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I have a a Large RasterStack of temperatures and a 10570 points in a Large SpatialPointsDataFrame and I'm using extract() to assign the temperatures to each point in R.

pts@data <- data.frame(pts@data, extract(sub, pts))

This gives me a table with a column for each raster:

DATE2       BICHO   X2000.01.01   X2000.01.02   (...)   X2012.12.31
2009-04-08  Woody      20.7          19.2        ...         9.1
2009-04-09  Woody      20.5          19.3        ...         9.5
2009-04-10  Woody      20.7          19.2        ...         9.6
2004-11-30  Woody      20.9          19.1        ...         9.8
2004-12-01  Buzz       20.3          19.4        ...         10
2004-12-02  Buzz       20.7          19.2        ...         9.5
2012-12-05  Buzz       20.6          19.2        ...         9.8
2012-12-05  Andy      -99.99        -99.99       ...        -99.99
2012-12-05  Rex        20.5          19.3        ...         9.1

The problem is, when there are repeated dates, the temperature value of one of the dates is set to -99. How can I solve this problem?

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What is temp@layers? You should not be using the @ operator btw, where did this code come from? – mdsumner Apr 15 '14 at 12:14
temp is the initial stack file. In that line I'm subsetting the initial stack from years 1850-2013 to 2000-2013. – JMarcelino Apr 15 '14 at 12:38
just use sub <- subset(temp, 18263:23011) and then (admittedly I don't know what should happen here, sp can be overly prescriptive) use your second line as you did. I suspect your -99 thing is due to a problem with the coordinates themselves, but you don't provide enough info here. – mdsumner Apr 15 '14 at 13:20
up vote 1 down vote accepted

I found the problem, the temperature RasterStack does not cover all the extent of the country I'm working on.
I'm using E-OBS gridded dataset from European Climate Assessment & Dataset, by the way.

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