Re: [R] Getting all possible contingency tables
Thanks Ted for your correction. I was depressed thinking that I did not
understand the theory. However now it comes as just a plotting mistake!
Thanks,
On 02 December 2012 20:47:48, (Ted Harding) wrote:
On 02-Dec-2012 14:17:20 Christofer Bogaso wrote:
Thanks Ted (and other) for your suggestion. Here I have implemented
following:
Tab <- matrix(c(8, 10, 12, 6), nr = 2)
Simu_Number <- 5
Tab_Simulate <- vector("list", length = Simu_Number)
for (i in 1:Simu_Number) {
Tab_Simulate[[i]] <- matrix(rmultinom(1, sum(Tab), rep(0.25,
4)), nrow = 2) ## All Cells have equal probability
}
Sample_ChiSq <- sapply(Tab_Simulate, function(x) {
Statistic <-
sum((chisq.test(as.table(x))$observed -
chisq.test(as.table(x))$expected)^2/chisq.test(as.table(x))$expected)
return(Statistic)
})
length(Sample_ChiSq[Sample_ChiSq < qchisq(0.95, 1)])/Simu_Number
hist(Sample_ChiSq, freq = FALSE)
lines(dchisq(seq(min(Sample_ChiSq), max(Sample_ChiSq), by = 0.5), 1))
However I think I am making some serious mistake as histogram did not
match the density curve.
Can somebody help me where I am making mistake?
Thanks and regards,
[the remainder (copies of previous posts) snipped]
The reasons for the mis-match are:
A: that you have put the curve in the wrong place, by not
supplying x-coordinates to lines(), so that it plots its
points at x = 1,2,3,4,...
B: that you need to multiply the plotted density by the width
of the histogram cells, so as to match the density curve to the
discrete density of the histogram. It will also then look better
when the chis-squared curve is plotted at the mid-points of the cells.
Hence, try something like:
hist(Sample_ChiSq, freq = FALSE, breaks=0.5*(0:40))
x0 <- 0.25+0.5*(0:20)
lines(x0,dchisq(x0,1))
Hoping this helps,
Ted.
-
E-Mail: (Ted Harding)
Date: 02-Dec-2012 Time: 15:02:45
This message was sent by XFMail
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Re: [R] Getting all possible contingency tables
On 02-Dec-2012 14:17:20 Christofer Bogaso wrote:
> Thanks Ted (and other) for your suggestion. Here I have implemented
> following:
>
> Tab <- matrix(c(8, 10, 12, 6), nr = 2)
>
> Simu_Number <- 5
> Tab_Simulate <- vector("list", length = Simu_Number)
> for (i in 1:Simu_Number) {
> Tab_Simulate[[i]] <- matrix(rmultinom(1, sum(Tab), rep(0.25,
> 4)), nrow = 2) ## All Cells have equal probability
> }
> Sample_ChiSq <- sapply(Tab_Simulate, function(x) {
> Statistic <-
> sum((chisq.test(as.table(x))$observed -
> chisq.test(as.table(x))$expected)^2/chisq.test(as.table(x))$expected)
> return(Statistic)
> })
>
> length(Sample_ChiSq[Sample_ChiSq < qchisq(0.95, 1)])/Simu_Number
>
> hist(Sample_ChiSq, freq = FALSE)
> lines(dchisq(seq(min(Sample_ChiSq), max(Sample_ChiSq), by = 0.5), 1))
>
>
> However I think I am making some serious mistake as histogram did not
> match the density curve.
>
> Can somebody help me where I am making mistake?
>
> Thanks and regards,
> [the remainder (copies of previous posts) snipped]
The reasons for the mis-match are:
A: that you have put the curve in the wrong place, by not
supplying x-coordinates to lines(), so that it plots its
points at x = 1,2,3,4,...
B: that you need to multiply the plotted density by the width
of the histogram cells, so as to match the density curve to the
discrete density of the histogram. It will also then look better
when the chis-squared curve is plotted at the mid-points of the cells.
