[R-sig-Geo] dismo package: using biasfile when calling maxent

[Julie Lee-Yaw]

Hi All,

Does anyone know how to incorporate a biasfile into a maxent run set up from the R package dismo?

Or is it even possible to run dismo's maxent command with a bias file?

Here's what I've tried:

mybias<-raster(file.choose())  # load bias grid of same extent and resolution as raster layers

## Attempt 1
test1<-maxent(rasters,localities,removeDuplicates=TRUE, args="biasfile=mybias")

# Result
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file '/var/folders/rm/kftt7_jj5h70d5kgypw6njwr0000gn/T/R_raster_tmp/maxent/7322841707/species.lambdas': No such file or directory

## Attempt 2
test2<-maxent(rasters,localities,removeDuplicates=TRUE, args="biasfile=/Users/Documents/mybias.asc") # use path name instead

# Result
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file '/var/folders/rm/kftt7_jj5h70d5kgypw6njwr0000gn/T/R_raster_tmp/maxent/02810774444/species.lambdas': No such file or directory


## Attempt 3

test4<-maxent(rasters,localities,removeDuplicates=TRUE, biasfile=mybias)

# This runs but the bias file seems to be ignored. That is, the bias file isn't listed as a parameter in the html file of the results (when running maxent directly the output html file mentions the bias file under the "Raw data output and control parameters" section)

Thanks!

Julie