Re: [R] rpart cutpoint interpretation

[Kishor Tappita]

Thank you so much for the clarification Terry.

On Thu, Oct 8, 2015 at 6:03 PM, Therneau, Terry M., Ph.D.  wrote:

> The cutpoint is on the predictor, so the interpretation is the same as it
> is for any other rpart model.  The subjects with predictor < cutpoint form
> one group and those > cutpoint the other.  The cutpoint is chosen to give
> the greatest difference in "average y" between the groups.  For poisson
> "averge y" is an event rate.
>
>
> On 10/08/2015 05:00 AM, r-help-requ...@r-project.org wrote:
>
>> I am trying to derive cutpoint/threshold with a poisson distributed
>> dependent variable. I know how to interpret cutpoint with binary dependent
>> variable based on direction. Can some on help me to intrepret cutpoint for
>> poisson case with one independent variable with the derived threshold.
>>
>

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[R] rpart cutpoint interpretation

[Kishor Tappita]

Hi All,

I am trying to derive cutpoint/threshold with a poisson distributed
dependent variable. I know how to interpret cutpoint with binary dependent
variable based on direction. Can some on help me to intrepret cutpoint for
poisson case with one independent variable with the derived threshold.

Thanks in advance.

Regards,
Kishor

[[alternative HTML version deleted]]

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[R] BioNet::runFastHeinz error

[Kishor Tappita]

Dear R-Users,

I am trying to perform network analysis using BioNet. I am having
issues with the runFastHeinz function. I extracted the sub network and
computed the scores and fed to the function. I even tried to run the
function from the example data in the help function. I get the same
error. Please help me solve this issue. I tried accessing the
igraph.from.graphNEL function from igraph as
igraph::igraph.from.graphNEL. But still it didnt fix the error.

library(DLBCL)
data(dataLym)
data(interactome)
interactome <- subNetwork(dataLym$label, interactome)
p.values <- dataLym$t.pval
names(p.values) <- dataLym$label
bum <- fitBumModel(p.values, plot=TRUE)
scores <- scoreNodes(network=interactome, fb=bum, fdr=0.0001)
module <- runFastHeinz(network=interactome, scores=scores)

Error in graph[[9]][[3]] : subscript out of bounds

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_SG   LC_NUMERIC=C LC_TIME=en_SG
 [4] LC_COLLATE=en_SG LC_MONETARY=en_SGLC_MESSAGES=en_SG
 [7] LC_PAPER=C   LC_NAME=CLC_ADDRESS=C
[10] LC_TELEPHONE=C   LC_MEASUREMENT=en_SG LC_IDENTIFICATION=C

attached base packages:
[1] grid  stats graphics  grDevices utils datasets  methods
[8] base

other attached packages:
 [1] hash_2.2.6  DLBCL_1.3.5 BioNet_1.18.0
 [4] RBGL_1.34.0 Biobase_2.18.0  BiocGenerics_0.4.0
 [7] igraph0_0.5.5-3 maanova_1.28.0  samr_2.0
[10] matrixStats_0.8.12  impute_1.32.0   limma_3.14.4
[13] Rgraphviz_2.2.1 graph_1.36.2GeneNet_1.2.8
[16] igraph_0.6.6fdrtool_1.2.11  longitudinal_1.1.8
[19] corpcor_1.6.6   BiocInstaller_1.8.3

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.20.7 DBI_0.2-7IRanges_1.16.6
[4] parallel_2.15.1  R.methodsS3_1.5.2RSQLite_0.11.4
[7] stats4_2.15.1tools_2.15.1


Thanks,
Regards,
Kishor

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Re: [R] ordinal data with binary response

[Kishor Tappita]

Dear John,

Thanks for the information. It is quite helpful.

Regards,
Kishor

On Thu, Oct 24, 2013 at 9:24 PM, John Sorkin
 wrote:
> Kishor,
> It sounds like you will need to use logistic regression. Although the
> following URL might help you better understand logistic regression,
> http://ww2.coastal.edu/kingw/statistics/R-tutorials/logistic.html  it would
> probably be most helpful if you would see help from a local statistician.
> John
>
>
> John David Sorkin M.D., Ph.D.
> Professor of Medicine
> Chief, Biostatistics and Informatics
> University of Maryland School of Medicine Division of Gerontology and
> Geriatric Medicine
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
>>>> Kishor Tappita  10/24/2013 5:15 AM >>>
>
> Dear R-users,
>
> I am trying to analyze data with ordinal independent variables and
> binary response . Could some one suggest me an appropriate statistic
> for this kind of analysis.
>
> Thanks,
> Regards,
> Kishir
>
> __
> 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.
>
>
> Confidentiality Statement:
>
> This email message, including any attachments, is for ...{{dropped:6}}

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[R] ordinal data with binary response

[Kishor Tappita]

Dear R-users,

I am trying to analyze data with ordinal independent variables and
binary response . Could some one suggest me an appropriate statistic
for this kind of analysis.

