Re: [R] Need help putting histograms on the diagonal of a splom plot
On 8/30/07, Marc Paterno [EMAIL PROTECTED] wrote:
Hello,
I am in need of help in putting histograms on the diagonal of a plot
produced with splom().
The plot matrix I am trying to produce is to have standard scatterplots
in the upper-left triangle, contour plots in the lower-right triangle,
and histograms on the diagonal. I have a function that does the first
two, but the histograms on the diagonal has been beyond my ability.
Here is my function:
require(lattice)
require(MASS)
my.plot = function(data)
{
splom( ~data
, lower.panel=function(x,y, ...)
{
xy=kde2d(x,y)
xy.tr=con2tr(xy)
panel.contourplot( xy.tr$x
, xy.tr$y
, xy.tr$z
, subscripts=seq(nrow(xy.tr))
, contour=TRUE
, region=TRUE
, labels = FALSE
, col.regions = terrain.colors
)
}
, upper.panel=function(x,y, ...)
{
panel.grid(-1,-1)
panel.xyplot(x,y, cex=0.5)
}
#, diag.panel=function(x, ...)
# {
#panel.histogram(x, ...)
# }
)
}
It can be called, for example, with:
my.plot(subset(iris, select = Sepal.Length:Petal.Width))
(the subset is necessary to get rid of a variable that is a factor; my
function can not deal with factors).
I have commented out my best guess at the code needed to produce the
histograms along the diagonal, which fails.
Well, basically the y-axis range of the diagonal panels are not right.
What you want is simpler if you are happy with a density estimate:
my.plot = function(data)
{
splom( ~data
#, lower.panel=...
#, upper.panel=...
, diag.panel = function(x, ...)
{
yrng - current.panel.limits()$ylim
d - density(x)
d$y - with(d, yrng[1] + 0.95 * diff(yrng) * y / max(y) )
panel.lines(d)
})
}
my.plot(iris[1:4])
For a histogram, things are a bit more complicated, but still easy enough:
my.plot = function(data)
{
splom( ~data
#, lower.panel=...
#, upper.panel=...
, diag.panel = function(x, ...)
{
yrng - current.panel.limits()$ylim
d - density(x)
d$y - with(d, yrng[1] + 0.95 * diff(yrng) * y / max(y) )
panel.lines(d)
})
}
-Deepayan
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Need help putting histograms on the diagonal of a splom plot
Hello,
I am in need of help in putting histograms on the diagonal of a plot
produced with splom().
The plot matrix I am trying to produce is to have standard scatterplots
in the upper-left triangle, contour plots in the lower-right triangle,
and histograms on the diagonal. I have a function that does the first
two, but the histograms on the diagonal has been beyond my ability.
Here is my function:
require(lattice)
require(MASS)
my.plot = function(data)
{
splom( ~data
, lower.panel=function(x,y, ...)
{
xy=kde2d(x,y)
xy.tr=con2tr(xy)
panel.contourplot( xy.tr$x
, xy.tr$y
, xy.tr$z
, subscripts=seq(nrow(xy.tr))
, contour=TRUE
, region=TRUE
, labels = FALSE
, col.regions = terrain.colors
)
}
, upper.panel=function(x,y, ...)
{
panel.grid(-1,-1)
panel.xyplot(x,y, cex=0.5)
}
#, diag.panel=function(x, ...)
# {
#panel.histogram(x, ...)
# }
)
}
It can be called, for example, with:
my.plot(subset(iris, select = Sepal.Length:Petal.Width))
(the subset is necessary to get rid of a variable that is a factor; my
function can not deal with factors).
I have commented out my best guess at the code needed to produce the
histograms along the diagonal, which fails.
Any guidance would be greatly appreciated.
best regards,
Marc
__
R-help@stat.math.ethz.ch 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] need help with pdf-plot
Thank you both! The hint with the pty=s was very useful. I did not know it before. Ciao, Antje Ivar Herfindal schrieb: Dear Antje I cannot see that you have got any replies yet, so I will make and attempt. However, I am sure other have more formally correct solutions. When you call the pdf(), you can set paper=a4 (or a4r for landscape). However, the width and the height of your plot should then not exceed the size of the paper (which is approximately 8.27*11.69 inches for a4). Try (I have only tested on windows XP, R 2.5.0): pdf(test1.pdf, width=10, heigh=5, paper=a4r) par(mfrow=c(1,3), pty=s) #pty=s gives square plotting regions plot(rnorm(100)) plot(rnorm(100)) plot(rnorm(100)) dev.off() Hope this helps Ivar Antje skrev: I still have this problem. Does anybody know any solution? Antje Antje schrieb: Hello, I'm trying to plot a set of barplots like a matrix (2 rows, 10 columns fromreduced_mat) to a pdf. It works with the following parameters: pdf(test.pdf,width=ncol(reduced_mat)*2, height=nrow(reduced_mat)*2, pointsize = 12) par(mfcol = c(nrow(reduced_mat),ncol(reduced_mat)), oma = c(0,0,0,0), lwd=48/96, cex.axis = 0.5, las = 2, cex.main = 1.0) The I get a long narrow page format with the quadratic barplots. But I would like to have a A4 format in the end and the plots not filling the whole page (they should stay somehow quadratic and not be stretched...). What shall I look for to achieve this? Antje __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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@stat.math.ethz.ch 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] need help to manipulate function and time interval
Hi,
data are extracted from MS Access with the format: (%d/%m%Y %H%M%S); ex:
16/09/2006 03:38:37
I still have error messneger
Thank you for your help.
Lassana KOITA
Chargé d'Etudes de Sécurité Aéroportuaire et d'Analyse Statistique /
Project Engineer Airport Safety Studies Statistical analysis
Service Technique de l'Aviation Civile (STAC) / Civil Aviation Technical
Department
Direction Générale de l'Aviation Civile (DGAC) / French Civil Aviation
Headquarters
Tel: 01 49 56 80 60
Fax: 01 49 56 82 14
E-mail: [EMAIL PROTECTED]
http://www.stac.aviation-civile.gouv.fr/
Uwe Ligges [EMAIL PROTECTED]
12/08/2007 15:24
A
Matthew Walker [EMAIL PROTECTED]
cc
Henrique Dallazuanna [EMAIL PROTECTED], r-help@stat.math.ethz.ch, KOITA
Lassana - STAC/ACE [EMAIL PROTECTED]
Objet
Re: [R] need help to manipulate function and time interval
Matthew Walker wrote:
Uwe Ligges wrote:
Henrique Dallazuanna wrote:
Hi,
Try whit:
if(time[j] = 18:00:00 23:59:59)
This code is obviously wrong and does not help for the next few lines
in the questioner's message, please do not post unsensible stuff.
Uwe Ligges
Actually, I would have said that was quite an interesting solution. If
the time is guaranteed to be in this 8 character format, then that
idea's quite easily implemented:
# Returns true if time is between 18:00:00 and 23:59:59
check_time - function(time_string) {
if (nchar(time_string)!=8) stop (Incorrect format)
time_string = 18:00:00 time_string = 23:59:59
}
check_time(19:59:00)
[1] TRUE
check_time(16:59:00)
[1] FALSE
check_time(18:00:00)
[1] TRUE
check_time(23:59:59)
[1] TRUE
check_time(24:00:00)
[1] FALSE
check_time(18:05)
Error in check_time(18:05) : Incorrect format
Perhaps there is an issue if the locale does not sort character-based
numbers in the same way as ASCII? But Otherwise, I can't see why this
solution wouldn't do the job.
A more robust solution solution would parse the strings (?strptime) and
then check their days/hours/mins/seconds (?DateTimeClasses). But
perhaps the above is sufficient?
Well, the interesting part of the original question that everynody seems
to omit now was the second part:
if (time[j] is between 22:00:00 and 05:59:59)
hence the answer is still not sufficient (even if the syntax error has
been corrected) - and hence I asked for the format the time is
originally in.
Uwe Ligges
Cheers,
Matthew
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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] need help to manipulate function and time interval
KOITA Lassana - STAC/ACE wrote:
Hi,
data are extracted from MS Access with the format: (%d/%m%Y %H%M%S); ex:
16/09/2006 03:38:37
1. the example you gave in your first message is still not reproducible,
you gave the following:
myfunc - function(mytab, Time, Level)
{
vect - rep(0, length(mytab))
for(i in 1:length(vect))
{
for(j in 1:length(Time))
if(time[j] is between 18:00:00 and 23:59:59)
L[i] - L[j]+5
vect[i] - 10^((L[i])/10
if (time[j] is between 22:00:00 and 05:59:59)
L[i] - L[j]+10
vect[i] - 10^((L[i])/10
else
L[i] = L[j]
vect[i] - 10^((L[i])/10
}
}
a) Please check the parentheses (some closing ) are missing, you also
probably want to group some code {} that is executed in some of the
if conditions rather than executing the (syntactically erroneous) line
vect[i] - 10^((L[i])/10
three times for each inner loop. Particularly, the else is
syntactically incorrect with not preceding if.
So my guess is you want something like
myfunc - function(mytab, Time, Level)
{
vect - rep(0, length(mytab))
for(i in 1:length(vect))
{
for(j in 1:length(Time))
{
if(time[j] is between 18:00:00 and 23:59:59){
L[i] - L[j]+5
vect[i] - 10^(L[i]/10)
}
if (time[j] is between 22:00:00 and 05:59:59){
L[i] - L[j]+10
vect[i] - 10^(L[i]/10)
} else {
L[i] - L[j]
vect[i] - 10^(L[i]/10)
}
}
}
But I am really not sure about that and why you subsitute L[i] so many
times...!
b) What are mytab, Time and Level?
2. Which is the format do you have?
(%d/%m%Y %H%M%S)
*or*
16/09/2006 03:38:37
If the latter, you can use
dat - strptime(16/09/2006 03:38:37, %d/%m/%Y %H:%M:%S)
in order to get some POSIXlt object for later calculations.
3. What do you mean with
time[j] is between 22:00:00 and 05:59:59
Is the day of the date important or not for this comparison?
Uwe Ligges
I still have error messneger
Thank you for your help.
Lassana KOITA
Chargé d'Etudes de Sécurité Aéroportuaire et d'Analyse Statistique /
Project Engineer Airport Safety Studies Statistical analysis
Service Technique de l'Aviation Civile (STAC) / Civil Aviation Technical
Department
Direction Générale de l'Aviation Civile (DGAC) / French Civil Aviation
Headquarters
Tel: 01 49 56 80 60
Fax: 01 49 56 82 14
E-mail: [EMAIL PROTECTED]
http://www.stac.aviation-civile.gouv.fr/
Uwe Ligges [EMAIL PROTECTED]
12/08/2007 15:24
A
Matthew Walker [EMAIL PROTECTED]
cc
Henrique Dallazuanna [EMAIL PROTECTED], r-help@stat.math.ethz.ch, KOITA
Lassana - STAC/ACE [EMAIL PROTECTED]
Objet
Re: [R] need help to manipulate function and time interval
Matthew Walker wrote:
Uwe Ligges wrote:
Henrique Dallazuanna wrote:
Hi,
Try whit:
if(time[j] = 18:00:00 23:59:59)
This code is obviously wrong and does not help for the next few lines
in the questioner's message, please do not post unsensible stuff.
Uwe Ligges
Actually, I would have said that was quite an interesting solution. If
the time is guaranteed to be in this 8 character format, then that
idea's quite easily implemented:
# Returns true if time is between 18:00:00 and 23:59:59
check_time - function(time_string) {
if (nchar(time_string)!=8) stop (Incorrect format)
time_string = 18:00:00 time_string = 23:59:59
}
check_time(19:59:00)
[1] TRUE
check_time(16:59:00)
[1] FALSE
check_time(18:00:00)
[1] TRUE
check_time(23:59:59)
[1] TRUE
check_time(24:00:00)
[1] FALSE
check_time(18:05)
Error in check_time(18:05) : Incorrect format
Perhaps there is an issue if the locale does not sort character-based
numbers in the same way as ASCII? But Otherwise, I can't see why this
solution wouldn't do the job.
A more robust solution solution would parse the strings (?strptime) and
then check their days/hours/mins/seconds (?DateTimeClasses). But
perhaps the above is sufficient?
Well, the interesting part of the original question that everynody seems
to omit now was the second part:
if (time[j] is between 22:00:00 and 05:59:59)
hence the answer is still not sufficient (even if the syntax error has
been corrected) - and hence I asked for the format the time is
originally in.
Uwe Ligges
Cheers,
Matthew
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
Re: [R] need help to manipulate function and time interval
a) I agreed with your suggestion about the condition else. L = Level of
noise fluctuates during the various moments of the day (i.e L= L+5 between
18:00:00 and 21:59:59; L=L+10 between 22:00:00 and 05:59:59 and L = L
else).
b)
mytab is a data table including Time column, Level column, ,
Time - Table[,time] and Level - Table[, Levele]
c) Time format is 16/09/2006 03:38:37
d)
the time interval [ 18:00:00 ; 21:59:59 ]and [ 22:00:00 ; 05:59:59] is
very important for me.
Best regards
Lassana KOITA
Chargé d'Etudes de Sécurité Aéroportuaire et d'Analyse Statistique /
Project Engineer Airport Safety Studies Statistical analysis
Service Technique de l'Aviation Civile (STAC) / Civil Aviation Technical
Department
Direction Générale de l'Aviation Civile (DGAC) / French Civil Aviation
Headquarters
Tel: 01 49 56 80 60
Fax: 01 49 56 82 14
E-mail: [EMAIL PROTECTED]
http://www.stac.aviation-civile.gouv.fr/
Uwe Ligges [EMAIL PROTECTED]
Envoyé par : [EMAIL PROTECTED]
13/08/2007 10:39
A
KOITA Lassana - STAC/ACE [EMAIL PROTECTED]
cc
r-help@stat.math.ethz.ch
Objet
Re: [R] need help to manipulate function and time interval
KOITA Lassana - STAC/ACE wrote:
Hi,
data are extracted from MS Access with the format: (%d/%m%Y %H%M%S);
ex:
16/09/2006 03:38:37
1. the example you gave in your first message is still not reproducible,
you gave the following:
myfunc - function(mytab, Time, Level)
{
vect - rep(0, length(mytab))
for(i in 1:length(vect))
{
for(j in 1:length(Time))
if(time[j] is between 18:00:00 and 23:59:59)
L[i] - L[j]+5
vect[i] - 10^((L[i])/10
if (time[j] is between 22:00:00 and 05:59:59)
L[i] - L[j]+10
vect[i] - 10^((L[i])/10
else
L[i] = L[j]
vect[i] - 10^((L[i])/10
}
}
a) Please check the parentheses (some closing ) are missing, you also
probably want to group some code {} that is executed in some of the
if conditions rather than executing the (syntactically erroneous) line
vect[i] - 10^((L[i])/10
three times for each inner loop. Particularly, the else is
syntactically incorrect with not preceding if.
So my guess is you want something like
myfunc - function(mytab, Time, Level)
{
vect - rep(0, length(mytab))
for(i in 1:length(vect))
{
for(j in 1:length(Time))
{
if(time[j] is between 18:00:00 and 23:59:59){
L[i] - L[j]+5
vect[i] - 10^(L[i]/10)
}
if (time[j] is between 22:00:00 and 05:59:59){
L[i] - L[j]+10
vect[i] - 10^(L[i]/10)
} else {
L[i] - L[j]
vect[i] - 10^(L[i]/10)
}
}
}
But I am really not sure about that and why you subsitute L[i] so many
times...!
b) What are mytab, Time and Level?
2. Which is the format do you have?
(%d/%m%Y %H%M%S)
*or*
16/09/2006 03:38:37
If the latter, you can use
dat - strptime(16/09/2006 03:38:37, %d/%m/%Y %H:%M:%S)
in order to get some POSIXlt object for later calculations.
3. What do you mean with
time[j] is between 22:00:00 and 05:59:59
Is the day of the date important or not for this comparison?
Uwe Ligges
I still have error messneger
Thank you for your help.
Lassana KOITA
Chargé d'Etudes de Sécurité Aéroportuaire et d'Analyse Statistique /
Project Engineer Airport Safety Studies Statistical analysis
Service Technique de l'Aviation Civile (STAC) / Civil Aviation Technical
Department
Direction Générale de l'Aviation Civile (DGAC) / French Civil Aviation
Headquarters
Tel: 01 49 56 80 60
Fax: 01 49 56 82 14
E-mail: [EMAIL PROTECTED]
http://www.stac.aviation-civile.gouv.fr/
Uwe Ligges [EMAIL PROTECTED]
12/08/2007 15:24
A
Matthew Walker [EMAIL PROTECTED]
cc
Henrique Dallazuanna [EMAIL PROTECTED], r-help@stat.math.ethz.ch, KOITA
Lassana - STAC/ACE [EMAIL PROTECTED]
Objet
Re: [R] need help to manipulate function and time interval
Matthew Walker wrote:
Uwe Ligges wrote:
Henrique Dallazuanna wrote:
Hi,
Try whit:
if(time[j] = 18:00:00 23:59:59)
This code is obviously wrong and does not help for the next few lines
in the questioner's message, please do not post unsensible stuff.
