[R] Object not found using GAMs in MGCV Package

[Sarah Goslee]

See inline:

On Mon, Jan 16, 2012 at 6:29 PM, ruggeddon24 <smithdon2469 at gmail.com> wrote:
> This is my first time running GAMs in R.
> My csv file has these column headings:
>
> "X"         "Y"         "Sound"     "Atlantic"  "Blacktip"  "Bonnet"
> "Bull"      "Finetooth" "Lemon"     "Scalloped" "Sandbar"   "Spinner"
> "Abundance" "Diversity" "Depth"     "Distance"  "Width"     "System"
> "Channel"   "Profile"  "Bathy"     "Slope"     "Salinity"
>  X is longitude and Y is Latitude.

Your csv file? You read it into R with read.table() or read.csv(), right?

> I typed in the code below and received the reply "Error in eval(expr, envir,
> enclos) : object 'Atlantic' not found".
>
>> library(mgcv)
> This is mgcv 1.7-6. For overview type 'help("mgcv-package")'.
>> help("mgcv-package")
> starting httpd help server ... done
>> gam(Atlantic ~ s(depth, bs="sos", k=4) + s(distance, bs="sos", k=4))
> Error in eval(expr, envir, enclos) : object 'Atlantic' not found

You need the data=mydataframe argument to gam(), with whatever the name
of your data frame is. Otherwise R has no idea where to look for Atlantic,
so it just looks for an object with that name, which there isn't.

> I do not have a clue how to fix this problem. Do I have too many variables
> or do I need to remove my x and y from the file? This data is being used to
> assess the spatial distribution of shark abundance in relation to
> environmental variables. I really cannot remove the x and y anyway. Help
> would be greatly appreciated.

Sarah

-- 
Sarah Goslee
http://www.functionaldiversity.org