[R] readMat - how to retrieve the variables

[Joshua Wiley]

Hi Ed,

Here are some different ways of structuring and storing data in R as
well as how to access them.

Hope this helps,

Josh

#########################################################################

set.seed(10)
## Option 1a (closest to what you want?)
a1a <- list(river1 = data.frame(flow = 1:10, precipitation = runif(10)),
  river2 = data.frame(flow = 11:20, precipitation = runif(10)))

set.seed(10)
## Option 1b (a slight variant), lists + named vectors
a1b <- list(river1 = list(flow = 1:10, precipitation = runif(10)),
  river2 = list(flow = 11:20, precipitation = runif(10)))

set.seed(10)
## Option 2 (a.k.a. 'long' format)
a2 <- data.frame(flow = 1:20, precipitation = runif(20),
  river = factor(rep(1:2, each = 10)))

set.seed(10)
## Option 3 (a.k.a. 'wide' format)
a3 <- data.frame(r1.flow = 1:10, r2.flow = 11:20,
  r1.precipitation = runif(10), r2.precipitation = runif(10))

## compare the str()uctures of all four objects

str(a1a)
str(a1b)
str(a2)
str(a3)

## Access "flow" from "river1" in option 1a
## four equivalent options
a1a$river1$flow
a1a[["river1"]][,"flow"]
a1a[[1]][, 1]
a1a[[c(1, 1)]]

## Option 1b
a1b$river1$flow ## works
a1b[[1]][, 1] ## does not work, used vectors not a dataframe
a1b[[c(1, 1)]] ## works

## Option 2
a2$flow ## both rivers' flow, useful for plotting
a2[, 1]
a2[, "flow"]
## for example:
require(lattice)
xyplot(flow ~ precipitation | river, data = a2)

## Option 3
a3$r1.flow
a3[, 1]
a3[, "r1.flow"]

##################################################################

On Sun, Mar 13, 2011 at 3:42 PM, Eduardo M. A. M.Mendes
<emammendes at gmail.com> 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).
>
> 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/
>
>



-- 
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/