Re: [R] readMat - how to retrieve the variables

From: David Winsemius <dwinsemius_at_comcast.net>
Date: Sun, 13 Mar 2011 20:15:31 -0400

On Mar 13, 2011, at 7:48 PM, Eduardo M. A. M.Mendes wrote:

> Hi there
>
> ... means that I have not copied all the data that R showed on the
> screen.

I fail to see the point in posting mangled dput output.

-- 
David.

>
> Cheers
>
> Ed
>
>
> -----Original Message-----
> From: David Winsemius [mailto:dwinsemius_at_comcast.net]
> Sent: Sunday, March 13, 2011 8:37 PM
> To: Eduardo M. A. M.Mendes
> Cc: 'Joshua Wiley'; R-help_at_r-project.org
> Subject: Re: [R] readMat - how to retrieve the variables
>
>
> On Mar 13, 2011, at 7:27 PM, Eduardo M. A. M.Mendes wrote:
>
>> Hello there
>>
>> Here is the output of the command
>>
>> structure(list(a =
>> structure(list(structure(list(structure(c(16.259746877453,
>> 17.7125316239611, 17.7801266531401, 18.7370886410339,
>> 18.5622784910323, 19. ....
>
> That seems pretty unlikely. All of those "...." are not in the
> output from
> dput are they? The dimension of 3683 implies otherwise.
>
>> ....
>> ), .Dim = c(3683L, 1L)), structure(c(0, 0, 6.7, 46.1, 2, 0, 29.5,
>> 93.7, 4.5, 39.6, 1.4, 5.5, 9, 12.2, 5.7, 0, 0, 0, 0, 8, 0, 19.5,
>> 30 ....
>> ....
>> ), .Dim = c(3683L, 1L))), .Dim = c(2L, 1L, 1L), .Dimnames = list(
>> c("flow", "precip"), NULL, NULL)), structure(list(structure(c(42,
>> 42, 44, 60, 84, 97, 113, 357, 613, 495, 401, 295, 250, 228, 202,
>> 174 ....
>> ....
>> 12, 36, 0, 2, 0, 6, 13, 0, 1, 0, 12, 0, 0, 32, 0, 0, 1, 36, 7, 36,
>> 48,
>> 27, 7), .Dim = c(3683L, 1L))), .Dim = c(2L, 1L, 1L), .Dimnames =
>> list(
>> c("flow", "precip"), NULL, NULL))), .Dim = c(2L, 1L, 1L), .Dimnames
>> = list(
>> c("river1", "river2"), NULL, NULL))), .Names = "a", header =
>> structure(list(
>> description = "MATLAB 5.0 MAT-file, Platform: PCWIN, Created on:
>> Sun Mar
>> 13 18:51:54 2011 ",
>> version = "5", endian = "little"), .Names = c("description",
>> "version", "endian")))
>>
>> Cheers
>>
>> Ed
>>
>>
>> -----Original Message-----
>> From: David Winsemius [mailto:dwinsemius_at_comcast.net]
>> Sent: Sunday, March 13, 2011 8:01 PM
>> To: Eduardo M. A. M.Mendes
>> Cc: 'Joshua Wiley'; R-help_at_r-project.org
>> Subject: Re: [R] readMat - how to retrieve the variables
>>
>>
>> On Mar 13, 2011, at 6:42 PM, Eduardo M. A. M.Mendes wrote:
>>
>>>
>>> Hi Joshua
>>>
>>> Many thanks.
>>>
>>> The values of flow can be accessed in a weird way and we can used
>>> them for some calculations. Since I am a newbie as far as using R
>>> is
>>> concerned I wonder whether you could tell me how to create a
>>> structure in R that looks like the one I have in matlab (that is, a
>>> variable a that contains river1 and river2 that contains flow and
>>> precipitation).
>>
>> If you posted the results of dput(a) , we might be able to test our
>> pet theories, but here is my hapless first guess:
>>
>> mat.R.struc <- with(b$a[,,1], #looks like it was a matrix that had
>> lists as elements
>> cbind(as.data.frame(river1), as.data.frame(river2) )
>> )
>>
>> It's not so much that it will "look like" your Matlab structure, but
>> it could be something that you can work with. This will create a
>> long-
>> format structure which is a typical one for plotting ans regression.
>> Another option would be an R array which, unlike matrices, can have
>> more than 2 dimensions.
>>
>>
>>>
>>> Cheers
>>>
>>> Ed
>>>
>>>
>>> -----Original Message-----
>>> From: Joshua Wiley [mailto:jwiley.psych_at_gmail.com]
>>> Sent: Sunday, March 13, 2011 7:20 PM
>>> To: Eduardo M. A. M.Mendes
>>> Cc: R-help_at_r-project.org
>>> Subject: Re: [R] readMat - how to retrieve the variables
>>>
>>> On Sun, Mar 13, 2011 at 2:56 PM, Eduardo M. A. M.Mendes