Hence, try something like:
hist(Sample_ChiSq, freq = FALSE, breaks=0.5*(0:40))
x0 <- 0.25+0.5*(0:20)
lines(x0,dchisq(x0,1))
Hoping this helps,
Ted.
-
E-Mail: (Ted Harding)
Date: 02-Dec-2012 Time: 15:02:45
This message was sent by XFMail
__
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] Getting all possible contingency tables
Thanks Ted (and other) for your suggestion. Here I have implemented
following:
Tab <- matrix(c(8, 10, 12, 6), nr = 2)
Simu_Number <- 5
Tab_Simulate <- vector("list", length = Simu_Number)
for (i in 1:Simu_Number) {
Tab_Simulate[[i]] <- matrix(rmultinom(1, sum(Tab), rep(0.25,
4)), nrow = 2) ## All Cells have equal probability
}
Sample_ChiSq <- sapply(Tab_Simulate, function(x) {
Statistic <-
sum((chisq.test(as.table(x))$observed -
chisq.test(as.table(x))$expected)^2/chisq.test(as.table(x))$expected)
return(Statistic)
})
length(Sample_ChiSq[Sample_ChiSq < qchisq(0.95, 1)])/Simu_Number
hist(Sample_ChiSq, freq = FALSE)
lines(dchisq(seq(min(Sample_ChiSq), max(Sample_ChiSq), by = 0.5), 1))
However I think I am making some serious mistake as histogram did not
match the density curve.
Can somebody help me where I am making mistake?
Thanks and regards,
On 01-12-2012 21:45, (Ted Harding) wrote:
You will need to be clear about whether you are conditioning on
the marginal totals as well as on the overall total. As stated,
you are only asking for the overall total (36) to be fixed.
In that case, one possible (and by no means unique) approach
would be to:
[A]: Choose any four "random integers" a,b,c,d that add up to 36
(even there, you still have to make a choice about what distribution
to adopt for the "random integers").
[B]: Place the results into the 2x2 matrix; then evaluate chi-squared.
[C]: Repeat until you have enough cases.
Example (using equiprobable multinomial to generate 4 "random integers")
Tab <- matrix(rmultinom(1,36,c(1,1,1,1)/4), nrow=2)
A more specific choice would be to fix the row and column probablilties
(but not the sample row and column totals), e.g.:
P.row1 <- 0.25 ; P.row2 <- 1 - P.row1
P.col1 <- 0.50 ; P.col2 <- 1 - P.col1
Then, adopting the hypothesis of independence between rows and columns:
P11 <- P.row1*P.col1
P21 <- P.row2*P.col1
P12 <- P.row1*P.col2
P22 <- P.row2*P.col2
Tab <- matrix(rmultinom(1,36,c(P11,P21,P12,P22)), nrow=2)
On the other hand, if you want to also fix the sample row margins
and column margins, then your sampled table needs to be generated
using a hypergeometric distribution, (which is the basis of the
fisher.test mentioned by Bert Gunter). Since explaining how to
do this is a bit mjore complicated than the above, please first
confirm what constraints (e.g. only total count; row-margins
only; col-margins only; both row- & col-margins) you wich to impose.
Hoping this helps,
Ted.
On 01-Dec-2012 14:28:24 Christofer Bogaso wrote:
Thanks Bert for your reply.
I am trying to understand/visualize the Sample Chi-Squared Statistic's
Null distribution. Therefore I need all possible Contingency tables
under Independence case.
What could be better way to visualize that?
Thanks and regards,
On 01 December 2012 20:03:00, Bert Gunter wrote:
Christopher:
Don't do this!
If I understand you correctly, you want FIsher's exact test. This is
already available in R, using far smarter algorithms then you would. See:
?fisher.test
-- Bert
On Sat, Dec 1, 2012 at 5:48 AM, Christofer Bogaso
mailto:bogaso.christo...@gmail.com>> wrote:
Thanks John for your reply. However still not clear how I should
proceed.
My goal is to generate all possible contingency tables. Basically
I want to see the distribution of Chi-squared Statistic under
independence (NULL).
