[R] Managing axis labels
Dear R-users, I would like to ask probably a silly thing. For some reason, I need x-axis and y-axis labels to be of different size. Here is a little example where I want "ϑ" to appear bigger than "Concentration". I have tried in the following way, but it is not working. x<-seq(1,10,1) y<-seq(2,20,2) plot(x, y, xlab=expression(vartheta), ylab="Concentration", cex.axis=1.5) axis(1, cex.lab=3.0) axis(2, cex.lab=2.0) Any suggestion will be much appreciated. Kind Regards, Jamil. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] No visible binding for global variable
Dear Prof John,
I have got the points now. Many thanks for your suggestions.
Regards,
Jamil.
On 28 January 2017 at 00:27, Fox, John <j...@mcmaster.ca> wrote:
> Dear Jamil,
>
> Presumably, the variables alloc.dose, r0, r1, and r2 will exist in the
> global environment when you call the compiled function lf1.c(), but didn’t
> exist when you compiled the function. If so, then lf1.c() should work
> properly despite the notes (not errors, or even warnings) that was printed.
>
> On the other hand, relying on global data in a function is poor
> programming style — it would be better to make alloc.dose, etc., arguments
> to the function. As well, if you’re compiling the function to improve
> efficiency, then you probably also want to compile psi0(), etc.
>
> I hope that this helps,
> John
>
> John Fox
> Sen. William McMaster Professor of Social Statistics
> McMaster University
> Hamilton, Ontario, Canada
> Web: http::/socserv.mcmaster.ca/jfox
>
> > On Jan 27, 2017, at 10:43 AM, Naser Jamil <jamilnase...@gmail.com>
> wrote:
> >
> > Dear R-users,
> > I would like to seek your suggestion. I have the following code which
> runs
> > smoothly. But when I compile the function (lf1.c), it shows "no visible
> > binding for global variable" for some of the arguments.
> >
> > ###
> >
> > library(compiler)
> >
> >
> > psi0<-function(theta1,theta2,theta3,theta4,x){
> > z1<-exp(theta1+theta2*x)
> > z2<-exp(theta3+theta4*x)
> > 1/((1+z1)*(1+z2))
> > }
> >
> > psi1<-function(theta1,theta2,theta3,theta4,x){
> > z1<-exp(theta1+theta2*x)
> > z2<-exp(theta3+theta4*x)
> > z1/((1+z1)*(1+z2))
> > }
> > psi2<-function(theta3,theta4,x) {
> > z2<-exp(theta3+theta4*x)
> > z2/(1+z2)
> >}
> >
> >
> >
> > lf1<-function(w) {
> > v<-1
> > w1<-w[1]
> > w2<-w[2]
> > w3<-w[3]
> > w4<-w[4]
> > for (i in 1:length(alloc.dose)) {
> > dose.i<-alloc.dose[i]
> > r0.i<-r0[i]
> > r1.i<-r1[i]
> > r2.i<-r2[i]
> > z1<-exp(w1+w2*dose.i)
> > z2<-exp(w3+w4*dose.i)
> > psi0<-1/((1+z1)*(1+z2))
> > psi1<-z1*psi0
> > v<-v*(psi0^r0.i)*(psi1^r1.i)*((1-psi0-psi1)^r2.i)
> > }
> > return(v)
> > }
> >
> >
> > lf1.c<-cmpfun(lf1)
> >
> > ###
> >
> > May I know how to avoid this message? If I leave the code as it is, will
> > that affect the result anyway?
> >
> > Thanks in advance.
> >
> >
> > Regards,
> > Jamil.
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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]]
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[R] No visible binding for global variable
Dear R-users,
I would like to seek your suggestion. I have the following code which runs
smoothly. But when I compile the function (lf1.c), it shows "no visible
binding for global variable" for some of the arguments.
###
library(compiler)
psi0<-function(theta1,theta2,theta3,theta4,x){
z1<-exp(theta1+theta2*x)
z2<-exp(theta3+theta4*x)
1/((1+z1)*(1+z2))
}
psi1<-function(theta1,theta2,theta3,theta4,x){
z1<-exp(theta1+theta2*x)
z2<-exp(theta3+theta4*x)
z1/((1+z1)*(1+z2))
}
psi2<-function(theta3,theta4,x) {
z2<-exp(theta3+theta4*x)
z2/(1+z2)
}
lf1<-function(w) {
v<-1
w1<-w[1]
w2<-w[2]
w3<-w[3]
w4<-w[4]
for (i in 1:length(alloc.dose)) {
dose.i<-alloc.dose[i]
r0.i<-r0[i]
r1.i<-r1[i]
r2.i<-r2[i]
z1<-exp(w1+w2*dose.i)
z2<-exp(w3+w4*dose.i)
psi0<-1/((1+z1)*(1+z2))
psi1<-z1*psi0
v<-v*(psi0^r0.i)*(psi1^r1.i)*((1-psi0-psi1)^r2.i)
}
return(v)
}
lf1.c<-cmpfun(lf1)
###
May I know how to avoid this message? If I leave the code as it is, will
that affect the result anyway?
