[R-sig-Geo] spacetime EOF error "variable names are limited to 10000 bytes"
Andrew Vitale
vitale232 at gmail.com
Tue Oct 14 20:48:21 CEST 2014
Thanks for the quick fix, Edzer!
I was unfamiliar with installing a development version of a package from
GitHub. If anyone comes across this, it's pretty easy with the devtools
library:
library(raster)
library(spacetime)
library(devtools)
## Create a raster object that mimics my data
## I actually have 20,708 layers in the raster stack
a = array(rnorm(9*9*10000), c(9,9,10000))
b = brick(a)
b = setValues(b, a)
z = seq(as.Date('1980-01-01'), as.Date('2007-05-18'),
by = 'day')
b = setZ(b, z)
## Turn on dev_mode in devtools to easily
## compile spacetime from GitHub
dev_mode(on=TRUE)
install_github('edzer/spacetime')
## coerce the raster stack to an STFDF object
stfdf = as(b, 'STFDF')
## attempt to compute EOFs
eof_time = EOF(stfdf, 'temporal')
eof_space = EOF(stfdf, 'spatial')
On Tue, Oct 14, 2014 at 12:27 AM, Edzer Pebesma <
edzer.pebesma at uni-muenster.de> wrote:
> Thanks for the clear example & diagnostic.
>
> I committed a patch (github) that now uses the first name only to
> address all layers (i.e.: "layer.1"). I'm all ears for a better suggestion!
>
> On 10/14/2014 08:00 AM, Frede Aakmann Tøgersen wrote:
> > Hi Andrew
> >
> > Try this
> >
> >> nchar(names(stfdf at data))
> > [1] 108893
> >>
> >
> > Really long name. Here is a snipped version.
> >
> >> names(stfdf at data)
> > [1]
> "layer.1.layer.2.layer.3.layer.4.layer.5.layer.6.layer.7.layer.8.layer.9.layer.10.layer.11.layer.12.layer.13.layer.14.layer.15.layer.16.layer.17.layer.18.layer.19.layer.20.layer.21.layer.22.layer.23.layer.24.layer.25.layer.26.layer.27.layer.28.layer.29.layer.30.layer.31.layer.32.layer.33.layer.34.layer.35.layer.36.layer.37.layer.38.layer.39.layer.40.layer.41.layer.42.layer.43.layer.44.layer.45.layer.46.layer.47.layer.48.layer.49.layer.50.layer.51.layer.52.layer.53.layer.54.layer.55.layer.56.layer.57.layer.58.layer.59.layer.60.layer.61.layer.62.layer.63.layer.64.layer.65.layer.66.layer.67.layer.68.layer.69.layer.70.layer.71.layer.72.layer.73.layer.74.layer.75.layer.76.layer.77.layer.78.layer.79.layer.80.layer.81.layer.82.layer.83.layer.84.layer.85.layer.86.layer.87.layer.88.layer.89.layer.90.layer.91.layer.92.layer.93.layer.94.layer.95.layer.96.layer.97.layer.98.layer.99.layer.100.layer.101.layer.102.layer.103.layer.104.layer.105.layer.106.layer.107.layer.108.layer.109.layer.110.
>
> layer.111.layer.112.layer.113.layer.114.layer.115.layer.116.layer.117.layer.118.layer.119.layer.120.layer.121.layer.122.layer.123.layer.124.layer.125.layer.126.layer.127.layer.128.layer.129.layer.130.layer.131.layer.132.layer.133.layer.134.layer.135.layer.136.layer.137.layer.138.layer.139.layer.140.lay
> > < SNIP>
> 946.layer.9947.layer.9948.layer.9949.layer.9950.layer.9951.layer.9952.layer.9953.layer.9954.layer.9955.layer.9956.layer.9957.layer.9958.layer.9959.layer.9960.layer.9961.layer.9962.layer.9963.layer.9964.layer.9965.layer.9966.layer.9967.layer.9968.layer.9969.layer.9970.layer.9971.layer.9972.layer.9973.layer.9974.layer.9975.layer.9976.layer.9977.layer.9978.layer.9979.layer.9980.layer.9981.layer.9982.layer.9983.layer.9984.layer.9985.layer.9986.layer.9987.layer.9988.layer.9989.layer.9990.layer.9991.layer.9992.layer.9993.layer.9994.layer.9995.layer.9996.layer.9997.layer.9998.layer.9999.layer.10000"
> >>
> >
> > If you do this:
> >
> > names(stfdf at data) <- "all_layers"
> >
> > EOF() will work.