Uwe Ligges
Actually, I would have said that was quite an interesting solution. If
the time is guaranteed to be in this 8 character format, then that
idea's quite easily implemented:
# Returns true if time is between 18:00:00 and 23:59:59
check_time - function(time_string) {
if (nchar(time_string)!=8) stop (Incorrect format)
time_string = 18:00:00 time_string = 23:59:59
}
check_time(19:59:00)
[1] TRUE
check_time(16:59:00)
[1] FALSE
check_time(18:00:00)
[1] TRUE
check_time(23:59:59)
[1] TRUE
check_time(24:00:00)
[1] FALSE
check_time(18:05)
Error in check_time(18:05) : Incorrect format
Perhaps there is an issue if the locale does not sort character-based
numbers in the same
Re: [R] need help to manipulate function and time interval
Matthew Walker wrote:
Uwe Ligges wrote:
Henrique Dallazuanna wrote:
Hi,
Try whit:
if(time[j] = 18:00:00 23:59:59)
This code is obviously wrong and does not help for the next few lines
in the questioner's message, please do not post unsensible stuff.
Uwe Ligges
Actually, I would have said that was quite an interesting solution. If
the time is guaranteed to be in this 8 character format, then that
idea's quite easily implemented:
# Returns true if time is between 18:00:00 and 23:59:59
check_time - function(time_string) {
if (nchar(time_string)!=8) stop (Incorrect format)
time_string = 18:00:00 time_string = 23:59:59
}
check_time(19:59:00)
[1] TRUE
check_time(16:59:00)
[1] FALSE
check_time(18:00:00)
[1] TRUE
check_time(23:59:59)
[1] TRUE
check_time(24:00:00)
[1] FALSE
check_time(18:05)
Error in check_time(18:05) : Incorrect format
Perhaps there is an issue if the locale does not sort character-based
numbers in the same way as ASCII? But Otherwise, I can't see why this
solution wouldn't do the job.
A more robust solution solution would parse the strings (?strptime) and
then check their days/hours/mins/seconds (?DateTimeClasses). But
perhaps the above is sufficient?
Well, the interesting part of the original question that everynody seems
to omit now was the second part:
if (time[j] is between 22:00:00 and 05:59:59)
hence the answer is still not sufficient (even if the syntax error has
been corrected) - and hence I asked for the format the time is
originally in.
Uwe Ligges
Cheers,
Matthew
__
R-help@stat.math.ethz.ch 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] need help to manipulate function and time interval
Uwe Ligges wrote:
Henrique Dallazuanna wrote:
Hi,
Try whit:
if(time[j] = 18:00:00 23:59:59)
This code is obviously wrong and does not help for the next few lines in
the questioner's message, please do not post unsensible stuff.
Uwe Ligges
Actually, I would have said that was quite an interesting solution. If
the time is guaranteed to be in this 8 character format, then that
idea's quite easily implemented:
# Returns true if time is between 18:00:00 and 23:59:59
check_time - function(time_string) {
if (nchar(time_string)!=8) stop (Incorrect format)
time_string = 18:00:00 time_string = 23:59:59
}
check_time(19:59:00)
[1] TRUE
check_time(16:59:00)
[1] FALSE
check_time(18:00:00)
[1] TRUE
check_time(23:59:59)
[1] TRUE
check_time(24:00:00)
[1] FALSE
check_time(18:05)
Error in check_time(18:05) : Incorrect format
Perhaps there is an issue if the locale does not sort character-based
numbers in the same way as ASCII? But Otherwise, I can't see why this
solution wouldn't do the job.
A more robust solution solution would parse the strings (?strptime) and
then check their days/hours/mins/seconds (?DateTimeClasses). But
perhaps the above is sufficient?
Cheers,
Matthew
__
R-help@stat.math.ethz.ch 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] need help with pdf-plot
I still have this problem. Does anybody know any solution? Antje Antje schrieb: Hello, I'm trying to plot a set of barplots like a matrix (2 rows, 10 columns fromreduced_mat) to a pdf. It works with the following parameters: pdf(test.pdf,width=ncol(reduced_mat)*2, height=nrow(reduced_mat)*2, pointsize = 12) par(mfcol = c(nrow(reduced_mat),ncol(reduced_mat)), oma = c(0,0,0,0), lwd=48/96, cex.axis = 0.5, las = 2, cex.main = 1.0) The I get a long narrow page format with the quadratic barplots. But I would like to have a A4 format in the end and the plots not filling the whole page (they should stay somehow quadratic and not be stretched...). What shall I look for to achieve this? Antje __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] need help to manipulate function and time interval
Hi R-users,
I have to define a noise level function L and its energy in the various
moment of the day by:
if time is between 18:00:00 and 23:59:59 then L[j] - L[j]+5 and W -
10^((L+5)/10)
if time is between 22:00:00 and 05:59:59 == L - L+10 and W -
10^((L+10)/10)
else
L=L and W = W
Could someone help me to realize this function please? You will find my
following proposal code, but my main problem is to handle the time
interval.
Best regard
###
myfunc - function(mytab, Time, Level)
{
vect - rep(0, length(mytab))
for(i in 1:length(vect))
{
for(j in 1:length(Time))
if(time[j] is between 18:00:00 and 23:59:59)
L[i] - L[j]+5
vect[i] - 10^((L[i])/10
if (time[j] is between 22:00:00 and 05:59:59)
L[i] - L[j]+10
vect[i] - 10^((L[i])/10
else
L[i] = L[j]
vect[i] - 10^((L[i])/10
}
}
###
Lassana KOITA
Chargé d'Etudes de Sécurité Aéroportuaire et d'Analyse Statistique /
Project Engineer Airport Safety Studies Statistical analysis
Service Technique de l'Aviation Civile (STAC) / Civil Aviation Technical
Department
Direction Générale de l'Aviation Civile (DGAC) / French Civil Aviation
Headquarters
Tel: 01 49 56 80 60
Fax: 01 49 56 82 14
E-mail: [EMAIL PROTECTED]
http://www.stac.aviation-civile.gouv.fr/
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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] need help to manipulate function and time interval
Hi,
Try whit:
if(time[j] = 18:00:00 23:59:59)
...
...
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
On 10/08/07, KOITA Lassana - STAC/ACE [EMAIL PROTECTED]
wrote:
Hi R-users,
I have to define a noise level function L and its energy in the various
moment of the day by:
if time is between 18:00:00 and 23:59:59 then L[j] - L[j]+5 and W -
10^((L+5)/10)
if time is between 22:00:00 and 05:59:59 == L - L+10 and W -
10^((L+10)/10)
else
L=L and W = W
Could someone help me to realize this function please? You will find my
following proposal code, but my main problem is to handle the time
interval.
Best regard
###
myfunc - function(mytab, Time, Level)
{
vect - rep(0, length(mytab))
for(i in 1:length(vect))
{
for(j in 1:length(Time))
if(time[j] is between 18:00:00 and 23:59:59)
L[i] - L[j]+5
vect[i] - 10^((L[i])/10
if (time[j] is between 22:00:00 and 05:59:59)
L[i] - L[j]+10
vect[i] - 10^((L[i])/10
else
L[i] = L[j]
vect[i] - 10^((L[i])/10
}
}
###
Lassana KOITA
Chargé d'Etudes de Sécurité Aéroportuaire et d'Analyse Statistique /
Project Engineer Airport Safety Studies Statistical analysis
Service Technique de l'Aviation Civile (STAC) / Civil Aviation Technical
Department
Direction Générale de l'Aviation Civile (DGAC) / French Civil Aviation
Headquarters
Tel: 01 49 56 80 60
Fax: 01 49 56 82 14
E-mail: [EMAIL PROTECTED]
http://www.stac.aviation-civile.gouv.fr/
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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] need help to manipulate function and time interval
Henrique Dallazuanna wrote: Hi, Try whit: if(time[j] = 18:00:00 23:59:59) This code is obviously wrong and does not help for the next few lines in the questioner's message, please do not post unsensible stuff. Uwe Ligges ... ... __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] need help to manipulate function and time interval
KOITA Lassana - STAC/ACE wrote:
Hi R-users,
I have to define a noise level function L and its energy in the various
moment of the day by:
if time is between 18:00:00 and 23:59:59 then L[j] - L[j]+5 and W -
10^((L+5)/10)
What kind of object is time? Just a character or some Time/Date format?
Do you know the day?
If time is between 18:00:00 and 23:59:59, should the next point (time is
between 22:00:00 and 05:59:59) be executed additionally if time is,
e.g., 23:00:00 or is there any other condition I cannot see?
All the information is quite essential in order to help...
BTW: I don't think the rest of your code is sensible (at least, some
braces are missing).
Uwe Ligges
if time is between 22:00:00 and 05:59:59 == L - L+10 and W -
10^((L+10)/10)
else
L=L and W = W
Could someone help me to realize this function please? You will find my
following proposal code, but my main problem is to handle the time
interval.
Best regard
###
myfunc - function(mytab, Time, Level)
{
vect - rep(0, length(mytab))
for(i in 1:length(vect))
{
for(j in 1:length(Time))
if(time[j] is between 18:00:00 and 23:59:59)
L[i] - L[j]+5
vect[i] - 10^((L[i])/10
if (time[j] is between 22:00:00 and 05:59:59)
L[i] - L[j]+10
vect[i] - 10^((L[i])/10
else
L[i] = L[j]
vect[i] - 10^((L[i])/10
}
}
###
Lassana KOITA
Chargé d'Etudes de Sécurité Aéroportuaire et d'Analyse Statistique /
Project Engineer Airport Safety Studies Statistical analysis
Service Technique de l'Aviation Civile (STAC) / Civil Aviation Technical
Department
Direction Générale de l'Aviation Civile (DGAC) / French Civil Aviation
Headquarters
Tel: 01 49 56 80 60
Fax: 01 49 56 82 14
E-mail: [EMAIL PROTECTED]
http://www.stac.aviation-civile.gouv.fr/
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] need help with pdf-plot
Dear Antje I cannot see that you have got any replies yet, so I will make and attempt. However, I am sure other have more formally correct solutions. When you call the pdf(), you can set paper=a4 (or a4r for landscape). However, the width and the height of your plot should then not exceed the size of the paper (which is approximately 8.27*11.69 inches for a4). Try (I have only tested on windows XP, R 2.5.0): pdf(test1.pdf, width=10, heigh=5, paper=a4r) par(mfrow=c(1,3), pty=s) #pty=s gives square plotting regions plot(rnorm(100)) plot(rnorm(100)) plot(rnorm(100)) dev.off() Hope this helps Ivar Antje skrev: I still have this problem. Does anybody know any solution? Antje Antje schrieb: Hello, I'm trying to plot a set of barplots like a matrix (2 rows, 10 columns fromreduced_mat) to a pdf. It works with the following parameters: pdf(test.pdf,width=ncol(reduced_mat)*2, height=nrow(reduced_mat)*2, pointsize = 12) par(mfcol = c(nrow(reduced_mat),ncol(reduced_mat)), oma = c(0,0,0,0), lwd=48/96, cex.axis = 0.5, las = 2, cex.main = 1.0) The I get a long narrow page format with the quadratic barplots. But I would like to have a A4 format in the end and the plots not filling the whole page (they should stay somehow quadratic and not be stretched...). What shall I look for to achieve this? Antje __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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@stat.math.ethz.ch 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] Need Help: Installing/Using xtable package
Hi all, Let me know if I need to ask this question of the bioconductor group. I used the bioconductor utility to install this package and also the CRAN package.install function. My computer crashed a week ago. Today I reinstalled all my bioconductor/R packages. One of my scripts is giving me the following error: in my script I set: library(xtable) print.xtable( and receive this error: Error : could not find function print.xtable This is a new error and I cannot find the source. I reinstalled xtable with the messages below(which are the same whether I use CRAN or bioconductor): Any help is appreciated! Thanks! Matt biocLite(xtable) Running biocinstall version 2.0.8 with R version 2.5.1 Your version of R requires version 2.0 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependenc ies, : argument 'lib' is missing: using '/home/mdj/R/i486-pc-linux-gnu-library /2.5' trying URL 'http://cran.fhcrc.org/src/contrib/xtable_1.5-1.tar.gz' Content type 'application/x-gzip' length 134758 bytes opened URL == downloaded 131Kb * Installing *source* package 'xtable' ... ** R ** data ** inst ** preparing package for lazy loading ** help Building/Updating help pages for package 'xtable' Formats: text html latex example print.xtable texthtmllatex stringtexthtmllatex table.attributes texthtmllatex tli texthtmllatex xtabletexthtmllatex example ** building package indices ... * DONE (xtable) The downloaded packages are in /tmp/RtmpGThCuI/downloaded_packages __ R-help@stat.math.ethz.ch 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] Need Help: Installing/Using xtable package
M. Jankowski wrote: Hi all, Let me know if I need to ask this question of the bioconductor group. I used the bioconductor utility to install this package and also the CRAN package.install function. My computer crashed a week ago. Today I reinstalled all my bioconductor/R packages. One of my scripts is giving me the following error: in my script I set: library(xtable) print.xtable( and receive this error: Error : could not find function print.xtable This is a new error and I cannot find the source. Looks like the current xtable is no longer exporting its print methods. Why were you calling print.xtable explicitly in the first place? __ R-help@stat.math.ethz.ch 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] Need Help: Installing/Using xtable package
Peter Dalgaard [EMAIL PROTECTED] writes: M. Jankowski wrote: Hi all, Let me know if I need to ask this question of the bioconductor group. I used the bioconductor utility to install this package and also the CRAN package.install function. My computer crashed a week ago. Today I reinstalled all my bioconductor/R packages. One of my scripts is giving me the following error: in my script I set: library(xtable) print.xtable( and receive this error: Error : could not find function print.xtable This is a new error and I cannot find the source. Looks like the current xtable is no longer exporting its print methods. Why were you calling print.xtable explicitly in the first place? Indeed, xtable now has a namespace. The S3 methods are not exported because they should not be called directly; rather, the generic function (in this case print) should be called. The addition of the namespace is really a good. Yes, it will cause some hicups for folks who were calling the methods directory (tsk tsk). But the addition fixes breakage that was occuring due to internal xtable helper functions being masked. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/ __ R-help@stat.math.ethz.ch 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] Need Help: Installing/Using xtable package
Ok, I got it now. Just: print(xtable(...),) Thanks! Matt On 8/9/07, Seth Falcon [EMAIL PROTECTED] wrote: Peter Dalgaard [EMAIL PROTECTED] writes: M. Jankowski wrote: Hi all, Let me know if I need to ask this question of the bioconductor group. I used the bioconductor utility to install this package and also the CRAN package.install function. My computer crashed a week ago. Today I reinstalled all my bioconductor/R packages. One of my scripts is giving me the following error: in my script I set: library(xtable) print.xtable( and receive this error: Error : could not find function print.xtable This is a new error and I cannot find the source. Looks like the current xtable is no longer exporting its print methods. Why were you calling print.xtable explicitly in the first place? Indeed, xtable now has a namespace. The S3 methods are not exported because they should not be called directly; rather, the generic function (in this case print) should be called. The addition of the namespace is really a good. Yes, it will cause some hicups for folks who were calling the methods directory (tsk tsk). But the addition fixes breakage that was occuring due to internal xtable helper functions being masked. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/ __ R-help@stat.math.ethz.ch 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] need help with pdf-plot
Hello, I'm trying to plot a set of barplots like a matrix (2 rows, 10 columns fromreduced_mat) to a pdf. It works with the following parameters: pdf(test.pdf,width=ncol(reduced_mat)*2, height=nrow(reduced_mat)*2, pointsize = 12) par(mfcol = c(nrow(reduced_mat),ncol(reduced_mat)), oma = c(0,0,0,0), lwd=48/96, cex.axis = 0.5, las = 2, cex.main = 1.0) The I get a long narrow page format with the quadratic barplots. But I would like to have a A4 format in the end and the plots not filling the whole page (they should stay somehow quadratic and not be stretched...). What shall I look for to achieve this? Antje __ R-help@stat.math.ethz.ch 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] Need Help: User Defined R Functions in Sweave/Latex
On Wed, 2007-06-20 at 22:50 -0500, M. Jankowski wrote:
Dear all,
I want to start my post by expressing my sincere gratitude for all the
help this group has given me in Sweave/Latex/R. The tools are
excellent and so is the community!
On to the question.
My Sweave code is intended to make lots of plots and create a *.pdf
document. Sweave is perfect for this. The only problem is that I find
myself using the same R code, within my Sweave input file over an
over. I know about Latex macros and I can even get R functions,
essentially used as subroutines, to sort of work. \Sexpr{} will not
work because the R code I want to use over and over is in the R
environment. I've tried numerous ways to tackle this process and could
really use some help. If there is some easier way to do this please
let me know!
This is the R function:
basicplot - function(x, nplots, sectionname){
# Begin to make figure here
file = paste(scatter,nplots, .pdf, sep=)
pdf(file = file,paper=special, width=6, height = 6)
plot(x)
dev.off()
cat(\\begin{figure}\n)
cat(\\includegraphics{,file,}\n, sep=)
cat(\\caption{, sectionname,}\n, sep = )
cat(\\end{figure}\n)
#End figure making
}
The aim is to generate Latex code which will have some basic
information as part of the caption. The trouble seems to be that the
output from the function appears to latex as if it is protected R code
when I really want to create output that pdflatex will act on.