So I was thinking if I can generate all possible permutation of
integer numbers having sum equal to (8 + 10 + 12 + 6) = 36. Is
there any R function to do that?
Thanks and regards,
On 01-12-2012 18:39, John Kane wrote:
Are you basically asking for all possible permutations of the
table? If so see ?permn in the combinat package.
John Kane
Kingston ON Canada
-Original Message-
From:bogaso.christo...@gmail.com
<mailto:bogaso.christo...@gmail.com>
Sent: Sat, 01 Dec 2012 18:10:15 +0545
To:r-help@r-project.org <mailto:r-help@r-project.org>
Subject: [R] Getting all possible contingency tables
Hello all,
Let say I have 2-way contingency table:
Tab <- matrix(c(8, 10, 12, 6), nr = 2)
and the Chi-squared test could not reject the independence:
> chisq.test(Tab)
Pearson's Chi-squared test with Yates'
continuity correction
data: Tab
X-squared = 1.0125, df = 1, p-value = 0.3143
However I want to get all possible contingency tables
under this
independence scenario (one of them would obviously be
Re: [R] Getting all possible contingency tables
I believe you are looking for a detailed construction of Fisher's Exact
Test. I have an example
with code in my book and R package.
The book discussion is Section 15.2 of
Heiberger, Richard M., and Burt Holland (2004). Statistical Analysis and
Data
Display: An Intermediate Course with Examples in S-Plus, R, and SAS.
Springer--Verlag, New York.
http://springer.com/0-387-40270-5
Table 15.2 shows the full set of tables for the example.
The package is HH
install.packages("HH")
The code to construct Table 15.2 is in file
library/HH/scripts/Ch15-twtb.r
Search for the line:
## study the construction of the Fisher Exact test
and read through to the end of the glasses example.
Rich
On Sat, Dec 1, 2012 at 7:25 AM, Christofer Bogaso <
bogaso.christo...@gmail.com> wrote:
> Hello all,
>
> Let say I have 2-way contingency table:
>
> Tab <- matrix(c(8, 10, 12, 6), nr = 2)
>
> and the Chi-squared test could not reject the independence:
>
> > chisq.test(Tab)
>
> Pearson's Chi-squared test with Yates' continuity correction
>
> data: Tab
> X-squared = 1.0125, df = 1, p-value = 0.3143
>
>
> However I want to get all possible contingency tables under this
> independence scenario (one of them would obviously be the given table as,
> we could not reject the independence), and for each such table I want to
> calculate the Ch-sq statistic.
>
> Can somebody help me how to generate all such tables?
>
> Thanks and regards,
>
> __**
> 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]]
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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.
Re: [R] Getting all possible contingency tables
On Dec 1, 2012, at 7:28 AM, Christofer Bogaso wrote: Thanks Bert for your reply. I am trying to understand/visualize the Sample Chi-Squared Statistic's Null distribution. Therefore I need all possible Contingency tables under Independence case. What could be better way to visualize that? In your quest for enlightenment, consider looking at the example in: ?r2dtable -- David. Thanks and regards, On 01 December 2012 20:03:00, Bert Gunter wrote: Christopher: Don't do this! If I understand you correctly, you want FIsher's exact test. This is already available in R, using far smarter algorithms then you would. See: ?fisher.test -- Bert On Sat, Dec 1, 2012 at 5:48 AM, Christofer Bogaso mailto:bogaso.christo...@gmail.com>> wrote: Thanks John for your reply. However still not clear how I should proceed. My goal is to generate all possible contingency tables. Basically I want to see the distribution of Chi-squared Statistic under independence (NULL). So I was thinking if I can generate all possible permutation of integer numbers having sum equal to (8 + 10 + 12 + 6) = 36. Is there any R function to do that? Thanks and regards, On 01-12-2012 18:39, John Kane wrote: Are you basically asking for all possible permutations of the table? If so see ?permn in the combinat package. John Kane Kingston ON Canada -Original Message- From: bogaso.christo...