Thanks in advance.
Regards,
Jamil.
[[alternative HTML version deleted]]
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Superimposing graphs
Dear Richard and Duncan,
your suggestions are absolutely serving what I need. But I would like to
see x-axis to be up to 30 instead of 20. Do you have any suggestion on that?
Many thanks for your kind help.
Regards,
Jamil.
On 12 August 2014 01:22, Duncan Mackay dulca...@bigpond.com wrote:
Hi
If you want a 1 package and 1 function approach try this
xyplot(conc ~ time | factor(subject, levels = c(2,1,3)), data = data.d,
par.settings = list(strip.background = list(col = transparent)),
layout = c(3,1),
aspect = 1,
type = c(b,g),
scales = list(alternating = FALSE),
panel = function(x,y,...){
panel.xyplot(x,y,...)
# f1-function(x,v,cl,t)
# (x/v)*exp(-(cl/v)*t) f1(0.5,0.5,0.06,t),
panel.curve((0.5/0.5)*exp(-(0.06/0.5)*x),0,30)
}
)
# par.settings ... if you are publishing show text better
# with factor if you want 1:3 omit the levels
# has advantage of doing more things than in groupedData as Doug Bates has
said
Regards
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
Armidale NSW 2351
Email: home: mac...@northnet.com.au
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On
Behalf Of Naser Jamil
Sent: Monday, 11 August 2014 19:06
To: R help
Subject: [R] Superimposing graphs
Dear R-user,
May I seek your help to sort out a little problem. I have the following
codes
to draw two graphs. I want to superimpose the second one on each of the
first one.
library(nlme)
subject-c(1,1,1,2,2,2,3,3,3)
time-c(0.0,5.4,21.0,0.0,5.4,21.0,0.0,5.4,21.0)
con.cohort-c(1.10971703,0.54535512,0.07176724,0.75912539,0.47825282,
0.10593292,1.20808375,0.47638394,0.02808967)
data.d=data.frame(subject=subject,time=time,conc=con.cohort)
grouped.data-groupedData(formula=conc~time | subject, data =data.d)
plot(grouped.data)
##
f1-function(x,v,cl,t) {
(x/v)*exp(-(cl/v)*t)
}
t-seq(0,30, .01)
plot(t,f1(0.5,0.5,0.06,t),type=l,pch=18, ylim=c(), xlab=time,
ylab=conc)
###
Any suggestion will really be helpful.
Regards,
Jamil.
[[alternative HTML version deleted]]
__
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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.
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Superimposing graphs
That's perfect! Many thanks.
On 12 August 2014 14:32, Richard M. Heiberger r...@temple.edu wrote:
Yes, use xlim=c(0, 30) in your definition of P1
On Tue, Aug 12, 2014 at 7:26 AM, Naser Jamil jamilnase...@gmail.com
wrote:
Dear Richard and Duncan,
your suggestions are absolutely serving what I need. But I would like to
see x-axis to be up to 30 instead of 20. Do you have any suggestion on
that?
Many thanks for your kind help.
Regards,
Jamil.
On 12 August 2014 01:22, Duncan Mackay dulca...@bigpond.com wrote:
Hi
If you want a 1 package and 1 function approach try this
xyplot(conc ~ time | factor(subject, levels = c(2,1,3)), data = data.d,
par.settings = list(strip.background = list(col =
transparent)),
layout = c(3,1),
aspect = 1,
type = c(b,g),
scales = list(alternating = FALSE),
panel = function(x,y,...){
panel.xyplot(x,y,...)
