Reshaping an array - how does it work in R

Fri, Mar 18, 2016 3:15 PM

Thanks.  That is what I needed to know.  I don?t want to play around with some of the other suggestions, as I don?t totally understand what they do, and don?t want to risk messing up something and not be aware of it.

There is a way to read in the data chunks at a time and reshape it and put, it into the (reshaped) larger array, harder to program but probably worth the pain to be certain of what I am doing.

I had a feeling a copy was made, just wanted to make certain of it.

Thanks again,

-Roy

On Mar 18, 2016, at 2:56 PM, D?nes T?th <toth.denes at ttk.mta.hu> wrote:

Hi Roy,

R (usually) makes a copy if the dimensionality of an array is modified, even if you use this syntax:
x <- array(1:24, c(2, 3, 4))
dim(x) <- c(6, 4)

See also ?tracemem, ?data.table::address, ?pryr::address and other tools to trace if an internal copy is done.

Workaround: use data.table::setattr or bit::setattr to modify the dimensions in place (i.e., without making a copy). Risk: if you modify an object by reference, all other objects which point to the same memory address will be modified silently, too.

HTH,
 Denes



On 03/18/2016 10:28 PM, Roy Mendelssohn - NOAA Federal wrote:

Hi All:

I am working with a very large array. if noLat is the number of latitudes, noLon the number of longitudes and noTime the number of time periods, the array is of the form:

myData[noLat, no Lon, noTime].

It is read in this way because that is how it is stored in a (series) of netcdf files. For the analysis I need to do, I need instead the array:

myData[noLat*noLon, noTime]. Normally this would be easy:

myData<- array(myData,dim=c(noLat*noLon,noTime))

My question is how does this command work in R - does it make a copy of the existing array, with different indices for the dimensions, or does it just redo the indices and leave the given array as is? The reason for this question is my array is 30GB in memory, and I don?t have enough space to have a copy of the array in memory. If the latter I will have to figure out a work around to bring in only part of the data at a time and put it into the proper locations.

Thanks,

-Roy

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new address and phone***
110 Shaffer Road
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new address and phone***
110 Shaffer Road
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

Reshaping an array - how does it work in R

Thread (14 messages)