[R-sig-Geo] gdistance transition objects: dealing with NAs in source cost raster

[chris english]

Toby,

I've only just installed Jacob's gdistance package and don't know as yet
the underlying assumptions nor the, what I will term 'services', his
package offers. Were I in your position, having my DEM, and knowing what
you already know about using gdistance, I would swap out my sea NA(s) for
0.0(s), in my case probably using GDAL, and see how things went thereafter.

Jacob will have a much better suggestion, but basically it seems like
'package x doesn't like my data, so I'll make my data more consumable for
package x'. Wish I could be of more help but I'm playing in a different
distance space than Hausdorf and probably shouldn't comment further, except
as to what I'd try to finagle as to my DEM.

Chris

On Thu, Jun 2, 2016 at 7:28 PM, T C Wilkinson <open at tobywilkinson.co.uk>
wrote:

> Dear Chris, dear Jacob,
>
> Many thanks indeed for suggestions and help.
>
> 1. The input raster (dem) definitely shows NA in the areas of sea using
> click().
>
> 2. Tried the 0.0 in the ifelse: no luck, same result.
>
> I tried plotting and clicking for the values of the initial `slope`
> TransitionLayer: here the area of the sea reports as a value of NaN, so
> perhaps the problem is not in the transition function, but in the later
> conversion of slope to cost (in sw_conductance).
>
> I tried changing adjacent() to adjacencyFromTransition(), which does
> indeed result in the sea being plotted as NA (or presumably NaN), but the
> values of the conductance on land now don’t seem correct (i.e. some areas
> that I know are flat are shown as relatively lower conductance than areas
> which are sloping).
>
> Any ideas?
>
> Thank you again,
> Toby
>
>
>
> sw_slope <- function(dem, dirs=16, symm=FALSE){
>   # calculate the altitudinal differences between cells:
>   #altDiffFunction <- function(x){x[2] - x[1]}
>   # with a little help from Jacob van Etten and Chris English:
>   altDiffFunction <- function(x){ifelse(((!is.na(x[2])) & (!is.na(x[1]))),
> (x[2] - x[1]), 0.0)}
>
>   heightDiff <- transition(dem, altDiffFunction, directions=dirs,
> symm=symm)
>   #divide by the distance between cells
>   slope <- geoCorrection(heightDiff)
>   return(slope)
> }
>
> slope <- sw_slope(dem)
> plot(raster(slope))
> click(raster(slope))
>
> sw_conductance <- function(dem, dirs=16, symm=FALSE){
>   #first find slope
>   slope <- sw_slope(dem, dirs, symm)
>
>   #create an index for adjacent cells (adj) with the function adjacent
>   #adj <- adjacent(dem, cells=1:ncell(dem), pairs=TRUE, directions=16)
>   adj <- adjacencyFromTransition(slope)
>   cost <- slope
>
>   #extract and replace adjacent cells
>   #note the 1/ to convert from resistivity (as cited in publication above)
> to conductivity
>   cost[adj] <- 1 / ((((1337.8 * cost[adj]^6) + (278.19 * cost[adj]^5) -
> (517.39 * cost[adj]^4) - (78.199 * cost[adj]^3) + (93.419 * cost[adj]^2) +
> (19.825 * cost[adj]) + 1.64)))
>
>   #correction to take account of distance between cell centres
>   gc <- geoCorrection(cost)
>
>   return(gc)
> }
>
> plot(raster(sw_conductance(dem))
>
>
>
> On 2 June 2016 at 14:29:42, chris english (englishchristophera at gmail.com)
> wrote:
> > Toby,
> >
> > This may seem silly, and a thousandth of something is not zero, but
> perhaps
> > this is a kind of preallocation issue and using Jacob's if else with 0.0
> > as else might do the trick.
> >
> > Fingers crossed?
> > Chris
> > On Jun 2, 2016 16:07, "T C Wilkinson" wrote:
> >
> > > Dear Jacob,
> > >
> > > Many thanks for fast reply. [Apologies for the typo and potential
> > > confusion on gdistance, I am still relative new to R — and thus
> borrowing
> > > camelCase habit from previous coding.]
> > >
> > > I’ve tried your suggested re-worked function to avoid NA in the
> > > transition, but I still get the same result.
> > >
> > > When plotted, the `plot(raster(conductance))` still colours the sea
> (i.e.
> > > doesn’t show it in the colNA colour) and the resultant accCosts etc
> include
> > > the sea as part of the result surface.
> > >
> > > An interactive `click(raster(conductance))` reveals the sea to be a
> > > uniform value of 0.001436461.
> > >
> > > Thanks again,
> > > Toby
> > >
> > >
> > >
> > > On 2 June 2016 at 12:30:43, Jacob van Etten (jacobvanetten at yahoo.com)
> > > wrote:
> > > > Dear Toby,
> > > > TransitionLayers should normally not hold NA values. If you want to
> set
> > > cell connections
> > > > to zero conductance, the transitionFunction should give a value zero
> if
> > > it finds an NA.
> > > > Your function gives an NA as result, which is not what you want:
> > > > ifelse(((!is.na(x[2])) & (!is.na(x[1]))),(x[2] - x[1]),NA)
> > > >
> > > > You probably want to do:
> > > > ifelse(((!is.na(x[2])) & (!is.na(x[1]))), (x[2] - x[1]), 0)
> > > >
> > > > Also, note that gDistance is not the name of the package.
> > > > Best,
> > > > Jacob
> > >
> > > _______________________________________________
> > > R-sig-Geo mailing list
> > > R-sig-Geo at r-project.org
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
>
>

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