# f1-function(x,v,cl,t)
# (x/v)*exp(-(cl/v)*t) f1(0.5,0.5,0.06,t),
panel.curve((0.5/0.5)*exp(-(0.06/0.5)*x),0,30)
}
)
# par.settings ... if you are publishing show text better
# with factor if you want 1:3 omit the levels
# has advantage of doing more things than in groupedData as Doug Bates
has
said
Regards
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
Armidale NSW 2351
Email: home: mac...@northnet.com.au
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org
]
On
Behalf Of Naser Jamil
Sent: Monday, 11 August 2014 19:06
To: R help
Subject: [R] Superimposing graphs
Dear R-user,
May I seek your help to sort out a little problem. I have the following
codes
to draw two graphs. I want to superimpose the second one on each of the
first one.
library(nlme)
subject-c(1,1,1,2,2,2,3,3,3)
time-c(0.0,5.4,21.0,0.0,5.4,21.0,0.0,5.4,21.0)
con.cohort-c(1.10971703,0.54535512,0.07176724,0.75912539,0.47825282,
0.10593292,1.20808375,0.47638394,0.02808967)
data.d=data.frame(subject=subject,time=time,conc=con.cohort)
grouped.data-groupedData(formula=conc~time | subject, data =data.d)
plot(grouped.data)
##
f1-function(x,v,cl,t) {
(x/v)*exp(-(cl/v)*t)
}
t-seq(0,30, .01)
plot(t,f1(0.5,0.5,0.06,t),type=l,pch=18, ylim=c(), xlab=time,
ylab=conc)
###
Any suggestion will really be helpful.
Regards,
Jamil.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Superimposing graphs
Dear R-user,
May I seek your help to sort out a little problem. I have the following
codes
to draw two graphs. I want to superimpose the second one on each of the
first one.
library(nlme)
subject-c(1,1,1,2,2,2,3,3,3)
time-c(0.0,5.4,21.0,0.0,5.4,21.0,0.0,5.4,21.0)
con.cohort-c(1.10971703,0.54535512,0.07176724,0.75912539,0.47825282,
0.10593292,1.20808375,0.47638394,0.02808967)
data.d=data.frame(subject=subject,time=time,conc=con.cohort)
grouped.data-groupedData(formula=conc~time | subject, data =data.d)
plot(grouped.data)
##
f1-function(x,v,cl,t) {
(x/v)*exp(-(cl/v)*t)
}
t-seq(0,30, .01)
plot(t,f1(0.5,0.5,0.06,t),type=l,pch=18, ylim=c(), xlab=time,
ylab=conc)
###
Any suggestion will really be helpful.
Regards,
Jamil.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] skipping an error message
Hi Jim, Thanks for the suggestion. What I understand is trying something like tryCatch(nlme(conc~f2(dose,Theta1,Theta 2,Theta3,t), fixed=Theta1+Theta2+Theta3~1, data=grouped.data, random=Theta1+Theta2+Theta3~1, start=list(fixed=ini.pkpara)) ) Is that correct? Once again thanks. Regards, Jamil. On 6 April 2014 23:51, Jim Lemon j...@bitwrit.com.au wrote: On 04/06/2014 08:21 PM, Naser Jamil wrote: Dear R-user, May I seek your suggestion on an issue. I'm fitting non-linear mixed effects model as a part of my large R program. But sometimes I get error messages from it and the code stops working. In such cases, I want to skip the iterations and want to move to the next iteration ignoring all the subsequent computations. The following is only that part of the code which fits the mixed effects model. I tried with tryCatch as shown below, but it's not serving my purpose. I guess something is wrong in my approach. ### grouped.data-groupedData(formula = conc ~ t | subject, data = data.d) model.d-nlme(conc~f2(dose,Theta1,Theta2,Theta3,t), fixed=Theta1+Theta2+Theta3~1, data=grouped.data, random=Theta1+Theta2+Theta3~1, start=list(fixed=ini.pkpara)) summ-summary(model.d) # summary of the model tryCatch(summ, error = function() next) ### Hi Jamil, I think you have to pass the expression: nlme(conc~f2(dose,Theta1,Theta2,Theta3,t), fixed=Theta1+Theta2+Theta3~1, data=grouped.data, random=Theta1+Theta2+Theta3~1, start=list(fixed=ini.pkpara)) not the result of the expression. Jim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] skipping an error message
Hi Bill,
Many thanks for such a nice illustration. I tried the first option and it's
working. More specifically,
model.d - tryCatch(nlme(blah blah blah), error=function(e)NULL)
if(!is.null(model.d)) {
furtherProcessTheModel(model.d)
}
But instead of !is.null, I want something so that when 'model.d' under
tryCatch is OK, I can do further computations based on its results.
Once again thanks.
Regards,
Jamil
On 7 April 2014 16:35, William Dunlap wdun...@tibco.com wrote:
Thanks for the suggestion. What I understand is trying something like
tryCatch(nlme(conc~f2(dose,Theta1,Theta
2,Theta3,t),
fixed=Theta1+Theta2+Theta3~1,
data=grouped.data,
random=Theta1+Theta2+Theta3~1,
start=list(fixed=ini.pkpara))
)
Is that correct?
No.
