Combining polygons and calculating their area (i.e. number of cells)

On Fri, Dec 20, 2013 at 5:38 AM, Roger Bivand <Roger.Bivand at nhh.no> wrote:

On Thu, 19 Dec 2013, Josh O'Brien wrote:

 On Thu, Dec 19, 2013 at 4:23 AM, Roger Bivand <Roger.Bivand at nhh.no>

wrote:

 On Wed, 18 Dec 2013, Josh O'Brien wrote:

<...snip...>

By the way, always avoid accessing S4 objects directly using @, do use

slot(obj, "slotname") - the sapply should read:

area = sapply(slot(SPclus, "polygons"), slot, "area")

for the SO version with possibly incorrect areas, and

area = gArea(SPclus, byid=TRUE)

for correct ones.

Would you mind explaining why the functional form, slot(obj, "slotname"),
should always be used instead of obj at slotname ? I've seen this admonition
repeatedly -- I think just from you -- and don't know whether it's a
purely
stylistic preference on your part, or whether there  is some other
rationale for preferring that form.

When sp was written (2003-5), we chose to use S4 (new style) classes. We
used Chambers (1998), referring to Ch. 7, and on slots pp. 290-292. There
the distinction between S3 (old style) "$" and "$<-" access and replacement
methods, and S4 "@" and particularly "@<-" was made more forcefully than in
Chambers (2008). Contemporary uses described in Venables and Ripley (2000)
also distinguish between the two.

All of these point to the formal use of S4 class definitions, not least to
ensure that storage mode checking when using .C() and .Call() cease to be
so time-consuming. This is an issue with S3 classes, because there is
nothing to stop the user modifying the storage mode of list components,
with potentially bad consequences in compiled code. Defensive changes in
the underlying R engine to detect mode mismatch were introduced very much
later, I believe, so mode mismatch could crash the engine until them.

For both S3 and S4 classes, the user is encouraged to use access functions
where provided. If the classes and methods are sufficiently well written,
there should only be a few occasions in which the user might want to access
components (S3) or slots (S4) that are not exposed via methods. If scripts
consistently contain @, and no access or replacement methods are provided,
consider asking the package maintainer to add the missing functionality.
slot() is a little less ugly, but the user shouldn't really need it either,
unless something inside an object has to be shown or manipulated.

In this case, the "area" slot is documented, but precisely because it is
not intended to be used as a measure of area, there is no access method.

The danger is that "@<-" and "$<-" are used to insert values into
components/slots without sufficient care being taken; access is perhaps
less of a problem.

I particularly react to usages such as:

sdf at data$var

for sdf a Spatial*DataFrame object, as "$" and "$<-" methods *are*
provided to let these objects appear to be data.frame objects. This usage
is redundant, and displays ignorance about the class/method systems in S
and R. Of course, all are free to write what they like, so my preferences
may be just a matter of taste, but at least they are based on the books
written to establish the structure of the language.

Hope this clarifies,

Roger

None of that seems like just a matter of taste _except_ perhaps for the
preference for slot(obj, "slotname") over obj at slotname (which, by the way,
is used extensively in the sp package's code base).

Thanks for your thoughtful and enlightening reply,

- Josh

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