Essentially, the resulting *.pdf contains the lines output by the cat
function in basicplot. Or:
\begin{figure}
\includegraphics{scatter1.pdf}
\caption{myname}
\end{figure}
These lines are not in the environment acted by Latex. I tried a
variant of the function where results=tex,echo=FALSE and received
the same result. Below are the files *.Snw - *.tex - *.pdf and the
output I received while compiling. If there is anything else I can
give to help you help me just let me know. Thanks!
Matt
Matt,
I don't know if you have reviewed the Sweave manual, but section 3.4
provides insight into reusing named code chunks, as an alternative to
looping or creating LaTeX macros as proposed by Dieter. These can be
nested within other named code chunks and/or R code.
If you don't yet have the manual, it is available here from Fritz' site:
http://www.ci.tuwien.ac.at/~leisch/Sweave/Sweave-manual-20060104.pdf
You could consider using a figure chunk, if the sole output is the plot
and not text. That way you don't have to worry about explicitly cat()ing
the figure related LaTeX markup as you are doing above. Thus, the LaTeX
markup for things like captions will be in LaTeX sections of the .Rnw
file and you can use \Sexpr{}'s to include derived scalar values.
The preferred approach may be to an extent dependent upon whether your
final document will simply have several plots on one or more pages in
sequence, or whether you will need to have text between the plots, such
that you really need LaTeX sections between the figure/code chunks.
Back to Dieter's solution for a moment, take note of the Sweave FAQ
(also in the above manual), specifically FAQ A.9, which covers the issue
of figure chunks and multiple plots, proposing a looping approach
consistent with Dieter's.
I hope that this might give you some other insights into alternative
approaches.
HTH,
Marc Schwartz
__
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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] Need Help: User Defined R Functions in Sweave/Latex
Back to Dieter's solution for a moment, take note of the Sweave FAQ (also in the above manual), specifically FAQ A.9, which covers the issue of figure chunks and multiple plots, proposing a looping approach consistent with Dieter's. I hope that this might give you some other insights into alternative approaches. HTH, Marc Schwartz Marc, You sure did help me. I reviewed A.9 and found that I simply needed to set: results=tex, echo=false = in the initial function call. Then the route I was pursuing worked smashingly. The rest of your post has me thinking about my approach. I have more than enough data, in my mind at least, to justify the extra effort (and possible confusion) of including captions. I'll need to look at the options for the pdf function to see if it already has the functionality I am looking for. Thank you very much for the nice reply to my post! Matt __ R-help@stat.math.ethz.ch 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] Need Help: User Defined R Functions in Sweave/Latex
Dear all,
I want to start my post by expressing my sincere gratitude for all the
help this group has given me in Sweave/Latex/R. The tools are
excellent and so is the community!
On to the question.
My Sweave code is intended to make lots of plots and create a *.pdf
document. Sweave is perfect for this. The only problem is that I find
myself using the same R code, within my Sweave input file over an
over. I know about Latex macros and I can even get R functions,
essentially used as subroutines, to sort of work. \Sexpr{} will not
work because the R code I want to use over and over is in the R
environment. I've tried numerous ways to tackle this process and could
really use some help. If there is some easier way to do this please
let me know!
This is the R function:
basicplot - function(x, nplots, sectionname){
# Begin to make figure here
file = paste(scatter,nplots, .pdf, sep=)
pdf(file = file,paper=special, width=6, height = 6)
plot(x)
dev.off()
cat(\\begin{figure}\n)
cat(\\includegraphics{,file,}\n, sep=)
cat(\\caption{, sectionname,}\n, sep = )
cat(\\end{figure}\n)
#End figure making
}
The aim is to generate Latex code which will have some basic
information as part of the caption. The trouble seems to be that the
output from the function appears to latex as if it is protected R code
when I really want to create output that pdflatex will act on.
Essentially, the resulting *.pdf contains the lines output by the cat
function in basicplot. Or:
\begin{figure}
\includegraphics{scatter1.pdf}
\caption{myname}
\end{figure}
These lines are not in the environment acted by Latex. I tried a
variant of the function where results=tex,echo=FALSE and received
the same result. Below are the files *.Snw - *.tex - *.pdf and the
output I received while compiling. If there is anything else I can
give to help you help me just let me know. Thanks!
Matt
My system:
T41 IBM Thinkpad
Ubuntu Feisty (7.04)
R version 2.5
testmacro3.Snw:
[EMAIL PROTECTED]:~/mydocs/R$ more testmacro3.Snw
\documentclass[a4paper]{article}
\usepackage{fullpage}
echo=f=
basicplot - function(x, nplots, sectionname){
# Begin to make figure here
file = paste(scatter,nplots, .pdf, sep=)
pdf(file = file,paper=special, width=6, height = 6)
plot(x)
dev.off()
cat(\\begin{figure}\n)
cat(\\includegraphics{,file,}\n, sep=)
cat(\\caption{, sectionname,}\n, sep = )
cat(\\end{figure}\n)
#End figure making
}
@
\begin{document}
Filler text here.\\
=
library(flowCore)
x - read.FCS(/home/mdj/data/yifacs2/NL7_PHA03_1.fcs, transformation = FALSE,
alter.names = TRUE);
basicplot(x, nplots = 1, sectionname=myname)
@
End text here \\
\end{document}
testmacro3.tex
\usepackage{/usr/share/R/share/texmf/Sweave}
\begin{document}
Filler text here.\\
\begin{Schunk}
\begin{Sinput}
library(flowCore)
\end{Sinput}
\begin{Soutput}
Scalable Robust Estimators with High Breakdown Point (version 0.3-05)
\end{Soutput}
\begin{Sinput}
x - read.FCS(/home/mdj/data/yifacs2/NL7_PHA03_1.fcs, transformation = FALSE
,
+ alter.names = TRUE)
basicplot(x, nplots = 1, sectionname = myname)
\end{Sinput}
\begin{Soutput}
\begin{figure}
\includegraphics{scatter1.pdf}
\caption{myname}
\end{figure}
\end{Soutput}
\end{Schunk}
End text here \\
\end{document}
testmacro3.pdf:
Filler text here.
library(flowCore)
Scalable Robust Estimators with High Breakdown Point (version 0.3-05)
x - read.FCS(/home/mdj/data/yifacs2/NL7_PHA03_1.fcs, transformation =
FALSE,
+ alter.names = TRUE)
basicplot(x, nplots = 1, sectionname = myname)
\begin{figure}
\includegraphics{scatter1.pdf}
\caption{myname}
\end{figure}
End text here
Output:
[EMAIL PROTECTED]:~/mydocs/R$ R CMD Sweave testmacro3.Snw
[1] Welcome to my custom R eenvironment!
library(utils); Sweave(testmacro3.Snw)
Writing to file testmacro3.tex
Processing code chunks ...
1 : term verbatim
2 : echo term verbatim
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: rrcov
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
You can now run LaTeX on 'testmacro3.tex'
[EMAIL PROTECTED]:~/mydocs/Rpdflatex testmacro3.tex
This is pdfeTeX, Version 3.141592-1.21a-2.2 (Web2C 7.5.4)
entering extended mode
(./testmacro3.tex
LaTeX2e 2003/12/01
Babel v3.8d and hyphenation patterns for american, french, german, ngerman, b
ahasa, basque, bulgarian, catalan, croatian, czech, danish, dutch, esperanto, e
stonian, finnish, greek, icelandic, irish, italian, latin, magyar, norsk, polis
h, portuges, romanian, russian, serbian, slovak, slovene, spanish, swedish, tur
kish, ukrainian, nohyphenation, loaded.
(/usr/share/texmf-tetex/tex/latex/base/article.cls
Document Class: article 2004/02/16 v1.4f Standard LaTeX document class
(/usr/share/texmf-tetex/tex/latex/base/size10.clo))
[R] Need Help with Dendrogram and DataFrame Leaf names
I having problem with dendrogram leaf names when I read a tab delimited
file into dataframe;
I have a text file, tab delimited, using read.table into a data frame as
follows:
test1-read.table(c:\\R\\data\\Tremont4.txt, header=TRUE, sep=\t)
When I do this the test1 data frame is picking up my first column
names as
part of the data and not the case names, the leafs are the numbers on
the left 1-13
As opposed to the text names to the right.
Example Output from displaying dataframe:
test1
row.names X1.31.2004 X2.29.2004 X3.31.2004 X4.30.2004
X5.31.2004 X6.30.2004 X7.31.2004 X8.31.2004 X9.30.2004 X10.31.2004
1 ConvertibleArbitrage 0.014 0.003 0.004 0.005
-0.013 -0.008 -0.002 0.003 -0.001 -0.003
2 DedicatedShortBias -0.017 0.003 -0.026 0.042
0.008 -0.013 0.081 0.013 -0.019 -0.018
3 EmergingMarkets 0.025 0.014 0.018 -0.033
-0.018 0.009 -0.001 0.018 0.023 0.024
4MarketNeutral 0.008 0.008 -0.001 -0.003
0.002 0.008 0.003 0.021 0.005 0.000
5 EventDriven 0.022 0.010 0.005 0.005
0.001 0.010 0.000 0.005 0.013 0.012
6 Distressed 0.024 0.009 0.006 0.007
0.003 0.011 0.005 0.006 0.012 0.019
7 EventdriveMultiStrategy 0.020 0.011 0.003 0.005
-0.001 0.009 -0.003 0.004 0.014 0.007
8RiskArbitrage 0.008 0.005 0.007 -0.006
0.004 0.003 -0.015 0.002 0.006 0.009
9 FixedIncomeArbitrage 0.012 0.009 -0.005 0.013
0.006 0.007 0.007 -0.004 -0.008 0.011
10 GlobalMacro 0.015 0.012 0.010 0.001
0.001 0.005 0.008 -0.008 -0.005 0.012
11 LongShortEquity 0.020 0.018 0.002 -0.014
-0.004 0.007 -0.014 0.001 0.024 0.014
12 ManagedFutures 0.011 0.069 -0.009 -0.065
-0.011 -0.028 -0.020 -0.015 0.020 0.048
13 Multi-Strategy 0.016 0.004 0.004 0.003
-0.001 0.001 -0.003 0.004 0.006 0.006
Input file looks like this:
row.names 1/31/2004 2/29/2004 3/31/2004
4/30/2004 5/31/2004 6/30/2004 7/31/2004
8/31/2004
ConvertibleArbitrage0.0140.003 0.004 0.005-0.013
-0.008 -0.002 0.003
DedicatedShortBias -0.017 0.003 -0.026 0.042 0.008
-0.013 0.081 0.013
EmergingMarkets 0.0250.0140.018-0.033
-0.0180.009 -0.001 0.018
MarketNeutral 0.0080.008-0.001 -0.003 0.002
0.008 0.003 0.021
Etc...
Would appreciate why the read.table into dataframe sees the text as part
of the data oand
Not the observation names and is making the numbers the leaf names and
observation names.
Thanks for any help,
Neil Gottlieb
This information is being sent at the recipient's request or...{{dropped}}
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Re: [R] Need Help with robustbase package: fitnorm2 and plotnorm2
On Fri, 8 Jun 2007, M. Jankowski wrote: This is my first post requesting help to this mailing list. I am new to R. My apologies for any breach in posting etiquette. For future reference, telling us your version of R and exact OS would have helped here. The R posting guide suggests showing the output of sessionInfo(). Also, to help the readers, fitNorm2 (R is case-sensitive) is in 'prada', and the missing package is rrcov not robustbase. I am new to this language and just learning my way around. I am attempting to run some sample code and and am confused by the error message: Loading required package: rrcov Error in fitNorm2(fdat[, FSC-H], fdat[, SSC-H], scalefac = ScaleFactor) : Required package rrcov could not be found. In addition: Warning message: there is no package called 'rrcov' in: library(package, lib.loc = lib.loc, character.only = TRUE, logical = TRUE, that I get when I attempt to run the following sample snippet of code. The error above is taken from the code below. I am running Ubuntu Linux with all the r packages listed in the Synaptic package manager (universa). I loaded the prada bioconductor package as instructed in the comments and the robustbase was downloaded and installed with the command: sudo R CMD INSTALL robustbase_0.2- 7.tar.gz, the robustbase folder is in /usr/local/lib/R/site-library/ When I type in 'library(robustbase)' no error appears; I believe robustbase is installed correctly. The sample code was taken from FCS-prada.pdf. The sample code was written in 2005, I understand that rrcov was made part of the robustbase package sometime in the past year. This may be the cause of the problem, but, if it is, I have no idea how to fix it. That is not the case: rrcov is a separate package, and one prada depends on. So somehow you have managed to install prada without an essential dependency 'rrcov'. That looks like a problem in the Debian/Ubuntu packaging of prada. (There is a list R-sig-debian for such issues.) Running install.packages(rrcov) inside R should fix this for you: if your R is not current (i.e. 2.5.0) you may need to run R as root for that session. (There may be a Debian package for rrcov for your OS and R version, but without further details I cannot check.) In the current version of prada (1.12.0 for BioC-2.0 for R 2.5.0) rrcov is in Imports, so probably your version of BioC is not current either. [...] -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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] Need Help with robustbase package: fitnorm2 and plotnorm2
This is my first post requesting help to this mailing list. I am new
to R. My apologies for any breach in posting etiquette. I am new to
this language and just learning my way around. I am attempting to run
some sample code and and am confused by the error message:
Loading required package: rrcov
Error in fitNorm2(fdat[, FSC-H], fdat[, SSC-H], scalefac = ScaleFactor) :
Required package rrcov could not be found.
In addition: Warning message:
there is no package called 'rrcov' in: library(package, lib.loc =
lib.loc, character.only = TRUE, logical = TRUE,
that I get when I attempt to run the following sample snippet of code.
The error above is taken from the code below. I am running Ubuntu
Linux with all the r packages listed in the Synaptic package manager
(universa). I loaded the prada bioconductor package as instructed in
the comments and the robustbase was downloaded and installed with the
command: sudo R CMD INSTALL robustbase_0.2- 7.tar.gz, the robustbase
folder is in /usr/local/lib/R/site-library/ When I type in
'library(robustbase)' no error appears; I believe robustbase is
installed correctly. The sample code was taken from FCS-prada.pdf. The
sample code was written in 2005, I understand that rrcov was made part
of the robustbase package sometime in the past year. This may be the
cause of the problem, but, if it is, I have no idea how to fix it.
Thank you in advance for helping out!
Below you will find the code that generates the error and the complete
output of the code. Let me know what I can do to get up and running!
Matt
#prada Bioconductor package
#http://www.bioconductor.org/repository/devel/vignette/norm2.pdf
# To install prada
#source(http://www.bioconductor.org/biocLite.R;)
#biocLite(prada)
library(prada)
filepath - system.file(extdata, fas-Bcl2-plate323-04-04.A01, package = pra
da)
print(filepath)
sampdat - readFCS(filepath)
fdat - exprs(sampdat)
print(dim(fdat))
print(colnames(fdat))
plot(fdat[, FSC-H], fdat[, SSC-H], pch = 20, col = #303030, xlab = FSC,
ylab = SSC, main = Scatter plot FSC vs SSC)
#All of this goes as the help documentation suggests it should
# 2. Show selections for various scale factors
savepar - par(mfrow=c(2,2))
for (Scalefactor in c(1.0, 1.5, 2.0, 2.5) )
{
# The next line gives the error I've included below.
nfit - fitNorm2 (fdat[, FSC-H], fdat[, SSC-H], scalefac = ScaleFactor)
plotnorm2(nfit, selection = TRUE, ellipse = TRUE,
xlab=FSC-H, ylab=SSC-H,
main=paste(SSC-H vs. FSC-H (ScaleFactor=,ScaleFactor,), sep=
))
}
par(savepar)
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: RColorBrewer
Loading required package: grid
Loading required package: geneplotter
Loading required package: annotate
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
[1] /usr/local/lib/R/site-library/prada/extdata/fas-Bcl2-plate323-04-04.A01
[1] 21158
$P1N$P2N$P3N$P4N$P5N$P6N$P7N$P8N
FSC-H SSC-H FL1-H FL2-H FL3-H FL2-A FL4-H Time
Loading required package: rrcov
Error in fitNorm2(fdat[, FSC-H], fdat[, SSC-H], scalefac = ScaleFactor) :
Required package rrcov could not be found.
