Re: [R] Whiskers on the default boxplot {graphics}
Just to put this topic to rest: The hinges match quantile(x, probs = c(1,3)/4, type = 2) except when n = 3 mod 4. I no longer have Tukey's EDA book, but I think that his idea was that hinges (aka quartiles) were defined as medians of the lower/upper halves of the (sorted, of course) data, where a 'half' would include the median for odd sample sizes. And that's how they are calculated in fivenum(). Thus hinges are a 10th definition of quartiles, but they don't lend themselves to generalization to arbitrary quantiles other than, say, octiles or other (1/2^k)-iles. -Peter On 2010-05-13 11:47, David Winsemius wrote: I agree. I was convinced by Ehlers' example that type =2 was a better match to fivenum's result -- Peter Ehlers University of Calgary __ R-help@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.
Re: [R] Whiskers on the default boxplot {graphics}
Hi Peter, You're absolutely correct! The description for 'range' in 'boxplot' help file is a little bit confusing by using the words interquartile range. I think it should be changed to the length of the box to be exact and consistent with those in the help file for boxplot.stats. The issue is probably that there are multiple ways (9 to be exact) of defining quantiles in R. See 'type= ' arguement for ?quantile. The quantile function uses type=7 by default which matches the quantile definition used by S-Plus(?), but differs from that used by SPSS. Doesn't fivenum essentially use the equivalent of a different type= arguement (maybe 2 or 5) in constructing the hinges? It seems perfectly reasonable to talk about 'length of box' (or 'box height' depending how you display the boxplot), but aren't the hinges simply Q1 and Q3 defined by one of the possible quartile definitions (as Peter points out the one used by fivenum)? The box height does not necesarily match the distance produced by IQR() which also seems to use the equivalent of quantile(..., type=7), but it is still an IQR, is it not? Quantiles apparantly can be defined in more than one acceptable way (sort of like dealing with ties in rank statistics). The OP seemed to want an exact explanation of the wiskers, and I think Peter has pointed us at the definition of quartiles used by fivenum, as opposed to the default used with quantile(..., type=7). All that said, I'm not convinced that it is wrong to speak of interquartile range in 'boxplot' help. Rob __ R-help@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.
Re: [R] Whiskers on the default boxplot {graphics}
On May 13, 2010, at 10:25 AM, Robert Baer wrote:
Hi Peter,
You're absolutely correct! The description for 'range' in
'boxplot' help file is a little bit confusing by using the words
interquartile range. I think it should be changed to the length
of the box to be exact and consistent with those in the help file
for boxplot.stats.
The issue is probably that there are multiple ways (9 to be exact)
of defining quantiles in R. See 'type= ' arguement for ?quantile.
The quantile function uses type=7 by default which matches the
quantile definition used by S-Plus(?), but differs from that used by
SPSS. Doesn't fivenum essentially use the equivalent of a different
type= arguement (maybe 2 or 5) in constructing the hinges?
It seems perfectly reasonable to talk about 'length of box' (or 'box
height' depending how you display the boxplot), but aren't the
hinges simply Q1 and Q3 defined by one of the possible quartile
definitions (as Peter points out the one used by fivenum)? The box
height does not necesarily match the distance produced by IQR()
which also seems to use the equivalent of quantile(..., type=7), but
it is still an IQR, is it not?
Quantiles apparantly can be defined in more than one acceptable
way (sort of like dealing with ties in rank statistics). The OP
seemed to want an exact explanation of the wiskers, and I think
Peter has pointed us at the definition of quartiles used by fivenum,
as opposed to the default used with quantile(..., type=7).
Yes, and experimentation leads me to the conclusion that the only
possible candidate for matching up the results of fivenum[c(2,4] with
quantile(y, c(1,3)/4, type=i) is for type=5. I'm not able to prove
that to myself from mathematical arguments. since I do not quite
understand the formalism in the quantile page. If the match is not
exact, this would be a tenth definition of IQR.
set.seed(123)
y - rexp(300, .02)
fivenum(y)
[1] 0.2183685 15.8740466 42.1147820 74.0362517 360.5503788
for (i in 4:9) {print(quantile(y, c(1,3)/4, type=i) ) }
25% 75%
15.82506 73.93080
25% 75%
15.87405 74.03625
25% 75%
15.84955 74.08898
25% 75%
15.89854 73.98352
25% 75%
15.86588 74.05383
25% 75%
15.86792 74.04943
--
David.
All that said, I'm not convinced that it is wrong to speak of
interquartile range in 'boxplot' help.
Rob
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Re: [R] Whiskers on the default boxplot {graphics}
David,
try this:
fivenum(1:101)
quantile(1:101, c(1,3)/4, type=5)
-Peter
On 2010-05-13 8:55, David Winsemius wrote:
On May 13, 2010, at 10:25 AM, Robert Baer wrote:
Hi Peter,
You're absolutely correct! The description for 'range' in 'boxplot'
help file is a little bit confusing by using the words interquartile
range. I think it should be changed to the length of the box to be
exact and consistent with those in the help file for boxplot.stats.
The issue is probably that there are multiple ways (9 to be exact) of
defining quantiles in R. See 'type= ' arguement for ?quantile. The
quantile function uses type=7 by default which matches the quantile
definition used by S-Plus(?), but differs from that used by SPSS.
Doesn't fivenum essentially use the equivalent of a different type=
arguement (maybe 2 or 5) in constructing the hinges?
It seems perfectly reasonable to talk about 'length of box' (or 'box
height' depending how you display the boxplot), but aren't the hinges
simply Q1 and Q3 defined by one of the possible quartile definitions
(as Peter points out the one used by fivenum)? The box height does not
necesarily match the distance produced by IQR() which also seems to
use the equivalent of quantile(..., type=7), but it is still an IQR,
is it not?
Quantiles apparantly can be defined in more than one acceptable way
(sort of like dealing with ties in rank statistics). The OP seemed to
want an exact explanation of the wiskers, and I think Peter has
pointed us at the definition of quartiles used by fivenum, as opposed
to the default used with quantile(..., type=7).
Yes, and experimentation leads me to the conclusion that the only
possible candidate for matching up the results of fivenum[c(2,4] with
quantile(y, c(1,3)/4, type=i) is for type=5. I'm not able to prove that
to myself from mathematical arguments. since I do not quite understand
the formalism in the quantile page. If the match is not exact, this
would be a tenth definition of IQR.
set.seed(123)
y - rexp(300, .02)
fivenum(y)
[1] 0.2183685 15.8740466 42.1147820 74.0362517 360.5503788
for (i in 4:9) {print(quantile(y, c(1,3)/4, type=i) ) }
25% 75%
15.82506 73.93080
25% 75%
15.87405 74.03625
25% 75%
15.84955 74.08898
25% 75%
15.89854 73.98352
25% 75%
15.86588 74.05383
25% 75%
15.86792 74.04943
--
Peter Ehlers
University of Calgary
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Re: [R] Whiskers on the default boxplot {graphics}
And try this (which seems to leave us with type=2) and is listed in
?quantile as Discontinuous sample quantile types 1, 2, and 3
quantile(1:101, c(1,3)/4, type=2)
25% 75%
26 76
David,
try this:
fivenum(1:101)
quantile(1:101, c(1,3)/4, type=5)
-Peter
On 2010-05-13 8:55, David Winsemius wrote:
On May 13, 2010, at 10:25 AM, Robert Baer wrote:
Hi Peter,
You're absolutely correct! The description for 'range' in 'boxplot'
help file is a little bit confusing by using the words interquartile
range. I think it should be changed to the length of the box to be
exact and consistent with those in the help file for boxplot.stats.
The issue is probably that there are multiple ways (9 to be exact) of
defining quantiles in R. See 'type= ' arguement for ?quantile. The
quantile function uses type=7 by default which matches the quantile
definition used by S-Plus(?), but differs from that used by SPSS.