Thanks,
Regards,
Kishir

__
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Re: [R] problem installing RDCOMEvents

[Kishor Tappita]

Dear Prof Ripley,

Thanks for your reply. I tried with R -versions (R-3.0.1 & R-2.15.2)
but was having problem with installing the dependencies such as
SWinRegistry,SWinTypeLibs. With R version 2.9.1, I was able to install
all the dependencies but am having problem with installing
RDCOMEvents.

As suggested by you I will contact the package maintainer.

Thanks,
Regards,
Kishor


On Fri, Aug 16, 2013 at 3:29 PM, Prof Brian Ripley
 wrote:
> Are you serious: 'R version 2.9.1 (2009-06-26)' ?
>
> Please see the posting guide (see the footer of this message), and
>
> 1) Update your R.
>
> 2) If this still does not work, ask the package maintainer.
>
>
>
> On 16/08/2013 09:29, Kishor Tappita wrote:
>>
>> Dear R-Users,
>>
>> I am getting the below error when I am trying to install "RDCOMEvents"
>> from Omegahat. All the dependencies were installed .Please help me
>> resolve this issue.
>>
>>> library(RDCOMEvents)
>>
>> Loading required package: RDCOMServer
>> Loading required package: SWinRegistry
>>
>> Attaching package: 'SWinRegistry'
>>
>>
>>  The following object(s) are masked from package:base :
>>
>>   append
>>
>> Loading required package: Ruuid
>> Loading required package: RDCOMClient
>> Loading required package: SWinTypeLibs
>> Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source
>> = keep.source) :
>>in 'RDCOMEvents' methods for export not found: findConnectionPoint,
>> createCOMEventServer
>> In addition: There were 18 warnings (use warnings() to see them)
>> Error: package/namespace load failed for 'RDCOMEvents'
>>
>>> sessionInfo()
>>
>> R version 2.9.1 (2009-06-26)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>>
>> other attached packages:
>> [1] SWinTypeLibs_0.5-1 RDCOMClient_0.92-0 RDCOMServer_0.6-2  Ruuid_1.22.0
>> [5] SWinRegistry_0.3-3
>>
>>
>> Thanks,
>> Regards,
>> Kishor
>>
>> __
>> 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.
>>
>
>
> --
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> 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

__
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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] problem installing RDCOMEvents

[Kishor Tappita]

Dear R-Users,

I am getting the below error when I am trying to install "RDCOMEvents"
from Omegahat. All the dependencies were installed .Please help me
resolve this issue.

> library(RDCOMEvents)
Loading required package: RDCOMServer
Loading required package: SWinRegistry

Attaching package: 'SWinRegistry'


The following object(s) are masked from package:base :

 append

Loading required package: Ruuid
Loading required package: RDCOMClient
Loading required package: SWinTypeLibs
Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source
= keep.source) :
  in 'RDCOMEvents' methods for export not found: findConnectionPoint,
createCOMEventServer
In addition: There were 18 warnings (use warnings() to see them)
Error: package/namespace load failed for 'RDCOMEvents'

> sessionInfo()
R version 2.9.1 (2009-06-26)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] SWinTypeLibs_0.5-1 RDCOMClient_0.92-0 RDCOMServer_0.6-2  Ruuid_1.22.0
[5] SWinRegistry_0.3-3


Thanks,
Regards,
Kishor

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Re: [R] problem installing RDCOMClient on Windows 7

[Kishor Tappita]

Dear Uwe,

Thank you for your repsonse. I installed the latest version of R
(R-3.0.1) . I get the below errors when I try to install RDCOMClient.