@gmail.com <mailto:bogaso.christo...@gmail.com> Sent: Sat, 01 Dec 2012 18:10:15 +0545 To: r-help@r-project.org <mailto:r-help@r-project.org> Subject: [R] Getting all possible contingency tables Hello all, Let say I have 2-way contingency table: Tab <- matrix(c(8, 10, 12, 6), nr = 2) and the Chi-squared test could not reject the independence: > chisq.test(Tab) Pearson's Chi-squared test with Yates' continuity correction data: Tab X-squared = 1.0125, df = 1, p-value = 0.3143 However I want to get all possible contingency tables under this independence scenario (one of them would obviously be the given table as, we could not reject the independence), and for each such table I want to calculate the Ch-sq statistic. Can somebody help me how to generate all such tables? Thanks and regards, David Winsemius, MD Alameda, CA, USA __ 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] Getting all possible contingency tables
> > > > My goal is to generate all possible contingency tables. Basically I want > > to see the distribution of Chi-squared Statistic under independence > > (NULL). > > > > So I was thinking if I can generate all possible permutation of integer > > numbers having sum equal to (8 + 10 + 12 + 6) = 36. Is there any R > > function to do that? I think R *can* do this (thanks to Robin Hankin): library(partitions) str(parts(36)) 'partition' int [1:36, 1:17977] 36 0 0 0 0 0 0 0 0 0 ... I'm not quite clear on how you're going to take these results and turn them into possible tables, but I guess you do ... You might also be interested in the simulate.p.value option to chisq.test and the randomizer (which preserves row and column totals): from the code of chisq.test, tmp <- .Call(C_chisq_sim, sr, sc, B, E) > >>> -Original Message- > >>> From: bogaso.christofer gmail.com > >>> Let say I have 2-way contingency table: > >>> > >>> Tab <- matrix(c(8, 10, 12, 6), nr = 2) > >>> > >>> and the Chi-squared test could not reject the independence: > >>> > >>> > chisq.test(Tab) > >>> > >>> Pearson's Chi-squared test with Yates' continuity correction > >>> > >>> data: Tab > >>> X-squared = 1.0125, df = 1, p-value = 0.3143 > >>> > >>> > >>> However I want to get all possible contingency tables under this > >>> independence scenario (one of them would obviously be the given table > >>> as, we could not reject the independence), and for each such table I > >>> want to calculate the Ch-sq statistic. > >>> > >>> Can somebody help me how to generate all such tables? __ 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] Getting all possible contingency tables
You will need to be clear about whether you are conditioning on the marginal totals as well as on the overall total. As stated, you are only asking for the overall total (36) to be fixed. In that case, one possible (and by no means unique) approach would be to: [A]: Choose any four "random integers" a,b,c,d that add up to 36 (even there, you still have to make a choice about what distribution to adopt for the "random integers"). [B]: Place the results into the 2x2 matrix; then evaluate chi-squared. [C]: Repeat until you have enough cases. Example (using equiprobable multinomial to generate 4 "random integers") Tab <- matrix(rmultinom(1,36,c(1,1,1,1)/4), nrow=2) A more specific choice would be to fix the row and column probablilties (but not the sample row and column totals), e.g.: P.row1 <- 0.25 ; P.row2 <- 1 - P.row1 P.col1 <- 0.50 ; P.col2 <- 1 - P.col1 Then, adopting the hypothesis of independence between rows and columns: P11 <- P.row1*P.col1 P21 <- P.row2*P.col1 P12 <- P.row1*P.col2 P22 <- P.row2*P.col2 Tab <- matrix(rmultinom(1,36,c(P11,P21,P12,P22)), nrow=2) On the other hand, if you want to also fix the sample row margins and column margins, then your sampled table needs to be generated using a hypergeometric