Doesn't fivenum essentially use the equivalent of a different type=
arguement (maybe 2 or 5) in constructing the hinges?
It seems perfectly reasonable to talk about 'length of box' (or 'box
height' depending how you display the boxplot), but aren't the hinges
simply Q1 and Q3 defined by one of the possible quartile definitions
(as Peter points out the one used by fivenum)? The box height does not
necesarily match the distance produced by IQR() which also seems to
use the equivalent of quantile(..., type=7), but it is still an IQR,
is it not?
Quantiles apparantly can be defined in more than one acceptable way
(sort of like dealing with ties in rank statistics). The OP seemed to
want an exact explanation of the wiskers, and I think Peter has
pointed us at the definition of quartiles used by fivenum, as opposed
to the default used with quantile(..., type=7).
Yes, and experimentation leads me to the conclusion that the only
possible candidate for matching up the results of fivenum[c(2,4] with
quantile(y, c(1,3)/4, type=i) is for type=5. I'm not able to prove that
to myself from mathematical arguments. since I do not quite understand
the formalism in the quantile page. If the match is not exact, this
would be a tenth definition of IQR.
set.seed(123)
y - rexp(300, .02)
fivenum(y)
[1] 0.2183685 15.8740466 42.1147820 74.0362517 360.5503788
for (i in 4:9) {print(quantile(y, c(1,3)/4, type=i) ) }
25% 75%
15.82506 73.93080
25% 75%
15.87405 74.03625
25% 75%
15.84955 74.08898
25% 75%
15.89854 73.98352
25% 75%
15.86588 74.05383
25% 75%
15.86792 74.04943
--
Peter Ehlers
University of Calgary
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Whiskers on the default boxplot {graphics}
On May 13, 2010, at 12:18 PM, Robert Baer wrote:
And try this (which seems to leave us with type=2) and is listed in ?
quantile as Discontinuous sample quantile types 1, 2, and 3
quantile(1:101, c(1,3)/4, type=2)
25% 75%
26 76
I think Peter may be right,. If I do it with the rnorm function I
repeatedly get the same result for fivenum[2] and the type 2 first
quartile. I did not test those types because they were designed for
discrete values variables, but I suppose everything is really discrete
on computers, eh?
fivenum(x - rnorm(101) )
[1] -2.6224338 -0.9682586 -0.1897377 0.5999332 2.5409711
quantile(x, c(1,3)/4, type=2)
25%75%
-0.9682586 0.5999332
fivenum(x - rnorm(101) )
[1] -3.8251928 -0.6495966 0.1816233 0.7101774 2.3789054
quantile(x, c(1,3)/4, type=2)
25%75%
-0.6495966 0.7101774
--
David.
David,
try this:
fivenum(1:101)
quantile(1:101, c(1,3)/4, type=5)
-Peter
On 2010-05-13 8:55, David Winsemius wrote:
On May 13, 2010, at 10:25 AM, Robert Baer wrote:
Hi Peter,
You're absolutely correct! The description for 'range' in
'boxplot'
help file is a little bit confusing by using the words
interquartile
range. I think it should be changed to the length of the box
to be
exact and consistent with those in the help file for
boxplot.stats.
The issue is probably that there are multiple ways (9 to be
exact) of
defining quantiles in R. See 'type= ' arguement for ?quantile. The
quantile function uses type=7 by default which matches the quantile
definition used by S-Plus(?), but differs from that used by SPSS.
Doesn't fivenum essentially use the equivalent of a different
type=
arguement (maybe 2 or 5) in constructing the hinges?
It seems perfectly reasonable to talk about 'length of box' (or
'box
height' depending how you display the boxplot), but aren't the
hinges
simply Q1 and Q3 defined by one of the possible quartile
definitions
(as Peter points out the one used by fivenum)? The box height
does not
necesarily match the distance produced by IQR() which also seems to
use the equivalent of quantile(..., type=7), but it is still an
IQR,
is it not?
Quantiles apparantly can be defined in more than one acceptable
way
(sort of like dealing with ties in rank statistics). The OP
seemed to
want an exact explanation of the wiskers, and I think Peter has
pointed us at the definition of quartiles used by fivenum, as
opposed
to the default used with quantile(..., type=7).
Yes, and experimentation leads me to the conclusion that the only
possible candidate for matching up the results of fivenum[c(2,4]
with
quantile(y, c(1,3)/4, type=i) is for type=5. I'm not able to prove
that
to myself from mathematical arguments. since I do not quite
understand
the formalism in the quantile page. If the match is not exact, this
would be a tenth definition of IQR.
set.seed(123)
y - rexp(300, .02)
fivenum(y)
[1] 0.2183685 15.8740466 42.1147820 74.0362517 360.5503788
for (i in 4:9) {print(quantile(y, c(1,3)/4, type=i) ) }
25% 75%
15.82506 73.93080
25% 75%
15.87405 74.03625
25% 75%
15.84955 74.08898
25% 75%
15.89854 73.98352
25% 75%
15.86588 74.05383
25% 75%
15.86792 74.04943
--
Peter Ehlers
University of Calgary
David Winsemius, MD
West Hartford, CT
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Re: [R] Whiskers on the default boxplot {graphics}
On Thu, May 13, 2010 at 7:55 AM, David Winsemius dwinsem...@comcast.net wrote:
Yes, and experimentation leads me to the conclusion that the only possible
candidate for matching up the results of fivenum[c(2,4] with quantile(y,
c(1,3)/4, type=i) is for type=5. I'm not able to prove that to myself from
mathematical arguments. since I do not quite understand the formalism in the
quantile page. If the match is not exact, this would be a tenth definition
of IQR.
David,
Here is some sample data, and the most parsimonious code I could come
up with for how quantile() computes the quartiles when using type=5.
The code for fivenum() seems simple enough, but I am not quite able to
make enough sense of the code for type=5 from quantile() to say
confidently why they are different.
I am open to the possibility that my attempts to extract relevant code
from quantile were flawed, but my tentative conclusion is that
quantile(x, type=5) != fivenum(x).
##
x - c(0.643796386452606, -0.605277531056206, -0.339239367816402,
1.12408365699422, 0.615753476531243, -1.10545696568758,
0.666533406841698, 1.42794492209271, 0.624752921945051,
2.02317205214712, -0.365586657432646, 0.821742701084307,
-0.874753498321076, -0.0298783402061118, 1.18037670706428,
-0.178274986836195, 0.308703365439049, 0.619700844646392,
0.54977981430092, -1.82161514610448, -1.28413556650749,
-0.0443852992196351, 0.704196760556652, -1.88596816676741,
-0.420811351737096)
oldx - x #this is just a backup because x will be transformed
##Start from quantile()
probs - c(0, 0.25, 0.5, 0.75, 1)
type - 5
n - length(x)
switch(type - 3, {
a - 0
b - 1
}, a - b - 0.5, a - b - 0, a - b - 1, a - b - 1/3, a - b - 3/8)
fuzz - 4 * .Machine$double.eps
nppm - a + probs * (n + 1 - a - b)
j - floor(nppm + fuzz)
h - nppm - j
h - ifelse(abs(h) fuzz, 0, h)
x - sort(x, partial = unique(c(1, j[j 0L j = n], (j + 1)[j 0L
j n], n)))
x - c(x[1L], x[1L], x, x[n], x[n])
qs - x[j + 2L]
qs[h == 1] - x[j + 3L][h == 1]
other - (h 0) (h 1)
if (any(other)) qs[other] - ((1 - h) * x[j + 2L] + h * x[j + 3L])[other]
##End from quantile
qs # from the calculations above
quantile(oldx, type=5) #this should match qs
fivenum(oldx) #the 25% does not match
everything else snipped
Josh
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Re: [R] Whiskers on the default boxplot {graphics}
I agree. I was convinced by Ehlers' example that type =2 was a better
match to fivenum's result
--
David..