Executing tryCatch(someExpression) is equivalent to executing just
someExpression because you haven't set up any condition handlers.
If you did something like
model.d - tryCatch(nlme(blah blah blah), error=function(e)NULL)
then model.d would contain the return value of the call to nlme if
all went well and NULL otherwise. You could then use
if(!is.null(model.d)) {
furtherProcessTheModel(model.d)
}
to do things that only make sense when the model could be fitted.
Now NULL may be a legitimate return value from a function and
it also doesn't give you any hint about what went wrong, so you could
have the error handler return an object of a class that no normal
function would return and have it contain the error message. E.g.,
model.d - tryCatch(nlme(notAFormula),
error=function(e)structure(conditionMessage(e),class=ERROR))
and then you can test for errors with
if (inherits(model.d, ERROR)) {
message(Iteration , i, failed with error: , model.d)
} else {
furtherProcessTheModel(model.d)
}
You could also look at the error message that model.d contains in that
case.
The try() function is essentially that call to tryCatch: it gives its
error output
the class 'try-error'.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf
Of Naser Jamil
Sent: Monday, April 07, 2014 1:46 AM
To: Jim Lemon
Cc: R help
Subject: Re: [R] skipping an error message
Hi Jim,
Thanks for the suggestion. What I understand is trying something like
tryCatch(nlme(conc~f2(dose,Theta1,Theta
2,Theta3,t),
fixed=Theta1+Theta2+Theta3~1,
data=grouped.data,
random=Theta1+Theta2+Theta3~1,
start=list(fixed=ini.pkpara))
)
Is that correct?
Once again thanks.
Regards,
Jamil.
On 6 April 2014 23:51, Jim Lemon j...@bitwrit.com.au wrote:
On 04/06/2014 08:21 PM, Naser Jamil wrote:
Dear R-user,
May I seek your suggestion on an issue. I'm fitting non-linear mixed
effects
model as a part of my large R program. But sometimes I get error
messages
from it and the code stops working. In such cases, I want to skip the
iterations and
want to move to the next iteration ignoring all the subsequent
computations.
The following is only that part of the code which fits the mixed
effects
model. I tried with tryCatch as shown below, but it's not serving my
purpose. I guess something is wrong in my approach.
###
grouped.data-groupedData(formula = conc ~ t | subject,
data = data.d)
model.d-nlme(conc~f2(dose,Theta1,Theta2,Theta3,t),
fixed=Theta1+Theta2+Theta3~1,
data=grouped.data,
random=Theta1+Theta2+Theta3~1,
start=list(fixed=ini.pkpara))
summ-summary(model.d) # summary of the model
tryCatch(summ, error = function() next)
###
Hi Jamil,
I think you have to pass the expression:
nlme(conc~f2(dose,Theta1,Theta2,Theta3,t),
fixed=Theta1+Theta2+Theta3~1,
data=grouped.data,
random=Theta1+Theta2+Theta3~1,
start=list(fixed=ini.pkpara))
not the result of the expression.
Jim
[[alternative HTML version deleted]]
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] skipping an error message
Dear R-user, May I seek your suggestion on an issue. I'm fitting non-linear mixed effects model as a part of my large R program. But sometimes I get error messages from it and the code stops working. In such cases, I want to skip the iterations and want to move to the next iteration ignoring all the subsequent computations. The following is only that part of the code which fits the mixed effects model. I tried with tryCatch as shown below, but it's not serving my purpose. I guess something is wrong in my approach. ### grouped.data-groupedData(formula = conc ~ t | subject, data = data.d) model.d-nlme(conc~f2(dose,Theta1,Theta2,Theta3,t), fixed=Theta1+Theta2+Theta3~1, data=grouped.data, random=Theta1+Theta2+Theta3~1, start=list(fixed=ini.pkpara)) summ-summary(model.d) # summary of the model tryCatch(summ, error = function() next) ### Any suggestion will be more than great. Thank you very much. Regards, Jamil [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] functions and matrices
Thanks to everyone for such nice illustrations. It will guide me for sure.
On 2 July 2013 02:56, David Winsemius dwinsem...@comcast.net wrote:
With permission I offer this exchange. Rolf and I have different notions
of what u %*% v should mean, but the arbiter is obviously the original
poster:
Begin forwarded message:
From: David Winsemius dwinsem...@comcast.net
Subject: Re: [R] functions and matrices
Date: July 1, 2013 6:21:09 PM PDT
To: Rolf Turner rolf.tur...@xtra.co.nz
On Jul 1, 2013, at 5:09 PM, Rolf Turner wrote:
On 02/07/13 11:37, David Winsemius wrote:
On Jul 1, 2013, at 3:32 PM, Rolf Turner wrote:
Basically R does things *numerically* and what you want to do really
amounts to symbolic manipulation. Of course R could be cajoled into
doing it --- see fortune(Yoda) --- but probably only with a great
deal of
effort and code-writing.
