thanks for your help!
>> >
>> > beloitstudent
>> > --
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