[R-sig-eco] How to extract values from contiguous raster cells that ate not touched by SpatialLines?

[Andre Rovai]

Hi Julian, apologies for my late feedback to the group. I was able to
extract the values from adjacent cells using adjacent() function from
raster package. I must thank Santiago Sanchez for his help after looking up
my post.
Best,
Andre

*Andre Rovai, Ph.D.*
Research Associate V
Department of Oceanography and Coastal Sciences
Energy, Coast, and Environment Bldg., Room 3201
Louisiana State University, Baton Rouge, LA 70803
Phone: *225 578 6422*, Cell: *225 439 5559*
Email: *arovai1 at lsu.edu* <arovai1 at lsu.edu>, *asrovai at gmail.com*
<asrovai at gmail.com>
oceanography.lsu.edu/twilleylab
<http://oceanography.lsu.edu/twilleylab/index.html>
lattes.cnpq.br/3739236195138235

2017-08-31 10:41 GMT-05:00 Julian M. Burgos <julian.burgos at hafogvatn.is>:

> Hi Andre,
>
> Your description is very confusing.  Could you clarify exactly what you
> want?  You have a) a raster, and b) some lines.  What are you trying to
> do exactly?
>
> Julian
>
>
> Andre Rovai writes:
>
> > Hi all,
> >
> > I've been trying to extract values from a single attribute raster (area,
> in
> > m2) that overlaps with lines (that is, a .shp SpatialLines).
> >
> > The problem is that, along these lines, my raster sometimes goes from one
> > to several contiguous cells in all directions.  Using the
> > extract function only values from cells that are touched by the lines are
> > extracted.  Thus, when I add up the extracted values from all lines a
> > significant amount of area (m2) is lost due to cells that were not
> touched
> > by the line and therefore values were not extracted.
> >
> > I tried to work it around by:
> >
> > Step 1 - first aggregating my raster to a lower resolution (i.e.
> increasing
> > the fact argument) and then
> > Step 2 - rasterizing the lines using this aggregated raster (created in
> > step 1) as a mold to make sure the rasterized lines would get thick
> enough
> > to cover the horizontal spread of cells in my original resolution raster.
> > Step 3 - Then I resample the rasterized lines (created in step 2) back to
> > the original resolution I started with.
> > Step 4 - Finally, extracted the values from the resampled rasterized
> lines
> > (created in step 3).
> >
> > However, it didn't quite work as now the total area (m2) varies according
> > to the fact="" value I use when first aggregating the raster (in step 1).
> >
> > I really appreciate if anyone has already dealt with a similar problem
> and
> > can help me out here.  Here are the codes I've been running to try to get
> > it to work:
> >
> >
> > # input raster file
> >
> > g.025 <- raster("ras.asc")
> >
> > g.1 <- aggregate(g.025, fact=2, fun=sum)
> >
> >
> >
> > # input SpatialLines
> >
> > Spline1 <- readOGR("/Users/xxxxx.shp")
> >
> > Spline2 <- readOGR("/Users/xxxxx.shp")
> >
> > Spline3 <- readOGR("/Users/xxxxx.shp")
> >
> >
> >
> > # rasterizing using low resolution raster (aggregated)
> >
> > c1 <- rasterize(Spline1, g.1, field=Spline1$type, fun=sum)
> >
> > c2 <- rasterize(Spline2, g.1, field=Spline2$type, fun=sum)
> >
> > c3 <- rasterize(Spline3, g.1, field=Spline3$type, fun=sum)
> >
> >
> >
> > # resampling back to higher resolution
> >
> > c1 <- resample(c1, g.025)
> >
> > c2 <- resample(c2, g.025)
> >
> > c3 <- resample(c3, g.025)
> >
> >
> >
> > # preparing to extract area (m2) values from raster “g.025”
> >
> > c1tab <- as.data.frame(c1, xy=T)
> >
> > c2tab <- as.data.frame(c2, xy=T)
> >
> > c3tab <- as.data.frame(c3, xy=T)
> >
> > c1tab <- c1tab[which(is.na(c1tab$layer)!=T),]
> >
> > c2tab <- c2tab[which(is.na(c2tab$layer)!=T),]
> >
> > c3tab <- c3tab[which(is.na(c3tab$layer)!=T),]
> >
> >
> >
> > # extracting area (m2) values from raster “g.025”
> >
> > c1tab[,4] <- extract(g.025, c1tab[,1:2])
> >
> > c2tab[,4] <- extract(g.025, c2tab[,1:2])
> >
> > c3tab[,4] <- extract(g.025, c3tab[,1:2])
> >
> > names(c1tab)[4] <- "area_m2"
> >
> > names(c2tab)[4] <- "area_m2"
> >
> > names(c3tab)[4] <- "area_m2"
> >
> >
> >
> > # sum total area (m2)
> >
> > c1_area <- sum(c1tab$area_m2)
> >
> > c2_area <- sum(c2tab$area_m2)
> >
> > c3_area <- sum(c3tab$area_m2)
> >
> > tot_area <- sum(c1_area, c2_area, c3_area)
> >
> >
> > Thanks!
> >
> > Andre Rovai
> > Department of Oceanography and Coastal Sciences
> > Louisiana State University
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-ecology mailing list
> > R-sig-ecology at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>
>
> --
> Julian Mariano Burgos, PhD
> Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
> Marine and Freshwater Research Institute
> Skúlagata 4, 121 Reykjavík, Iceland
> Sími/Telephone : +354-5752037
> Bréfsími/Telefax:  +354-5752001
> Netfang/Email: julian.burgos at hafogvatn.is
>

	[[alternative HTML version deleted]]