> >
> >
> > 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-sig-geo-bounces at r-project.org [mailto:r-sig-geo-bounces at r-
> >> project.org] On Behalf Of Andrew Vitale
> >> Sent: 14. oktober 2014 01:24
> >> To: r-sig-geo
> >> Subject: [R-sig-Geo] spacetime EOF error "variable names are limited to
> >> 10000 bytes"
> >>
> >> Hello,
> >>
> >> I have a raster brick of sea level pressure anomalies that I would like
> to
> >> analyze using empirical orthogonal functions. Each layer of the brick
> >> represents a daily observation, with a total of 20,718 days worth of
> >> observations (nlayer=20,718).
> >>
> >> I can easily coerce the raster brick to a spacetime STFDF object.
> However,
> >> when I try to run the spacetime:::EOF function, I get the following
> error:
> >> "Error in eval(as.call(c(expression(data.frame), x, check.names =
> >> !optional, :
> >> variable names are limited to 10000 bytes"
> >>
> >> It seems that the error originates from the third line of the EOF code,
> >> where the STFDF is coerced to an xts object.
> >>
> >> Does anyone know of a workaround for this error, or is this merely a
> >> limitation of R?
> >>
> >> Here's a code that mimics my issue and my sessionInfo():
> >>
> >> library(raster)
> >> library(spacetime)
> >>
> >> ## Create a raster object that mimics my data
> >> ## I actually have 20,708 layers in the raster stack
> >> a = array(rnorm(9*9*10000), c(9,9,10000))
> >> b = brick(a)
> >> b = setValues(b, a)
> >> z = seq(as.Date('1980-01-01'), as.Date('2007-05-18'),
> >> by = 'day')
> >> b = setZ(b, z)
> >>
> >> ## coerce the raster stack to an STFDF object
> >> stfdf = as(b, 'STFDF')
> >>
> >> ## attempt to compute EOFs
> >> eof_time = EOF(stfdf, 'temporal')
> >> eof_space = EOF(stfdf, 'space')
> >>
> >> #### restultant error:
> >> # Error in eval(as.call(c(expression(data.frame), x, check.names =
> >> !optional, :
> >> # variable names are limited to 10000 bytes
> >>
> >> # > sessionInfo()
> >> # R version 3.1.1 (2014-07-10)
> >> # Platform: x86_64-pc-linux-gnu (64-bit)
> >>
> >> # locale:
> >> # [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> >> # [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> >> # [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> >> # [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> >> # [9] LC_ADDRESS=C LC_TELEPHONE=C
> >> # [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >>
> >> # attached base packages:
> >> # [1] grid stats graphics grDevices utils datasets
> methods
> >> # [8] base
> >>
> >> # other attached packages:
> >> # [1] spacetime_1.1-0 ncdf4_1.13 fields_7.1 maps_2.3-7
> >> # [5] spam_1.0-1 rgdal_0.8-16 raster_2.2-31 sp_1.0-15
> >>
> >> # loaded via a namespace (and not attached):
> >> # [1] intervals_0.14.0 lattice_0.20-29 rgeos_0.3-4 tcltk_3.1.1
> >> # [5] tools_3.1.1 xts_0.9-7 zoo_1.7-11
> >>
> >>
> >>
> >>
> >> Thanks,
> >> Andrew
> >> --
> >> *Andrew P. Vitale*
> >> Masters Student
> >> Department of Geography
> >> University of Nevada, Reno
> >> vitale232 at gmail.com
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
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> >> R-sig-Geo at r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > R-sig-Geo at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
>
> --
> Edzer Pebesma, Co-Editor-in-Chief Computers & Geosciences
> Institute for Geoinformatics (ifgi), University of Münster
> Heisenbergstraße 2, 48149 Münster, Germany. Phone: +49 251
> 83 33081 http://ifgi.uni-muenster.de GPG key ID 0xAC227795
>
>
> _______________________________________________
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>
>
--
*Andrew P. Vitale*
Masters Student
Department of Geography
University of Nevada, Reno
vitale232 at gmail.com
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