wpeterman
commented
1 year ago It's not clear what you're attempting to do. It looks like you're creating resistance surfaces with known parameters, then using these with MS optim. There really isn't a need to specify resistance values a priori as this is done during optimization.
I am not certain what the error is that you received. However, support for gdistanceis largely discontinued in favor of using Circuitscape with Julia. See the vignettes in latest GitHub release of ResistanceGA for downloading, installing, and examples. If you continue to have issues, I'm happy to troubleshoot if you can share input files used in the analysis.
I received this error when running MS_optim. I checked all .asc files and all parameters and they are all correct. The code I'm using is here:
CS.inputs <- CS.prep(n.Pops = length(sample.locales), CS_Point.File = paste0(write.dir2,"samples.txt"), CS.program = CS.program, response = wcpw)
Run this for each layer to write .asc files to directory
CS.response7 <- Run_CS(CS.inputs = CS.inputs, r=Culv, CurrentMap = TRUE, EXPORT.dir = "C:/Users/rwatson17/Desktop/Watson_Opt/MS/")
now you should have multiple .asc files in your directory
GA.inputs <- GA.prep(ASCII.dir = write.dir2, Results.dir = write.dir2, method = "LL", max.cat = 100, max.cont = 100, parallel = 6)
gdist.inputs <- gdist.prep(length(sample.locales), samples = sample.locales, method = 'commuteDistance') # Optimize using commute distance
PARM must be in the order of the rasters, check order: Culv, Cond, Elev, NLCD, Slope, SS
GA.inputs$layer.names
Fill in parm using the outputs from SS_optim (?Combine_Surfaces) for categorical put all the feature #s in order
PARM <- c(1.7,1,43.4,88.5,100,3,11.5,21.9,1,13.7,5.1,1,14.5,41.6,1,7.3,100,1,9.3,100)
Combine resistance surfaces
Resist <- Combine_Surfaces(PARM = PARM, gdist.inputs = gdist.inputs, GA.inputs = GA.inputs, out = NULL, rescale = TRUE)
View combined surface
plot(Resist, main = "scaled composite resistance")
Create the true resistance/response surface
gdist.response <- Run_gdistance(gdist.inputs = gdist.inputs, r = Resist) gdist.inputs <- gdist.prep(n.Pops = length(sample.locales), samples = sample.locales, response = as.vector(gdist.response), method = 'commuteDistance')
Multi.Surface_optim <- MS_optim(gdist.inputs = gdist.inputs, GA.inputs = GA.inputs)
Error in { : task 3 failed - "duplicate "by" values not allowed"