[R] Loop to extract from variables in the workspace

Tue Apr 22 07:04:16 CEST 2014

Well, sticking to your loop that you seem comfortable with try this:

## list to hold dataframes
extracList <- vector("list", length(1981:2010))

cnt <- 0
for(i in 1981:2010){
	cnt <- cnt + 1
	rasterObj <-get( c(paste("RR_", i, "_1", sep="")))
      	extractList[[cnt]]<- extract(rasterObj, coords, df=T)}
 }

See ?get which is kind of the opposite of assign.

To coerce the list of dataframes into one dataframe several methods are available:

do.call("rbind", extractList)

plyr::rbind.fill(extractList)

plyr::ldply(extractList, data.frame)

as.data.frame(data.table::rbindlist(extractList))

This was taken from http://stackoverflow.com/questions/2851327/converting-a-list-of-data-frames-into-one-data-frame-in-r where you get get some pros and cons on the methods.

The fastest way will probably be to create a huge dataframe and during the loop calculated the row indices of that dataframe for each raster into the result from extract should be put.

Yours sincerely / Med venlig hilsen

Frede Aakmann Tøgersen
Specialist, M.Sc., Ph.D.
Plant Performance & Modeling

Technology & Service Solutions
T +45 9730 5135
M +45 2547 6050
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> -----Original Message-----
> From: Beatriz R. Gonzalez Dominguez [mailto:aguitatierra at hotmail.com]
> Sent: 21. april 2014 16:27
> To: Frede Aakmann Tøgersen; r-help at r-project.org
> Subject: Re: [R] Loop to extract from variables in the workspace
> 
> Hi Frede,
> 
> Many thanks for your reply.
> 1. The first argument in extract is a Formal class RasterLayer in the
> Workspace (e.g RR_1981_1 ).
> 
> 2. I created an intermediate name to hold the result fromthe extract
> function because I'd like to create several dataframes with the output
> of the iterative (loop) extraction. I'd like to get the same result as
> when I do:
> 
> PE.coords_01_1981 <- extract(RR_1981_1, coords, df=T)
> PE.coords_01_1982 <- extract(RR_1982_1, coords, df=T)
> PE.coords_01_1983 <- extract(RR_1983_1, coords, df=T)
> PE.coords_01_1984 <- extract(RR_1984_1, coords, df=T)
> [... this works no problem]
> 
> 3. 'coords' is a SpatialPointsDataFrame.
> 
> 4. I used assign in the loop becuase I thought it was the way forward to
> create new variables out of it. Isn't it?
> 
> What I'd like to do is to use coordinate points ('coords') to extract
> raster pixel values (eg. 'RR_1981_1') on which the points are overlying.
> Then I'd like to build a bigger data frame including the data from all
> the outputs (i.e. PE.coords_01_1981, PE.coords_01_1982).
> 
> Hope to have explained myself properly. Please let me know if anything
> else should be clarified.
> 
> Best wishes,
> 
> Bea
> 
> 
> On 21/04/2014 15:17, Frede Aakmann Tøgersen wrote:
> > Hi Beatriz
> >
> > Did you read the help for extract{raster} carefully?
> >
> > Several things can be wrong.
> >
> > 1) First argument to extract is not a file name but a raster object.
> > 2) In the loop you name an object extract as an intermediate name to hold
> the result from the extract function. Do you think there could be a name
> clash? R is clever but perhaps not clever enough.
> > 3) coords are of the right class (see ?extract).
> > 4) assign can be useful from time to time. But in a loop?
> >
> > I think the things you are doing are some intermediate results that needs
> more processing. Do you think this is the right way to do that. For instance
> instead of storing the immediate result as separate objects why not store
> those in a list.
> >
> > Perhaps if you tell us what you would like to do  overall, i.e. from first to
> last, then we will be able to help you to become more efficient.
> >
> >
> > Yours sincerely / Med venlig hilsen
> >
> >
> > Frede Aakmann Tøgersen
> > Specialist, M.Sc., Ph.D.
> > Plant Performance & Modeling
> >
> > Technology & Service Solutions
> > T +45 9730 5135
> > M +45 2547 6050
> > frtog at vestas.com
> > http://www.vestas.com
> >
> > Company reg. name: Vestas Wind Systems A/S
> > This e-mail is subject to our e-mail disclaimer statement.
> > Please refer to www.vestas.com/legal/notice
> > If you have received this e-mail in error please contact the sender.
> >
> >
> >> -----Original Message-----
> >> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org]
> >> On Behalf Of Beatriz R. Gonzalez Dominguez
> >> Sent: 21. april 2014 14:53
> >> To: r-help at r-project.org
> >> Subject: [R] Loop to extract from variables in the workspace
> >>
> >> Dear all,
> >>
> >> I'm starting to work with loops and I'm stucked on something.
> >> I've been searching and trying different possibilities but I don't get
> >> to the solution.
> >> I'd be very grateful if you could share any ideas that you think may help.
> >>
> >> library("raster")
> >>
> >> # All my variables are in the workspace
> >>
> >> # This is what I'd like to obtain, but with a loop (I'm working with
> >> several years and variables).
> >> PE.coords_01_1981 <- extract(RR_1981_1, coords, df=T)
> >> PE.coords_01_1982 <- extract(RR_1982_1, coords, df=T)
> >> PE.coords_01_1983 <- extract(RR_1983_1, coords, df=T)
> >> PE.coords_01_1984 <- extract(RR_1984_1, coords, df=T)
> >> PE.coords_01_1985 <- extract(RR_1985_1, coords, df=T)
> >> PE.coords_01_1986 <- extract(RR_1986_1, coords, df=T)
> >> PE.coords_01_1987 <- extract(RR_1987_1, coords, df=T)
> >> PE.coords_01_1988 <- extract(RR_1988_1, coords, df=T)
> >> PE.coords_01_1989 <- extract(RR_1989_1, coords, df=T)
> >> PE.coords_01_1990 <- extract(RR_1990_1, coords, df=T)
> >>
> >>
> >> # This is one of the things I've tried.
> >>
> >> for(i in 1981:2010){
> >> file <- c(paste("RR_", i, "_1", sep=""))
> >> extract <- extract(file, coords, df=T)}
> >> names.a <- paste("PE.coords_01_", i, sep="")
> >> assign(names.a, value=extract)
> >> }
> >>
> >> # I get the following error.
> >> Error in (function (classes, fdef, mtable) :
> >> unable to find an inherited method for function 'extract'
> >> for signature '"character", "SpatialPointsDataFrame"'
> >> # I think the error must be something when I'm defining 'file'
> >>
> >> Thanks a lot for any help!
> >>
> >> ______________________________________________
> >> 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.