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@data,b2@data,b3@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graphical parameter "type" is obsolete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 : graphical parameter "type" is obsolete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 : graphical parameter "type" is obsolete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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