[R] Loop to extract from variables in the workspace

[Beatriz R. Gonzalez Dominguez]

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
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>
>> -----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!
>>
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