On May 13, 2010, at 1:36 PM, Joshua Wiley wrote:
On Thu, May 13, 2010 at 7:55 AM, David Winsemius dwinsem...@comcast.net
wrote:
Yes, and experimentation leads me to the conclusion that the only
possible
candidate for matching up the results of fivenum[c(2,4] with
quantile(y,
c(1,3)/4, type=i) is for type=5. I'm not able to prove that to
myself from
mathematical arguments. since I do not quite understand the
formalism in the
quantile page. If the match is not exact, this would be a tenth
definition
of IQR.
David,
Here is some sample data, and the most parsimonious code I could come
up with for how quantile() computes the quartiles when using type=5.
The code for fivenum() seems simple enough, but I am not quite able to
make enough sense of the code for type=5 from quantile() to say
confidently why they are different.
I am open to the possibility that my attempts to extract relevant code
from quantile were flawed, but my tentative conclusion is that
quantile(x, type=5) != fivenum(x).
##
x - c(0.643796386452606, -0.605277531056206, -0.339239367816402,
1.12408365699422, 0.615753476531243, -1.10545696568758,
0.666533406841698, 1.42794492209271, 0.624752921945051,
2.02317205214712, -0.365586657432646, 0.821742701084307,
-0.874753498321076, -0.0298783402061118, 1.18037670706428,
-0.178274986836195, 0.308703365439049, 0.619700844646392,
0.54977981430092, -1.82161514610448, -1.28413556650749,
-0.0443852992196351, 0.704196760556652, -1.88596816676741,
-0.420811351737096)
oldx - x #this is just a backup because x will be transformed
##Start from quantile()
probs - c(0, 0.25, 0.5, 0.75, 1)
type - 5
n - length(x)
switch(type - 3, {
a - 0
b - 1
}, a - b - 0.5, a - b - 0, a - b - 1, a - b - 1/3, a - b -
3/8)
fuzz - 4 * .Machine$double.eps
nppm - a + probs * (n + 1 - a - b)
j - floor(nppm + fuzz)
h - nppm - j
h - ifelse(abs(h) fuzz, 0, h)
x - sort(x, partial = unique(c(1, j[j 0L j = n], (j + 1)[j 0L
j n], n)))
x - c(x[1L], x[1L], x, x[n], x[n])
qs - x[j + 2L]
qs[h == 1] - x[j + 3L][h == 1]
other - (h 0) (h 1)
if (any(other)) qs[other] - ((1 - h) * x[j + 2L] + h * x[j + 3L])
[other]
##End from quantile
qs # from the calculations above
quantile(oldx, type=5) #this should match qs
fivenum(oldx) #the 25% does not match
everything else snipped
Josh
David Winsemius, MD
West Hartford, CT
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Re: [R] Whiskers on the default boxplot {graphics}
Hi Robert,
Your points are well taken. However, I reserve mine, b/c I think without this
detailed discussion, an average R user would simply confused the interquartile
range said in boxplot help file with the results of IQR. Changing it to
length of box makes it more exact and consistent, as I stated earlier. With
all these being said, this is up to the R core team to decide.
...Tao
- Original Message
From: Robert Baer rb...@atsu.edu
To: Shi, Tao shida...@yahoo.com; Peter Ehlers ehl...@ucalgary.ca
Cc: R Project Help R-help@r-project.org
Sent: Thu, May 13, 2010 7:25:09 AM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
Hi Peter,
You're absolutely correct! The description
for 'range' in 'boxplot' help file is a little bit confusing by using the
words
interquartile range. I think it should be changed to the length of the
box
to be exact and consistent with those in the help file for
boxplot.stats.
The issue is probably that there are multiple ways (9 to
be exact) of defining quantiles in R. See 'type= ' arguement for
?quantile. The quantile function uses type=7 by default which matches the
quantile definition used by S-Plus(?), but differs from that used by SPSS.
Doesn't fivenum essentially use the equivalent of a different type=
arguement
(maybe 2 or 5) in constructing the hinges?
It seems perfectly reasonable
to talk about 'length of box' (or 'box height' depending how you display the
boxplot), but aren't the hinges simply Q1 and Q3 defined by one of the
possible
quartile definitions (as Peter points out the one used by fivenum)? The
box height does not necesarily match the distance produced by IQR() which
also
seems to use the equivalent of quantile(..., type=7), but it is still an IQR,
is
it not?
Quantiles apparantly can be defined in more than one acceptable
way (sort of like dealing with ties in rank statistics). The OP seemed to
want an exact explanation of the wiskers, and I think Peter has pointed us
at
the definition of quartiles used by fivenum, as opposed to the default
used with quantile(..., type=7).
All that said, I'm not convinced that
it is wrong to speak of interquartile range in 'boxplot'
help.
Rob
__
R-help@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.
Re: [R] Whiskers on the default boxplot {graphics}
Hi:
Let's do some math :)
On Tue, May 11, 2010 at 8:55 PM, Jason Rupert jasonkrup...@yahoo.comwrote:
Okay...Let me see if I've got it...
I'm just trying to use the default boxplot {graphics} capability in R...
So I call something like the following:
boxplot(mpg~cyl,data=mtcars, main=Car Milage Data, xlab=Number of
Cylinders, ylab=Miles Per Gallon) \
That produces something as shown in the following:
http://www.statmethods.net/graphs/images/boxplot1.jpg
When that default boxplot is called, i.e. boxplot {graphics}, as shown in
the line of code above, it is actually calling into boxplot.stats
{grDevices}. When boxplot.stats {grDevices} is called it has a default
value for coef of 1.5, i.e. coef = 1.5.
If I understand the purpose of coef correctly, it means that the
whiskers should extend out 1.5 times the length of the box away from the
box. Is that correct?
If by 'length of the box' you mean the interquartile range (IQR = Q_3 - Q_1
where Q refers to quartile), then assuming that
x is the numeric vector of interest for a boxplot,
upper whisker = min(max(x), Q_3 + 1.5 * IQR)
lower whisker = max(min(x), Q_1 - 1.5 * IQR)
So the upper whisker is located at the *smaller* of the maximum x value and
Q_3 + 1.5 IQR,
whereas the lower whisker is located at the *larger* of the smallest x value
and Q_1 - 1.5 IQR.
In your terms, the whiskers should extend out a *maximum* of 1.5 times the
length of the box
away from the box.
Visually, this means that individual points more extreme in value than Q3 +
1.5 IQR are plotted
separately at the high end, and those below Q1 - 1.5 IQR are plotted
separately on the low
end. Depending on the source, the separately plotted points are called
'outside values'. On
the other hand, if the maximum or minimum values of x are closer than 1.5
IQR in distance from
its nearest quartile, then that is where the whisker is positioned.
Does that make sense?
HTH,
Dennis
Now I look back at the plot, and I'm not sure how 1.5 times the length of
the box corresponds with the whisker lengths shown in the image:
http://www.statmethods.net/graphs/images/boxplot1.jpg
Is it that the whisker length is a total of 1.5 the length of the box and
centered about the median (2nd Quartile)?
Just trying to get a handle on this, so thanks again for all the help in
deciphering this.
From: RJ Cunningham ro...@iinet.net.au
ast.net
Cc: R Project Help R-help@r-project.org
Sent: Tue, May 11, 2010 9:57:48 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
I think not. Isn't the secret here?
Arguments:
x: a numeric vector for which the boxplot will be constructed
('NA's and 'NaN's are allowed and omitted).
coef: this determines how far the plot 'whiskers' extend out
from the box. If 'coef' is positive, the whiskers extend
to the most extreme data point which is no more than
'coef' times the length of the box away from the box. A
value of zero causes the whiskers to extend to the data
extremes (and no outliers be returned).
do.conf,do.out: logicals; if 'FALSE', the 'conf' or 'out'
component respectively will be empty in the result.
