Make a function return updateable result
Creates a function wrapper that stores a call in the object returned by its
argument FUN.
updateable(FUN, eval.args = NULL, Class) get_call(x) ## updateable wrapper for mgcv::gamm and gamm4::gamm4 uGamm(formula, random = NULL, ..., lme4 = inherits(random, "formula"))
FUN |
function to be modified, found via |
eval.args |
optionally a character vector of function arguments' names to be evaluated in the stored call. See ‘Details’. |
Class |
optional character vector naming class(es) to be set onto the
result of |
x |
an object from which the call should be extracted. |
formula, random, ... |
arguments to be passed to |
lme4 |
if |
Most model fitting functions in R return an object that can be updated or
re-fitted via update. This is thanks to the call
stored in the object, which can be used (possibly modified) later on. It is
also utilised by dredge to generate sub-models. Some functions (such
as gamm or MCMCglmm) do not provide their result with the
call element. To work that around, updateable can be used on
that function to store the call. The resulting “wrapper” should be
used in exactly the same way as the original function.
Argument eval.args specifies names of function arguments that should
be evaluated in the stored call. This is useful when, for example, the model
object does not have formula element. The default formula
method tries to retrieve formula from the stored call,
which works unless the formula has been given as a variable and value of
that variable changed since the model was fitted (the last ‘example’
demonstrates this).
updateable returns a function with the same arguments as FUN,
wrapping a call to FUN and adding an element named call to its
result if possible, otherwise an attribute "call" (if the returned
value is atomic or a formal S4 object).
get_call is similar to getCall (defined in package
stats), but it can also extract the call when it is an
attribute (and not an element of the object). Because the
default getCall method cannot do that, the default update method
will not work with atomic or S4 objects resulting from updateable
wrappers.
uGamm sets also an appropriate class onto the result ("gamm4"
and/or "gamm"), which is needed for some generics defined in MuMIn
to work (note that unlike the functions created by updateable it has no
formal arguments of the original function). As of version 1.9.2,
MuMIn::gamm is no longer available.
Kamil Bartoń
# Simple example with cor.test:
# From example(cor.test)
x <- c(44.4, 45.9, 41.9, 53.3, 44.7, 44.1, 50.7, 45.2, 60.1)
y <- c( 2.6, 3.1, 2.5, 5.0, 3.6, 4.0, 5.2, 2.8, 3.8)
ct1 <- cor.test(x, y, method = "kendall", alternative = "greater")
uCor.test <- updateable(cor.test)
ct2 <- uCor.test(x, y, method = "kendall", alternative = "greater")
getCall(ct1) # --> NULL
getCall(ct2)
#update(ct1, method = "pearson") --> Error
update(ct2, method = "pearson")
update(ct2, alternative = "two.sided")
## predefined wrapper for 'gamm':
set.seed(0)
dat <- gamSim(6, n = 100, scale = 5, dist = "normal")
fmm1 <- uGamm(y ~s(x0)+ s(x3) + s(x2), family = gaussian, data = dat,
random = list(fac = ~1))
getCall(fmm1)
class(fmm1)
###
## Not run:
library(caper)
data(shorebird)
shorebird <- comparative.data(shorebird.tree, shorebird.data, Species)
fm1 <- crunch(Egg.Mass ~ F.Mass * M.Mass, data = shorebird)
uCrunch <- updateable(crunch)
fm2 <- uCrunch(Egg.Mass ~ F.Mass * M.Mass, data = shorebird)
getCall(fm1)
getCall(fm2)
update(fm2) # Error with 'fm1'
dredge(fm2)
## End(Not run)
###
## Not run:
# "lmekin" does not store "formula" element
library(coxme)
uLmekin <- updateable(lmekin, eval.args = "formula")
f <- effort ~ Type + (1|Subject)
fm1 <- lmekin(f, data = ergoStool)
fm2 <- uLmekin(f, data = ergoStool)
f <- wrong ~ formula # reassigning "f"
getCall(fm1) # formula is "f"
getCall(fm2)
formula(fm1) # returns the current value of "f"
formula(fm2)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.