OTOH you could quite easily write a function that would calculate
det(u%*%v)(x) for any given numerical value of x:
foo - function(a,b,x){
a1 - apply(a,c(1,2),function(m,x){m[[1]](x)},x=x)
b1 - apply(b,c(1,2),function(m,x){m[[1]](x)},x=x)
det(a1%*%b1)
}
Then doing
foo(u,v,2)
I would have thought that (u %*% v) would be:
u[1,1]( v[1,1](x) ) + u[1,2]( v[2,1](x) ) u[1,1]( v[1,2](x) ) +
u[1,2]( v[2,2](x) )
u[2,1]( v[1,1](x) ) + u[2,2]( v[2,1](x) ) u[2,1]( v[2,1](x) ) +
u[2,2]( v[2,2](x) )
(Crossing my fingers that I got the row and column conventions correct
for matrix multiplication.)
SNIP
Not quite sure what you're getting at here. It looks to me that you are
calculating the *composition* of the functions rather than their
*product*.
Exactly. That is how I understood successive application of functions
embedded in matrices . The symbol used in my differential topology course
lo those 40 years ago was an open circle, but I assumed the OP wanted
something along those lines to perform a composite mapping:
compose - function(u, v, x) matrix( c(
u[1,1][[1]]( v[1,1][[1]](x) ) + u[1,2][[1]]( v[2,1][[1]](x) ) ,
u[1,1][[1]]( v[1,2][[1]](x) ) + u[1,2][[1]]( v[2,2][[1]](x) ),
u[2,1][[1]]( v[1,1][[1]](x) ) + u[2,2][[1]]( v[2,1][[1]](x) ),
u[2,1][[1]]( v[2,1][[1]](x) ) + u[2,2][[1]]( v[2,2][[1]](x) ) ),
2,2,byrow=TRUE)
compose(u,v,2)
[,1][,2]
[1,] 751332
[2,] 5427 1680128
(Noting that I may have reversed the roles of u and v.)
I.e. you are taking the (i,j)th entry of u%*%v (evaluated at x) to be
the
sum over k of
u[i,k](v[k,j](x))
This is not what I understood the OP to want. I assumed he wanted the
product of the function values rather than the composition of the
functions,
i.e. that he wanted the (i,j)th entry to be the sum over k of
u[i,k](x) * v[k,j](x)
which is what my function provides. This seems to me to be the most
reasonable interpretation, but I could be wrong.
BTW --- you cannot actually do u[i,k](x). E.g.
u[1,2](2)
gives Error: attempt to apply non-function. One needs to do
u[1,2][[1]](2)
(which gives 4, as it should).
Yes. I was playing fast and loose with notation. I didn't think the code
would really run as offered.I was a bit surprise that this worked, but I
suppose you bear credit (and blame?) for pushing my program closer to
completion.
v[1,1][[1]]( u[1,1][[1]]( 2 ))
[1] 11
Any problem with me copying this to the list?
cheers,
Rolf
Best;
David Winsemius
Alameda, CA, USA
David Winsemius
Alameda, CA, USA
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[R] functions and matrices
Dear R-user,
May I seek your help, please. I have two matrices, u and v, elements of
which are some functions
of x. I just want to multiply them and express the determinant of the
resulting matrix as a function of
x and of course, this is for some reason. Actually the original problem has
more matrices to multiply and I'm just wondering whether I can simplify it
anyway through the R codes. It may even be non-sense, but just want to hear
from you. The below is the code.
-
f1-function(x) {x}
f2-function(x) {x^2}
f3-function(x) {x^3}
f4-function(x) {x^4}
f5-function(x) {x^2+7}
f6-function(x) {x^3+14*x}
f7-function(x) {x^2+2*x}
f8-function(x) {x^4+10*x}
u-matrix(c(f1,f2,f3,f4), nrow=2, ncol=2, byrow=TRUE)
v-matrix(c(f5,f6,f7,f8), nrow=2, ncol=2, byrow=TRUE)
det(u %*% v) # Is that possible?
Any suggestion will be more than great!
Regards,
Jamil.