Details:
The two 'hinges' are versions of the first and third quartile,...
On Wed May 12 10:35 , Jason Rupert sent:
HummMaybe I need to look some place else than boxplot.stats {grDevices}
for a definition of how the upper/lower whiskers are produced.
By any chance are they the lowest datum still within 1.5 IQR of the lower
quartile, and the highest datum still within 1.5 IQR of the upper quartile?
None of the links from boxplot.stats {grDevices} seemed to reveal the
secret definition of the R whiskers.
Thanks again.
- Original Message
To: David Winsemius dwinsem...@comcast.net
Cc: R Project Help R-help@r-project.org
Sent: Tue, May 11, 2010 9:26:25 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
Wowzers...
From ?boxplot.stats:
Details
The two hinges are versions of the first and third quartile, i.e., close
to quantile(x, c(1,3)/4). The hinges equal the quartiles for odd n (where n
- length(x)) and differ for even n. Whereas the quartiles only equal
observations for n %% 4 == 1 (n = 1 mod 4), the hinges do so additionally
for n %% 4 == 2 (n = 2 mod 4), and are in the middle of two observations
otherwise.
The notches (if requested) extend to +/-1.58 IQR/sqrt(n). This seems to be
based on the same calculations as the formula with 1.57 in Chambers et al.
(1983, p. 62), given in McGill et al. (1978, p. 16). They are based on
asymptotic normality of the median and roughly equal sample sizes for the
two medians being compared, and are said to be rather insensitive to the
underlying distributions of the samples. The idea appears to be to give
roughly a 95% confidence interval for the difference in two medians.
Is a notch equal to the upper/lower whisker
Re: [R] Whiskers on the default boxplot {graphics}
Fantastic!
It would be great if the description could be modified to include the
mysterious bit about the upper and lower bound whisker positions:
upper whisker = min(max(x), Q_3 + 1.5 * IQR)
lower whisker = max(min(x), Q_1 - 1.5 * IQR)
Maybe that is clearly written in the description of boxplot.stats {grDevices},
but evidently I missed it numerous times and also did not pick up on this
intent from the original description of boxplot {graphics}.
Your type of descriptive answer and helpfulness is much appreciated and one of
the reasons I continue to endorse the R tool over numerous others.
More like you and the tool may be headed for domination in the market.
Thanks again!
From: Dennis Murphy djmu...@gmail.com
Cc: R Project Help R-help@r-project.org
Sent: Wed, May 12, 2010 2:50:19 AM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
Hi:
Let's do some math :)
e:
Okay...Let me see if I've got it...
I'm just trying to use the default boxplot {graphics} capability in R...
So I call something like the following:
boxplot(mpg~cyl,data=mtcars, main=Car Milage Data, xlab=Number of
Cylinders, ylab=Miles Per Gallon) \
That produces something as shown in the following:
http://www.statmethods.net/graphs/images/boxplot1.jpg
When that default boxplot is called, i.e. boxplot {graphics}, as shown in the
line of code above, it is actually calling into boxplot.stats {grDevices}.
When boxplot.stats {grDevices} is called it has a default value for coef of
1.5, i.e. coef = 1.5.
If I understand the purpose of coef correctly, it means that the
âwhiskersâ should extend out 1.5 times the length of the box away from
the box. Is that correct?
If by 'length of the box' you mean the interquartile range (IQR = Q_3 - Q_1
where Q refers to quartile), then assuming that
x is the numeric vector of interest for a boxplot,
upper whisker = min(max(x), Q_3 + 1.5 * IQR)
lower whisker = max(min(x), Q_1 - 1.5 * IQR)
So the upper whisker is located at the *smaller* of the maximum x value and Q_3
+ 1.5 IQR,
whereas the lower whisker is located at the *larger* of the smallest x value
and Q_1 - 1.5 IQR.
In your terms, the whiskers should extend out a *maximum* of 1.5 times the
length of the box
away from the box.
Visually, this means that individual points more extreme in value than Q3 + 1.5
IQR are plotted
separately at the high end, and those below Q1 - 1.5 IQR are plotted separately
on the low
end. Depending on the source, the separately plotted points are called 'outside
values'. On
the other hand, if the maximum or minimum values of x are closer than 1.5 IQR
in distance from
its nearest quartile, then that is where the whisker is positioned.
Does that make sense?
HTH,
Dennis
Now I look back at the plot, and I'm not sure how 1.5 times the length of the
box corresponds with the whisker lengths shown in the image:
http://www.statmethods.net/graphs/images/boxplot1.jpg
Is it that the whisker length is a total of 1.5 the length of the box and
centered about the median (2nd Quartile)?
Just trying to get a handle on this, so thanks again for all the help in
deciphering this.
From: RJ Cunningham ro...@iinet.net.au
ast.net
Cc: R Project Help R-help@r-project.org
Sent: Tue, May 11, 2010 9:57:48 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
I think not. Isn't the secret here?
Arguments:
x: a numeric vector for which the boxplot will be constructed
('NA's and 'NaN's are allowed and omitted).
coef: this determines how far the plot 'whiskers' extend out
from the box. If 'coef' is positive, the whiskers extend
to the most extreme data point which is no more than
'coef' times the length of the box away from the box. A
value of zero causes the whiskers to extend to the data
extremes (and no outliers be returned).
do.conf,do.out: logicals; if 'FALSE', the 'conf' or 'out'
component respectively will be empty in the result.
Details:
The two 'hinges' are versions of the first and third quartile,...
On Wed May 12 10:35 , Jason Rupert sent:
HummMaybe I need to look some place else than boxplot.stats {grDevices}
for a definition of how the upper/lower whiskers are produced.
By any chance are they the lowest datum still within 1.5 IQR of the lower
quartile, and the highest datum still within 1.5 IQR of the upper quartile?
None of the links from boxplot.stats {grDevices} seemed to reveal the secret
definition of the R whiskers.
Thanks again.
- Original Message
To: David Winsemius dwinsem...@comcast.net
Cc: R Project Help R-help@r-project.org
Sent: Tue, May 11, 2010 9:26:25 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
Wowzers...
From ?boxplot.stats:
Details
The two âhingesâ are versions of the first and third quartile, i.e.,
close to quantile(x, c(1,3)/4). The hinges equal the quartiles for odd n
(where n - length(x
Re: [R] Whiskers on the default boxplot {graphics}
- Original Message - Fantastic! It would be great if the description could be modified to include the mysterious bit about the upper and lower bound whisker positions: upper whisker = min(max(x), Q_3 + 1.5 * IQR) lower whisker = max(min(x), Q_1 - 1.5 * IQR) -- snip -- -- NOT quite! The boxplot.stats help reads under the coef argument: ... the whiskers extend to the most extreme data point which is no more than coef times the length of the box away from the box. If there are outliers, and the most extreme data point within 1.5 *IQR of Q1 or Q3 is less than 1.5 IQRs, and the wisker may end earlier than 1.5*IQR, but the data point at which it ends may NOT be max(x) or min(x). __ R-help@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.
Re: [R] Whiskers on the default boxplot {graphics}
Hi: Point well taken, Robert. This is a good example of the difference between how something is defined mathematically as opposed to how it is applied computationally. Thank you for the clarification. Regards, Dennis On Wed, May 12, 2010 at 9:51 AM, Robert Baer rb...@atsu.edu wrote: - Original Message - Fantastic! It would be great if the description could be modified to include the mysterious bit about the upper and lower bound whisker positions: upper whisker = min(max(x), Q_3 + 1.5 * IQR) lower whisker = max(min(x), Q_1 - 1.5 * IQR) -- snip -- -- NOT quite! The boxplot.stats help reads under the coef argument: ... the whiskers extend to the most extreme data point which is no more than coef times the length of the box away from the box. If there are outliers, and the most extreme data point within 1.5 *IQR of Q1 or Q3 is less than 1.5 IQRs, and the wisker may end earlier than 1.5*IQR, but the data point at which it ends may NOT be max(x) or min(x). [[alternative HTML version deleted]] __ R-help@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.