distribution, (which is the basis of the fisher.test mentioned by Bert Gunter). Since explaining how to do this is a bit mjore complicated than the above, please first confirm what constraints (e.g. only total count; row-margins only; col-margins only; both row- & col-margins) you wich to impose. Hoping this helps, Ted. On 01-Dec-2012 14:28:24 Christofer Bogaso wrote: > Thanks Bert for your reply. > > I am trying to understand/visualize the Sample Chi-Squared Statistic's > Null distribution. Therefore I need all possible Contingency tables > under Independence case. > > What could be better way to visualize that? > > Thanks and regards, > > On 01 December 2012 20:03:00, Bert Gunter wrote: >> Christopher: >> >> Don't do this! >> >> If I understand you correctly, you want FIsher's exact test. This is >> already available in R, using far smarter algorithms then you would. See: >> >> ?fisher.test >> >> -- Bert >> >> On Sat, Dec 1, 2012 at 5:48 AM, Christofer Bogaso >> mailto:bogaso.christo...@gmail.com>> wrote: >> >> Thanks John for your reply. However still not clear how I should >> proceed. >> >> My goal is to generate all possible contingency tables. Basically >> I want to see the distribution of Chi-squared Statistic under >> independence (NULL). >> >> So I was thinking if I can generate all possible permutation of >> integer numbers having sum equal to (8 + 10 + 12 + 6) = 36. Is >> there any R function to do that? >> >> Thanks and regards, >> >> >> On 01-12-2012 18:39, John Kane wrote: >> >> Are you basically asking for all possible permutations of the >> table? If so see ?permn in the combinat package. >> >> John Kane >> Kingston ON Canada >> >> >> -Original Message- >> From: bogaso.christo...@gmail.com >> <mailto:bogaso.christo...@gmail.com> >> Sent: Sat, 01 Dec 2012 18:10:15 +0545 >> To: r-help@r-project.org <mailto:r-help@r-project.org> >> Subject: [R] Getting all possible contingency tables >> >> Hello all, >> >> Let say I have 2-way contingency table: >> >> Tab <- matrix(c(8, 10, 12, 6), nr = 2) >> >> and the Chi-squared test could not reject the independence: >> >> > chisq.test(Tab) >> >> Pearson's Chi-squared test with Yates' >> continuity correction >> >> data: Tab >> X-squared = 1.0125, df = 1, p-value = 0.3143 >> >> >> However I want to get all possible contingency tables >> under this >> independence scenario (one of them would obviously be the >> given table >> as, we could not reject the independence), and for each >> such table I >> want to calculate the Ch-sq statistic. >> >> Can somebody help me how to generate all such tables? >> >> Thanks and regards, - E-Mail: (Ted Harding) Date: 01-Dec-2012 Time: 16:00:16 This message was sent by XFMail __ 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] Getting all possible contingency tables
Thanks Bert for your reply.
I am trying to understand/visualize the Sample Chi-Squared Statistic's
Null distribution. Therefore I need all possible Contingency tables
under Independence case.
What could be better way to visualize that?
Thanks and regards,
On 01 December 2012 20:03:00, Bert Gunter wrote:
Christopher:
Don't do this!
If I understand you correctly, you want FIsher's exact test. This is
already available in R, using far smarter algorithms then you would. See:
?fisher.test
-- Bert
On Sat, Dec 1, 2012 at 5:48 AM, Christofer Bogaso
mailto:bogaso.christo...@gmail.com>> wrote:
Thanks John for your reply. However still not clear how I should
proceed.
My goal is to generate all possible contingency tables. Basically
I want to see the distribution of Chi-squared Statistic under
independence (NULL).
So I was thinking if I can generate all possible permutation of
integer numbers having sum equal to (8 + 10 + 12 + 6) = 36. Is
there any R function to do that?
Thanks and regards,
On 01-12-2012 18:39, John Kane wrote:
Are you basically asking for all possible permutations of the
table? If so see ?permn in the combinat package.