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[R] R for windows GUI front-end has stopped working
Dear R-users, May I seek your attention please! I have a long R code, which runs most of the time quite nicely and provides necessary results. However, often it provides a message like R for windows GUI front-end has stopped working and just stops working. I'm running the program in Windows 2007. Is there any way out? Any suggestion in this regard will be more than great!! Many thanks for your time. Regards, Jamil. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] scan in R
Dear R-user, May I seek your help over a issue, probably a simple one. I just one to scan the following numbers, avoiding [1]s, [2]. By the way, I know how to scan numbers in the absence of such [1] and [2]. -- [1] 18 18 17 14 17 13 13 18 13 16 16 14 [1] 12 19 15 21 13 17 10 13 18 14 17 13 [2] 13 15 20 14 18 15 10 12 20 17 17 17 -- Any suggestion would be more than great! Regards, Jamil. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] scanning data in R
Dear R-user, May I seek your suggestion. I have a data file 'stop' to be scanned in R. But I want to ignore one specific number '21' there. Putting differently, I want to get all numbers in the file except 21. Is there any command to achieve it? -- b-scan(F:\\stop.txt) -- Many thanks for your kind attention. Regards, Jamil. 15 15 16 15 17 16 16 15 17 15 16 17 19 17 19 15 16 16 19 18 19 17 17 19 16 17 16 20 15 16 16 15 18 19 17 18 16 18 16 17 21 21 17 15 15 20 16 20 17 21 19 15 15 15 18 20 16 17 16 15 16 15 16 16 18 16 15 21 20 15 16 17 18 18 20 17 18 18 21 16 15 16 20 17 19 17 18 19 17 21 21 16 15 19 21 15 20 20 16 16 20 18 21 21 15 15 19 15 16 15 17 15 21 20 16 15 16 16 18 17 16 18 16 16 16 21 16 15 20 16 19 17 14 17 15 16 15 17 16 15 15 20 15 16 15 15 16 15 20 19 15 15 17 17 15 18 16 15 14 21 19 20 15 17 15 15 17 19 15 15 16 18 17 16 16 16 16 18 21 15 16 16 21 19 17 15 16 15 18 16 20 17 16 16 21 15 17 20 21 16 16 17 21 16 16 20 19 17 15 16 18 16 16 15 16 18 19 16 15 21 20 19 20 20 20 16 18 16 15 20 16 16 18 19 16 18 21 16 21 19 19 17 18 15 18 16 19 17 20 20 16 18 16 19 20 21 15 16 18 19 16 17 16 15 17 16 15 21 16 15 18 18 15 21 19 16 19 15 15 17 18 17 16 15 16 18 18 19 17 16 21 16 19 16 15 16 20 17 17 21 21 20 16 17 19 16 15 19 18 17 15 15 15 19 20 18 21 16 15 15 20 20 17 19 15 19 16 15 15 19 16 16 19 15 15 19 18 21 15 15 18 21 16 16 17 17 16 15 18 16 15 20 17 20 15 16 15 15 20 15 16 17 16 17 16 21 17 18 17 15 20 18 16 17 16 17 15 15 17 20 17 18 15 16 20 16 15 15 18 16 18 16 18 15 16 18 15 17 18 18 16 15 19 16 19 21 15 20 17 18 15 16 19 17 16 18 18 15 19 15 15 17 15 19 19 16 20 16 16 15 19 15 16 15 16 15 15 17 20 15 20 16 20 15 17 16 15 16 16 16 17 16 16 21 21 15 15 17 16 16 19 20 16 16 16 16 15 16 16 20 16 16 20 18 19 15 21 16 15 15 21 20 20 19 17
Re: [R] scanning data in R
Many thanks, Prof. David. It's exactly what I wanted! On 3 April 2013 17:26, David L Carlson dcarl...@tamu.edu wrote: You can certainly do it after scanning all the numbers in with b - scan(F:\\stop.txt, what=integer()) b - b[b!=21] -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Naser Jamil Sent: Wednesday, April 03, 2013 4:33 AM To: R help Subject: [R] scanning data in R Dear R-user, May I seek your suggestion. I have a data file 'stop' to be scanned in R. But I want to ignore one specific number '21' there. Putting differently, I want to get all numbers in the file except 21. Is there any command to achieve it? -- b-scan(F:\\stop.txt) -- Many thanks for your kind attention. Regards, Jamil. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] vertical lines in R plot
Dear All,
May I seek your suggestion on a simple issue. I want to draw vertical lines
at some positions in the following R plot. To be more specific, I wish to
draw vertical lines at d=c(5.0,5.5,6) and they should go till
p=c(0.12,0.60,0.20) . I haven't found any way out, though made several
attempts. Please run the following commands first if you are interested in!