Re: [R] Whiskers on the default boxplot {graphics}
On 2010-05-12 10:51, Robert Baer wrote:
- Original Message - Fantastic!
It would be great if the description could be modified to include the
mysterious bit about the upper and lower bound whisker positions:
upper whisker = min(max(x), Q_3 + 1.5 * IQR)
lower whisker = max(min(x), Q_1 - 1.5 * IQR)
-- snip --
--
NOT quite!
The boxplot.stats help reads under the coef argument:
... the whiskers extend to the most extreme data point which is no more
than coef times the length of the box away from the box.
If there are outliers, and the most extreme data point within 1.5 *IQR
of Q1 or Q3 is less than 1.5 IQRs, and the wisker may end earlier than
1.5*IQR, but the data point at which it ends may NOT be max(x) or min(x).
But even this is not quite correct.
The help page (quoted above) is, as is so often the case,
quite precise: the *length of the box* is multiplied by 1.5,
not the *IQR*. The difference is probably insignificant in most
applications, but then this question was about the precise
definition of the whiskers.
The box length is defined by the hinges, for whose definition
it's probably easiest to look at the code in fivenum() which
is used by boxplot.stats(). (The relevant code consists of three
short lines.) For the calculation of the whisker extremes, one
can peruse the boxplot.stats() code, which also is quite brief.
Essentially, it determines which observations lie outside the
boundaries established by (lower hinge - 1.5 * boxlength) and
(upper hinge + 1.5 * boxlength) and then uses the range of
the remaining data values to determine the whisker extremes.
(I've assumed the default value of coef=1.5).
Here's an example:
set.seed(1)
y - rexp(30, .02)
y - sort(round(y))
fivenum(y)
#[1] 3 22 38 61 221
boxplot.stats(y)$stats
#[1] 3 22 38 61 118
# The hinges are 22, 61;
# The whisker extremes are 3, 118;
quantile(y, c(1,3)/4)
# 25% 75%
#23.25 60.50
# The hinges do not equal the quartiles.
# Upper cut-off ('fence'):
61 + 1.5 * (61 - 22)
#[1] 119.5
tail(y)
#[1] 70 94 118 145 198 221
# So 118 is the largest data value less than or equal to 119.5.
60.5 + 1.5 * IQR(y)
#[1] 116.375
# Using quartiles and the IQR would take the upper whisker to 94.
--
Peter Ehlers
__
R-help@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.
Re: [R] Whiskers on the default boxplot {graphics}
Jason,
All these are clearly defined in the help file for 'boxplot' under 'range'.
Don't understand how you missed that.
...Tao
- Original Message
From: Jason Rupert jasonkrup...@yahoo.com
To: Dennis Murphy djmu...@gmail.com
Cc: R Project Help R-help@r-project.org
Sent: Wed, May 12, 2010 3:40:12 AM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
Fantastic!
It would be great if the description could be modified to
include the mysterious bit about the upper and lower bound whisker
positions:
upper whisker = min(max(x), Q_3 + 1.5 * IQR)
lower whisker
= max(min(x), Q_1 - 1.5 * IQR)
Maybe that is clearly written in the
description of boxplot.stats {grDevices}, but evidently I missed it numerous
times and also did not pick up on this intent from the original description
of
boxplot {graphics}.
Your type of descriptive answer and
helpfulness is much appreciated and one of the reasons I continue to endorse
the
R tool over numerous others.
More like you and the tool may be
headed for domination in the market.
Thanks
again!
From:
Dennis Murphy
href=mailto:djmu...@gmail.com;djmu...@gmail.com
Cc: R Project
Help
href=mailto:R-help@r-project.org;R-help@r-project.org
Sent: Wed,
May 12, 2010 2:50:19 AM
Subject: Re: [R] Whiskers on the default boxplot
{graphics}
Hi:
Let's do some math
:)
e:
Okay...Let me see if I've got
it...
I'm just trying to use the default boxplot {graphics}
capability in R...
So I call something like the
following:
boxplot(mpg~cyl,data=mtcars, main=Car Milage Data,
xlab=Number of Cylinders, ylab=Miles Per Gallon) \
That
produces something as shown in the
following:
http://www.statmethods.net/graphs/images/boxplot1.jpg
When
that default boxplot is called, i.e. boxplot {graphics}, as shown in the line
of
code above, it is actually calling into boxplot.stats {grDevices}. When
boxplot.stats {grDevices} is called it has a default value for coef of 1.5,
i.e. coef = 1.5.
If I understand the purpose of coef
correctly, it means that the ‘whiskers’ should extend out 1.5 times the
length
of the box away from the box. Is that correct?
If by
'length of the box' you mean the interquartile range (IQR = Q_3 - Q_1 where Q
refers to quartile), then assuming that
x is the numeric vector of interest
for a boxplot,
upper whisker = min(max(x), Q_3 + 1.5 * IQR)
lower
whisker = max(min(x), Q_1 - 1.5 * IQR)
So the upper whisker is located at
the *smaller* of the maximum x value and Q_3 + 1.5 IQR,
whereas the lower
whisker is located at the *larger* of the smallest x value and Q_1 - 1.5
IQR.
In your terms, the whiskers should extend out a *maximum* of 1.5
times the length of the box
away from the box.
Visually, this means
that individual points more extreme in value than Q3 + 1.5 IQR are
plotted
separately at the high end, and those below Q1 - 1.5 IQR are plotted
separately on the low
end. Depending on the source, the separately plotted
points are called 'outside values'. On
the other hand, if the maximum or
minimum values of x are closer than 1.5 IQR in distance from
its nearest
quartile, then that is where the whisker is positioned.
Does that make
sense?
HTH,
Dennis
Now I look back at the plot, and
I'm not sure how 1.5 times the length of the box corresponds with the whisker
lengths shown in the image:
href=http://www.statmethods.net/graphs/images/boxplot1.jpg; target=_blank
http://www.statmethods.net/graphs/images/boxplot1.jpg
Is
it that the whisker length is a total of 1.5 the length of the box and
centered
about the median (2nd Quartile)?
Just trying to get a handle
on this, so thanks again for all the help in deciphering
this.
From:
RJ Cunningham
href=mailto:ro...@iinet.net.au;ro...@iinet.net.au
target=_blank href=http://ast.net;ast.net
Cc: R Project
Help
href=mailto:R-help@r-project.org;R-help@r-project.org
Sent:
Tue, May 11, 2010 9:57:48 PM
Subject: Re: [R] Whiskers on the
default boxplot {graphics}
I think not. Isn't the
secret here?
Arguments:
x: a
numeric vector for which the boxplot will be constructed
('NA's and
'NaN's are allowed and omitted).
coef: this determines how
far the plot 'whiskers' extend out
from the box. If 'coef' is
positive, the whiskers extend
to the most extreme data point which is
no more than
'coef' times the length of the box away from the box.
A
value of zero causes the whiskers to extend to the
data
extremes (and no outliers be
returned).
do.conf,do.out: logicals; if 'FALSE', the 'conf'
or 'out'
component respectively will be empty in the
result.
Details:
The two 'hinges' are
versions of the first and third quartile,...
On Wed
May 12 10:35 , Jason Rupert sent:
HummMaybe
I need to look some place else than boxplot.stats {grDevices} for a
definition
of how
Re: [R] Whiskers on the default boxplot {graphics}
On 2010-05-12 13:27, Shi, Tao wrote: Jason, All these are clearly defined in the help file for 'boxplot' under 'range'. Don't understand how you missed that. ...Tao You've made me re-read the help page for boxplot. I notice that there's a difference in the description of 'range' on that page and the description of the equivalent 'coef' on the help page for boxplot.stats. boxplot.stats has it right. This should be made consistent. [previous posts snipped] -- Peter Ehlers University of Calgary __ R-help@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.
