Yes-I did look through the CRAN view and could not find any package that
featured a function whereby an MRI set was transformed into Talairach or MNI
space.
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PLEASE do rea
I need to analyze multiple T1 contrast enhanced MRI studies from different
patients. They are all in DICOM format. I see that there are different
packages for loading individual studies in DICOM format, however I have had
limited luck so far researching how the different studies can be tranformed
i
I did.But could only find the citation-not an implementation.
On Tuesday, January 1, 2013, David Winsemius wrote:
>
> On Dec 31, 2012, at 4:38 PM, moleps wrote:
>
> Dear all,
>> Is there an implementation of Simon & Makuch method of plotting the
>> survival
Dear all,
Is there an implementation of Simon & Makuch method of plotting the survival
function with time-dependent variables. I´m only able to find event.chart in
Hmisc for the purpose and I would prefer the Simon and Makuch method. I believe
stata has it implemented for this purpose, but I can
Dear all,
I´m trying to get a output table for age and the summary of a and b, stratified
by epo as follows using summary.formula
h<-data.frame(a=sample(c("A",NA),100,replace=T),b=sample(c("B",NA),100,replace=T),age=rnorm(100,50,25),epo=sample(c("Y","N"),100,T))
library(rms)
summary.formula(ep
Yup, thats the culprit. Thx.
//M
On 28. apr. 2011, at 18.36, Achim Zeileis wrote:
> On Thu, 28 Apr 2011, moleps wrote:
>
>> sessionInfo yields the following:
>
> OK, the "Design" package causes the problem here. When you load the Design
> package, it pr
ced
> your error.
>
> It is also recommended that you try simply upgrading R to the latest
> version and see if you get an error with the latest version of
> 'party'. My guess is that the error will go away.
>
> On Wed, Apr 27, 2011 at 3:40 PM, moleps wro
Forgot to mention that the ctree command is from the party library.
//M
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and provide commented,
Dear all,
I was intrigued by the ctree command and wanted to check it out. I first ran
the demo with example(ctree) and did get the survival graphs in the end. Upon
doing this with my own data and yielding a "Invalid operation on a survival
time" I tried to rerun example(ctree) and now I also g
Dear all,
Is there a package that allows me to run a sensitivy analysis on a
matched dataset created using MatchIt? I am aware of both rbounds and
the sensitivy function in the twang package but they do not allow
matched objects from MatchIt as input.
//M
Feb 1, 2011, at 2:31 PM, moleps wrote:
>
>>
>> My terminology is probably way off. I´ll try again in plain english.
>>
>> I´d like to generate a scatter plot of r1 & r2 and color code each pair
>> according to the probability of observing the pair given that
ons.
rr<-data.frame(r1=-rnorm(1000,10,5),r2=-rnorm(1000,220,5))
with(rr,plot(r1,r2))
Best,
//M
On 31. jan. 2011, at 23.13, Peter Ehlers wrote:
> On 2011-01-31 12:42, moleps wrote:
>> Dear all,
>>
>> Given
>>
>> rr<-data.frame(r1<-rnorm(1000,10,5),r2<
Dear all,
Given
rr<-data.frame(r1<-rnorm(1000,10,5),r2<-rnorm(1000,220,5))
How can I add a column (rr$p) for the joint probability of each r1 & r2 pair?
I know how to add the column.. I just dont know how to compute the p value for
joint probabilities given the two samples.
//M
__
011, moleps islon wrote:
>
>> Dear all,
>>
>> Using the SetInternet2(TRUE) option works wonders with R in my sealed
>> down work-environment. However, I'd like to use RCurl and apparently
>> the proxy settings are not carried over. Is it possible to figure out
>
Dear all,
Using the SetInternet2(TRUE) option works wonders with R in my sealed
down work-environment. However, I'd like to use RCurl and apparently
the proxy settings are not carried over. Is it possible to figure out
the proxy-IP and port number from R after invoking SetInternet2?
//M
Is it at all possible to specify this so that different tests display different
parameters,
ie have the continous test display F, df and p while tes categorical test
display only P values?
sf1 <- summary(trt~sex+ascites+age,data=ex,test=T,method="reverse",catTest=u)
print(sf1, prtest = "P")
/
Allright..Works like a charm. However I do believe that the prtest vector
should have been mentioned in the catTest or conTest option. Appreciate your
time and effort.
Best,
//M
On 6. jan. 2011, at 23.24, Erik Iverson wrote:
>
>> Does the prtest argument help when you actually use the 'print'
Dear all,
I´m specifying the fisher.exact test for use with summary.formula as follows:
u<-function(a,b){
j<-fisher.test(a)
p<-list(P=j$p.value,stat=NA,df=NA,testname=j$method,statname="")
return(p)
}
However I´m also required to specify stat
I´m trying to run a logistic joinpoint regression utilising the ljr package.