In addition: Warning message:
there is no package called 'rrcov' in: library(package, lib.loc =
lib.loc, character.only = TRUE, logical = TRUE,
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[R] Need Help
Hi, I have 2 text files the first one is in the following format: CC: Some statements ... this is continued for 11-12 lines of variable length. then a line containing the variable names used in the file and then the variable fields with their observations...there are in all 684 observations. The next file is a text file containing 3 variables and 684 observations but are not numbered , I mean 1 to 684. Only th variable values are there along with thew column headers. My target is to merge these 2 text files and create a new text file preserving the format of the first one becos the subsequent steps of the main program uses the format of the first file. I have to create an id variable that numbers the observations from 1 to 684 and then merge th 2 files with that id, because the first one has the id variable numbered from 1 to 684. Please help me to achieve this in R. Regards Chandramouli Banerjee - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Need Help on Joining 2 text files in R
Hi, I have 2 text files , the first one looks like this : CC: some statements this is followed by 10-12 lines in the similar pattern and then the next line is a comment and from the 14th line all the columns are aligned and the variable values are filled in The next file is a text file with 3 columns with column names and the 2 files have the same number of rows in both. I want to concatanate these 2 files side by side to make a complete file, keeping the structure of the first file same.. More explicitly the first file looks like: CC:some statement. CC:same as above... .this pattern is followed upto say 10-12 lines and then some variables , I mean columns used in the file is listed as a string like nuclear_intensity; cell_intensity ;and so on ... and then in the next row onwards the column headers start with column names and then the variable values are plugged in ...I wish I could have sent you the file but it is in the intranet system and can't be sent over in email... The second file looks simple with column headers and field values.The 2 files are both in the text format. What I really need to know is how to join the 2 text files and make it into one keeping the structure of the first one intact...I need to join the columns with the column names from the second file to the first one. I will wait for any help of how to achieve this is R. Thanks and Regards Chandramouli Banerjee 23rd May 2007 - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Need Help on Joining 2 text files in R
On Wednesday 23 May 2007 07:31:47 am CHANDRAMOULI BANERJEE wrote: Hi, I have 2 text files , the first one looks like this : CC: some statements this is followed by 10-12 lines in the similar pattern and then the next line is a comment and from the 14th line all the columns are aligned and the variable values are filled in The next file is a text file with 3 columns with column names and the 2 files have the same number of rows in both. I want to concatanate these 2 files side by side to make a complete file, keeping the structure of the first file same.. More explicitly the first file looks like: CC:some statement. CC:same as above... .this pattern is followed upto say 10-12 lines and then some variables , I mean columns used in the file is listed as a string like nuclear_intensity; cell_intensity ;and so on ... and then in the next row onwards the column headers start with column names and then the variable values are plugged in ...I wish I could have sent you the file but it is in the intranet system and can't be sent over in email... If the file has read access, then it can always be copied and attached, unless you are prohibited from distributing the file in public domain. The second file looks simple with column headers and field values.The 2 files are both in the text format. What I really need to know is how to join the 2 text files and make it into one keeping the structure of the first one intact...I need to join the columns with the column names from the second file to the first one. I will wait for any help of how to achieve this is R. The cheapest way (if possible) is to use an editor that supports block selection (like, kate, emacs) then block select the 3 columns from the second file and paste them beside the last column in the first one. Done. Now, if the merging has to be done in R, one way is to read.table the first file with 'skip=13' that way you will get only the data. Then read.table from the second file and cbind the two data.frames. Finally write.table into a new file. By this the data will merged but to add the comments, I think you will have to do it manually, copy from the first file and paste into the new file, using whatever text editor you use. (I assume the file is a text file) HTH, PK __ R-help@stat.math.ethz.ch 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] Need help imputing missing data using mice and outputting them
Hello!
I am trying to impute missing data and output the results of the imputation.
My data set is called: MyData.
I have a bunch of variables all of which start with Q20_ - and some of them
have missing values.
Here is what I've been doing:
imputationmodel-mice( MyData[ c (grep(Q20_, names(MyData)) ) ] )
multipledataset-complete(imputationmodel,action=long)
write.table(as.data.frame(lapply(multipledataset,function(x)
{as.numeric(is.element(x,5))} )), sep=\t,file=multiset.txt,row.names=F)
The last line (write.table) makes it so that all the values get changed into 0s
and 1s. How could I output the original imputed values (in my case, they should
be 1s or 2s or 3s or 4s or 5s) rather than 0s and 1s?
Thank you very much!
Dimitri
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[R] need help in reading TOMS observed ASCII data file
Hello R Users, I am new to R. I have two data sets i) TOMS aerosol optical depth(AOD) and ii) TOMS ozone(O3). AOD data is on 1x1 grid and O3 data is on 5x5 grid. First I want to read AOD and O3 as it is and then I want to regrid AOD on 5x5 grid as O3. Reading is first problem. FIRST PROBLEM READING AOD: AOD data is in following format: # Latitute: 89.5 167 0 0 0 0 0 182 0 0 0 0 0 0 0 0 0 0 0 0 200 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 155 0 0 0 0 0 156 0 0 0 0 0 0 ... Latitude: 88.5 . Lat. . ... .. Latitude: -88.5 180 0 0 0 0 0 182 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 655 0 0 0 0 0 156 0 0 0 0 0 0 .. . ## After each latitude header there is 360 AOD values (1x1 grid). This is monthly mean data. I have many years of data file. So the first problem is how to read the data by omiting latitude header, also data is written along row not along column ? SECOND PROBLEM READING O3: O3 data is in following format: ozone(72,12,324) 72: Longitude -177.5,-172.5,...,177.5' 12: Latitude -27.5,-22.5,...,27.5' 324: Month Jan79,Feb79,,Dec05' ### Month index:0 20.8 22.1 20.0 19.0 16.3 20.0 24.4 23.5 27.9 23.7 0.0 32.4 21.6 23.8 20.4 17.9 16.0 22.2 25.3 25.1 31.1 27.4 0.0 30.3 23.2 23.9 20.7 17.3 16.5 23.1 25.9 25.4 30.4 29.3 0.0 29.9 26.1 24.7 21.3 15.9 16.8 22.8 25.3 25.8 29.8 30.1 0.0 31.6 -- Month index: 323 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.00.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - - # 12 columns and 72 rows (latitudexlongitude) THIRD PROBLEM regriding AOD: How to regrid 1x1 AOD data on 5x5 grid as O3. Many thanks for yours help. Regards, Yogesh -- Dr. Yogesh K. Tiwari, Scientist, Indian Institute of Tropical Meteorology, Homi Bhabha Road, Pashan, Pune-411008 INDIA Phone: 0091-99 2273 9513 (Cell) : 0091-20-258 93 600 (O) ( Ext.250) Fax: 0091-20-258 93 825 -- Dr. Yogesh K. Tiwari, Scientist 'B', Indian Institute of Tropical Meteorology, Homi Bhabha Road, Pashan, Pune-411008 INDIA Phone: 0091-99 2273 9513 (Cell) : 0091-20-258 93 600 (O) (Ext.250) Fax: 0091-20-258 93 825 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] need help in reading TOMS observed ASCII data file
Here is a script that will read in you O3 data. It assumes that the data is
perfect. You will have to either prescan the data for errors, or add code
to catch them.
# setup to read your file
# this procedure works if the data is 'perfect'; it does not catch errors
# 'result' is a list of matrices of the data
f.1 - file(/jph/r-help/TOMS_O3.txt, r)
result - list()
while(length(month - readLines(f.1, n=1))){
+ # read in 12*72 real numbers from the file after reading the 'month'
header
+ data.in - matrix(scan(f.1, what=0, n=12*72), ncol=12, byrow=TRUE)
+ # extract just the number and use it as the index into the list to
save the matrix
+ result[[gsub(.*(\\d file://d/+), \\1 file://0.0.0.1/, month,
perl=TRUE)]] - data.in
+ }
Read 864 items
Read 864 items
Read 864 items
Read 864 items
str(result)
List of 4
$ 0: num [1:72, 1:12] 20.8 21.6 23.2 26.1 26.2 29 22.2 18.5 19 20.5 ...
$ 1: num [1:72, 1:12] 22.7 22.4 20.4 19.7 16.9 20.8 24 25.1 24.7 24.7 ...
$ 2: num [1:72, 1:12] 25.4 24.6 27 28 29.9 33.3 32.4 28.2 24.5 21.6 ...
$ 3: num [1:72, 1:12] 31 31 31 30 30.1 27.4 20.5 19 18.8 19.2 ...
On 2/19/07, Yogesh Tiwari [EMAIL PROTECTED] wrote:
Hello R Users,
I am new to R.
I have two data sets i) TOMS aerosol optical depth(AOD) and ii) TOMS
ozone(O3).
AOD data is on 1x1 grid and O3 data is on 5x5 grid.
First I want to read AOD and O3 as it is and then I want to regrid AOD
on
5x5 grid as O3.
Reading is first problem.
FIRST PROBLEM READING AOD:
AOD data is in following format:
#
Latitute: 89.5
167 0 0 0 0 0 182 0 0 0 0 0 0 0 0 0 0 0 0 200 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 155 0 0 0 0 0 156 0 0 0 0 0 0
...
Latitude: 88.5
.
Lat.
.
...
..
Latitude: -88.5
180 0 0 0 0 0 182 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 655 0 0 0 0 0 156 0 0 0 0 0 0
..
.
##
After each latitude header there is 360 AOD values (1x1 grid). This is
monthly mean data. I have many years of data file.
So the first problem is how to read the data by omiting latitude header,
also data is written along row not along column ?
SECOND PROBLEM READING O3:
O3 data is in following format:
ozone(72,12,324)
72: Longitude -177.5,-172.5,...,177.5'
12: Latitude -27.5,-22.5,...,27.5'
324: Month Jan79,Feb79,,Dec05'
###
Month index:0
20.8 22.1 20.0 19.0 16.3 20.0 24.4 23.5 27.9 23.7 0.0 32.4
21.6 23.8 20.4 17.9 16.0 22.2 25.3 25.1 31.1 27.4 0.0 30.3
23.2 23.9 20.7 17.3 16.5 23.1 25.9 25.4 30.4 29.3 0.0
29.9
26.1 24.7 21.3 15.9 16.8 22.8 25.3 25.8 29.8 30.1 0.0 31.6
--
Month index: 323
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.00.0 0.0 0.0 0.0
0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
-
-
#
12 columns and 72 rows (latitudexlongitude)
THIRD PROBLEM regriding AOD:
How to regrid 1x1 AOD data on 5x5 grid as O3.
Many thanks for yours help.
Regards,
Yogesh
--
Dr. Yogesh K. Tiwari,
Scientist,
Indian Institute of Tropical Meteorology,
Homi Bhabha Road,
Pashan,
Pune-411008
INDIA
Phone: 0091-99 2273 9513 (Cell)
: 0091-20-258 93 600 (O) ( Ext.250)
Fax: 0091-20-258 93 825
--
Dr. Yogesh K. Tiwari,
Scientist 'B',
Indian Institute of Tropical Meteorology,
Homi Bhabha Road,
Pashan,
Pune-411008
INDIA
Phone: 0091-99 2273 9513 (Cell)
: 0091-20-258 93 600 (O) (Ext.250)
Fax: 0091-20-258 93 825
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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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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and provide commented, minimal, self-contained, reproducible code.
[R] Need help writing a faster code
Hi,
I apologize for this repeat posting, which I first posted yesterday. I would
appreciate any hints on solving this problem:
I have two matrices A (m x 2) and B (n x 2), where m and n are large
integers (on the order of 10^4). I am looking for an efficient way to
create another matrix, W (m x n), which can be defined as follows:
for (i in 1:m){
for (j in 1:n) {
W[i,j] - g(A[i,], B[j,])
} }
where g(x,y) is a function that takes two vectors and returns a scalar.
The following works okay, but is not fast enough for my purpose. I am sure
that I can do better:
for (i in 1:m) {
W[i,] - apply(B, 1, y=A[i,], function(x,y) g(y,x))
}
How can I do this in a faster manner? I attempted outer, kronecker,
expand.grid, etc, but with no success.
Here is an example:
m - 2000
n - 5000
A - matrix(rnorm(2*m),ncol=2)
B - matrix(rnorm(2*n),ncol=2)
W - matrix(NA, m, n)
for (i in 1:m) {
W[i,] - apply(B, 1, y=A[i,], function(x,y) g(y,x))
}
g - function(x,y){
theta - atan((y[2]-x[2]) / (y[1] - x[1]))
theta + 2*pi*(theta 0)
}
Thanks for any suggestions.
Best,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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] Need help writing a faster code
the following seems to be a first improvement:
m - 2000
n - 5000
A - matrix(rnorm(2*m), ncol=2)
B - matrix(rnorm(2*n), ncol=2)
W1 - W2 - matrix(0, m, n)
##
##
g1 - function(x, y){
theta - atan((y[2] - x[2]) / (y[1] - x[1]))
theta + 2*pi*(theta 0)
}
invisible({gc(); gc()})
system.time(for (i in 1:m) {
W1[i, ] - apply(B, 1, y = A[i,], function(x, y) g1(y, x))
})
##
g2 - function(x){
out - tB - x
theta - atan(out[2, ] / out[1, ])
theta + 2*pi*(theta 0)
}
tB - t(B)
invisible({gc(); gc()})
system.time(for (i in 1:m) {
W2[i, ] - g2(A[i, ])
})
## or
invisible({gc(); gc()})
system.time(W3 - t(apply(A, 1, g2)))
all.equal(W1, W2)
all.equal(W1, W3)
I hope it helps.
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
http://www.student.kuleuven.be/~m0390867/dimitris.htm
- Original Message -
From: Ravi Varadhan [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Sent: Thursday, February 01, 2007 4:10 PM
Subject: [R] Need help writing a faster code
Hi,
I apologize for this repeat posting, which I first posted yesterday.
I would
appreciate any hints on solving this problem:
I have two matrices A (m x 2) and B (n x 2), where m and n are large
integers (on the order of 10^4). I am looking for an efficient way
to
create another matrix, W (m x n), which can be defined as follows:
for (i in 1:m){
for (j in 1:n) {
W[i,j] - g(A[i,], B[j,])
} }
where g(x,y) is a function that takes two vectors and returns a
scalar.
The following works okay, but is not fast enough for my purpose. I
am sure
that I can do better:
for (i in 1:m) {
W[i,] - apply(B, 1, y=A[i,], function(x,y) g(y,x))
}
How can I do this in a faster manner? I attempted outer,
kronecker,
expand.grid, etc, but with no success.
Here is an example:
m - 2000
n - 5000
A - matrix(rnorm(2*m),ncol=2)
B - matrix(rnorm(2*n),ncol=2)
W - matrix(NA, m, n)
for (i in 1:m) {
W[i,] - apply(B, 1, y=A[i,], function(x,y) g(y,x))
}
g - function(x,y){
theta - atan((y[2]-x[2]) / (y[1] - x[1]))
theta + 2*pi*(theta 0)
}
Thanks for any suggestions.
Best,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage:
http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
__
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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] Need help writing a faster code
Hi
A - matrix(runif(10),ncol=2)
B - matrix(runif(10),ncol=2)
g - function(i4){theta - atan2( (i4[4]-i4[2]),(i4[3]-i4[1]))
+ return(theta + 2*pi*(theta0))}
apply(A,1,function(x){apply(B,1,function(y){g(c(x,y))})})
[,1] [,2] [,3][,4] [,5]
[1,] 1.1709326 2.6521457 3.857477 0.219274562 1.2948374
[2,] 1.1770919 4.2109056 4.057313 4.918552967 1.9733967
[3,] 0.9171661 0.6721475 4.193675 0.434253839 0.9781060
[4,] 0.9181475 0.6911804 4.213295 0.455127422 0.9771797
[5,] 1.0467449 4.9263243 3.983248 0.004371504 1.1693707
HTH
rksh
On 1 Feb 2007, at 15:10, Ravi Varadhan wrote:
Hi,
I apologize for this repeat posting, which I first posted
yesterday. I would
appreciate any hints on solving this problem:
I have two matrices A (m x 2) and B (n x 2), where m and n are large
integers (on the order of 10^4). I am looking for an efficient way to
create another matrix, W (m x n), which can be defined as follows:
for (i in 1:m){
for (j in 1:n) {
W[i,j] - g(A[i,], B[j,])
} }
where g(x,y) is a function that takes two vectors and returns a
scalar.
The following works okay, but is not fast enough for my purpose. I
am sure
that I can do better:
for (i in 1:m) {
W[i,] - apply(B, 1, y=A[i,], function(x,y) g(y,x))
}
How can I do this in a faster manner? I attempted outer,
kronecker,
expand.grid, etc, but with no success.
Here is an example:
m - 2000
n - 5000
A - matrix(rnorm(2*m),ncol=2)
B - matrix(rnorm(2*n),ncol=2)
W - matrix(NA, m, n)
for (i in 1:m) {
W[i,] - apply(B, 1, y=A[i,], function(x,y) g(y,x))
}
g - function(x,y){
theta - atan((y[2]-x[2]) / (y[1] - x[1]))
theta + 2*pi*(theta 0)
}
Thanks for any suggestions.
Best,
Ravi.
--
--
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/
Varadhan.html
--
--
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
--
This e-mail (and any attachments) is confidential and intend...{{dropped}}
__
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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] Need help writing a faster code
Thank you, Dimitris and Robin.
Dimitris - your solution(s) works very well. Although my g function is a
lot more complicated than that in the simple example that I gave, I think
that I can use your idea of taking the whole matrix inside the function and
working directly with it.
Robin - using two applys doesn't make the code any faster, it just produces
a compact one-liner.
