Dear Frede,
Sorry for the late reply, yesterday I was out of office.
Thanks so much for your code! It has just compacted in a few lines what
I had written in several 'paragraphs'!
To be honest, I'm not familiar to work with lists in R. I think one of
its main advantages is the reduced size of the outputs.
Thanks again and have a nice day,
Bea
On 22.04.2014 07:04, Frede Aakmann Tøgersen wrote:
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
fr...@vestas.com
http://www.vestas.com
Company reg. name: Vestas Wind Systems A/S
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-----Original Message-----
From: Beatriz R. Gonzalez Dominguez [mailto:aguitatie...@hotmail.com]
Sent: 21. april 2014 16:27
To: Frede Aakmann Tøgersen; r-help@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
fr...@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-boun...@r-project.org [mailto:r-help-bounces@r-
project.org]
On Behalf Of Beatriz R. Gonzalez Dominguez
Sent: 21. april 2014 14:53
To: r-help@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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and provide commented, minimal, self-contained, reproducible code.