John Kane
Kingston ON Canada
-Original Message-
From: bogaso.christo...@gmail.com
<mailto:bogaso.christo...@gmail.com>
Sent: Sat, 01 Dec 2012 18:10:15 +0545
To: r-help@r-project.org <mailto:r-help@r-project.org>
Subject: [R] Getting all possible contingency tables
Hello all,
Let say I have 2-way contingency table:
Tab <- matrix(c(8, 10, 12, 6), nr = 2)
and the Chi-squared test could not reject the independence:
> chisq.test(Tab)
Pearson's Chi-squared test with Yates'
continuity correction
data: Tab
X-squared = 1.0125, df = 1, p-value = 0.3143
However I want to get all possible contingency tables
under this
independence scenario (one of them would obviously be the
given table
as, we could not reject the independence), and for each
such table I
want to calculate the Ch-sq statistic.
Can somebody help me how to generate all such tables?
Thanks and regards,
R-help@r-project.org <mailto: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.
__
FREE ONLINE PHOTOSHARING - Share your photos online with your
friends and family!
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<http://www.R-project.org/posting-guide.html>
and provide commented, minimal, self-contained, reproducible code.
--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.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] Getting all possible contingency tables
Christopher: Don't do this! If I understand you correctly, you want FIsher's exact test. This is already available in R, using far smarter algorithms then you would. See: ?fisher.test -- Bert On Sat, Dec 1, 2012 at 5:48 AM, Christofer Bogaso < bogaso.christo...@gmail.com> wrote: > Thanks John for your reply. However still not clear how I should proceed. > > My goal is to generate all possible contingency tables. Basically I want > to see the distribution of Chi-squared Statistic under independence (NULL). > > So I was thinking if I can generate all possible permutation of integer > numbers having sum equal to (8 + 10 + 12 + 6) = 36. Is there any R function > to do that? > > Thanks and regards, > > > On 01-12-2012 18:39, John Kane wrote: > >> Are you basically asking for all possible permutations of the table? If >> so see ?permn in the combinat package. >> >> John Kane >> Kingston ON Canada >> >> >> -Original Message- >>> From: bogaso.christo...@gmail.com >>> Sent: Sat, 01 Dec 2012 18:10:15 +0545 >>> To: r-help@r-project.org >>> Subject: [R] Getting all possible contingency tables >>> >>> Hello all, >>> >>> Let say I have 2-way contingency table: >>> >>> Tab <- matrix(c(8, 10, 12, 6), nr = 2) >>> >>> and the Chi-squared test could not reject the independence: >>> >>> > chisq.test(Tab) >>> >>> Pearson's Chi-squared test with Yates' continuity correction >>> >>> data: Tab >>> X-squared = 1.0125, df = 1, p-value = 0.3143 >>> >>> >>> However I want to get all possible contingency tables under this >>> independence scenario (one of them would obviously be the given table >>> as, we could not reject the independence), and for each such table I >>> want to calculate the Ch-sq statistic. >>> >>> Can somebody help me how to generate all such tables? >>> >>> Thanks and regards, >>> >>> __** >>> 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. >>> >> __**__ >> FREE ONLINE PHOTOSHARING - Share your photos online with your friends and >> family! >> Visit >> http://www.inbox.com/**photosharing<http://www.inbox.com/photosharing>to >> find out more! >> >> >> >> > __** > 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. > -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm [[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] Getting all possible contingency tables
R can usually do almost anything but if the function exists I am not aware of it. Sorry. I did misunderstand what you were doing. John Kane Kingston ON Canada > -Original Message- > From: bogaso.christo...@gmail.com > Sent: Sat, 01 Dec 2012 19:33:09 +0545 > To: jrkrid...@inbox.com > Subject: Re: [R] Getting all possible contingency tables > > Thanks John for your reply. However still not clear how I should proceed. > > My goal is to generate all possible contingency tables. Basically I want > to see the distribution of Chi-squared Statistic under independence > (NULL). > > So I was thinking if I can generate all possible permutation of integer > numbers having sum equal to (8 + 10 + 12 + 6) = 36. Is there any R > function to do that? > > Thanks and regards, > > > On 01-12-2012 18:39, John Kane wrote: >> Are you basically asking for all possible permutations of the table? If >> so see ?permn in the combinat package. >> >> John Kane >> Kingston ON Canada >> >> >>> -Original Message- >>> From: bogaso.christo...