Best,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: Dimitris Rizopoulos [mailto:[EMAIL PROTECTED]
Sent: Thursday, February 01, 2007 10:33 AM
To: Ravi Varadhan
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Need help writing a faster code
the following seems to be a first improvement:
m - 2000
n - 5000
A - matrix(rnorm(2*m), ncol=2)
B - matrix(rnorm(2*n), ncol=2)
W1 - W2 - matrix(0, m, n)
##
##
g1 - function(x, y){
theta - atan((y[2] - x[2]) / (y[1] - x[1]))
theta + 2*pi*(theta 0)
}
invisible({gc(); gc()})
system.time(for (i in 1:m) {
W1[i, ] - apply(B, 1, y = A[i,], function(x, y) g1(y, x))
})
##
g2 - function(x){
out - tB - x
theta - atan(out[2, ] / out[1, ])
theta + 2*pi*(theta 0)
}
tB - t(B)
invisible({gc(); gc()})
system.time(for (i in 1:m) {
W2[i, ] - g2(A[i, ])
})
## or
invisible({gc(); gc()})
system.time(W3 - t(apply(A, 1, g2)))
all.equal(W1, W2)
all.equal(W1, W3)
I hope it helps.
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
http://www.student.kuleuven.be/~m0390867/dimitris.htm
- Original Message -
From: Ravi Varadhan [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Sent: Thursday, February 01, 2007 4:10 PM
Subject: [R] Need help writing a faster code
Hi,
I apologize for this repeat posting, which I first posted yesterday.
I would
appreciate any hints on solving this problem:
I have two matrices A (m x 2) and B (n x 2), where m and n are large
integers (on the order of 10^4). I am looking for an efficient way
to
create another matrix, W (m x n), which can be defined as follows:
for (i in 1:m){
for (j in 1:n) {
W[i,j] - g(A[i,], B[j,])
} }
where g(x,y) is a function that takes two vectors and returns a
scalar.
The following works okay, but is not fast enough for my purpose. I
am sure
that I can do better:
for (i in 1:m) {
W[i,] - apply(B, 1, y=A[i,], function(x,y) g(y,x))
}
How can I do this in a faster manner? I attempted outer,
kronecker,
expand.grid, etc, but with no success.
Here is an example:
m - 2000
n - 5000
A - matrix(rnorm(2*m),ncol=2)
B - matrix(rnorm(2*n),ncol=2)
W - matrix(NA, m, n)
for (i in 1:m) {
W[i,] - apply(B, 1, y=A[i,], function(x,y) g(y,x))
}
g - function(x,y){
theta - atan((y[2]-x[2]) / (y[1] - x[1]))
theta + 2*pi*(theta 0)
}
Thanks for any suggestions.
Best,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage:
http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
__
R-help@stat.math.ethz.ch 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] Need help writing a faster code
Dear Dimitris,
I implemented your solution on my actual problem. I was able to generate my
large transition matrix in 56 seconds, compared to the previous time of
around 27 minutes. Wow!!!
I thank you very much for the help. R and the R-user group are truly
amazing!
Best regards,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: Dimitris Rizopoulos [mailto:[EMAIL PROTECTED]
Sent: Thursday, February 01, 2007 10:33 AM
To: Ravi Varadhan
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Need help writing a faster code
the following seems to be a first improvement:
m - 2000
n - 5000
A - matrix(rnorm(2*m), ncol=2)
B - matrix(rnorm(2*n), ncol=2)
W1 - W2 - matrix(0, m, n)
##
##
g1 - function(x, y){
theta - atan((y[2] - x[2]) / (y[1] - x[1]))
theta + 2*pi*(theta 0)
}
invisible({gc(); gc()})
system.time(for (i in 1:m) {
W1[i, ] - apply(B, 1, y = A[i,], function(x, y) g1(y, x))
})
##
g2 - function(x){
out - tB - x
theta - atan(out[2, ] / out[1, ])
theta + 2*pi*(theta 0)
}
tB - t(B)
invisible({gc(); gc()})
system.time(for (i in 1:m) {
W2[i, ] - g2(A[i, ])
})
## or
invisible({gc(); gc()})
system.time(W3 - t(apply(A, 1, g2)))
all.equal(W1, W2)
all.equal(W1, W3)
I hope it helps.
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
http://www.student.kuleuven.be/~m0390867/dimitris.htm
- Original Message -
From: Ravi Varadhan [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Sent: Thursday, February 01, 2007 4:10 PM
Subject: [R] Need help writing a faster code
Hi,
I apologize for this repeat posting, which I first posted yesterday.
I would
appreciate any hints on solving this problem:
I have two matrices A (m x 2) and B (n x 2), where m and n are large
integers (on the order of 10^4). I am looking for an efficient way
to
create another matrix, W (m x n), which can be defined as follows:
for (i in 1:m){
for (j in 1:n) {
W[i,j] - g(A[i,], B[j,])
} }
where g(x,y) is a function that takes two vectors and returns a
scalar.
The following works okay, but is not fast enough for my purpose. I
am sure
that I can do better:
for (i in 1:m) {
W[i,] - apply(B, 1, y=A[i,], function(x,y) g(y,x))
}
How can I do this in a faster manner? I attempted outer,
kronecker,
expand.grid, etc, but with no success.
Here is an example:
m - 2000
n - 5000
A - matrix(rnorm(2*m),ncol=2)
B - matrix(rnorm(2*n),ncol=2)
W - matrix(NA, m, n)
for (i in 1:m) {
W[i,] - apply(B, 1, y=A[i,], function(x,y) g(y,x))
}
g - function(x,y){
theta - atan((y[2]-x[2]) / (y[1] - x[1]))
theta + 2*pi*(theta 0)
}
Thanks for any suggestions.
Best,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage:
http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
__
R-help@stat.math.ethz.ch 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] need help with debug package
I think I have figured out part of the answer, when I entered a debugger, the
calling environment (parent frame)
refers to the debugger program, instead of the mainfun( ). But is there
anyway to solve this problem ?
thanks
- Original Message -
From: Tong Wang [EMAIL PROTECTED]
Date: Wednesday, January 3, 2007 9:30 pm
Subject: need help with debug package
To: R help r-help@stat.math.ethz.ch
Hi all,
I met a problem while using the debug package, I have the
following program:
mainfun- function(){
beta-1
result-subfun(beta+x)
}
subfun-function(expr){
y - eval(expr, envir=list(x=c(1,2)),enclos =
parent.frame()) return(y)
}
I have no problem using this program without calling the debug
package. but once
I mtrace(subfun), the debugger can't find all the beta after
entering subfun , and give
the message : Error in beta : non-numeric argument to binary
operator
Is there anyway to get around ?
thanks a lot
happy new year
__
R-help@stat.math.ethz.ch 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] need help with debug package
Hi all,
I met a problem while using the debug package, I have the following
program:
mainfun- function(){
beta-1
result-subfun(beta+x)
}
subfun-function(expr){
y - eval(expr, envir=list(x=c(1,2)),enclos = parent.frame())
return(y)
}
I have no problem using this program without calling the debug package. but
once
I mtrace(subfun), the debugger can't find all the beta after entering subfun ,
and give
the message : Error in beta : non-numeric argument to binary operator
Is there anyway to get around ?
thanks a lot
happy new year
__
R-help@stat.math.ethz.ch 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] need help with barplot
Hello, I do this a=c(10.2,0.4,0.2,5.2,8.6,1.6,0.0,1.0,6.3,1.4,0.4,0.2) b=matrix(a,nrow=4) rownames(b)=c(20/04/2002,21/04/2002,22/04/2002,23/04/2002) colnames(b)=c(p1,p2,p3) barplot(b,beside=T,col=(c(red,orange,yellow))) then I have http://www.mif.vu.lt/~roka5178/barplot1.JPGhttp://www.mif.vu.lt/%7Eroka5178/barplot1.JPG but I need to have http://www.mif.vu.lt/~roka5178/barplot.JPGhttp://www.mif.vu.lt/%7Eroka5178/barplot.JPG how can i do this? i need to to change axis x whit y -- Robertas [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] need help with barplot
You need the transpose of the matrix (or create it differently in the first place!). Changing the last line to barplot(t(b),beside=T,col=(c(red,orange,yellow))) should do the trick. On 29/11/06, Robertas Kavaliūnas [EMAIL PROTECTED] wrote: Hello, I do this a=c(10.2,0.4,0.2,5.2,8.6,1.6,0.0,1.0,6.3,1.4,0.4,0.2) b=matrix(a,nrow=4) rownames(b)=c(20/04/2002,21/04/2002,22/04/2002,23/04/2002) colnames(b)=c(p1,p2,p3) barplot(b,beside=T,col=(c(red,orange,yellow))) then I have http://www.mif.vu.lt/~roka5178/barplot1.JPGhttp://www.mif.vu.lt/%7Eroka5178/barplot1.JPG but I need to have http://www.mif.vu.lt/~roka5178/barplot.JPGhttp://www.mif.vu.lt/%7Eroka5178/barplot.JPG how can i do this? i need to to change axis x whit y -- Robertas [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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 Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch 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] need help with barplot
--- Robertas Kavaliûnas [EMAIL PROTECTED] wrote: Hello, I do this a=c(10.2,0.4,0.2,5.2,8.6,1.6,0.0,1.0,6.3,1.4,0.4,0.2) b=matrix(a,nrow=4) rownames(b)=c(20/04/2002,21/04/2002,22/04/2002,23/04/2002) colnames(b)=c(p1,p2,p3) barplot(b,beside=T,col=(c(red,orange,yellow))) then I have http://www.mif.vu.lt/~roka5178/barplot1.JPGhttp://www.mif.vu.lt/%7Eroka5178/barplot1.JPG but I need to have http://www.mif.vu.lt/~roka5178/barplot.JPGhttp://www.mif.vu.lt/%7Eroka5178/barplot.JPG how can i do this? i need to to change axis x whit y Robertas This is dirty code but it works. Just transpose the matrix before you plot it. a=c(10.2,0.4,0.2,5.2,8.6,1.6,0.0,1.0,6.3,1.4,0.4,0.2) b= matrix(a,nrow=4) rownames(b)=c(20/04/2002,21/04/2002,22/04/2002,23/04/2002) colnames(b)=c(p1,p2,p3) b1 - t(b)# Transpose of 'b' barplot(b1,beside=T,col=(c(red,orange,yellow))) __ R-help@stat.math.ethz.ch 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] Need help in nlmeODE
I've never used nlmeODE, but this post is almost 3 days old, so I'll offer some comments. I didn't see an example in the 'nlmeODE' help file, but I did find a reference to 'PKPDmodels', and the help file for 'PKPDmodels' includes several examples. Have you worked through those? If you have and you still would like some help, please submit another post with a copy to the 'nlmeODE' maintainer [identified, e.g., via help(package='nlmeODE')]. In that post, please include minimal, self-contained, reproducible code showing something you tried and explaining why it doesn't meet your needs (as suggested in the posting guide www.R-project.org/posting-guide.html). Hope this helps. Spencer Graves Ron Fisher wrote: I am trying to use nlmeODE. But I don't know what is ObsEq. How you can get it from your ODEs system? Could someone help me out? Best, Ron __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] Need help in nlmeODE
I am trying to use nlmeODE. But I don't know what is ObsEq. How you can get it from your ODEs system? Could someone help me out? Best, Ron __ R-help@stat.math.ethz.ch 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] Need help in waveslim package: imodwt and universal.thresh.modwt
Hi: I have encountered problems with imodwt and universal.thresh.modwt and cannot find any reference in R Search. Hope someone can give me some ideas: Starting with modwt.la8 - modwt(xdata, la8, n.level=6) -- this seems to work fine (1) ydata - imodwt(modwt.la8) will always give ydata as numeric(0) (no values) instead of being a time series data with the same lenght as xdata. (2) thred.la8 - universal.thresh.modwt(modwt.la8, max.level=4, hard=F) will give me error at: abs(wc.fine) - cannot contain non-numeric field. Any help is much appreciated. Regards ___ YM - Â÷½u°T®§ ´Nºâ§A¨S¦³¤Wºô¡A§AªºªB¤Í¤´¥i¥H¯d¤U°T®§µ¹§A¡A·í§A¤Wºô®É´N¯à¥ß§Y¬Ý¨ì¡A¥ô¦ó»¡¸Ü³£ÉN¨«¥¢¡C [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Need help in waveslim package: imodwt and universal.thresh.modwt
The first two commands worked fine to me. I used xdata = rnorm(128). To let us help you more, specify your R version, some data, OS etc, as usually asked. Rogerio Porto. -- Cabeçalho original --- De: [EMAIL PROTECTED] Para: r-help@stat.math.ethz.ch Cópia: Data: Sun, 12 Nov 2006 16:02:45 +0800 (CST) Assunto: [R] Need help in waveslim package: imodwt and universal.thresh.modwt Hi: I have encountered problems with imodwt and universal.thresh.modwt and cannot find any reference in R Search. Hope someone can give me some ideas: Starting with modwt.la8 - modwt(xdata, la8, n.level=6) -- this seems to work fine (1) ydata - imodwt(modwt.la8) will always give ydata as numeric(0) (no values) instead of being a time series data with the same lenght as xdata. (2) thred.la8 - universal.thresh.modwt(modwt.la8, max.level=4, hard=F) will give me error at: abs(wc.fine) - cannot contain non-numeric field. Any help is much appreciated. Regards ___ YM - Â÷½u°T®§ ´Nºâ§A¨S¦³¤Wºô¡A§AªºªB¤Í¤´¥i¥H¯d¤U°T®§µ¹§A¡A·í§A¤Wºô®É´N¯à¥ß§Y¬Ý¨ì¡A¥ô¦ó»¡¸Ü³£ÉN¨«¥¢¡C [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Need help with barplots
On 2006-10-13 10:55, David Barron wrote: First, produce two barplots for comparison: par(mfrow=c(2,1) ) barplot(VADeaths,beside=TRUE) barplot(VADeaths) The same information is in both plots; in the top, it is displayed as 5 separate bars for each group, and in the stacked plot it is shown as 5 separate regions in each of the four bars. The hight of each of these regions is the same as the hight of the corresponding bar in the side-by-side plot. The stacked plot enables you to see overall differences more easily (easier to see that the death rate is highest for Urban Males), but it is harder to compare the sizes of the categories. Take a look at ?spineplot. HTH, Henric On 13/10/06, laba diena [EMAIL PROTECTED] wrote: I`ve read all the manuals and still couln`t find what is the difference between the stacked and side-by-side barplots ? Could you explain me ? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] Need help with barplots
I`ve read all the manuals and still couln`t find what is the difference between the stacked and side-by-side barplots ? Could you explain me ? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Need help with barplots
laba diena [EMAIL PROTECTED] writes: I`ve read all the manuals and still couln`t find what is the difference between the stacked and side-by-side barplots ? Could you explain me ? Did you try par(ask=TRUE) example(barplot) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch 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] Need help with barplots
First, produce two barplots for comparison: par(mfrow=c(2,1) ) barplot(VADeaths,beside=TRUE) barplot(VADeaths) The same information is in both plots; in the top, it is displayed as 5 separate bars for each group, and in the stacked plot it is shown as 5 separate regions in each of the four bars. The hight of each of these regions is the same as the hight of the corresponding bar in the side-by-side plot. The stacked plot enables you to see overall differences more easily (easier to see that the death rate is highest for Urban Males), but it is harder to compare the sizes of the categories. On 13/10/06, laba diena [EMAIL PROTECTED] wrote: I`ve read all the manuals and still couln`t find what is the difference between the stacked and side-by-side barplots ? Could you explain me ? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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 Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch 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] Need help with tables
