[R] coda sweave

[Brian Diggs]

On 4/27/2010 1:42 PM, Randall Wrong wrote:
> Thank you so much Ista.
>
> I have problems with pictures too.
>
> \begin{figure}
> \centering
> <<fig=true>>=
> xyplot( mcmc(x) )
> @
> \end{figure}
>
> Why doesn't this work ? Sorry for posting all these questions :-(
>
> Best,
> Randall

Check out FAQ 7.22.  You need to use

print(xyplot(mcmc(x)))

since inside an Sweave evaluation, you are not at the command line and 
it does not print by default.

> 2010/4/27 Ista Zahn<istazahn at gmail.com>
>
>> Hi Randall,
>>
>> Sounds like you need to make friends with the str() function, and
>> perhaps read the documentation about data types in R. For your
>> particular problem:
>>
>> library(coda)
>> m1<- matrix(runif(100), nrow=10)
>> m1.sum<- summary(mcmc(m1))
>> str(m1.sum)
>>
>> library(xtable)
>> xtable(m1.sum$statistics)
>> xtable(m1.sum$quantiles)
>>
>> Best,
>> Ista
>>
>> On Tue, Apr 27, 2010 at 12:22 PM, Randall Wrong<randall.wrong at gmail.com>
>> wrote:
>>> This is the kind of output I get with summary(mcmc(x)). I would like it
>> in
>>> LaTeX. There are two tables.
>>>
>>> Iterations = 1:10
>>> Thinning interval = 1
>>> Number of chains = 1
>>> Sample size per chain = 10
>>> 1. Empirical mean and standard deviation for each variable,
>>>    plus standard error of the mean:
>>>         Mean    SD Naive SE Time-series SE
>>> [1,]  0.7237 3.374    1.067          1.252
>>> [2,] -1.7883 4.317    1.365          1.644
>>> [3,]  0.8384 3.422    1.082          1.047
>>> [4,]  1.0750 3.195    1.010          1.087
>>> 2. Quantiles for each variable:
>>>         2.5%      25%     50%     75% 97.5%
>>> var1 -1.5408 -0.91681 -0.1798  0.7134 7.929
>>> var2 -4.1454 -3.89975 -3.5207 -2.1781 7.706
>>> var3 -2.0412 -0.79606  0.3247  1.0445 7.999
>>> var4 -0.9809 -0.08847  0.1895  0.4980 8.015
>>>
>>> Thank you very much for any help,
>>> Randall
>>>
>>> 2010/4/27 Randall Wrong<randall.wrong at gmail.com>
>>>
>>>> I forgot to say that the coda package is loaded.
>>>>
>>>> Randall
>>>>
>>>> 2010/4/27 Randall Wrong<randall.wrong at gmail.com>
>>>>
>>>>   Dear R users,
>>>>>
>>>>> I have a matrix x of simulated values. Each column corresponds to one
>>>>> variable.
>>>>>
>>>>> summary(mcmc(x)) works fine
>>>>>
>>>>> I would like however to transform the ouput into a nice LaTeX code.
>>>>>
>>>>> xtable( summary(mcmc(x)) ) does not work.
>>>>>
>>>>> Thanks
>>>>> Randall
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-help at 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<http://www.r-project.org/posting-guide.html>
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>>
>>
>>   --
>> Ista Zahn
>> Graduate student
>> University of Rochester
>> Department of Clinical and Social Psychology
>> http://yourpsyche.org
>>
>
> 	[[alternative HTML version deleted]]
>

--
Brian Diggs
Senior Research Associate, Department of Surgery, Oregon Health & 
Science University