@gmail.com >>> Sent: Sat, 01 Dec 2012 18:10:15 +0545 >>> To: r-help@r-project.org >>> Subject: [R] Getting all possible contingency tables >>> >>> Hello all, >>> >>> Let say I have 2-way contingency table: >>> >>> Tab <- matrix(c(8, 10, 12, 6), nr = 2) >>> >>> and the Chi-squared test could not reject the independence: >>> >>> > chisq.test(Tab) >>> >>> Pearson's Chi-squared test with Yates' continuity correction >>> >>> data: Tab >>> X-squared = 1.0125, df = 1, p-value = 0.3143 >>> >>> >>> However I want to get all possible contingency tables under this >>> independence scenario (one of them would obviously be the given table >>> as, we could not reject the independence), and for each such table I >>> want to calculate the Ch-sq statistic. >>> >>> Can somebody help me how to generate all such tables? >>> >>> Thanks and regards, >>> >>> __ >>> 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. >> >> FREE ONLINE PHOTOSHARING - Share your photos online with your friends >> and family! >> Visit http://www.inbox.com/photosharing to find out more! >> >> >> FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! __ 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] Getting all possible contingency tables
Thanks John for your reply. However still not clear how I should proceed. My goal is to generate all possible contingency tables. Basically I want to see the distribution of Chi-squared Statistic under independence (NULL). So I was thinking if I can generate all possible permutation of integer numbers having sum equal to (8 + 10 + 12 + 6) = 36. Is there any R function to do that? Thanks and regards, On 01-12-2012 18:39, John Kane wrote: Are you basically asking for all possible permutations of the table? If so see ?permn in the combinat package. John Kane Kingston ON Canada -Original Message- From: bogaso.christo...@gmail.com Sent: Sat, 01 Dec 2012 18:10:15 +0545 To: r-help@r-project.org Subject: [R] Getting all possible contingency tables Hello all, Let say I have 2-way contingency table: Tab <- matrix(c(8, 10, 12, 6), nr = 2) and the Chi-squared test could not reject the independence: > chisq.test(Tab) Pearson's Chi-squared test with Yates' continuity correction data: Tab X-squared = 1.0125, df = 1, p-value = 0.3143 However I want to get all possible contingency tables under this independence scenario (one of them would obviously be the given table as, we could not reject the independence), and for each such table I want to calculate the Ch-sq statistic. Can somebody help me how to generate all such tables? Thanks and regards, __ 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. FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/photosharing to find out more! __ 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] Getting all possible contingency tables
Are you basically asking for all possible permutations of the table? If so see ?permn in the combinat package. John Kane Kingston ON Canada > -Original Message- > From: bogaso.christo...@gmail.com > Sent: Sat, 01 Dec 2012 18:10:15 +0545 > To: r-help@r-project.org > Subject: [R] Getting all possible contingency tables > > Hello all, > > Let say I have 2-way contingency table: > > Tab <- matrix(c(8, 10, 12, 6), nr = 2) > > and the Chi-squared test could not reject the independence: > > > chisq.test(Tab) > > Pearson's Chi-squared test with Yates' continuity correction > > data: Tab > X-squared = 1.0125, df = 1, p-value = 0.3143 > > > However I want to get all possible contingency tables under this > independence scenario (one of them would obviously be the given table > as, we could not reject the independence), and for each such table I > want to calculate the Ch-sq statistic. > > Can somebody help me how to generate all such tables? > > Thanks and regards, > > __ > 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. FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/photosharing to find out more! __ 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] Getting all possible contingency tables
Hello all, Let say I have 2-way contingency table: Tab <- matrix(c(8, 10, 12, 6), nr = 2) and the Chi-squared test could not reject the independence: > chisq.test(Tab) Pearson's Chi-squared test with Yates' continuity correction data: Tab X-squared = 1.0125, df = 1, p-value = 0.3143 However I want to get all possible contingency tables under this independence scenario (one of them would obviously be the given table as, we could not reject the independence), and for each such table I want to calculate the Ch-sq statistic. Can somebody help me how to generate all such tables? Thanks and regards, __ 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.
