wpeterman
commented
5 years ago The development version of ResistanceGA supports use of the Julia language version of CIRCUITSCAPE. devtools::install_github("wpeterman/ResistanceGA", ref = "julia_dev")
You'll need to install Julia https://julialang.org/ (>= v 1.0), and then get the Circuitscape package for Julia https://github.com/Circuitscape/Circuitscape.jl.
Use of ResistanceGA isn't too different when using Julia. You'll need to use the jl.prep function prior to running analyses, and this has a few different arguments to specify (e.g., where is Julia located on your system).
Let me know if you have any questions, and good luck!
Bill Peterman Assistant Professor School of Environment and Natural Resources The Ohio State University 2021 Coffey Road Columbus, OH 43210-1085 Phone: 614.292.9795 Web Page https://goo.gl/4Gc15W Terrestrial Wildlife Ecology Lab http://www.twel.osu.edu
Bill Peterman
On Tue, Sep 17, 2019 at 4:35 AM Clarkhsiung notifications@github.com wrote:
I tried to use ResistanceGA in Ubuntu 16.04. I installed Circuitscape 4.0.5 through source https://github.com/Circuitscape/Circuitscape. And use this command below.
library(raster) library(ResistanceGA) library(gdistance) library(parallel) library(doParallel) data(resistance_surfaces) dir.create("test_cir") setwd("~/test_cir/") write.dir="./"
continuous <- resistance_surfaces[[2]] writeRaster(continuous,filename =paste0(write.dir,"cont.asc"),overwrite = TRUE) data(samples) write.table(samples,file=paste0(write.dir,"samples.txt"),sep="\t",col.names=F,row.names=F) sample.locales <-SpatialPoints(samples[,c(2,3)])
GA.inputs <-GA.prep(ASCII.dir = write.dir,Results.dir = write.dir, max.cat = 500, max.cont = 500, select.trans = "M", method = "LL", seed = 555)
CS.inputs <- CS.prep(n.Pops = length(samples), CS_Point.File = paste0(write.dir,"samples.txt"), CS.program ='csrun.py',platform="other")
SS_RESULTS <- SS_optim(CS.inputs=CS.inputs, GA.inputs=GA.inputs)
And I get some error message bellow.
Iteration took 0.01 seconds LL = -99999 EXCLUDED TRANSFORMATION
Reading maps Processing maps Resistance/conductance map has 2500 nodes Traceback (most recent call last): File "/usr/local/bin/csrun.py", line 13, in
resistances = cs.compute() File "/usr/local/lib/python2.7/dist-packages/circuitscape/profiler.py", line 144, in wrapper return func(args) File "/usr/local/lib/python2.7/dist-packages/circuitscape/compute.py", line 31, in compute return self.compute_raster() File "/usr/local/lib/python2.7/dist-packages/circuitscape/profiler.py", line 144, in wrapper return func(args) File "/usr/local/lib/python2.7/dist-packages/circuitscape/compute.py", line 152, in compute_raster resistances, solver_failed = self.pairwise_module(self.state.g_map, self.state.poly_map, self.state.points_rc) File "/usr/local/lib/python2.7/dist-packages/circuitscape/profiler.py", line 144, in wrapper return func(*args) File "/usr/local/lib/python2.7/dist-packages/circuitscape/compute.py", line 367, in pairwise_module g_habitat = HabitatGraph(g_map=g_map, poly_map=poly_map, connect_using_avg_resistances=self.options.connect_using_avg_resistances, connect_four_neighbors_only=self.options.connect_four_neighbors_only) File "/usr/local/lib/python2.7/dist-packages/circuitscape/compute_base.py", line 510, in init if None != g_map: ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() Error in file(file, "rt") : cannot open the connection In addition: Warning messages: 1: In system(paste(CS.inputs$CS.program, CS.ini), hidden) : running command 'csrun.py ./tmp/resist_surface.ini' had status 1 2: In file(file, "rt") : cannot open file './tmp/resist_surface_resistances.out': No such file or directory Is it possible to run ResistanceGA with Circuitscape 4.0.5 in Ubuntu 16.04?
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Clarkhsiung
I tried to use ResistanceGA in Ubuntu 16.04. I installed Circuitscape 4.0.5 through source. And use this command below.
And I get some error message bellow.
Is it possible to run ResistanceGA with Circuitscape 4.0.5 in Ubuntu 16.04?