g++ -m32 -I"D:/R-3.0.1/include" -DNDEBUG -D_GNU_ -DNO_PYCOM_IPROVIDECLASSINFO -
.-I"d:/RCompile/CRANpkg/extralibs64/local/include"  -Wno-deprecated-O2
Wall  -mtune=core2 -c connect.cpp -o connect.o
In file included from d:\mingw\bin\../lib/gcc/mingw32/4.6.2/include/c++/cstdio:
4:0,
 from D:/R-3.0.1/include/Rinternals.h:25,
 from D:/R-3.0.1/include/Rdefines.h:29,
 from RUtils.h:1,
 from connect.cpp:20:
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:573:9:
error: 'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:574:9:
error:'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:575:9:
error:'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:586:9:
error:'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:587:9: error:
'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:589:9: error:
'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:591:9: error:
'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:632:9: error:
'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:633:9: error:
'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:638:9: error:
'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:639:9: error:
'wint_t' does not name a type
make: *** [connect.o] Error 1
ERROR: compilation failed for package 'RDCOMClient'
* removing 'D:/R-3.0.1/library/RDCOMClient'



> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C   LC_TIME=English_United
States.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base
>

Thanks,
Regards,
Kishor



On Mon, Aug 5, 2013 at 9:03 PM, Uwe Ligges
 wrote:
> Please try with a recent version of R. Yours is 6 major updates behind
>
> Best,
> Uwe Ligges
>
>
>
> On 05.08.2013 16:11, Kishor Tappita wrote:
>>
>> Dear R-Users,
>>
>> I am trying to install RDCOMClient package as it is a dependency for
>> installing excel.link package. I get the below error while trying to
>> install RDCOMClient on 64-bit Windows 7 operating system.
>>
>>
>> g++ -I"D:/R-2.10.0/include" -D_GNU_ -DNO_PYCOM_IPROVIDECLASSINFO -I.
>>   -Wno-deprecated-O2 -Wall  -c RUtils.c -o RUtils.o
>>
>> RUtils.c: In function 'SEXPREC* R_createRCOMUnknownObject(void*, const
>> char*)':
>> RUtils.c:151:52: error: invalid conversion from 'int' to 'Rboolean'
>> [-fpermissive]
>> D:/R-2.10.0/include/Rinternals.h:692:6: error:   initializing argument
>> 3 of 'void R_RegisterCFinalizerEx(SEXP, R_CFinalizer_t, Rboolean)'
>> [-fpermissive]
>> RUtils.c: In function 'Rboolean ISSInstanceOf(SEXP, const char*)':
>> RUtils.c:245:26: error: invalid conversion from 'int' to 'Rboolean'
>> [-fpermissive]
>>
>> make: *** [RUtils.o] Error 1
>>
>> Please help me to resolve this issue. RDCOMClient_0.93-0.tar.gz is the
>> source file that I am using. Below is my session information.
>>
>>> sessionInfo()
>>
>> R version 2.10.0 (2009-10-26)
>> i386-pc-mingw32
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>>
>> Thanks,
>> Kishor
>>
>> __
>> 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.
>>
>

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] problem installing RDCOMClient on Windows 7

[Kishor Tappita]

Dear R-Users,

I am trying to install RDCOMClient package as it is a dependency for
installing excel.link package. I get the below error while trying to
install RDCOMClient on 64-bit Windows 7 operating system.


g++ -I"D:/R-2.10.0/include" -D_GNU_ -DNO_PYCOM_IPROVIDECLASSINFO -I.
 -Wno-deprecated-O2 -Wall  -c RUtils.c -o RUtils.o

RUtils.c: In function 'SEXPREC* R_createRCOMUnknownObject(void*, const char*)':
RUtils.c:151:52: error: invalid conversion from 'int' to 'Rboolean'
[-fpermissive]
D:/R-2.10.0/include/Rinternals.h:692:6: error:   initializing argument
3 of 'void R_RegisterCFinalizerEx(SEXP, R_CFinalizer_t, Rboolean)'
[-fpermissive]
RUtils.c: In function 'Rboolean ISSInstanceOf(SEXP, const char*)':
RUtils.c:245:26: error: invalid conversion from 'int' to 'Rboolean'
[-fpermissive]

make: *** [RUtils.o] Error 1

Please help me to resolve this issue. RDCOMClient_0.93-0.tar.gz is the
source file that I am using. Below is my session information.

> sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

Thanks,
Kishor

__
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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] mvpart - legend help

[Kishor Tappita]

Dear R-Users,

I was able to use mvpart package for my multi-response data and was able to
generate the decision tree.

