[R-sig-Geo] Problem with raster::extract

[Agustin Lobo]

I confirm the problem is solved in  raster_1.8-16

Thanks!

Agus

2011/4/28 Robert J. Hijmans <r.hijmans at gmail.com>:
> This was caused by raster incorrectly interpreting the highest
> possible INT2U value (65530) as NA. Now fixed (version 1.8-16), at
> least for this case. Thanks for reporting, Robert
>
> On Wed, Apr 27, 2011 at 8:52 AM, Robert J. Hijmans <r.hijmans at gmail.com> wrote:
>> Hello Agus,
>>
>> The NaN suggests that there are only NA values for that polygon/layer.
>> To investigate this I would do
>>
>> v <- extract(SGRGBF40, calibf2, nl=3)
>>
>> # i.e. do not use a function and then inspect
>>
>> v[[7]]
>>
>>
>> All functions must accept an na.rm argument (even if they choose to
>> ignore it. So for length you can do something like:
>>
>> vl <- extract(SGRGBF40, calibf2, fun=function(x,...)length(x), nl=3)
>>
>>
>> Hope this helps, Robert
>>
>>> v
>> [1] 387.8158 329.3913
>>> v <- extract(r, polys, length)
>> Error in FUN(X[[1L]], ...) :
>>  2 arguments passed to 'length' which requires 1
>>> v <- extract(r, polys, function(x,...)length(x))
>>> v
>> [1] 38 23
>>>
>>
>>
>> On Wed, Apr 27, 2011 at 3:14 AM, Agustin Lobo <alobolistas at gmail.com> wrote:
>>> Hi!
>>>
>>> I'm doing
>>>
>>> SGRGBF40 = brick("/media/Iomega_HDD/UAVetal/CALIBRACIONRADIOM/TESTCASA/CALSEL/SGRGB/SGRGBWBPS125F40.tif")
>>> calibf2 = readOGR(dsn="/media/Iomega_HDD/UAVetal/CALIBRACIONRADIOM/TESTCASA/CALSEL",layer="calibf2",stringsAsFactors=F)
>>> projection(SGRGBF40) = projection(calibf2)
>>> #I make sure vector calibf2 and raster SGRGBF40 do overlap:
>>> plot(subset(SGRGBF40,1))
>>> plot(calibf2,add=T)
>>>
>>> #Calculate mean values for each polygon:
>>> v <- extract(SGRGBF40, calibf2,fun=mean,na.rm=T,nl=3)
>>> summary(v)
>>> SGRGBF40data = cbind(calibf2 at data,v)
>>>
>>> But then, despite na.rm=T:
>>>> SGRGBF40data[7,]
>>>  ID code codetxt SGRGBWBPS125F40_1 SGRGBWBPS125F40_2 SGRGBWBPS125F40_3
>>> 6  7    7      C7               NaN          39781.02                 3
>>>
>>>> summary(v)
>>>  SGRGBWBPS125F40_1 SGRGBWBPS125F40_2 SGRGBWBPS125F40_3
>>>  Min.   :18444     Min.   :  119.4   Min.   :    3
>>>  1st Qu.:34098     1st Qu.:25875.7   1st Qu.:15633
>>>  Median :37776     Median :36668.2   Median :22374
>>>  Mean   :41314     Mean   :36882.2   Mean   :29737
>>>  3rd Qu.:52236     3rd Qu.:49452.6   3rd Qu.:48116
>>>  Max.   :65396     Max.   :65417.5   Max.   :63826
>>>  NA's   :    3
>>>
>>> While there are no NA in the raster brick:
>>>> summary(SGRGBF40)
>>> Cells:  4646400
>>> NAs  :  0 0 0
>>>
>>>            1     2     3
>>> Min.     1777     3     3
>>> 1st Qu. 34910 22460 18640
>>> Median  42660 27540 24420
>>> Mean    41070 28570 25170
>>> 3rd Qu. 48470 33320 29060
>>> Max.    65520 65530 64220
>>>
>>>
>>> A possibility would be a division by 0 (weird, because all polygons
>>> are large), so I've tried:
>>>> vl <- extract(SGRGBF40, calibf2,fun=length,nl=3)
>>> but...
>>> Error in t(sapply(res[!i], function(x) apply(x, 2, FUN = fun, na.rm =
>>> na.rm))) :
>>>  error in evaluating the argument 'x' in selecting a method for
>>> function 't': Error in FUN(newX[, i], ...) :
>>>  2 arguments passed to 'length' which requires 1
>>> Calls: sapply -> lapply -> FUN -> apply
>>> Calls: extract -> extract -> .polygonValues -> t
>>>
>>> Any hint?
>>>
>>> Data:
>>> http://dl.dropbox.com/u/3180464/SGRGBWBPS125F40.tif
>>> http://dl.dropbox.com/u/3180464/SGRGBWBPS125F40.tfw
>>> http://dl.dropbox.com/u/3180464/calibf2.zip
>>>
>>>> sessionInfo()
>>> R version 2.13.0 (2011-04-13)
>>> 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=en_US.UTF-8
>>>  [9] LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8
>>> [11] LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] grid      stats     graphics  grDevices utils     datasets  methods
>>> [8] base
>>>
>>> other attached packages:
>>> [1] gridExtra_0.7 ggplot2_0.8.9 rgdal_0.6-33  raster_1.7-29 sp_0.9-76
>>> [6] reshape_0.8.4 plyr_1.4      proto_0.3-8   rkward_0.5.6
>>>
>>> loaded via a namespace (and not attached):
>>> [1] lattice_0.19-26 tools_2.13.0
>>>>
>>>
>>> Agus
>>>
>>
>
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