Categorical variable being treated as continuous

[Sarah Sam]

Hi,

I am trying to use Maxent to do some species distribution mapping using 10 predictor variables (9 continuous and 1 categorical).  When I import my categorical raster into R, it treats it as continuous.  I am including the factors argument in the model to indicate that variable should be treated as categorical, but when I look at the responses curves, the output for this variable is a line graph rather than a bar graph. 

mod = maxent(x=pred.vars, p=pb, factors = "Soiltext",

             args=c("hinge",

                    "threshold=FALSE",

                    "noautofeature",

                    "noremoveduplicates", 

                    "-P","-J", 

                    "writeplotdata",

                    "outputformat=logistic", 

                    "threads=4",

                    "randomseed=FALSE"), 

             path=paste("S:/Thesis_Chapter_1/data/Output/Maxent/species")) ## folder for maxent output; 

I've tried setting the raster as a factor after I import and this appears to work.  However, I get an error when I try to plot it, and it still seems to be getting treated as a continuous variable in the model (i.e. response curve is still a line graph, not a bar graph).  

> # Set soil raster layer as a factor (categorical variable)

> Soiltext.f <- asFactor(Soiltext)

> # Check soil is set to factor 

> is.factor(Soiltext.f)

[1] TRUE

> plot(Soiltext.f)

Error in .checkLevels(levels(x)[[1]], value) : 

  the first column name of the raster attributes (factors) data.frame should be "ID"

> structure(Soiltext.f)

class      : RasterLayer 

dimensions : 2270, 3252, 7382040  (nrow, ncol, ncell)

resolution : 250, 250  (x, y)

extent     : 2126684, 2939684, 2259553, 2827053  (xmin, xmax, ymin, ymax)

crs        : +proj=lcc +lat_0=-37 +lon_0=145 +lat_1=-36 +lat_2=-38 +x_0=2500000 +y_0=2500000 +ellps=GRS80 +units=m +no_defs 

source     : S:/SEFS Research Data/Restricted/Fire Ecology & Biodiversity/Students/PhD/Current/Sarah/Thesis_Chapter_1/data/Soil Texture/soil_text_v4_clip3.tif 

names      : soil_text_v4_clip3 

values     : 1, 7  (min, max)

attributes :

       VALUE

 from:     1

  to :     7

Any suggestions for how I can fix this issue?

many thanks,

Sarah

[Sarah Sam]

Just an update to say that I've resolved this.  It turned out I needed to convert soil column in the dataframe to a categorical variable, rather than the original soil raster layer.