I realized that the colors (3) for the legend are being recycled.  In my
situation I have 12
dependent variables and would like to have 12 different colors for the
legend and barplots.
Otherwise please help me understand the reason for having 3 colors.

And also at each node, I see two values,  1. the number of cases and
another number. Please help me understand
what the other number means.

Thanks in advance.


> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

Regard,
Kishor

[[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.

Re: [R] problem with installing R pacakges

[Kishor Tappita]

Dear Uwe,

I will enter the correct user::password values and try again. As per your
suggestion I will contact the local sysadmin
if required.

Thanks for your help.

Regards,
Kishor

On Wed, Jul 18, 2012 at 12:46 AM, Uwe Ligges <
lig...@statistik.tu-dortmund.de> wrote:

>
>
> On 16.07.2012 14:45, Kishor Tappita wrote:
>
>> Dear R- Users,
>>
>> I am unable to install R packages over the internet. Below is my session
>> information. My guess is that this may be
>> a proxy issue. I have set the http_proxy_user : my user id(network id) :
>> password (machine password) .
>>
>
>
> Maybe not correctly?
>
> Please see what the R for Windows FAQs say about using proxies. If that
> does not help, ask your local sysadmin. We cannot help.
>
> Uwe Ligges
>
>
>
>> The error I get is as below
>>
>>  install.packages("MASS")
>>>
>> Warning: unable to access index for repository
>> http://ftp.iitm.ac.in/cran/**bin/windows/contrib/2.15<http://ftp.iitm.ac.in/cran/bin/windows/contrib/2.15>
>> Warning: unable to access index for repository
>> http://www.stats.ox.ac.uk/pub/**RWin/bin/windows/contrib/2.15<http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.15>
>> Warning message:
>> package ‘MASS’ is not available (for R version 2.15.1)
>>
>> Below is my session info. I searched in the archives but was not able to
>> find the issue. Please excuse me if this
>> is a repost.
>>
>>  sessionInfo()
>>>
>> R version 2.15.1 (2012-06-22)
>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>> locale:
>> [1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252
>> LC_MONETARY=English_India.1252 LC_NUMERIC=C
>> LC_TIME=English_India.1252
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>> loaded via a namespace (and not attached):
>> [1] tools_2.15.1
>>
>> Thanks in advance.
>>
>> Regards,
>> Kishor
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
>> __**
>> R-help@r-project.org 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 <http://www.R-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>

[[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.

[R] problem with installing R pacakges

[Kishor Tappita]

Dear R- Users,

I am unable to install R packages over the internet. Below is my session
information. My guess is that this may be
a proxy issue. I have set the http_proxy_user : my user id(network id) :
password (machine password) .

The error I get is as below

> install.packages("MASS")
Warning: unable to access index for repository
http://ftp.iitm.ac.in/cran/bin/windows/contrib/2.15
Warning: unable to access index for repository
http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.15
Warning message:
package ‘MASS’ is not available (for R version 2.15.1)

Below is my session info. I searched in the archives but was not able to
find the issue. Please excuse me if this
is a repost.

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252
LC_MONETARY=English_India.1252 LC_NUMERIC=C
LC_TIME=English_India.1252
attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base
loaded via a namespace (and not attached):
[1] tools_2.15.1

Thanks in advance.

Regards,
Kishor

[[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.

Re: [R] Survival Analysis

[Kishor Tappita]

Thanks a lot. I used survfit to generate KM plots but I will try to figure
out to find the corresponding returned value for KM estimate. Thank you for
your invaluable help.

On Mon, Jul 18, 2011 at 8:28 PM, David Winsemius wrote:

>
> On Jul 18, 2011, at 10:42 AM, Kishor Tappita wrote:
>
>  Ok David, Thanks for clearing my misconception. Then could you please
>> suggest me how I could get the KM estimate for a time point. I remember
>> reading the formula
>> for calculating the KM. Do, I have to write a method to compute the KM
>> estimate or will the survival package provide it for me?
>>
>
> ?survfit
> ?survfit.formula
>
> --
> david.
>
>
>
>>
>> Thank you so much in advance.
>>
>> Regards,
>> Kishor
>>
>> On Mon, Jul 18, 2011 at 7:52 PM, David Winsemius 
>> wrote:
>>
>> On Jul 18, 2011, at 10:10 AM, Kishor Tappita wrote:
>>
>>  Dear David,
>>>
>>> Thank you for your reply. I realized that the summary  function can help
>>> me in finding the the order of the curves.
>>> The 0.95UCL (95% upper confidence level) column in particular seems to
>>> follow the same pattern as the curves on the plot.
>>>
>>
>> That would not have been my prediction. The 95% UCL could be high simply
>> because the sample size in that group was small.
>>
>> --
>> David
>>
>>
>>> I am new to survival analysis, so  please correct me if I am wrong.
>>>
>>> Thanks,
>>> Kishor
>>>
>>>
>>>
>>> On Mon, Jul 18, 2011 at 3:21 AM, David Winsemius 
>>> wrote:
>>>
>>> On Jul 17, 2011, at 11:27 AM, Kishor Tappita wrote:
>>>
>>> Dear List,
>>>
>>> I used survival package of R and was able to generate KM plots. Now I
>>> need
>>>
>>> help in finding the top curve in a non-visualization way. I mean to say
>>> that
>>> I would like to know the order of curves through any existing methods
>>> rather
>>> than looking at the KM plots. I need this information as I am generating
>>> KM
>>> plots for thousands of genes.
>>>
>>> Why aren't you taking the KM estimate at a particular time?
>>>
>>> --
>>> David
>>>
>>>
>>> I would really appreciate if some one can direct me and help me.
>>>
>>> Thanks,
>>> Regards,
>>> Kishor
>>>
>>>   [[alternative HTML version deleted]]
>>>
>>> __**
>>> R-help@r-project.org 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 <http://www.R-project.org/posting-guide.html>
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>> David Winsemius, MD
>>> West Hartford, CT
>>>
>>>
>>>
>>
>> David Winsemius, MD
>> West Hartford, CT
>>
>>
>>
> David Winsemius, MD
> West Hartford, CT
>
>

[[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.

Re: [R] Survival Analysis

[Kishor Tappita]

Ok David, Thanks for clearing my misconception. Then could you please
suggest me how I could get the KM estimate for a time point. I remember
reading the formula
for calculating the KM. Do, I have to write a method to compute the KM
estimate or will the survival package provide it for me?


Thank you so much in advance.

Regards,
Kishor

On Mon, Jul 18, 2011 at 7:52 PM, David Winsemius wrote:

>
> On Jul 18, 2011, at 10:10 AM, Kishor Tappita wrote:
>
> Dear David,
>
> Thank you for your reply. I realized that the summary  function can help me
> in finding the the order of the curves.
> The 0.95UCL (95% upper confidence level) column in particular seems to
> follow the same pattern as the curves on the plot.
>
>
> That would not have been my prediction. The 95% UCL could be high simply
> because the sample size in that group was small.
>
> --
> David
>
>
> I am new to survival analysis, so  please correct me if I am wrong.
>
> Thanks,
> Kishor
>
>
>
> On Mon, Jul 18, 2011 at 3:21 AM, David Winsemius 
> wrote:
>
>>
>> On Jul 17, 2011, at 11:27 AM, Kishor Tappita wrote:
>>
>>  Dear List,
>>>
>>> I used survival package of R and was able to generate KM plots. Now I
>>> need
>>>
>>
>>  help in finding the top curve in a non-visualization way. I mean to say
>>> that
>>> I would like to know the order of curves through any existing methods
>>> rather
>>> than looking at the KM plots. I need this information as I am generating
>>> KM
>>> plots for thousands of genes.
>>>
>>
>> Why aren't you taking the KM estimate at a particular time?
>>
>> --
>> David
>>
>>
>>> I would really appreciate if some one can direct me and help me.
>>>
>>> Thanks,
>>> Regards,
>>> Kishor
>>>
>>>[[alternative HTML version deleted]]
>>>
>>> __**
>>> R-help@r-project.org 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 <http://www.R-project.org/posting-guide.html>
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>> David Winsemius, MD
>> West Hartford, CT
>>
>>
>
> David Winsemius, MD
> West Hartford, CT
>
>

[[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.

Re: [R] Survival Analysis

[Kishor Tappita]

Dear David,

Thank you for your reply. I realized that the summary  function can help me
in finding the the order of the curves.
The 0.95UCL (95% upper confidence level) column in particular seems to
follow the same pattern as the curves on the plot.

I am new to survival analysis, so  please correct me if I am wrong.