>>> <emammendes_at_gmail.com
>>>> wrote:
>>>> Hi Joshua
>>>>
>>>> Many thanks for the prompt reply.
>>>>
>>>> I have saved a short version of the matlab file and the output on R
>>>> is
>>>>
>>>>> b=readMat("testr.mat")
>>>>> b
>>>> $a
>>>> , , 1
>>>>
>>>> [,1]
>>>> river1 List,2
>>>> river2 List,2
>>>
>>> It looks like you are dealing with a special series of lists nested
>>> within three dimensional arrays within lists. My suggestion would
>>> be
>>> to double check that the matlab file has reasonable data (whatever
>>> that means) and try to double check your use of readmat (do you meet
>>> all the requirements for versions, etc.). That is not a common R
>>> structure so the extraction is similarly uncommon.
>>> Perhaps Henrik will be along with more helpful answers.
>>>
>>> Good luck,
>>>
>>> Josh
>>>>
>>>>
>>>> attr(,"header")
>>>> attr(,"header")$description
>>>> [1] "MATLAB 5.0 MAT-file, Platform: PCWIN, Created on: Sun Mar 13
>>>> 18:51:54 2011 "
>>>>
>>>> attr(,"header")$version
>>>> [1] "5"
>>>>
>>>> attr(,"header")$endian
>>>> [1] "little"
>>>>
>>>> When I issue the command b$a[,,1]$river1[,,1]$flow I see the flow
>>>> values.
>>>>
>>>> Unfortunately the data is confidential.
>>>>
>>>> Many thanks
>>>>
>>>> Ed
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Joshua Wiley [mailto:jwiley.psych_at_gmail.com]
>>>> Sent: Sunday, March 13, 2011 6:30 PM
>>>> To: Eduardo M. A. M.Mendes
>>>> Cc: R-help_at_r-project.org
>>>> Subject: Re: [R] readMat - how to retrieve the variables
>>>>
>>>> Hi Ed,
>>>>
>>>> Can you please provide *at least* the R output from running:
>>>>
>>>> str(data)
>>>>
>>>> where "data" is the variable name you stored the results of
>>>> readMat() in. If it is reasonably small and can be sent as
>>>> plaintext (I do not know Matlabs file format off hand), you could
>>>> send us the actual data so we can try to read it in, but at the
>>>> least str() will let us see how R is storing your data and give you
>>>> some explanation.
>>>>
>>>> Side note, as data() is a function, it might be worthwhile to call
>>>> your actual data something else (say, mydata, dat, etc.). For
>>>> anyone else interested, readMat() is in package "R.matlab".
>>>>
>>>> Cheers,
>>>>
>>>> Josh
>>>>
>>>> On Sun, Mar 13, 2011 at 2:07 PM, Eduardo M. A. M.Mendes
>>>> <emammendes_at_gmail.com
>>>>> wrote:
>>>>> Hello
>>>>>
>>>>> I have a matlab MAT file that contains one single variable: a.
>>>>> The
>>>>> structure of a is as follows:
>>>>>
>>>>> a.river1.flow (flow values)
>>>>> a.river1.date_flow (date)
>>>>> a.river1.precip (precipitation values) a.river1.date_precip
>>>>> a.river2.flow a.river2.date_flow a.river2.precip
>>>>> a.river2.date_precip
>>>>>
>>>>> I have used readMat to load the variable a in R, however I have no
>>>>> idea how readMat translates a. I managed to get some values out
>>>>> of
>>>>> data=readMat("matfile.mat")
>>>>>
>>>>> data$a[,,1]$river1[,,1]$flow -> Why do I need [,,1]? Why not
>>>>> data$a$river1$flow?
>>>>>
>>>>> Many thanks
>>>>>
>>>>> Ed
>>>>>
>>>>> ______________________________________________
>>>>> 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
>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>> --
>>> Joshua Wiley
>>> Ph.D. Student, Health Psychology
>>> University of California, Los Angeles http://www.joshuawiley.com/
>>>
>>> ______________________________________________
>>> 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
>>> 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 ______________________________________________ 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 and provide commented, minimal, self-contained, reproducible code.
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