I have a data file with 3 columns and I need to take only 2, how to do that ? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Need help with tables
I'm not quite sure what you mean, but if you are wanting to select columns of a data frame, have a look at help([) David On 13/10/06, laba diena [EMAIL PROTECTED] wrote: I have a data file with 3 columns and I need to take only 2, how to do that ? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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 Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch 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] Need help with tables
I suggest you look at one of the guides: http://cran.r-project.org/other-docs.html before answering questions like this to the mailing list... please read the posting guide! laba diena schrieb: I have a data file with 3 columns and I need to take only 2, how to do that ? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] Need help with tables
--- laba diena [EMAIL PROTECTED] wrote: I have a data file with 3 columns and I need to take only 2, how to do that Have a look at the manual? An Introduction to R 2.7 Index vectors; selecting and modifying subsets of a data set __ R-help@stat.math.ethz.ch 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] Need help to estimate the Coef matrices in mAr
I'm sorry, but I can't follow what you are asking. If you'd like more help, please provide commented, minimal, self-contained, reproducible code, as suggested in the posting guide www.R-project.org/posting-guide.html. http://www.R-project.org/posting-guide.html Please include a minimal data set, e.g., 10 simulated observations on 2 variables, with comments describing what you tried and what you don't understand about it. Hope this helps. Spencer Graves Arun Kumar Saha wrote: Dear Spencer, Thank you very much for your attention on my problem. According to your advice I did some home work on this problem, but unfortunately I could not solve my problem. Suppose I have a dataset of length 300 with 2 variables. And I want to fit a VAR model on this of order 2. I went through the function mAr.est and got understand that, here 'K' is a matrix with (300-2) rows and 7 columns. the first col. consists only 1, next two columns consist of lagged values of two variables with lag-length 2, next two col. consist of lagged value with lag length-1, and next two cols are for lag-length-0. Next, they add additional a 7-7 matrix to K. For this matrix diagonal elements are the square root of sum of square of elements of K (col. wise) and rest of the elements are 0. I feel that this matrix, that is added to K, is the key matrix for any type of modification that you prescribed. Therefore for experimental purpose I put NA against one of its off-diagonal elements. But I got error. However I cannot understand why they put such figures for diagonal and off-diagonal elements of that matrix. Can you suggest me any solution more specifically? Thanks and regards, Arun On 9/4/06, *Spencer Graves* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Have you tried 'RSiteSearch(multivariate autoregression, functions)'? This produced 14 hits for me just now, the first of which mentions a package 'MSBVAR'. Have you looked at that? If that failed, I don't think it would be too hard to modify 'mAr.est' to do what you want. If it were my problem, I might a local copy of the function, then add an argument accepting a 2 or 3-dimensional array with numbers for AR coefficients to be fixed and NAs for the coefficients. Then I'd use 'debug' to walk through the function line by line until I figured out how to modify the function to do what I wanted. I haven't checked all the details, so I don't know for sure if this would work, but the function contains a line 'R = qr.R(qr((rbind(K, diag(scale, complete = TRUE)' which I would start by decomposing, possibly starting as follows: Z - rbind(K, diag(scale) I'd figure out how the different columns of Z relate to my problem, then modify it appropriately to get what I wanted. Another alternative would be to program it from scratch using something like 'optim' to minimize the sum of squares of residuals over the free parameters in my AR matrices. I'm confident I could make this work, even if the I somehow could not get it with either of the other two. There may be something else better, e.g., a Kalman filter representation, but I can't think how to do that off the top if my head. Hope this helps. Spencer Graves Arun Kumar Saha wrote: Dear R users, I am using mAr package to fit a Vector autoregressive model to my data. But here I want to put some predetermined values for some elements in coefficient matrix that mAr.est going to estimate. For example if p=3 then I want to put A3[1,3] = 0 and keep rest of the elements of coefficient matrices to be determined by mAr.est. Can anyone please tell me how can I do that? Sincerely yours, Arun [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailto:R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help 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. -- Arun Kumar Saha, M.Sc.[C.U.] S T A T I S T I C I A N[Analyst] RISK MANAGEMENT DIVISION Transgraph Consulting [ www.transgraph.com http://www.transgraph.com] Hyderabad, INDIA Contact # Home: (91-033) 25558038 Office: (91-040) 30685012 Ext. 17 FAX: (91-040) 55755003 Mobile: 919989122010 E-Mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
Re: [R] Need help with boxplots
To prevent confusion you might want to use a red dot rather than a line: points(1:2, c(mean(a), mean(b)), col = red) and perhaps label it since its non-standard: text(1:2, c(mean(a), mean(b)), Mean, pos = 4) On 9/26/06, laba diena [EMAIL PROTECTED] wrote: How to add a mean line in the boxplot keeping the median line ? For example in this: set.seed(1) a - rnorm(10) b - rnorm(10) boxplot(a, b) [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] Need help with boxplots
How to add a mean line in the boxplot keeping the median line ? For example in this: set.seed(1) a - rnorm(10) b - rnorm(10) boxplot(a, b) [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Need help with boxplots
How to add a mean *line* in the boxplot keeping the median line ? Maybe it is possible to do using the *segments* function ? For example in this: set.seed(1) a - rnorm(10) b - rnorm(10) boxplot(a, b) [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Need help with boxplots
The problem with a line, I think, would be that the width of the boxes can vary depending on the number of boxes in the plot, etc. No doubt it could be done, but you'd probably have to look into the bxp function to see how the widths are calculated. On 26/09/06, laba diena [EMAIL PROTECTED] wrote: How to add a mean *line* in the boxplot keeping the median line ? Maybe it is possible to do using the *segments* function ? For example in this: set.seed(1) a - rnorm(10) b - rnorm(10) boxplot(a, b) [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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 Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch 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] Need help with boxplots
And if you really do want a line segment try this: M - c(mean(a), mean(b)) segments(1:2-0.4, M, 1:2+0.4, M, col = red) On 9/26/06, Gabor Grothendieck [EMAIL PROTECTED] wrote: To prevent confusion you might want to use a red dot rather than a line: points(1:2, c(mean(a), mean(b)), col = red) and perhaps label it since its non-standard: text(1:2, c(mean(a), mean(b)), Mean, pos = 4) On 9/26/06, laba diena [EMAIL PROTECTED] wrote: How to add a mean line in the boxplot keeping the median line ? For example in this: set.seed(1) a - rnorm(10) b - rnorm(10) boxplot(a, b) [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] Need help to estimate the Coef matrices in mAr
Dear Spencer, Thank you very much for your attention on my problem. According to your advice I did some home work on this problem, but unfortunately I could not solve my problem. Suppose I have a dataset of length 300 with 2 variables. And I want to fit a VAR model on this of order 2. I went through the function mAr.est and got understand that, here 'K' is a matrix with (300-2) rows and 7 columns. the first col. consists only 1, next two columns consist of lagged values of two variables with lag-length 2, next two col. consist of lagged value with lag length-1, and next two cols are for lag-length-0. Next, they add additional a 7-7 matrix to K. For this matrix diagonal elements are the square root of sum of square of elements of K (col. wise) and rest of the elements are 0. I feel that this matrix, that is added to K, is the key matrix for any type of modification that you prescribed. Therefore for experimental purpose I put NA against one of its off-diagonal elements. But I got error. However I cannot understand why they put such figures for diagonal and off-diagonal elements of that matrix. Can you suggest me any solution more specifically? Thanks and regards, Arun On 9/4/06, Spencer Graves [EMAIL PROTECTED] wrote: Have you tried 'RSiteSearch(multivariate autoregression, functions)'? This produced 14 hits for me just now, the first of which mentions a package 'MSBVAR'. Have you looked at that? If that failed, I don't think it would be too hard to modify 'mAr.est' to do what you want. If it were my problem, I might a local copy of the function, then add an argument accepting a 2 or 3-dimensional array with numbers for AR coefficients to be fixed and NAs for the coefficients. Then I'd use 'debug' to walk through the function line by line until I figured out how to modify the function to do what I wanted. I haven't checked all the details, so I don't know for sure if this would work, but the function contains a line 'R = qr.R(qr((rbind(K, diag(scale, complete = TRUE)' which I would start by decomposing, possibly starting as follows: Z - rbind(K, diag(scale) I'd figure out how the different columns of Z relate to my problem, then modify it appropriately to get what I wanted. Another alternative would be to program it from scratch using something like 'optim' to minimize the sum of squares of residuals over the free parameters in my AR matrices. I'm confident I could make this work, even if the I somehow could not get it with either of the other two. There may be something else better, e.g., a Kalman filter representation, but I can't think how to do that off the top if my head. Hope this helps. Spencer Graves Arun Kumar Saha wrote: Dear R users, I am using mAr package to fit a Vector autoregressive model to my data. But here I want to put some predetermined values for some elements in coefficient matrix that mAr.est going to estimate. For example if p=3 then I want to put A3[1,3] = 0 and keep rest of the elements of coefficient matrices to be determined by mAr.est. Can anyone please tell me how can I do that? Sincerely yours, Arun [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Arun Kumar Saha, M.Sc.[C.U.] S T A T I S T I C I A N[Analyst] RISK MANAGEMENT DIVISION Transgraph Consulting [www.transgraph.com] Hyderabad, INDIA Contact # Home: (91-033) 25558038 Office: (91-040) 30685012 Ext. 17 FAX: (91-040) 55755003 Mobile: 919989122010 E-Mail: [EMAIL PROTECTED] [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] -Need help with function
Hello everyone,
I have a function here that I wrote but doesn't seem to work quite
right. Attached is the code. In the calib funcion under the for loop
Bt[i+2]-(1-m)*Bt[i+1]+Rt[i]*Rerr-Ct[i+1] returns NA's for everything
after years 1983 and 1984. However the code works when it reads
Bt[i+2]-(1-m)*Bt[i+1]+Rt[i]*Rerr-Ct[i]. I don't quite understand why
since it should be calculating all of the necessary inputs prior to
calculating Bt[i+2]. Any help would be greatly appreciated.
Thanks
#Model parameters
B0-7500
m-0.3
R0-B0*m
z-0.8
a-B0/R0*(1-(z-0.2)/(0.8*z))
b-(z-0.2)/(0.8*z*R0)
dat-data.frame(years=seq(1983,2004),cobs=c(19032324,19032324,17531618,2
0533029,20298099,20793744,23519369,23131780,19922247,17274513,17034419,1
2448318,4551585,4226451,7183688,7407924,7538366,7336039,8869193,7902341,
6369089,6211886))
stdr-runif(100,0,0.5)
stdc-runif(100,0,0.5)
BC-runif(1000,0,100)
#model calibration
calib-function(x){
v-sample(stdr,1)
cr-sample(stdc,1)
N-rnorm(1)
Bq-sample(BC,1)
Rerr-exp(N*v-(v^2/2))
Cerr-exp(N*cr-(cr^2/2))
Bt-vector();Bt[1]=B0;Bt[2]=B0
Rt-vector()
Ct-vector()
for (i in 1:length(x$years)){
Ct[i]-1/Bq*Bt[i]*Cerr
Rt[i]-Bt[i]/(a+b*Bt[i])
Bt[i+2]-(1-m)*Bt[i+1]+Rt[i]*Rerr-Ct[i+1]
}
out-new.env()
out$yr-x$years[1:length(x$years)]
out$Bt-Bt[1:length(x$years)]
out$Rt-Rt[1:length(x$years)]
out$Ct-Ct[1:length(x$years)]
out$stdr-v
out$stdc-cr
out$Bq-Bq
out$Rerr-Rerr
out$Cerr-Cerr
return(as.list(out))
}
test-calib(dat)
Cameron Guenther, Ph.D.
Associate Research Scientist
FWC/FWRI, Marine Fisheries Research
100 8th Avenue S.E.
St. Petersburg, FL 33701
(727)896-8626 Ext. 4305
[EMAIL PROTECTED]
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] -Need help with function
You are referencing Ct[i+1] in the loop and it is not defined. From
then on everything is NA.
On 9/19/06, Guenther, Cameron [EMAIL PROTECTED] wrote:
Hello everyone,
I have a function here that I wrote but doesn't seem to work quite
right. Attached is the code. In the calib funcion under the for loop
Bt[i+2]-(1-m)*Bt[i+1]+Rt[i]*Rerr-Ct[i+1] returns NA's for everything
after years 1983 and 1984. However the code works when it reads
Bt[i+2]-(1-m)*Bt[i+1]+Rt[i]*Rerr-Ct[i]. I don't quite understand why
since it should be calculating all of the necessary inputs prior to
calculating Bt[i+2]. Any help would be greatly appreciated.
Thanks
#Model parameters
B0-7500
m-0.3
R0-B0*m
z-0.8
a-B0/R0*(1-(z-0.2)/(0.8*z))
b-(z-0.2)/(0.8*z*R0)
dat-data.frame(years=seq(1983,2004),cobs=c(19032324,19032324,17531618,2
0533029,20298099,20793744,23519369,23131780,19922247,17274513,17034419,1
2448318,4551585,4226451,7183688,7407924,7538366,7336039,8869193,7902341,
6369089,6211886))
stdr-runif(100,0,0.5)
stdc-runif(100,0,0.5)
BC-runif(1000,0,100)
#model calibration
calib-function(x){
v-sample(stdr,1)
cr-sample(stdc,1)
N-rnorm(1)
Bq-sample(BC,1)
Rerr-exp(N*v-(v^2/2))
Cerr-exp(N*cr-(cr^2/2))
Bt-vector();Bt[1]=B0;Bt[2]=B0
Rt-vector()
Ct-vector()
for (i in 1:length(x$years)){
Ct[i]-1/Bq*Bt[i]*Cerr
Rt[i]-Bt[i]/(a+b*Bt[i])
Bt[i+2]-(1-m)*Bt[i+1]+Rt[i]*Rerr-Ct[i+1]
}
out-new.env()
out$yr-x$years[1:length(x$years)]
out$Bt-Bt[1:length(x$years)]
out$Rt-Rt[1:length(x$years)]
out$Ct-Ct[1:length(x$years)]
out$stdr-v
out$stdc-cr
out$Bq-Bq
out$Rerr-Rerr
out$Cerr-Cerr
return(as.list(out))
}
test-calib(dat)
Cameron Guenther, Ph.D.
Associate Research Scientist
FWC/FWRI, Marine Fisheries Research
100 8th Avenue S.E.
St. Petersburg, FL 33701
(727)896-8626 Ext. 4305
[EMAIL PROTECTED]
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--
Jim Holtman
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+1 513 646 9390
What is the problem you are trying to solve?