###
psi1-function(alpha1,beta1,alpha2,beta2,d){
exp(alpha1+beta1*d)/((1+exp(alpha1+beta1*d))*(1+exp(alpha2+beta2*d)))
}
alpha1--3.5
beta1-1
alpha2--6
beta2-0.72
d-seq(0.5,10,0.01)
plot(d,psi1(alpha1,beta1,alpha2,beta2,d),type=l,pch=18, ylim=c(0,1),
xlab=Dose, ylab=Probabilitty)
##
Many thanks for the help!
Regards,
Jamil.
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Re: [R] vertical lines in R plot
Thank you guys. It was really worthy!
On 11 March 2013 16:10, William Dunlap wdun...@tibco.com wrote:
Also, type=h, in plot(), points(), or lines() draws vertical line
segments between (x,y)
and (x,0). E.g.,
points(x=c(5.0,5.5,6), y=c(0.12,0.60,0.20), type=h)
does the same as
segments(x0=c(5.0,5.5,6), y0=c(0,0,0), x1=c(5.0,5.5,6),
y1=c(0.12,0.60,0.20))
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf
Of Sarah Goslee
Sent: Monday, March 11, 2013 8:49 AM
To: Naser Jamil
Cc: R help
Subject: Re: [R] vertical lines in R plot
Like this:
segments(x0=c(5.0,5.5,6), y0=c(0,0,0), x1=c(5.0,5.5,6),
y1=c(0.12,0.60,0.20))
If you wanted them to extend the entire height of the plot,
abline(v=c(5.0,5.5,6))
is simpler.
Thanks for the reproducible example,
Sarah
On Mon, Mar 11, 2013 at 10:10 AM, Naser Jamil jamilnase...@gmail.com
wrote:
Dear All,
May I seek your suggestion on a simple issue. I want to draw vertical
lines
at some positions in the following R plot. To be more specific, I wish
to
draw vertical lines at d=c(5.0,5.5,6) and they should go till
p=c(0.12,0.60,0.20) . I haven't found any way out, though made
several
attempts. Please run the following commands first if you are
interested in!
###
psi1-function(alpha1,beta1,alpha2,beta2,d){
exp(alpha1+beta1*d)/((1+exp(alpha1+beta1*d))*(1+exp(alpha2+beta2*d)))
}
alpha1--3.5
beta1-1
alpha2--6
beta2-0.72
d-seq(0.5,10,0.01)
plot(d,psi1(alpha1,beta1,alpha2,beta2,d),type=l,pch=18, ylim=c(0,1),
xlab=Dose, ylab=Probabilitty)
##
Many thanks for the help!
Regards,
Jamil.
--
Sarah Goslee
http://www.functionaldiversity.org
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[R] Percentages in bar plot
Dear R-users, Though it's a silly thing to ask, but I'm not getting a way out. I wish to find the percentage distribution for a data vector 'stop'. The coomand below is giving the frequency distribution. May I know the option to see the percentages instead of frequencies. Similarly, what option I should put in a histogram plot to see the percentages instead of frequencies? - stop-c(8,6,6,6,8,6,6,8,8,6,6,6,8,8,8) barplot(table(stop)) Many thanks for your time. Regards, Jamil. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Integration in R
Hi R-users.
I'm having difficulty with an integration in R via
the package cubature. I'm putting it with a simple example here. I wish
to integrate a function like:
f(x1,x2)=2/3*(x1+x2) in the interval 0x1x27. To be sure I tried it
by hand and got 114.33, but the following R code is giving me 102.6667.
---
library(cubature)
f-function(x) { 2/3 * (x[1] + x[2] ) }
adaptIntegrate(f, lowerLimit = c(0, 0), upperLimit = c(x[2],7))
---
I guess something is wrong with the way I have assigned limits
in my codes. May I seek some advice from you.
Many thanks.
Regards,
Jamil.
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Re: [R] Integration in R
Thanks. But then how to implement condition like 0x1x27? I would be
happy to know that.
On 8 January 2013 18:41, David Winsemius dwinsem...@comcast.net wrote:
Please reply on list.
On Jan 8, 2013, at 10:27 AM, Naser Jamil wrote:
Hi David,
x[2] is the second variable, x2. It comes from the condition 0x1x27.
No, it doesn't come from those conditions. It is being grabbed from some
x-named object that exists in your workspace.
If your limits were 7 in both dimensions, then the code should be:
adaptIntegrate(f, lowerLimit = c(0, 0), upperLimit = c(7,7))
#
$integral
[1] 228.6667
(At this point I was trusting R's calculus abilities more than yours. I
wasn't too trusting of mine either, and so tried seeing if Wolfram Alpha
would accept this expression:
integrate 2/3 (x+y) over 0 x7, 0y7
; which it did and calculating the decimal expansion of the exact fraction:
686/3
[1] 228.6667
--
David.
