selfStart | R Documentation |
Construct self-starting nonlinear models to be used in
nls
, etc. Via function initial
to compute
approximate parameter values from data, such models are
“self-starting”, i.e., do not need a start
argument in,
e.g., nls()
.
selfStart(model, initial, parameters, template)
model |
a function object defining a nonlinear model or
a nonlinear |
initial |
a function object, taking arguments |
parameters |
a character vector specifying the terms on the right
hand side of |
template |
an optional prototype for the calling sequence of the
returned object, passed as the |
nls()
calls getInitial
and the
initial
function for these self-starting models.
This function is generic; methods functions can be written to handle specific classes of objects.
a function
object of class "selfStart"
, for the
formula
method obtained by applying deriv
to the right hand side of the model
formula. An
initial
attribute (defined by the initial
argument) is
added to the function to calculate starting estimates for the
parameters in the model automatically.
José Pinheiro and Douglas Bates
nls
, getInitial
.
Each of the following are "selfStart"
models (with examples)
SSasymp
, SSasympOff
, SSasympOrig
,
SSbiexp
, SSfol
, SSfpl
,
SSgompertz
, SSlogis
, SSmicmen
,
SSweibull
.
Further, package nlme's nlsList
.
## self-starting logistic model ## The "initializer" (finds initial values for parameters from data): initLogis <- function(mCall, data, LHS) { xy <- data.frame(sortedXyData(mCall[["input"]], LHS, data)) if(nrow(xy) < 4) stop("too few distinct input values to fit a logistic model") z <- xy[["y"]] ## transform to proportion, i.e. in (0,1) : rng <- range(z); dz <- diff(rng) z <- (z - rng[1L] 0.05 * dz)/(1.1 * dz) xy[["z"]] <- log(z/(1 - z)) # logit transformation aux <- coef(lm(x ~ z, xy)) pars <- coef(nls(y ~ 1/(1 exp((xmid - x)/scal)), data = xy, start = list(xmid = aux[[1L]], scal = aux[[2L]]), algorithm = "plinear")) setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("Asym", "xmid", "scal")]) } SSlogis <- selfStart(~ Asym/(1 exp((xmid - x)/scal)), initial = initLogis, parameters = c("Asym", "xmid", "scal")) # 'first.order.log.model' is a function object defining a first order # compartment model # 'first.order.log.initial' is a function object which calculates initial # values for the parameters in 'first.order.log.model' # # self-starting first order compartment model ## Not run: SSfol <- selfStart(first.order.log.model, first.order.log.initial) ## End(Not run) ## Explore the self-starting models already available in R's "stats": pos.st <- which("package:stats" == search()) mSS <- apropos("^SS..", where = TRUE, ignore.case = FALSE) (mSS <- unname(mSS[names(mSS) == pos.st])) fSS <- sapply(mSS, get, pos = pos.st, mode = "function") all(sapply(fSS, inherits, "selfStart")) # -> TRUE ## Show the argument list of each self-starting function: str(fSS, give.attr = FALSE)
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