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Re: [R] Need help with dataset formation problem
Tong Wang wrote: Hi, I have a data set , say, X : [1][2] mean 0 .8 sd1 3 I need to use it in do.call() , so when I refer to the first col of X, I need it to be a list with members mean, sd. thus I constructed X as a list of list : X[[1]]- list(mean=0, sd=1), X[[2]]-. . But this dataset is useless in other cases, for example, I can't pull out all the means as a vector. Can I get some suggestions on You can: sapply(X, [[, 1) Uwe Ligges what's the best way to handle it? (except preparing two copies of this data with different formats) Thanks a lot in advance. best __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] Need help to estimate the Coef matrices in mAr
Have you tried 'RSiteSearch(multivariate autoregression, functions)'? This produced 14 hits for me just now, the first of which mentions a package 'MSBVAR'. Have you looked at that? If that failed, I don't think it would be too hard to modify 'mAr.est' to do what you want. If it were my problem, I might a local copy of the function, then add an argument accepting a 2 or 3-dimensional array with numbers for AR coefficients to be fixed and NAs for the coefficients. Then I'd use 'debug' to walk through the function line by line until I figured out how to modify the function to do what I wanted. I haven't checked all the details, so I don't know for sure if this would work, but the function contains a line 'R = qr.R(qr((rbind(K, diag(scale, complete = TRUE)' which I would start by decomposing, possibly starting as follows: Z - rbind(K, diag(scale) I'd figure out how the different columns of Z relate to my problem, then modify it appropriately to get what I wanted. Another alternative would be to program it from scratch using something like 'optim' to minimize the sum of squares of residuals over the free parameters in my AR matrices. I'm confident I could make this work, even if the I somehow could not get it with either of the other two. There may be something else better, e.g., a Kalman filter representation, but I can't think how to do that off the top if my head. Hope this helps. Spencer Graves Arun Kumar Saha wrote: Dear R users, I am using mAr package to fit a Vector autoregressive model to my data. But here I want to put some predetermined values for some elements in coefficient matrix that mAr.est going to estimate. For example if p=3 then I want to put A3[1,3] = 0 and keep rest of the elements of coefficient matrices to be determined by mAr.est. Can anyone please tell me how can I do that? Sincerely yours, Arun [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] need help with an interaction term
Hello! Im fitting a model with glm(family binomial). The best model counts 9 Variables and includes an interaction term that was generated by the product of to continuous variables (a*b). All variables are correlated under a value of 0.7 (Spearman rank order) While the estimates of both main effects are negativ, the resulting interaction term is positiv. This change of sign makes it difficult to interpret the model and above all, is this perhaps due to a bad variable choice ? Thanks a lot for helping Christian ___ Viren-Scan für Ihren PC! Jetzt für jeden. Sofort, online und kostenlos. Gleich testen! http://www.pc-sicherheit.web.de/freescan/?mc=02 __ R-help@stat.math.ethz.ch 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] need help with an interaction term
Christian Jones wrote: Hello! I�m fitting a model with glm(family binomial). The best model counts 9 Variables and includes an interaction term that was generated by the product of to continuous variables (a*b). All variables are correlated under a value of 0.7 (Spearman rank order) While the estimates of both main effects are negativ, the resulting interaction term is positiv. This change of sign makes it difficult to interpret the model and above all, is this perhaps due to a bad variable choice ? Thanks a lot for helping Rather than trying to interpret the model coefficients directly, you might visualize the a*b interaction effect. The effects package by John Fox is very useful for this: http://cran.r-project.org/doc/packages/effects.pdf Christian ___ Viren-Scan für Ihren PC! Jetzt für jeden. Sofort, online und kostenlos. Gleich testen! http://www.pc-sicherheit.web.de/freescan/?mc=02 __ R-help@stat.math.ethz.ch 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. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch 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] need help with an interaction term
Hello Chuck, many thanks for your advice. IŽll go through the package and see if IŽll manage to visualize the interaction effect this time as I already tried it with a special tool for displaying models with interaction terms in 3D. http://www.uni-oldenburg.de/landeco/Download/Software/LR_Mesh/LR_Mesh.htm but could not yield any plausible results. Hopefully this time... best regards Christian -Ursprüngliche Nachricht- Von: Chuck Cleland [EMAIL PROTECTED] Gesendet: 31.08.06 14:16:12 An: Christian Jones [EMAIL PROTECTED] CC: r-help@stat.math.ethz.ch Betreff: Re: [R] need help with an interaction term Christian Jones wrote: Hello! Iï¿œm fitting a model with glm(family binomial). The best model counts 9 Variables and includes an interaction term that was generated by the product of to continuous variables (a*b). All variables are correlated under a value of 0.7 (Spearman rank order) While the estimates of both main effects are negativ, the resulting interaction term is positiv. This change of sign makes it difficult to interpret the model and above all, is this perhaps due to a bad variable choice ? Thanks a lot for helping Rather than trying to interpret the model coefficients directly, you might visualize the a*b interaction effect. The effects package by John Fox is very useful for this: http://cran.r-project.org/doc/packages/effects.pdf Christian ___ Viren-Scan für Ihren PC! Jetzt für jeden. Sofort, online und kostenlos. Gleich testen! http://www.pc-sicherheit.web.de/freescan/?mc=02 __ R-help@stat.math.ethz.ch 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. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch 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] Need help to estimate the Coef matrices in mAr
Dear R users, I am using mAr package to fit a Vector autoregressive model to my data. But here I want to put some predetermined values for some elements in coefficient matrix that mAr.est going to estimate. For example if p=3 then I want to put A3[1,3] = 0 and keep rest of the elements of coefficient matrices to be determined by mAr.est. Can anyone please tell me how can I do that? Sincerely yours, Arun [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Need help with difficulty loading page www.bioconductor.org
I didn't see a response to this, and am not an expert, but wanted to point you in the right direction. You should ask this question on the bioconductor mailing list. The site is very much alive at this end (though I'm very close to it, physically), so you'll need to provide some more information about the problems you're experiencing. At a minimum it would help to include the output of the R command sessionInfo() If you're using Windows you might also look at mailing list threads dealing with server proxies. Searchable archives are at http://dir.gmane.org/gmane.science.biology.informatics.conductor this link http://article.gmane.org/gmane.science.biology.informatics.conductor/2152/match=internet2 and searching for internet2 might be a good start. Martin Debashis Bhattacharya [EMAIL PROTECTED] writes: The page is either too busy, or there is something seriously wrong with access to this page. Most of the time, trying to reach www.bioconductor.org results in failure. Only once in a blue moon, do I get through. In fact, thus far, I have not been able to install bioconductor, since the first source(...) command from the R command window -- following instruction on www.bioconductor.org page, that I did manage to reach, one time -- has failed, every time. Please help. Debashis Bhattacharya. __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] Need help with difficulty loading page www.bioconductor.org
The page is either too busy, or there is something seriously wrong with access to this page. Most of the time, trying to reach www.bioconductor.org results in failure. Only once in a blue moon, do I get through. In fact, thus far, I have not been able to install bioconductor, since the first source(...) command from the R command window -- following instruction on www.bioconductor.org page, that I did manage to reach, one time -- has failed, every time. Please help. Debashis Bhattacharya. __ R-help@stat.math.ethz.ch 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] need help in building an R package with Fortran source
Hello all! Can someone give me instructions how to build on PC/Win an R package with some embedded Fortran functions (preferable source, not dll!). The package should then be compilable and work on PC/Win as well as on Unix derivatives. Thanks a lot Meinhard Ploner __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] need help in building an R package with Fortran source
Meinhard Ploner wrote: Hello all! Can someone give me instructions how to build on PC/Win an R package with some embedded Fortran functions (preferable source, not dll!). The package should then be compilable and work on PC/Win as well as on Unix derivatives. How to build source packages is described in the manual Writing R Extensions. Uwe Ligges Thanks a lot Meinhard Ploner __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] need help in building an R package with Fortran source
Uwe recommended the reading of help desk in Rnews 2005/2 http://cran.r-project.org/doc/Rnews/Rnews_2005-2.pdf Thanks, it looks good, as my problems were mainly due to Perl and some compilers!! Meinhard __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] need help for superpc package
Hi, I am using the superpc package. By superpc.train (data, type=regression) I calculated the standardized regression coefficients for measuring the univariate effect of each feature on a continuous response y. By superpc.cv(compute.fullcv=TRUE, compute.preval=FALSE, n.components=3, n.fold=10) I used cross validation to estimate the optimal feature threshold and choose only those features whose univariate coefficient exceeds the threshold. To choose the best threshold I plotted the cross-validation curves by superpc.plotcv(cv.type=full'). I work with 55 features and 43 samples. I noticed that by repeating the call of superpc.cv (with the same argument values) and then plotting the curves by superpc.plotcv, the curves change and sometimes the best threshold changes value. Please note that I chose compute.fullcv =TRUE, therefore full cross-validation is done. Moreover, if n.fold=10 the result is not significant for any threshold value (the three curves are under the three horizontal lines -likelihood ratio test). However with n.fold10 there are significant results. I tested also the example provided by the user manual for the explanation of the superpc.plotcv routine. In this case, by repeating the call of superpc.cv (with the same argument values) the three curves change, but they always remain under the three horizontal lines. So it seems that the result is always not significant (likelihood ratio). Is my interpretation of the likelihood ratio test correct? As the curves change, has someone any explanation or solution for the correct choice of the best threshold value? I also noticed that by following the instructions of the superpc tutorial (http://www-stat.stanford.edu/~tibs/superpc/tutorial.html) the obtained cv.plot is not similar to the one provided in the tutorial as pdf version. I use R 2.2.1 version. Is it possible that the rnorm() function (seed=4648) did not generate the same set of numbers as that used by R. Tibshirani? Thank You in advance Rossana --- Rossana Dell'Anna, PhD ITC-irst Centre for Scientific and Technological Research Via Sommarive, 18 - 38050 Trento, ITALY ph: +39 0461 314 486 e-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] need help in tune.nnet
You use tune function to find optimal parameters needed for particular classification algorithm. I had more experience with tune.svm but, I would try first to put parameters covering the whole possible range of each variable (in which algorithm do not crash), for example c(4^-2, 4^-1, 4^0, 4^1, 4^2) look at the results and than narrow down the search in the best ranges. For allowed ranges of parameters you will need to experiment or study documentation of your chosen classifier (nnet). Jarek Tuszynski -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of madhurima bhattacharjee Sent: Friday, March 10, 2006 5:38 AM To: r-help@stat.math.ethz.ch; Bioconductor Subject: [R] need help in tune.nnet Dear R people, I want to use the tune.nnet function of e1071 package to tune nnet . I am unable to understand the parameters of tune.nnet from the e1071 pdf document. I have performed nnet on a traindata and want to test it for class prediction with a testdata. I want to know the values of size,decay,range etc. parameters for which the prediction of testdata is best. Can anyone please tell me how to do this with the tune.nnet function. Anticipating quick response. Thanks and Regards, Madhurima. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] need help in tune.nnet
Dear R people, I want to use the tune.nnet function of e1071 package to tune nnet . I am unable to understand the parameters of tune.nnet from the e1071 pdf document. I have performed nnet on a traindata and want to test it for class prediction with a testdata. I want to know the values of size,decay,range etc. parameters for which the prediction of testdata is best. Can anyone please tell me how to do this with the tune.nnet function. Anticipating quick response. Thanks and Regards, Madhurima. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Need help on Coxph
Hi all,
I have a dataset which includes 84 rows and 4313 columns. Starting from the
2nd row, each row represents
a patient. The 1st column is for arrayID
2nd column is for time
3rd column is for cancer
4th column is for patientID
Starting for the 5th columns, each column's ID is like
CTC_232B23, RP11_181G12, RP11_62M23...
I extract first 5 rows and 7 columns and get the data in below:
arrayID time cancer patientID CTC_232B23 RP11_181G12 RP11_62M23
X1747_4224 37.633 0 30635 -0.02665-0.02665 -0.038025
X1750_4214 89.300 0 22158 -0.02665-0.02665 -0.038025
X1751_4208 53.333 0 31669 -0.02665-0.02665 -0.038025
X1754_4194 39.467 0 32849 -0.02665-0.02665 -0.038025
X1775_4497 84.900 0 33563 -0.02665-0.02665 -0.038025
Finally I would like to build the cox model for each column (starting from
the 5th column). The code would be like:
mod.allison - coxph( Surv(time, cancer) ~ CTC_232B23 , data=Rossi2)
mod.allison - coxph( Surv(time, cancer) ~ RP11_181G12 , data=Rossi2)
mod.allison - coxph( Surv(time, cancer) ~ RP11_62M23 , data=Rossi2)
I have no problem getting the result. However, since there are 4309 columns
(counted begining at the 5th column), I decide to make a 4309*1 matrix
(called BACs) to store the name of each column. Then run a loop like:
for (i in 1:4309){
mod.allison - coxph( Surv(time, cancer) ~ BAC[i,1], data=Rossi2)
}
mod.allison
However, I got the error. Would you like to give me some suggestions about
this?
Many thanks in advance!
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[R] need help in nnet
Hello Everybody, I would like to know how to interpret the result of nnet function of R. My result looks like this: # weights: 24 initial value 6.533893 iter 10 value 4.616299 iter 20 value 4.616120 iter 30 value 4.616109 iter 30 value 4.616109 final value 4.616109 converged cres true 1 1 10 2 3 Can anyone please help me asap? Thanks and Regards, Madhurima. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Need help for a statistical problem (See the posting guide)
In response to a thread where a statistical question unrelated to R was asked, Uwe Ligges wrote: PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Please ask a local statistical consultant for help. Uwe Ligges Perhaps Uwe's admonition to do read the posting guide was just a knee jerk reaction to an unrecognized poster's name. Of course, if the poster did read the posting guide, they would have learned that : Questions about statistics: The R mailing lists are primarily intended for questions and discussion about the R software. However, questions about statistical methodology are sometimes posted. If the question is well-asked and of interest to someone on the list, it may elicit an informative up-to-date answer. See also the Usenet groups sci.stat.consult (applied statistics and consulting) and sci.stat.math (mathematical stat and probability). The language here is so equivocal! OK, it is really for R, but statistical questions are asked and you might get an informative and up-to-date answer if you do it well. Sounds good to me! I might start using r-help for my statistical questions. Thanks for referring me to the posting guide Uwe (though I am not sure why it was relevant the the original post). My point: If r-help does not want statistical questions, and people who ask statistical questions are referred to the posting guide, shouldn't the posting guide *actually* say no statistical questions! Brett __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Need help for a statistical problem
Hello Dear I need to select among 700 objects a good representative sample. These objects could be residential houses, commercial buildings, trucks, etc. How to get a good sample size and select a set of objects that is very representative. The second part of my question is to find a statistical model in R that detects objects that are most likely used as their owners told the municipality. For example, if a restaurant is suppose to have 5 tables, we want to know that it doesn't have more. The goal is to have a model that flags such restaurant for inspection. Cheers, Dan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Need help for a statistical problem
james brown wrote: Hello Dear I need to select among 700 objects a good representative sample. These objects could be residential houses, commercial buildings, trucks, etc. How to get a good sample size and select a set of objects that is very representative. The second part of my question is to find a statistical model in R that detects objects that are most likely used as their owners told the municipality. For example, if a restaurant is suppose to have 5 tables, we want to know that it doesn't have more. The goal is to have a model that flags such restaurant for inspection. Cheers, Dan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Please ask a local statistical consultant for help. Uwe Ligges __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] need help with matrix manipulation
I hope my problem is not too basic to post here. I am a beginner having problems with some matrix manipulation. The data I am working with are sites with hourly ozone readings and is in a matrix where each row is a site and each column is an hourly reading. So for 10 sites, one day's worth of data is a 10x24 matrix - column 1 is the ozone measurement for midnight GMT, column 2 is ozone at 1:00am GMT, etc. My challenge is that I want to create a new matrix with the same sites, BUT I want the first column to be the hourly ozone reading at midnight LOCAL time. If all the sites were in the same time zone this would be easy - for the US Eastern time zone I could do something like: oz.est[, 1:19] - oz.gmt[, 6:24] The problem is the sites are in different time zones, and I have a separate vector that indicates which site belongs to which time zone. So sites in the Eastern time zone I want to extract columns 6-24 from the GMT matrix, sites in the Central time zone I want to extract columns 7-24 from the GMT matrix, etc. Is there a clever way to use matrix indices on my GMT matrix to extract the columns I need for the sites in the different time zones? I have been trying different things like this: # VECTOR WITH HOUR TIME DIFFERENCE BETWEEN SITE AND GMT start.hr - c(6,7,6,8,7,5,7,6,5,6) # THIS DOESN'T WORK oz.local[ , 1: (24-start.hr) ] - oz.gmt [, (start.hr+1) : 24 ] # THIS DOESN'T WORK EITHER oz.local[ , rep(1,nrow(oz.gmt)) : (24-start.hr) ] - oz.gmt [, (start.hr+1) : rep(24,nrow(oz.gmt)) ] Ultimately I will be working with over 10,000 sites and hourly data over 3 months so my data matrix will be something like 10,220 x 2208 I'd appreciate any suggestions. Thanks! Renee Jaramillo [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] need help with matrix manipulation
This will give a list, one element per row of oz.gmt, which contains the differently sized vectors as components: idx - seq(along = start.hr) f - function(i) oz.gmt[i, start.hr[i]:24] lapply(idx, f) On 12/5/05, Jaramillo, Renee [EMAIL PROTECTED] wrote: I hope my problem is not too basic to post here. I am a beginner having problems with some matrix manipulation. The data I am working with are sites with hourly ozone readings and is in a matrix where each row is a site and each column is an hourly reading. So for 10 sites, one day's worth of data is a 10x24 matrix - column 1 is the ozone measurement for midnight GMT, column 2 is ozone at 1:00am GMT, etc. My challenge is that I want to create a new matrix with the same sites, BUT I want the first column to be the hourly ozone reading at midnight LOCAL time. If all the sites were in the same time zone this would be easy - for the US Eastern time zone I could do something like: oz.est[, 1:19] - oz.gmt[, 6:24] The problem is the sites are in different time zones, and I have a separate vector that indicates which site belongs to which time zone. So sites in the Eastern time zone I want to extract columns 6-24 from the GMT matrix, sites in the Central time zone I want to extract columns 7-24 from the GMT matrix, etc. Is there a clever way to use matrix indices on my GMT matrix to extract the columns I need for the sites in the different time zones? I have been trying different things like this: # VECTOR WITH HOUR TIME DIFFERENCE BETWEEN SITE AND GMT start.hr - c(6,7,6,8,7,5,7,6,5,6) # THIS DOESN'T WORK oz.local[ , 1: (24-start.hr) ] - oz.gmt [, (start.hr+1) : 24 ] # THIS DOESN'T WORK EITHER oz.local[ , rep(1,nrow(oz.gmt)) : (24-start.hr) ] - oz.gmt [, (start.hr+1) : rep(24,nrow(oz.gmt)) ] Ultimately I will be working with over 10,000 sites and hourly data over 3 months so my data matrix will be something like 10,220 x 2208 I'd appreciate any suggestions. Thanks! Renee Jaramillo [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Need help on ARIMA (time series analysis)
Have you received a reply to this post? I have not seen one. If you
would still like some suggestions from this group, please provide more
detail on your question, as requested in the posting guide
(www.R-project.org/posting-guide.html), including which version of R
under which operating system.
If I understand your post, you have two questions: (1) the error
message and (2) the need for a loop.
Regarding the error message, I can not replicate it. The message
suggests a series that is nonstationary. However, I don't get that
message from 'arima(1:50, order=c(1,0,1))', which is clearly
nonstationary. What's in the file C:\\R\\arima.R? Can you replicate
the error without using a source command?
Regarding the need for a loop, I'm sorry, but I don't know enough
about time series in R to answer your question. I'm currently studying
Venables and Ripley (2002) Modern Applied Statistics with S, 4th ed.
(Springer), ch. 14. If you are not familiar with this book, I highly
recommend it. Ch. 14 is on time series. If you would like more
comments on your question regarding a loop, I suggest you rephrase your
question in terms of a standard example like lh, fitting to, e.g.,
windows of length 30 in this series of 48 observations, explaining also
very briefly what you are trying to accomplish with the loop.
spencer graves
park wrote:
Hi,
I am so novice in using R. I have some problems in my R script below
which fits time series data and predict it one-step ahead. Here is a
brief explanation on what I try to achieve
Th16k is time series data (500 data points). The size of window for
fitting and predicting is 50 (data points). As you can easily discover
from my code, (fixed) window is moving/sliding to get next one-step
ahead prediction. The predicted value will be saved in pth.
The problem is, every time I execute following script, I got error
saying
source(C:\\R\\arima.R)
Error in arima(temp, order = c(1, 0, 1)) :
non-stationary AR part from CSS
I think there should be better way to achieve this goal without using
for loop. If you can share your knowledge, please advise me!!! :-)
---
-
w - 50
pth - th16k[1:w]
limit - length(th16k)-w
for (i in 1:limit) {
ws - i
we - i+w-1
temp - th16k[ws:we]
fit - arima(temp, order=c(1, 0, 1))
pred - predict(fit, n.ahead=1)
pth[i+w] - pred$pred
}
plot(pth)
---
-
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Senior Development Engineer
PDF Solutions, Inc.
