masking error

[jmhallas]

Hello,

Thank you for you help with inputting ancestry values. I am running into another issue regarding masking.

I have tried using my own raster using the following code to mask by California state boundaries. I get the following error

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘mask’ for signature ‘"RasterStack", "data.frame"’

Code I am using below

require(rgdal)
CA <- readOGR(dsn = "/Users/jhallas/Documents/cdfw/lcdeer/popgen_analysis/California_State_Boundary/", layer = "California_State_Boundary")
gridsize <- 0.01
r <- raster(CA,res=gridsize)
rr <- rasterize(CA, r)

plot(qk4, long.lat, method = "map.max", cex = .4,  
     interpol = FieldsKrigModel(10),
    raster.filename = rr,
     main = "Ancestry coefficients",
     xlab = "Longitude", ylab = "Latitude", 
     col.palette = my.palette)

This fails, but works with raster.filename excluded.

Any advise is greatly appreciated.

Thank you for your time.

Josh

[francoio]

raster.filename must be a path to an external raster file, not to an R object

[francoio]

For an example, see the vignette https://bcm-uga.github.io/TESS3_encho_sen/articles/main-vignette.html. A raster file of Europe is downloaded for drawing a map of Q.

[jmhallas]

Thanks for the suggestion. I was able to mask the kriging. Is there a way to extend the range of the Kriging analysis? This is the range of the mask I would like to use.
tess_mask.pdf

However, when I run my analysis the lower right hand extant of the mask gets clipped.
tess_prelim1.pdf

This is the code I am running.

q.matrix <- as.matrix(qk47_info_noNA[1:4])
qk4 <- tess3r::as.qmatrix(q.matrix)

plot(qk4, long.lat, method = "map.max", cex = .4,  
     interpol = FieldsKrigModel(10),
     raster.filename = "/Users/jhallas/Documents/cdfw/lcdeer/popgen_analysis/California_State_Boundary/CA.asc",
     xlim= c(-124.5, -112.5), 
     ylim=c(32, 42.1), 
     main = "Ancestry coefficients",
     xlab = "Longitude", ylab = "Latitude", 
     col.palette = my.palette)

Thank you for you time and advise.

-josh