Re: [R] Whiskers on the default boxplot {graphics}
Hi Peter,
You're absolutely correct! The description for 'range' in 'boxplot' help file
is a little bit confusing by using the words interquartile range. I think it
should be changed to the length of the box to be exact and consistent with
those in the help file for boxplot.stats.
...Tao
- Original Message
From: Peter Ehlers ehl...@ucalgary.ca
To: Shi, Tao shida...@yahoo.com
Cc: Jason Rupert jasonkrup...@yahoo.com; Dennis Murphy djmu...@gmail.com;
R Project Help R-help@r-project.org; murdoch.dun...@gmail.com
Sent: Wed, May 12, 2010 2:11:24 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
On 2010-05-12 13:27, Shi, Tao wrote:
Jason,
All these
are clearly defined in the help file for 'boxplot' under 'range'. Don't
understand how you missed that.
...Tao
You've
made me re-read the help page for boxplot. I notice that
there's a difference
in the description of 'range' on that page
and the description of the
equivalent 'coef' on the help page
for boxplot.stats. boxplot.stats has it
right.
This should be made consistent.
[previous posts
snipped]
--
Peter Ehlers
University of Calgary
__
R-help@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.
[R] Whiskers on the default boxplot {graphics}
How are the lower/upper whiskers defined in the default version of boxplot
{graphics}?
I tried help(boxplot) and searching www.rseek.org, but I was unable to
determine an absolute answer.
I checked out the definition of boxplot according to Wikipedia
(http://en.wikipedia.org/wiki/Box_plot), but it also had several approaches
listed for how the whiskers could be determined, so I'm just curious how the
default
boxplot {graphics} does it.
Thanks for any feedback and insights.
__
R-help@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.
Re: [R] Whiskers on the default boxplot {graphics}
On May 11, 2010, at 9:45 PM, Jason Rupert wrote:
How are the lower/upper whiskers defined in the default version of
boxplot {graphics}?
I tried help(boxplot) and searching www.rseek.org, but I was unable
to determine an absolute answer.
You need to follow the links from the help pages and tin this case it
appears that you did not follow the one to
?boxplot.stats
I checked out the definition of boxplot according to Wikipedia (http://en.wikipedia.org/wiki/Box_plot
), but it also had several approaches
listed for how the whiskers could be determined, so I'm just curious
how the default
boxplot {graphics} does it.
Thanks for any feedback
Follow links with the R help system.
and insights.
David Winsemius, MD
West Hartford, CT
__
R-help@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.
Re: [R] Whiskers on the default boxplot {graphics}
Wowzers...
From ?boxplot.stats:
Details
The two ‘hinges’ are versions of the first and third quartile, i.e., close to
quantile(x, c(1,3)/4). The hinges equal the quartiles for odd n (where n -
length(x)) and differ for even n. Whereas the quartiles only equal observations
for n %% 4 == 1 (n = 1 mod 4), the hinges do so additionally for n %% 4 == 2 (n
= 2 mod 4), and are in the middle of two observations otherwise.
The notches (if requested) extend to +/-1.58 IQR/sqrt(n). This seems to be
based on the same calculations as the formula with 1.57 in Chambers et al.
(1983, p. 62), given in McGill et al. (1978, p. 16). They are based on
asymptotic normality of the median and roughly equal sample sizes for the two
medians being compared, and are said to be rather insensitive to the underlying
distributions of the samples. The idea appears to be to give roughly a 95%
confidence interval for the difference in two medians.
Is a notch equal to the upper/lower whisker? Is this just a difference of
terminology or something?
Thanks again for all the insights.
- Original Message
From: David Winsemius dwinsem...@comcast.net
To: Jason Rupert jasonkrup...@yahoo.com
Cc: R Project Help R-help@r-project.org
Sent: Tue, May 11, 2010 9:00:15 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
On May 11, 2010, at 9:45 PM, Jason Rupert wrote:
How are the lower/upper whiskers defined in the default version of boxplot
{graphics}?
I tried help(boxplot) and searching www.rseek.org, but I was unable to
determine an absolute answer.
You need to follow the links from the help pages and tin this case it appears
that you did not follow the one to
?boxplot.stats
I checked out the definition of boxplot according to Wikipedia
(http://en.wikipedia.org/wiki/Box_plot), but it also had several approaches
listed for how the whiskers could be determined, so I'm just curious how the
default
boxplot {graphics} does it.
Thanks for any feedback
Follow links with the R help system.
and insights.
David Winsemius, MD
West Hartford, CT
__
R-help@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.
Re: [R] Whiskers on the default boxplot {graphics}
HummMaybe I need to look some place else than boxplot.stats {grDevices} for
a definition of how the upper/lower whiskers are produced.
By any chance are they the lowest datum still within 1.5 IQR of the lower
quartile, and the highest datum still within 1.5 IQR of the upper quartile?
None of the links from boxplot.stats {grDevices} seemed to reveal the secret
definition of the R whiskers.
Thanks again.
- Original Message
From: Jason Rupert jasonkrup...@yahoo.com
To: David Winsemius dwinsem...@comcast.net
Cc: R Project Help R-help@r-project.org
Sent: Tue, May 11, 2010 9:26:25 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
Wowzers...
From ?boxplot.stats:
Details
The two ‘hinges’ are versions of the first and third quartile, i.e., close to
quantile(x, c(1,3)/4). The hinges equal the quartiles for odd n (where n -
length(x)) and differ for even n. Whereas the quartiles only equal observations
for n %% 4 == 1 (n = 1 mod 4), the hinges do so additionally for n %% 4 == 2 (n
= 2 mod 4), and are in the middle of two observations otherwise.
The notches (if requested) extend to +/-1.58 IQR/sqrt(n). This seems to be
based on the same calculations as the formula with 1.57 in Chambers et al.
(1983, p. 62), given in McGill et al. (1978, p. 16). They are based on
asymptotic normality of the median and roughly equal sample sizes for the two
medians being compared, and are said to be rather insensitive to the underlying
distributions of the samples. The idea appears to be to give roughly a 95%
confidence interval for the difference in two medians.
Is a notch equal to the upper/lower whisker? Is this just a difference of
terminology or something?
Thanks again for all the insights.
- Original Message
From: David Winsemius dwinsem...@comcast.net
To: Jason Rupert jasonkrup...@yahoo.com
Cc: R Project Help R-help@r-project.org
Sent: Tue, May 11, 2010 9:00:15 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
On May 11, 2010, at 9:45 PM, Jason Rupert wrote:
How are the lower/upper whiskers defined in the default version of boxplot
{graphics}?
I tried help(boxplot) and searching www.rseek.org, but I was unable to
determine an absolute answer.
You need to follow the links from the help pages and tin this case it appears
that you did not follow the one to
?boxplot.stats
I checked out the definition of boxplot according to Wikipedia
(http://en.wikipedia.org/wiki/Box_plot), but it also had several approaches
listed for how the whiskers could be determined, so I'm just curious how the
default
boxplot {graphics} does it.
Thanks for any feedback
Follow links with the R help system.
and insights.
David Winsemius, MD
West Hartford, CT
__
R-help@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.
__
R-help@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.
Re: [R] Whiskers on the default boxplot {graphics}
I think not. Isn't the secret here?
Arguments:
x: a numeric vector for which the boxplot will be constructed
('NA's and 'NaN's are allowed and omitted).
coef: this determines how far the plot 'whiskers' extend out
from the box. If 'coef' is positive, the whiskers extend
to the most extreme data point which is no more than
'coef' times the length of the box away from the box. A
value of zero causes the whiskers to extend to the data
extremes (and no outliers be returned).
do.conf,do.out: logicals; if 'FALSE', the 'conf' or 'out'
component respectively will be empty in the result.