I´ve been using the forward selection technique to get the number of knots for
the analysis, but I´m uncertain as to my results and the interpretation. The
documentation is rather brief ( in the package and the stats in
a<-subset(bar,h.r==x)
with(a, cdplot(wh~Age,ylab=x))
#plot.new()
})
Regards,
//M
On 8. sep. 2010, at 03.37, David Winsemius wrote:
>
> On Sep 7, 2010, at 8:02 PM, moleps wrote:
>
>> Dear all,
>>
>> I´m trying to create multiple g
Dear all,
I´m trying to create multiple graphs on the same page, but they are all stacked
on top of each other.
My code:
par(mfrow=c(2,2))
a<-list(levels(bar$h.r)[c(1,3,6)])
print(a)
lapply(a,function(x){
a<-subset(bar,h.r==x)
with(a,cdplot(wh~Age,ylab=x))
#plot.new()
Dear all,
With the latest update of Hmisc I no longer have any problems with latex.
However using the ctable option produces latex code that at least on both the
miktex distribution at work and mactex distribution at home refuses to run due
to an extra blank line inserted between the multicolum
glm(A~B+C+D+E+F,family = binomial(link = "logit"),data=tre,na.action=na.omit)
Error in `contrasts<-`(`*tmp*`, value = "contr.treatment") :
contrasts can be applied only to factors with 2 or more levels
however,
glm(A~B+C+D+E,family = binomial(link = "logit"),data=tre,na.action=na.omit)
runs
tre[,i]<-factor(dat[,i],labels=names(a[[i]]))
}
}
tre
Regards,
//M
On 25. aug. 2010, at 23.05, Bert Gunter wrote:
> ?attr
> ?attributes
>
> -- Bert Gunter
>
> On Wed, Aug 25, 2010 at 1:26 PM, moleps wrote:
>> Dear all,
>> I just received
Dear all,
I just received a file from a colleague in spss. The read.spss could not finish
the file due to an error (Unrecognized record type 7, subtype 18 encountered in
system file) so instead I converted the file using stat-transfer. Looking at my
data I see that most labels are in the attribu
Dear all,
Is it possible to impute a dataset and create a summary table with summary from
Hmisc and convert it to latex? I´m mostly familiar with cem and amelia hence
the example from the documentation in cem. The imbalance command is not exactly
what I was looking for...
library (cem)
if(req
correction...
Col and rows were mixed up and loop only worked when rows were less than or
equal to number of columns
//M
test<-function(a){
coef(summary(a))->lo
a<-colnames(lo)
b<-rownames(lo)
c<-length(a)
e<-character(0)
r<-NULL
for (x in (1:length(b))){
d<-rep(paste(a[1:c
coef(summary(a))->lo
a<-colnames(lo)
b<-rownames(lo)
c<-length(a)
e<-character(0)
r<-NULL
for (x in (1:c)){
d<-rep(paste(a[1:c],b[x],sep=" "))
e<-paste(c(e,d))
t<-lo[x,]
r<-c(r,t)
names(r)<-e
}
retu
avid Winsemius wrote:
>
> On Aug 9, 2010, at 7:51 AM, moleps wrote:
>
>> Dear all,
>>
>> I´m having trouble getting a list of regression variables back into a
>> dataframe.
>>
>> mydf <- data.frame(x1=rnorm(100), x2=rnorm(100), x3=rnorm(100)
Dear all,
I´m having trouble getting a list of regression variables back into a
dataframe.
mydf <- data.frame(x1=rnorm(100), x2=rnorm(100), x3=rnorm(100))
mydf$fac<-factor(sample((0:2),replace=T,100))
mydf$y<- mydf$x1+0.01+mydf$x2*3-mydf$x3*19+rnorm(100)
dlply(mydf,.(fac),function(df) lm(y~
Dear All,
I´ve been trying to find an option to scatter3D from rcmdr to remove the
individual points from the plots but to no help so far. Removing the residuals
is easy, but I cannot find a similar point option. Is there such an option that
can be set to FALSE?
Best,
//M
__
Dear all,
I did post this more or less identical mail in a follow up to another
question I posted, but under another heading. I try again, but now
under the correct header.
upon running this code (from the Hmisc library-latex function) I
believe the call to summary.formula is allright and produc
",
Nsize="smaller",long=TRUE, prmsd=TRUE, msdsize="smaller",middle.bold=TRUE,
ctable=TRUE)
This refused to run ( as long as the ctable=T was included), but without it
latex (s6)
I do get a nicely formated table, but again the numbers are all wrong... Also
latex(s6,
Jun 2010, Erik Iverson wrote:
>
>>
>>
>> moleps wrote:
>>> Dear R´ers
>>> I´m trying to get a summary table using latex and summary in the rms
>>> package to no avail. I´m running R 2.10.1, Mac OS X snow leopard and
>>> I have the mactex 200
Dear R´ers
I´m trying to get a summary table using latex and summary in the rms package
to no avail. I´m running R 2.10.1, Mac OS X snow leopard and I have the mactex
2009 distribution installed. Any obvious things I´m missing?
