[GRASS-stats] Raster maps from GRASS to R and back to GRASS?

[Roger Bivand]

On Mon, 13 Apr 2009, Dylan Beaudette wrote:

> On Monday 13 April 2009, Nikos Alexandris wrote:
>> GRASS_&_R-experts,
>> I really need some hand-of-help here.
>
> Hi Nilkos!
>
>> What I actually do is nothing but a PCA on a combination of different
>> bands. The fact is that bands a, b, c are of equal "length" in R and
>> have _more_ non-NULLs than bands d, e, f.
>
> I think that you are going to have to maintain a band-wise null mask in R, as
> opposed to a single null mask for the entire set of bands.
>
>> That is, bands d, e and f are of equal length compared to each other but
>> of different length comparing to bands a, b and c.
>>
>> I suspect this is the root of the problem. Any suggestion?
>> Thanks, Nikos
>
> It could be. The way that sp objects and their 'bands' (columns in the
> attached dataframe) function makes for some tricky NULL handling.
>
> One thing you might consider is generating a single NULL mask that represents
> NULL values that occur in any, or all bands -- akin to an OR operation. I
> think that na.omit(sp_object at data) may be able to return just the 'complete'
> data, along with a list of indices where NA values have been removed.

Would simply using complete.cases(x at data) be what you are looking for?

Roger

>
> The approach listed on the link you posted:
> x.vals <- which( !is.na(x at data$r1) & !is.na(x at data$r2) & !is.na(x at data$r3)
> & !is.na(x at data$r4))
>
> will only generate the non-NULL maks correctly when all bands have the same
> pattern of NULL values. Maybe I should add that hint.
>
> Hope that helps,
>
> Dylan
>
>
>
>
>>> Nikos:
>>>> I need a confirmation that I am doing the NA-work-around the _right_
>>>> way.
>>>
>>> Sorry, I fat-fingered the Send button before. For simplicity I tried to
>>> use small names instead of the long "original" names. Anyhow, I think
>>> it's clear what I am doing and what the problem is.
>>>
>>> The problem is:
>>>> I get several NULL's in the raster maps I write back in GRASS in
>>>> locations (=pixels) were the input raster map(s) have a NON-NULL value.
>>>
>>> For simplicity I tried to use small names instead of the long "original"
>>> names. Anyhow, I think it's clear what I am doing and what the problem
>>> is.
>>>
>>> Cheers,  Nikos
>>>
>>> # launch grass; launch R from within grass
>>> # load libraries and projection information
>>> library(spgrass6); G <- gmeta6()
>>>
>>> # load data
>>> raw <- readRAST6 (c('a', 'b', 'c', 'd', 'e', 'f'))
>>>
>>> # create vector pointing to values
>>> values <- which(!is.na(raw at data$a) & !is.na(raw at data$b) & !
>>> is.na(raw at data$c) & !is.na(raw at data$d) & !is.na(raw at data$e) & !
>>> is.na(raw at data$f))
>>>
>>> # get data
>>> data <- raw at data[values, ]
>>>
>>> # check structure
>>> str(data)
>>>
>>> # perform pca with prcomp(): SVD - SCALED
>>> prcomp.data <- prcomp(data, scale=TRUE)
>>> prcomp.data$rotation
>>> summary(prcomp.data)
>>>
>>> # add new columns to the original sp object #
>>> raw at data$pc1 <- NA
>>> raw at data$pc2 <- NA
>>> raw at data$pc3 <- NA
>>> raw at data$pc4 <- NA
>>> raw at data$pc5 <- NA
>>> raw at data$pc6 <- NA
>>> str(raw)
>>>
>>> # fill-in the PCs
>>> raw at data$pc1[values] <- prcomp.data$x[,"PC1"]
>>> raw at data$pc2[values] <- prcomp.data$x[,"PC1"]
>>> raw at data$pc3[values] <- prcomp.data$x[,"PC1"]
>>> raw at data$pc4[values] <- prcomp.data$x[,"PC1"]
>>> raw at data$pc5[values] <- prcomp.data$x[,"PC1"]
>>> raw at data$pc6[values] <- prcomp.data$x[,"PC1"]
>>>
>>> # write grass raster maps
>>> writeRAST6(raw, zcol=7, vname="prcomp1_0607", overwrite=TRUE)
>>> writeRAST6(raw, zcol=8, vname="prcomp1_0607", overwrite=TRUE)
>>> writeRAST6(raw, zcol=9, vname="prcomp1_0607", overwrite=TRUE)
>>> writeRAST6(raw, zcol=10, vname="prcomp1_0607", overwrite=TRUE)
>>> writeRAST6(raw, zcol=11, vname="prcomp1_0607", overwrite=TRUE)
>>> writeRAST6(raw, zcol=12, vname="prcomp1_0607", overwrite=TRUE)
>>
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>
>
>
>

-- 
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no