Thanks,
Kishor



On Mon, Jul 18, 2011 at 3:21 AM, David Winsemius wrote:

>
> On Jul 17, 2011, at 11:27 AM, Kishor Tappita wrote:
>
>  Dear List,
>>
>> I used survival package of R and was able to generate KM plots. Now I need
>>
>
>  help in finding the top curve in a non-visualization way. I mean to say
>> that
>> I would like to know the order of curves through any existing methods
>> rather
>> than looking at the KM plots. I need this information as I am generating
>> KM
>> plots for thousands of genes.
>>
>
> Why aren't you taking the KM estimate at a particular time?
>
> --
> David
>
>
>> I would really appreciate if some one can direct me and help me.
>>
>> Thanks,
>> Regards,
>> Kishor
>>
>>[[alternative HTML version deleted]]
>>
>> __**
>> R-help@r-project.org 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 <http://www.R-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> David Winsemius, MD
> West Hartford, CT
>
>

[[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.

[R] Survival Analysis

[Kishor Tappita]

Dear List,

I used survival package of R and was able to generate KM plots. Now I need
help in finding the top curve in a non-visualization way. I mean to say that
I would like to know the order of curves through any existing methods rather
than looking at the KM plots. I need this information as I am generating KM
plots for thousands of genes.

I would really appreciate if some one can direct me and help me.

Thanks,
Regards,
Kishor

[[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] Hmm Topology restriction

[Kishor Tappita]

Dear Ingmar,

Thanks a lot.

Regards,
Kishor

On Thu, Dec 2, 2010 at 6:39 PM, Ingmar Visser  wrote:
> depmixS4 enables linear constraints on parameters, best, Ingmar
>
> On Thu, Dec 2, 2010 at 12:01 PM, Kishor Tappita 
> wrote:
>>
>> Dear List,
>>
>> We are using RHmm to cluster data through HMM. We would like to
>> restrict the transition matrix of HMM, to get hierarchical connections
>> between clusters. But, RHmm doesn't seem to support these
>> restrictions. Can any one suggest a library to do that.
>>
>> Thanks,
>> Kishor
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>

__
R-help@r-project.org mailing list
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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] Hmm Topology restriction

[Kishor Tappita]

Dear List,

We are using RHmm to cluster data through HMM. We would like to
restrict the transition matrix of HMM, to get hierarchical connections
between clusters. But, RHmm doesn't seem to support these
restrictions. Can any one suggest a library to do that.

Thanks,
Kishor

__
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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] how to ignore or omit somethings while reading the data table

[Kishor Tappita]

Hi,

I have a tempoary fix but I think there can be a better way (R way) to solve
this.

If you have a unix account you can do it this way.

$ vi filename

For command prompt press Esc

: s/\$//g

Otherwise you can replace $ sign with a peculiar number say ''

:s/\$//g

This substitutes $ signs with  at all places and after u load the data
you can replace 
with $ sign using regular expressions in R.  There is some risk and you have
to be careful to chose
the peculiar number.

I am not familiar with regular expressions in R either you or someone in the
list can help.

Regards,
Kishor

On Jan 2, 2008 7:05 PM, mrafi <[EMAIL PROTECTED]> wrote:

>
> yeah...i'd have done that but it is a 20 mb csv file...and then there are
> other columns of data also..which could be distorted  by this...
>
> r_a_mueller wrote:
> >
> > Am Mittwoch, 2. Januar 2008 14:14 schrieb mrafi:
> >> hello respected ppl...
> >> am a engg. student...i was trying to use R in statistical calculations
> >> now the problem is..i imported a huge tsv file onto R...it has a column
> > csv?
> >> which gives cost...and it has "$" with each numerical value in this
> >> column...it is something like this..$.05,$.1,$.075...and so on..
> >> R is reading it as "character vector"...
> >> i tried using all the arguments but could only change it to a "factor"
> >> i want to read it as numericals...and perform further operations..
> >> i know it is a stupid problem but can any1 help me get outta this...
> >> thank you all...!!!
> > I'd like to have it simple... open your csv-file in a text editor, with
> > "find/replace" replace your "$" by ""
> >
> > --
> > Richard Müller - Am Spring 9 - D-58802 Balve-Eisborn
> > www.oeko-sorpe.de
> >
> > __
> > 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.
> >
> >
>
> --
> View this message in context:
> http://www.nabble.com/how-to-ignore-or-omit-somethings-while-reading-the-data-table-tp14578131p14578428.html
> Sent from the R help mailing list archive at Nabble.com
> .
>
> __
> 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.
>

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