coverscale {vegsoup} | R Documentation |
Vegsoup*
Objects Function Coverscale
creates an object of class Coverscale
containing a
definition for an ordinal scale, or alternatively setting up a Coverscale
object
representing species abundances on a continuous scale (counts, frequencies
or percentages). Objects of this class are mandatory for Vegsoup
and
it's extending classes.
Coverscale(name, codes, lims) ## S4 method for signature 'Vegsoup' coverscale(x) ## S4 replacement method for signature 'Vegsoup,Coverscale' coverscale(x) <- value ## S4 replacement method for signature 'Vegsoup,character' coverscale(x) <- value ## S4 method for signature 'Vegsoup' is.ordinal(x) ## S4 method for signature 'Vegsoup' is.continuous(x) ## S4 method for signature 'Vegsoup' is.occurence(x)
name |
character. Giving a name of a built in abundance scale, or a name to be referred to a user supplied definition. |
codes |
character. Vector assigning the level codes (ordinal scales). Need to not define zero. |
lims |
numeric. Vector defining the mean percentage cover for each entry
in |
x |
A |
value |
A |
The constructor Function Coverscale
creates an object of class "Coverscale"
, whereas method coverscale
(lower case letters!) returns the abundance scale set up for an Vegsoup*
object. The corresponding replacement method ("coverscale<-"
) can be used to assign a different scale for an object where it has already been set. Most of the time it is convenient to use one of the built in definitions. Call Coverscale()
without arguments to see which ones are available. Note, a continuous scale can simply be defined by having a value of NULL
for slots 'codes' and 'lims' (cf. Coverscale("percentage")
).
Coverscale("as.is")
is an alternative to percentage, frequency or counts. All treat the data as it is and do not translate it to percentage cover values. "as.is"
is appropriate, for example, if the data is coded with integers (e.g. Van der Maarel scale). Coverscale("ordinal")
defines breakpoints to translate to percentage cover values.
The methods is.continuous
and is.ordinal
test objects of class "Coverscale"
if they conform to the given type of cover scale. Note, this is just a simple test if slots 'codes' and 'lims' are NULL
. If so, the coverscale is treated as continuous, otherwise as ordinal. There are methods defined for Vegsoup*
object (see ‘Examples’).
The replacement function can also be used to transform a continuous scale to an ordinal one. This functionality is restricted to situations where is.continous(x)
evaluates to TRUE
and the "Coverscale"
object that is assigned (argument value
) can be treated as ordinal (is.ordinal(value)
evaluates to TRUE
). When doing so, the cover values stored in the Vegsoup*
object are transformed (the original data is lost) and a message is issued. Such a type of transformation makes sense, for example, when an output of function link{write.verbatim}
is intended.
Function Coverscale
returns an object of class "Coverscale"
.
Method coverscale
modifies a Vegsoup*
.
Roland Kaiser
There are many textbooks dealing with coverscale. A recent treatment is found in:
Peet, R.K. & Roberts D.W. (2013). Classification of natural and semi-natural vegetation. In Vegetation Ecology (van der Maarel, E. & Franklin, J. eds). Wiley-Blackwell.
Currall, J. (1987). A transformation of the Domin scale. Vegetatio, 72(2):81-87.
Pfadenhauer, J., Poschlod, P., and Buchwald, R. (1986). Überlegungen zu einem Konzept geobotanischer Dauerbeobachtungsflächen für Bayern, Teil I. Berichte der ANL, 10:41-60.
Coverscale-class
,
BraunBlanquetReduce
,
Vegsoup
in package vegsoup,
tv.coverperc
in package vegdata and
coverscale
in package vegan for the
ancestor of this implementation.
# show built in coverscales Coverscale() # test properties of coverscale objects is.ordinal(Coverscale("ordinal")) is.occurence(Coverscale("pa")) is.continuous(Coverscale("percentage")) # create coverscale from scratch Coverscale("foo", letters[1:5], 1:5) # data(barmstein) x <- barmstein # print reports name of coverscale x coverscale(x) # test properties of Vegsoup object is.ordinal(x) is.continuous(x) is.occurence(x) # use replace method to tarnsform covervalues # lower 9 point to 7 point Braun-Blanquet scale x1 <- x2 <- x coverscale(x1) <- "braun.blanquet2" coverscale(x2) <- Coverscale("braun.blanquet2") identical(coverscale(x1), coverscale(x2))