Details:
The two 'hinges' are versions of the first and third quartile,...
On Wed May 12 10:35 , Jason Rupert sent:
HummMaybe I need to look some place else than boxplot.stats
{grDevices} for a definition of how the upper/lower whiskers are produced.
By any chance are they the lowest datum still within 1.5 IQR of the lower
quartile, and the highest datum still within 1.5 IQR of the upper
quartile?
None of the links from boxplot.stats {grDevices} seemed to reveal the
secret definition of the R whiskers.
Thanks again.
- Original Message
From: Jason Rupert [1]jasonkrup...@yahoo.com
To: David Winsemius [2]dwinsem...@comcast.net
Cc: R Project Help [3]r-h...@r-project.org
Sent: Tue, May 11, 2010 9:26:25 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
Wowzers...
From ?boxplot.stats:
Details
The two âhingesâ are versions of the first and third quartile, i.e., close
to quantile(x, c(1,3)/4). The hinges equal the quartiles for odd n (where
n - length(x)) and differ for even n. Whereas the quartiles only equal
observations for n %% 4 == 1 (n = 1 mod 4), the hinges do so additionally
for n %% 4 == 2 (n = 2 mod 4), and are in the middle of two observations
otherwise.
The notches (if requested) extend to +/-1.58 IQR/sqrt(n). This seems to be
based on the same calculations as the formula with 1.57 in Chambers et al.
(1983, p. 62), given in McGill et al. (1978, p. 16). They are based on
asymptotic normality of the median and roughly equal sample sizes for the
two medians being compared, and are said to be rather insensitive to the
underlying distributions of the samples. The idea appears to be to give
roughly a 95% confidence interval for the difference in two medians.
Is a notch equal to the upper/lower whisker? Is this just a difference of
terminology or something?
Thanks again for all the insights.
- Original Message
From: David Winsemius [4]dwinsem...@comcast.net
To: Jason Rupert [5]jasonkrup...@yahoo.com
Cc: R Project Help [6]r-h...@r-project.org
Sent: Tue, May 11, 2010 9:00:15 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
On May 11, 2010, at 9:45 PM, Jason Rupert wrote:
How are the lower/upper whiskers defined in the default version of
boxplot {graphics}?
I tried help(boxplot) and searching [7]www.rseek.org, but I was unable
to determine an absolute answer.
You need to follow the links from the help pages and tin this case it
appears that you did not follow the one to
?boxplot.stats
I checked out the definition of boxplot according to Wikipedia
([8]http://en.wikipedia.org/wiki/Box_plot\), but it also had several
approaches
listed for how the whiskers could be determined, so I'm just curious how
the default
boxplot {graphics} does it.
Thanks for any feedback
Follow links with the R help system.
and insights.
David Winsemius, MD
West Hartford, CT
__
[9]r-h...@r-project.org mailing list
[10]https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
[11]http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
[12]r-h...@r-project.org mailing list
[13]https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
[14]http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
References
1.
javascript:top.opencompose%28%27jasonkrup...@yahoo.com%27,%27%27,%27%27,%27%27%29
2.
javascript:top.opencompose%28%27dwinsem...@comcast.net%27,%27%27,%27%27,%27%27%29
3.
javascript:top.opencompose%28%27r-h...@r-project.org%27,%27%27,%27%27,%27%27%29
4.
javascript:top.opencompose%28%27dwinsem...@comcast.net%27,%27%27,%27%27,%27%27%29
5.
javascript:top.opencompose%28%27jasonkrup...@yahoo.com%27,%27%27,%27%27,%27%27%29
6.
javascript:top.opencompose%28%27r-h...@r-project.org%27,%27%27,%27%27,%27%27%29
7. file://localhost/tmp/parse.pl
Re: [R] Whiskers on the default boxplot {graphics}
Okay...Let me see if I've got it...
I'm just trying to use the default boxplot {graphics} capability in R...
So I call something like the following:
boxplot(mpg~cyl,data=mtcars, main=Car Milage Data, xlab=Number of
Cylinders, ylab=Miles Per Gallon) \
That produces something as shown in the following:
http://www.statmethods.net/graphs/images/boxplot1.jpg
When that default boxplot is called, i.e. boxplot {graphics}, as shown in the
line of code above, it is actually calling into boxplot.stats {grDevices}.
When boxplot.stats {grDevices} is called it has a default value for coef of
1.5, i.e. coef = 1.5.
If I understand the purpose of coef correctly, it means that the
âwhiskersâ should extend out 1.5 times the length of the box away from the
box. Is that correct?
Now I look back at the plot, and I'm not sure how 1.5 times the length of the
box corresponds with the whisker lengths shown in the image:
http://www.statmethods.net/graphs/images/boxplot1.jpg
Is it that the whisker length is a total of 1.5 the length of the box and
centered about the median (2nd Quartile)?
Just trying to get a handle on this, so thanks again for all the help in
deciphering this.
From: RJ Cunningham ro...@iinet.net.au
ast.net
Cc: R Project Help R-help@r-project.org
Sent: Tue, May 11, 2010 9:57:48 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
I think not. Isn't the secret here?
Arguments:
x: a numeric vector for which the boxplot will be constructed
('NA's and 'NaN's are allowed and omitted).
coef: this determines how far the plot 'whiskers' extend out
from the box. If 'coef' is positive, the whiskers extend
to the most extreme data point which is no more than
'coef' times the length of the box away from the box. A
value of zero causes the whiskers to extend to the data
extremes (and no outliers be returned).
do.conf,do.out: logicals; if 'FALSE', the 'conf' or 'out'
component respectively will be empty in the result.
Details:
The two 'hinges' are versions of the first and third quartile,...
On Wed May 12 10:35 , Jason Rupert sent:
HummMaybe I need to look some place else than boxplot.stats {grDevices} for
a definition of how the upper/lower whiskers are produced.
By any chance are they the lowest datum still within 1.5 IQR of the lower
quartile, and the highest datum still within 1.5 IQR of the upper quartile?
None of the links from boxplot.stats {grDevices} seemed to reveal the secret
definition of the R whiskers.
Thanks again.
- Original Message
To: David Winsemius dwinsem...@comcast.net
Cc: R Project Help R-help@r-project.org
Sent: Tue, May 11, 2010 9:26:25 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
Wowzers...
From ?boxplot.stats:
Details
The two âhingesâ are versions of the first and third quartile, i.e., close
to quantile(x, c(1,3)/4). The hinges equal the quartiles for odd n (where n -
length(x)) and differ for even n. Whereas the quartiles only equal
observations for n %% 4 == 1 (n = 1 mod 4), the hinges do so additionally for
n %% 4 == 2 (n = 2 mod 4), and are in the middle of two observations otherwise.
The notches (if requested) extend to +/-1.58 IQR/sqrt(n). This seems to be
based on the same calculations as the formula with 1.57 in Chambers et al.
(1983, p. 62), given in McGill et al. (1978, p. 16). They are based on
asymptotic normality of the median and roughly equal sample sizes for the two
medians being compared, and are said to be rather insensitive to the
underlying distributions of the samples. The idea appears to be to give
roughly a 95% confidence interval for the difference in two medians.
Is a notch equal to the upper/lower whisker? Is this just a difference of
terminology or something?
Thanks again for all the insights.
- Original Message
From: David Winsemius dwinsem...@comcast.net
Cc: R Project Help R-help@r-project.org
Sent: Tue, May 11, 2010 9:00:15 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
On May 11, 2010, at 9:45 PM, Jason Rupert wrote:
How are the lower/upper whiskers defined in the default version of boxplot
{graphics}?
I tried help(boxplot) and searching www.rseek.org, but I was unable to
determine an absolute answer.
