The following came up when Roger Bivand and I discussed R's name spaces and overlap in packages, in the bus to the field trip during StatGIS, last Tuesday:
If two packages create the same class, say "variogram", and both are loaded, then using a method for an object of class "variogram" cannot discriminate between them and will call the method in the package loaded last. See example below.
I know what is happening, but for average users this may be extremely confusing, especially when loading the second package does not result in a warning that plot.variogram in the first is masked (gstat uses name spaces and "exports" plot.variogram through S3method(plot, variogram), geoR does not)
Shouldn't R know that objects created by functions in library x prefer there methods to be picked from library x, rather than the first in the search path? Isn't that one of the ideas behind name spaces?
Shouldn't R give an error message when a loaded library masks a method in another library, as it does when an object is masked (such as it does when loading gstat after spatial)?
If we are not going to deal with this, shouldn't CRAN reject (for now?) packages that create new classes and methods with names that are allready in other packages? -- Edzer
Executing the following commands:
library(gstat) data(meuse) v = variogram(log(zinc)~1, ~x+y, meuse) plot(v) # calls plot.variogram() in library gstat library(geoR) plot(v) # error: calls plot.variogram() in library geoR
gives the following output:
R> library(gstat) Loading required package: lattice Loading required package: grid
R> data(meuse)
R> v = variogram(log(zinc) ~ 1, ~x + y, meuse)
R> plot(v)
R> library(geoR)
------------------------------------------------- geoR - functions for geostatistical data analysis geoR version 1.3-16 (2003-09-17) is now loaded -------------------------------------------------
R> plot(v) Error in if (x$output.type == "bin") Ldots$type <- "p" : argument is of length zero In addition: Warning message: no finite arguments to max; returning -Inf
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