Thanks.
On 8 January 2013 18:11, David Winsemius dwinsem...@comcast.net wrote:
On Jan 8, 2013, at 9:43 AM, Naser Jamil wrote:
Hi R-users.
I'm having difficulty with an integration in R via
the package cubature. I'm putting it with a simple example here. I wish
to integrate a function like:
f(x1,x2)=2/3*(x1+x2) in the interval 0x1x27. To be sure I tried it
by hand and got 114.33, but the following R code is giving me 102.6667.
--**--**---
library(cubature)
f-function(x) { 2/3 * (x[1] + x[2] ) }
adaptIntegrate(f, lowerLimit = c(0, 0), upperLimit = c(x[2],7))
What is x[2]? On my machine it was 0.0761, so I obviously got a
different answer.
--
David Winsemius, MD
Alameda, CA, USA
David Winsemius, MD
Alameda, CA, USA
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[R] Minimizing Computational Time
Dear R-users,
May I seek some suggestions from you. I have a long programme written in R
with several 'for' loops inside. I just want to get them out by any elegant
way (if there is!) to reduce the computational time of the main programme.
For instance, is there any smart way for the following programme that will
lessen time?
---
dose-seq(0,10,.5)
alpha1--4
beta1-0.5
alpha2--6
beta2--.7
psi1-function(alpha1,beta1,alpha2,beta2,d){
z1-exp(alpha1+beta1*d)
z2-exp(alpha2+beta2*d)
z1/((1+z1)*(1+z2))
}
psi2-function(alpha2,beta2,d) {
z2-exp(alpha2+beta2*d)
z2/(1+z2)
}
psi1.hat=c()
psi2.hat=c()
for (i in 1:length(dose)){ # just want to avoid this 'for' loop
d-dose[i]
psi1.hat[i]-psi1(alpha1,beta1,alpha2,beta2,d)
psi2.hat[i]-psi2(alpha2,beta2,d)
}
print(psi1.hat)
print(psi2.hat)
Many thanks for your kind attention.
Regards,
Jamil.
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[R] PFIM 3.2
Dear R-user,
I'm having some difficulty with working PFIM 3.2, a package for
implementing population PK/PD in R. I wish to evaluate the determinant of
Fisher information matrix each time with successive dose from a pre defined
sequence of doses and want to store those values in a vector. It's
important to note that in my 'stdin.r' file, dose-c(u) and each time u is
to be replaced as I said. I think a quick look on the following R codes
will give a more clearer picture of the objective:
---
directory-F:\\PFIM3.2_examples\\experiment # working directory
directory.program-F:\\PFIM3.2.2\\PFIM3.2.2\\PFIM3.2.2\\Program #
program directory
true.dose-seq(0,10,0.5) # predefined sequence of doses
deter=c() # to store determinant values
for (i in 1:length(true.dose) {
u-true.dose[i]
source(F:\\PFIM3.2.2\\PFIM3.2.2\\PFIM3.2.2\\Program\\LibraryPK.r)
source(F:\\PFIM3.2_examples\\experiment\\model.r)
source(F:\\PFIM3.2_examples\\experiment\\stdin.r)
source(F:\\PFIM3.2_examples\\experiment\\PFIM3.2.r)
res-PFIM()
deter[i]-res$determinant
}
---
But it's not working anyway and of course showing some error messages.
I have attached the the associated files.
Any suggestion in this regard will help me a lot.
Thank you very much for the patience!
Regards,
Jamil.
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[R] Integration in R
Dear R-users,
I am facing problem with integrating in R a likelihood function which is a
function of four parameters. It's giving me the result at the end but
taking more than half an hour to run. I'm wondering is there any other
efficient way deal with. The following is my code. I am ready to provide
any other description of my function if you need to move forward.
library(cubature)
dose-c(2,3,5)
y0-c(2,1,0)
y1-c(1,1,1)
y2-c(0,1,2)
lf-function (x) {
v-1
for (i in 1:length(dose)) {
psi0-1/((1+exp(x[1]+x[2]*dose[i]))*(1+exp(x[3]+x[4]*dose[i])))
psi1-exp(x[1]+x[2]*dose[i])/((1+exp(x[1]+x[2]*dose[i]))*(1+exp(x[3]+x[4]*dose[i])))
v-v*(psi0^y0[i])*(psi1^y1[i])*((1-psi0-psi1)^y2[i])
}
return(v)
}
adaptIntegrate(lf, lowerLimit = c(-20, 0,-20,0), upperLimit = c(0,10,0,10))
-
Thanks for your attention.
Kind regards,
Jamil.
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