333 West San Carlos Street Suite 700
San Jose, CA 95110, USA
[EMAIL PROTECTED]
www.pdf.com http://www.pdf.com
Tel: 408-938-4420
Fax: 408-280-7915
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Re: [R] Need help on ARIMA (time series analysis)
Regarding the loop, the code below:
ws - i
we - i+w-1
temp - th16k[ws:we]
can be written as:
temp - th16k[seq(i, length = w)]
or you can get rid of the loop entirely using embed
or using running in package gtools or rapply in the zoo package.
park wrote:
Hi,
I am so novice in using R. I have some problems in my R script below
which fits time series data and predict it one-step ahead. Here is a
brief explanation on what I try to achieve
Th16k is time series data (500 data points). The size of window for
fitting and predicting is 50 (data points). As you can easily discover
from my code, (fixed) window is moving/sliding to get next one-step
ahead prediction. The predicted value will be saved in pth.
The problem is, every time I execute following script, I got error
saying
source(C:\\R\\arima.R)
Error in arima(temp, order = c(1, 0, 1)) :
non-stationary AR part from CSS
I think there should be better way to achieve this goal without using
for loop. If you can share your knowledge, please advise me!!! :-)
---
-
w - 50
pth - th16k[1:w]
limit - length(th16k)-w
for (i in 1:limit) {
ws - i
we - i+w-1
temp - th16k[ws:we]
fit - arima(temp, order=c(1, 0, 1))
pred - predict(fit, n.ahead=1)
pth[i+w] - pred$pred
}
plot(pth)
---
-
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Spencer Graves, PhD
Senior Development Engineer
PDF Solutions, Inc.
333 West San Carlos Street Suite 700
San Jose, CA 95110, USA
[EMAIL PROTECTED]
www.pdf.com http://www.pdf.com
Tel: 408-938-4420
Fax: 408-280-7915
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[R] Need help write a function
Dear all,
I am still learning R with write a small function for my self.
I was wondering if someone can help me to write a R function formula below:
Z_k (x) = \sum_{i=0}^{i=k} \binom{n}{i} (m-1)^i
Thanks a million in advance,
Sincerely,
Jan Sabee
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Re: [R] Need help write a function
Jan Sabee wrote:
Dear all,
I am still learning R with write a small function for my self.
I was wondering if someone can help me to write a R function formula below:
Z_k (x) = \sum_{i=0}^{i=k} \binom{n}{i} (m-1)^i
Thanks a million in advance,
Sincerely,
Jan Sabee
(This smells like a homework problem.)
What is m? Your Z_k is a function of x and there is no x on the RHS.
Are you trying to re-write pbinom?
--sundar
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[R] Need help on ARIMA (time series analysis)
Hi,
I am so novice in using R. I have some problems in my R script below
which fits time series data and predict it one-step ahead. Here is a
brief explanation on what I try to achieve
Th16k is time series data (500 data points). The size of window for
fitting and predicting is 50 (data points). As you can easily discover
from my code, (fixed) window is moving/sliding to get next one-step
ahead prediction. The predicted value will be saved in pth.
The problem is, every time I execute following script, I got error
saying
source(C:\\R\\arima.R)
Error in arima(temp, order = c(1, 0, 1)) :
non-stationary AR part from CSS
I think there should be better way to achieve this goal without using
for loop. If you can share your knowledge, please advise me!!! :-)
---
-
w - 50
pth - th16k[1:w]
limit - length(th16k)-w
for (i in 1:limit) {
ws - i
we - i+w-1
temp - th16k[ws:we]
fit - arima(temp, order=c(1, 0, 1))
pred - predict(fit, n.ahead=1)
pth[i+w] - pred$pred
}
plot(pth)
---
-
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[R] Need help understanding/resolving build error message
Can someone provide help to resolve this build failure?
Thank you,
John Zajd
C:\ConstellaGroup\EPA\RAGG\packagercmd check RAGG
* checking for working latex ... OK
* using log directory 'C:/ConstellaGroup/EPA/RAGG/package/RAGG.Rcheck'
* using R version 2.1.0, 2005-04-18
* checking for file 'RAGG/DESCRIPTION' ... OK
* this is package 'RAGG' version '1.5'
* checking if this is a source package ... OK
installing R.css in C:/ConstellaGroup/EPA/RAGG/package/RAGG.Rcheck
-- Making package RAGG
adding build stamp to DESCRIPTION
Error in if (regexpr(dep_regexp, dep) == -1) { :
missing value where TRUE/FALSE needed
Execution halted
make[2]: *** [frontmatter] Error 1
make[1]: *** [all] Error 2
make: *** [pkg-RAGG] Error 2
*** Installation of RAGG failed ***
Removing 'C:/ConstellaGroup/EPA/RAGG/package/RAGG.Rcheck/RAGG'
ERROR
Installation failed.
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Re: [R] need help
Weiwei Shi wrote:
Hi, there:
I think i need to re-phrase my question since last time I did not get
any reply but i think the question is not that hard, probably i did
not make the question clear:
I want to find cases like
35, 90, 330, 330, 335
from the rest which look like
3, 3, 3, 3.2, 3.3
4, 4.4, 4.5, 4.6, 4.7
basically there is one (or more) big 'gap' in the case i seek.
Hi Weiwei,
I think your method of defining a central value for the large proportion
of values and then setting a criterion for outliers is valid (or at
least as valid as many other ways of defining outliers). However, here
is a different method, sorting the vector of values and then looking for
a gap with a specified multiple (gap.prop) of the mean differences
between the smaller values. It returns the first value after the gap
(easily changed to all the values after). To account for vectors that
have negative values the minimum value is subtracted when calculating
newx and then added to the result. For your data, a gap.prop of 20
works, but the default value of 10 doesn't. It also won't work where
large values are typical and small ones are the outliers (well, it will
indicate where the gap is).
Jim
find.first.gap-function(x,gap.prop=10) {
lenx-length(x)
newx-sort(x)-min(x)
not.found-1
gap.pos-2
# set the
mean.diff-newx[2]-newx[1]
while(not.found gap.pos = lenx) {
this.diff-newx[gap.pos]-newx[gap.pos-1]
print(c(mean.diff,this.diff))
if(mean.diff != 0) {
if(this.diff/mean.diff = gap.prop) not.found-0
else gap.pos-gap.pos+1
}
else gap.pos-gap.pos+1
mean.diff-(this.diff+mean.diff*(gap.pos-1))/gap.pos
}
return(newx[gap.pos]+min(x))
}
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[R] need help
Hi, there: I think i need to re-phrase my question since last time I did not get any reply but i think the question is not that hard, probably i did not make the question clear: I want to find cases like 35, 90, 330, 330, 335 from the rest which look like 3, 3, 3, 3.2, 3.3 4, 4.4, 4.5, 4.6, 4.7 basically there is one (or more) big 'gap' in the case i seek. thanks, weiwei -- Weiwei Shi, Ph.D Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] need help
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Weiwei Shi Sent: Friday, August 12, 2005 2:05 PM To: r-help Subject: [R] need help Hi, there: I think i need to re-phrase my question since last time I did not get any reply but i think the question is not that hard, probably i did not make the question clear: I want to find cases like 35, 90, 330, 330, 335 from the rest which look like 3, 3, 3, 3.2, 3.3 4, 4.4, 4.5, 4.6, 4.7 basically there is one (or more) big 'gap' in the case i seek. thanks, weiwei -- Weiwei Shi, Ph.D Weiwei, You will have to specify what you mean by a big gap before anyone can help. And I still don't understand what your data look like. Is 35, 90, 330, 330, 335 supposed to represent a sequence or a row of a matrix (or data frame)? Dan Nordlund Bothell, WA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] need help
Hi, there: here is some part from my previous email: [,1] [,2] [,3] [,4] [,5] [1,] 34.216166 96.928587 330.125990 330.183222 330.201215 [2,] 2.819183 8.134491 8.275841 8.525256 8.828448 [3,] 2.819183 7.541680 7.550333 8.374636 8.690998 [4,] 4.672551 5.036353 5.072710 5.152218 5.223204 [5,] 5.470131 5.500513 5.674139 5.689151 5.770423 [6,] 4.480287 4.628300 4.797686 4.814106 4.823345 I want to filter out the first 3 cases from the rest and the criteria is I am looking for a gap. My way is using std(eachrow)/median(each) and set up a threshold, which is very naive, but fast and good enough. But I want it better and more academic. Please be advised. I think clustering might help, but it needs to be quick since t2 has 3 rows. Thanks, On 8/12/05, Daniel Nordlund [EMAIL PROTECTED] wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Weiwei Shi Sent: Friday, August 12, 2005 2:05 PM To: r-help Subject: [R] need help Hi, there: I think i need to re-phrase my question since last time I did not get any reply but i think the question is not that hard, probably i did not make the question clear: I want to find cases like 35, 90, 330, 330, 335 from the rest which look like 3, 3, 3, 3.2, 3.3 4, 4.4, 4.5, 4.6, 4.7 basically there is one (or more) big 'gap' in the case i seek. thanks, weiwei -- Weiwei Shi, Ph.D Weiwei, You will have to specify what you mean by a big gap before anyone can help. And I still don't understand what your data look like. Is 35, 90, 330, 330, 335 supposed to represent a sequence or a row of a matrix (or data frame)? Dan Nordlund Bothell, WA -- Weiwei Shi, Ph.D Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] need help on building packages
Good day, I have been trying to build packages for R unix, and the check always failed around the LaTeX area, altho LaTex was installed. I dont know wich test dosent pass check because there are a few test made and only one error message for all those test done in 3rd step of the check. Also could you refer me to a valid format of the package, because I am starting to believe the package format(directories+files) might have changed for version 2.0.0. I use R 2.0.1, I am completing a package for R-windows XP, and porting it to R for Unix. I need help to complete those tasks cause I have tried all I could to debug the package building error I was getting. Thank you Éric Lamontagne Université du Québec à Chicoutimi __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] need help on building packages
Erik Lamontagne wrote: Good day, I have been trying to build packages for R unix, and the check always failed around the LaTeX area, altho LaTex was installed. I dont know wich test dosent pass check because there are a few test made and only one error message for all those test done in 3rd step of the check. Usually there is useful information in the pkg.Rcheck directory that is left after the check. In particular, you'll see the .log file that latex produced, and it might be able to help you. Also could you refer me to a valid format of the package, because I am starting to believe the package format(directories+files) might have changed for version 2.0.0. See the R extensions manual. I use R 2.0.1, I am completing a package for R-windows XP, and porting it to R for Unix. I need help to complete those tasks cause I have tried all I could to debug the package building error I was getting. Does it pass Rcmd check in Windows? Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] need help on computing double summation
If I understood correctly, the following might be simpler (dat is the data
frame holding the data):
sum(ave(dat$x, dat$id, FUN=scale, scale=FALSE) *
+ ave(dat$y, dat$id, FUN=scale, scale=FALSE))
[1] 6.229377
Andy
From: Huntsinger, Reid
You could do something like
ids - unique(mydata$id)
ans - vector(length=length(ids), mode=list)
for (i in ids) {
g - which(mydata$id == i)
ans[[i]] - (length(g) - 1)*cov(mydata$x[g], mydata$y[g])
}
ans
but cov() returns NA for length 1 vectors, so you'd want an
if (length(g) ==
1) ans[i] - 0 else ans[i] - ... construction.
This is almost brute force; you could also use tapply, as follows:
sx - tapply(mydata$x,INDEX=mydata$id,FUN=sum)
sy - tapply(mydata$y,INDEX=mydata$id,FUN=sum)
sxy - tapply(mydata$x*mydata$y, INDEX=mydata$id, FUN=sum)
n - tapply(mydata$id,INDEX=mydata$id,FUN=length) # or use table()!
and now your inner sum is
sxy - 2*sx*(sy/n) + n*(sx/n)*(sy/n) = sxy - sx*sy/n
so
sum(sxy - sx*sy/n) should do.
One more approach is to make your dataset into a list of data
frames, one
for each id, then use lapply(). The list can be created by
split(). In one
line,
lapply(split(mydata,f=mydata$id),function(z) (length(z$x) -
1)*cov(z$x,z$y))
and take sum(,na.rm=TRUE) to remove the NAs due to single ids
that you want
to be zeros.
Reid Huntsinger
Reid Huntsinger
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Kerry Bush
Sent: Wednesday, June 15, 2005 11:41 AM
To: r-help@stat.math.ethz.ch
Subject: [R] need help on computing double summation
Dear helpers in this forum,
This is a clarified version of my previous
questions in this forum. I really need your generous
help on this issue.
Suppose I have the following data set:
..
Now I want to compute the following double summation:
sum_{i=1}^k
sum_{j=1}^{n_i}(x_{ij}-mean(x_i))*(y_{ij}-mean(y_i))
i is from 1 to k,
indexing the ith subject id; and j is from 1 to n_i,
indexing the jth observation for the ith subject.
in the above expression, mean(x_i) is the mean of x
values for the ith
subject, mean(y_i) is the mean of y values for the ith
subject.
Is there a simple way to do this in R?
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[R] need help on computing double summation
Dear helpers in this forum,
This is a clarified version of my previous
questions in this forum. I really need your generous
help on this issue.
Suppose I have the following data set:
id x y
023 1 2
023 2 5
023 4 6
023 5 7
412 2 5
412 3 4
412 4 6
412 7 9
220 5 7
220 4 8
220 9 8
..
Now I want to compute the following double summation:
sum_{i=1}^k
sum_{j=1}^{n_i}(x_{ij}-mean(x_i))*(y_{ij}-mean(y_i))
i is from 1 to k,
indexing the ith subject id; and j is from 1 to n_i,
indexing the jth observation for the ith subject.
in the above expression, mean(x_i) is the mean of x
values for the ith
subject, mean(y_i) is the mean of y values for the ith
subject.
Is there a simple way to do this in R?
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Re: [R] need help on computing double summation
You could do something like
ids - unique(mydata$id)
ans - vector(length=length(ids), mode=list)
for (i in ids) {
g - which(mydata$id == i)
ans[[i]] - (length(g) - 1)*cov(mydata$x[g], mydata$y[g])
}
ans
but cov() returns NA for length 1 vectors, so you'd want an if (length(g) ==
1) ans[i] - 0 else ans[i] - ... construction.
This is almost brute force; you could also use tapply, as follows:
sx - tapply(mydata$x,INDEX=mydata$id,FUN=sum)
sy - tapply(mydata$y,INDEX=mydata$id,FUN=sum)
sxy - tapply(mydata$x*mydata$y, INDEX=mydata$id, FUN=sum)
n - tapply(mydata$id,INDEX=mydata$id,FUN=length) # or use table()!
and now your inner sum is
sxy - 2*sx*(sy/n) + n*(sx/n)*(sy/n) = sxy - sx*sy/n
so
sum(sxy - sx*sy/n) should do.
One more approach is to make your dataset into a list of data frames, one
for each id, then use lapply(). The list can be created by split(). In one
line,
lapply(split(mydata,f=mydata$id),function(z) (length(z$x) - 1)*cov(z$x,z$y))
and take sum(,na.rm=TRUE) to remove the NAs due to single ids that you want
to be zeros.
Reid Huntsinger
Reid Huntsinger
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Kerry Bush
Sent: Wednesday, June 15, 2005 11:41 AM
To: r-help@stat.math.ethz.ch
Subject: [R] need help on computing double summation
Dear helpers in this forum,
This is a clarified version of my previous
questions in this forum. I really need your generous
help on this issue.
Suppose I have the following data set:
..
Now I want to compute the following double summation:
sum_{i=1}^k
sum_{j=1}^{n_i}(x_{ij}-mean(x_i))*(y_{ij}-mean(y_i))
i is from 1 to k,
indexing the ith subject id; and j is from 1 to n_i,
indexing the jth observation for the ith subject.
in the above expression, mean(x_i) is the mean of x
values for the ith
subject, mean(y_i) is the mean of y values for the ith
subject.
Is there a simple way to do this in R?
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[R] Need Help - Urgent
Hello, I am a student and some really urgent help.I am using R software and while creating a grid with eight elements its showing the error and while if i do it with seven it says that the memory is not sufficient... here is the line ...with the error Z-as.matrix(expand.grid(x,y,x,y,t,s,t,s)) Error in rep.int(rep.int(seq(length = nx), rep.int(rep.fac, nx)), orep) : cannot allocate vector of length 112896 Is it possible to somehow increase the default size of the matrix? please help.. THanking you nivesh pawar __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Need Help - Urgent
You're asking for a matrix with length(x)^2*length(y)^2*length(s)^2*length(t)^2 rows. What are these lengths? Is that what you're expecting? Perhaps you want the distinct factor levels in x,y,s,t rather than x,y,s,t themselves? Reid Huntsinger -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nivesh Pawar Sent: Friday, June 03, 2005 8:00 AM To: r-help@stat.math.ethz.ch Subject: [R] Need Help - Urgent Hello, I am a student and some really urgent help.I am using R software and while creating a grid with eight elements its showing the error and while if i do it with seven it says that the memory is not sufficient... here is the line ...with the error Z-as.matrix(expand.grid(x,y,x,y,t,s,t,s)) Error in rep.int(rep.int(seq(length = nx), rep.int(rep.fac, nx)), orep) : cannot allocate vector of length 112896 Is it possible to somehow increase the default size of the matrix? please help.. THanking you nivesh pawar __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
