[R-sig-Geo] Ecological Niche Factor Analysis

[alannie]

Hi,

I have been using ENFA in R to perform some analyses. 

I have gotten the procedure to work before, however I can't seem to
replicate the code. This is very important since I would like to do this
analysis for a wide range of species. 

Please advise of best practice for implementing the procedure.

Going from the very beginnings of the procedure:

1) read in .csv formatted locations data for the interested species

   /code/ species1<-read.csv("species1.csv",head=T, sep=",")
                    species1coords<-SpatialPoints(species1)

2) read in raster files (I am using the bioclim variables converted into
ASCII)

   /code/ b1<-read.asc("bio1.asc")
                    b2<-read.asc("bio2.asc")
                    b3<-read.asc("bio3.asc")

3) combine the maps into a single data frame and add slots to the individual
maps
   /code/ map<-cbind(b1 at data,b2 at data,b3 at data) *this form does not allow me
to visualize the maps using image(map)
                    map2<-cbind(b1,b2,b3) *this form, with out the slots,
does allow me to visualize the maps using image(map2)

4) following this step is making a histogram: hist(map, type = "l")  I
usually cannot make one, but when I am able to make a histogram, the
variables show up on a single graph with the warning:

Warning messages:
1: In title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
  graphical parameter "type" is obsolete
2: In axis(1, ...) : graphical parameter "type" is obsolete
3: In axis(2, ...) : graphical parameter "type" is obsolete

4) The tab:
   /code/ tab <- slot(map, "data"), I get this warning:
Error in slot(map, "data") : 
  cannot get a slot ("data") from an object of type "double"

Sometimes I get other warnings such as 'x is not numeric' or something about
NA values.

I will spare the rest of the issues I face.

I believe the origins of these issues are the starting data inputs. I would
appreciate any assistance in modifying the data inputs. I have tried to look
through other resources, however I have not found anything to help with my
specific issues. 

If I can get this worked out, I also hope to post some code somewhere to
aide others in their SDM adventures.

Thank you for reading!

A










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