You need to follow the links from the help pages and tin this case it appears
that you did not follow the one to
?boxplot.stats
I checked out the definition of boxplot according to Wikipedia
(http://en.wikipedia.org/wiki/Box_plot\), but it also had several approaches
listed for how the whiskers could be determined, so I'm just curious how the
default
boxplot {graphics} does it.
Thanks for any feedback
Follow links with the R help system.
and insights.
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch
Re: [R] Whiskers on the default boxplot {graphics}
On May 11, 2010, at 10:35 PM, Jason Rupert wrote:
HummMaybe I need to look some place else than boxplot.stats
{grDevices} for a definition of how the upper/lower whiskers are
produced.
By any chance are they the lowest datum still within 1.5 IQR of the
lower quartile, and the highest datum still within 1.5 IQR of the
upper quartile?
None of the links from boxplot.stats {grDevices} seemed to reveal
the secret definition of the R whiskers.
You didn't need to go to any other pages. You just needed to read
boxplot.stats ... apparently more than once.
--
David.
Thanks again.
- Original Message
From: Jason Rupert jasonkrup...@yahoo.com
To: David Winsemius dwinsem...@comcast.net
Cc: R Project Help R-help@r-project.org
Sent: Tue, May 11, 2010 9:26:25 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
Wowzers...
From ?boxplot.stats:
Details
The two ‘hinges’ are versions of the first and third quartile, i.e.,
close to quantile(x, c(1,3)/4). The hinges equal the quartiles for
odd n (where n - length(x)) and differ for even n. Whereas the
quartiles only equal observations for n %% 4 == 1 (n = 1 mod 4), the
hinges do so additionally for n %% 4 == 2 (n = 2 mod 4), and are in
the middle of two observations otherwise.
The notches (if requested) extend to +/-1.58 IQR/sqrt(n). This seems
to be based on the same calculations as the formula with 1.57 in
Chambers et al. (1983, p. 62), given in McGill et al. (1978, p. 16).
They are based on asymptotic normality of the median and roughly
equal sample sizes for the two medians being compared, and are said
to be rather insensitive to the underlying distributions of the
samples. The idea appears to be to give roughly a 95% confidence
interval for the difference in two medians.
Is a notch equal to the upper/lower whisker? Is this just a
difference of terminology or something?
Thanks again for all the insights.
- Original Message
From: David Winsemius dwinsem...@comcast.net
To: Jason Rupert jasonkrup...@yahoo.com
Cc: R Project Help R-help@r-project.org
Sent: Tue, May 11, 2010 9:00:15 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
On May 11, 2010, at 9:45 PM, Jason Rupert wrote:
How are the lower/upper whiskers defined in the default version of
boxplot {graphics}?
I tried help(boxplot) and searching www.rseek.org, but I was unable
to determine an absolute answer.
You need to follow the links from the help pages and tin this case
it appears that you did not follow the one to
?boxplot.stats
I checked out the definition of boxplot according to Wikipedia (http://en.wikipedia.org/wiki/Box_plot
), but it also had several approaches
listed for how the whiskers could be determined, so I'm just
curious how the default
boxplot {graphics} does it.
Thanks for any feedback
Follow links with the R help system.
and insights.
David Winsemius, MD
West Hartford, CT
__
R-help@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.
David Winsemius, MD
West Hartford, CT
__
R-help@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.
Re: [R] Whiskers on the default boxplot {graphics}
On May 11, 2010, at 11:55 PM, Jason Rupert wrote:
Okay...Let me see if I've got it...
I'm just trying to use the default boxplot {graphics} capability in
R...
So I call something like the following:
boxplot(mpg~cyl,data=mtcars, main=Car Milage Data, xlab=Number
of Cylinders, ylab=Miles Per Gallon) \
That produces something as shown in the following:
http://www.statmethods.net/graphs/images/boxplot1.jpg
When that default boxplot is called, i.e. boxplot {graphics}, as
shown in the line of code above, it is actually calling into
boxplot.stats {grDevices}. When boxplot.stats {grDevices} is called
it has a default value for coef of 1.5, i.e. coef = 1.5.
If I understand the purpose of coef correctly, it means that the
‘whiskers’ should extend out 1.5 times the length of the box away
from the box. Is that correct?
No. Read it again.
--
David.
Now I look back at the plot, and I'm not sure how 1.5 times the
length of the box corresponds with the whisker lengths shown in the
image:
http://www.statmethods.net/graphs/images/boxplot1.jpg
Is it that the whisker length is a total of 1.5 the length of the
box and centered about the median (2nd Quartile)?
Just trying to get a handle on this, so thanks again for all the
help in deciphering this.
From: RJ Cunningham ro...@iinet.net.au
ast.net
Cc: R Project Help R-help@r-project.org
Sent: Tue, May 11, 2010 9:57:48 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
I think not. Isn't the secret here?
Arguments:
x: a numeric vector for which the boxplot will be constructed
('NA's and 'NaN's are allowed and omitted).
coef: this determines how far the plot 'whiskers' extend out
from the box. If 'coef' is positive, the whiskers extend
to the most extreme data point which is no more than
'coef' times the length of the box away from the box. A
value of zero causes the whiskers to extend to the data
extremes (and no outliers be returned).
do.conf,do.out: logicals; if 'FALSE', the 'conf' or 'out'
component respectively will be empty in the result.
Details:
The two 'hinges' are versions of the first and third quartile,...
On Wed May 12 10:35 , Jason Rupert sent:
HummMaybe I need to look some place else than boxplot.stats
{grDevices} for a definition of how the upper/lower whiskers are
produced.
By any chance are they the lowest datum still within 1.5 IQR of
the lower quartile, and the highest datum still within 1.5 IQR of
the upper quartile?
None of the links from boxplot.stats {grDevices} seemed to reveal
the secret definition of the R whiskers.
Thanks again.
- Original Message
To: David Winsemius dwinsem...@comcast.net
Cc: R Project Help R-help@r-project.org
Sent: Tue, May 11, 2010 9:26:25 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
Wowzers...
From ?boxplot.stats:
Details
The two ‘hinges’ are versions of the first and third quartile,
i.e., close to quantile(x, c(1,3)/4). The hinges equal the
quartiles for odd n (where n - length(x)) and differ for even n.
Whereas the quartiles only equal observations for n %% 4 == 1 (n =
1 mod 4), the hinges do so additionally for n %% 4 == 2 (n = 2 mod
4), and are in the middle of two observations otherwise.
The notches (if requested) extend to +/-1.58 IQR/sqrt(n). This
seems to be based on the same calculations as the formula with 1.57
in Chambers et al. (1983, p. 62), given in McGill et al. (1978, p.
16). They are based on asymptotic normality of the median and
roughly equal sample sizes for the two medians being compared, and
are said to be rather insensitive to the underlying distributions
of the samples. The idea appears to be to give roughly a 95%
confidence interval for the difference in two medians.
Is a notch equal to the upper/lower whisker? Is this just a
difference of terminology or something?
Thanks again for all the insights.
- Original Message
From: David Winsemius dwinsem...@comcast.net
Cc: R Project Help R-help@r-project.org
Sent: Tue, May 11, 2010 9:00:15 PM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
On May 11, 2010, at 9:45 PM, Jason Rupert wrote:
How are the lower/upper whiskers defined in the default version of
boxplot {graphics}?
I tried help(boxplot) and searching www.rseek.org, but I was
unable to determine an absolute answer.
You need to follow the links from the help pages and tin this case
it appears that you did not follow the one to
?boxplot.stats
I checked out the definition of boxplot according to Wikipedia (http://en.wikipedia.org/wiki/Box_plot
\), but it also had several approaches
listed for how the whiskers could be determined, so I'm just
curious how the default
boxplot {graphics} does it.
Thanks for any feedback
Follow links with the R help system.
and insights