//M
options(digits=3)
set.seed(173)
sex <- factor(sample(c("m
Dear listers,
Does anyone have any experience running marginal structural models in r or can
point me in the direction of any good tutorials on this?
Regards,
//M
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PLEAS
ly
> nested inside another paste.
>
> --
> Gregory (Greg) L. Snow Ph.D.
> Statistical Data Center
> Intermountain Healthcare
> greg.s...@imail.org
> 801.408.8111
>
>
>> -Original Message-
>> From: r-help-boun...@r-project.org [mailto:r-he
t;
> $`rep(names(ts$a[3]),ts$a[3])`
> [1] "c" "c" "c"
>
> $`rep(names(ts$a[4]),ts$a[4])`
> [1] "d" "d" "d" "d"
>
> $`rep(names(ts$a[5]),ts$a[5])`
> [1] "e" "e" "e" "e"
Dear r-listers,
I need to pass a string to a function. However the length of the string is
dependent on the length of a vector.
b<-length(h)
v<-paste("rep(names(ts$a[",1:b,"]),ts$a[",1:b,"])",sep="")
Is it possible somehow to pass this as an argument to a function later on ?
Regards,
//
Appreciate it...
//M
On 5. juni 2010, at 20.11, Joshua Wiley wrote:
> On Sat, Jun 5, 2010 at 10:22 AM, moleps wrote:
>> thx.
>>
>> It was only the first instance that was class date. The rest were factors.
>> So that explains it.
>>
>> If I want to
I´m trying to tease out the minimum value from a row in a dataframe where all
the variables are dates.
apply(canc[,vec],1,function(x)min(x,na.rm=T))
However it only returns empty strings for the entire dataframe except for one
date value (which is not the minimum date).
I´ve also tried
app
Dear R´ers,
How can I create one single factor variable from two variables incorporating
all possible combinations of the values??
test<-sample(c("A",NA,"B"),100,replace=T)
test2<-sample(c("E",F,"A"),100,replace=T)
tes<-cbind(test,test2)
pseduocode:
r<-function(test,test2)
r
AE
AF
AA
NA
- Phil Spector
>Statistical Computing Facility
>Department of Statistics
>UC Berkeley
>spec...@stat.berkeley.edu
>
>
&g
Dear R´ers..
In this mock dataset how can I generate a logical variable based on whether
just tes or tes3 are NA in each row??
test<-sample(c("A",NA,"B"),100,replace=T)
test2<-sample(c("A",NA,"B"),100,replace=T)
test3<-sample(c("A",NA,"B"),100,replace=T)
tes<-cbind(test,test2,test3)
sam<-c("t
> On Apr 6, 2010, at 3:30 PM, David Winsemius wrote:
>
>>
>> On Apr 6, 2010, at 9:56 AM, moleps islon wrote:
>>
>>> OK... next question.. Which is still a data manipulation problem so I
>>> believe the heading is still OK.
>>>
>>>
tion quite often whereby I need to add
multiple columns based on another vector so I'd be very interested in
another more general approach.
//M
On Tue, Apr 6, 2010 at 9:41 PM, David Winsemius wrote:
>
> On Apr 6, 2010, at 3:30 PM, David Winsemius wrote:
>
>>
>> On Ap
tead of the original
yearly data. Do I have to program this from scratch or is it possible
to use an already existing function?
//M
qta<- table(cut(age,breaks = seq(0, 100, by = 10),include.lowest =
TRUE),cut(year,breaks=seq(1950,2010,by=5),include.lowest=TRUE
On Mon, Apr 5, 2010 at 10:11 P
include.lowest = TRUE)
>
> table(age.factor, year.factor)
>
> moleps wrote:
>> I already did try the regression modeling approach. However the
>> epidemiologists (referee) turns out to be quite fond of comparing the
>> incidence rates to different
kage).
> This avoids the arbitrariness and discontinuities of binning by age range.)
>
> Bert Gunter
> Genentech Nonclinical Biostatistics
>
> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
> Behalf Of moleps
&
Dear R´ers.
I´ve got a dataset with age and year of diagnosis. In order to age-standardize
the incidence I need to transform the data into a matrix with age-groups
(divided in 5 or 10 years) along one axis and year divided into 5 years along
the other axis. Each cell should contain the number o
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