nlme: nlsList – R documentation

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nlsList

List of nls Objects with a Common Model

Description

Data is partitioned according to the levels of the grouping factor defined in model and individual nls fits are obtained for each data partition, using the model defined in model.

Usage

nlsList(model, data, start, control, level, subset,
        na.action = na.fail, pool = TRUE, warn.nls = NA)
## S3 method for class 'nlsList'
update(object, model., ..., evaluate = TRUE)

Arguments

`object`	an object inheriting from class `nlsList`, representing a list of fitted `nls` objects.
`model`	either a nonlinear model formula, with the response on the left of a `~` operator and an expression involving parameters, covariates, and a grouping factor separated by the `\|` operator on the right, or a `selfStart` function. The method function `nlsList.selfStart` is documented separately.
`model.`	changes to the model – see `update.formula` for details.
`data`	a data frame in which to interpret the variables named in `model`.
`start`	an optional named list with initial values for the parameters to be estimated in `model`. It is passed as the `start` argument to each `nls` call and is required when the nonlinear function in `model` does not inherit from class `selfStart`.
`control`	a list of control values passed as the `control` argument to `nls`. Defaults to an empty list.
`level`	an optional integer specifying the level of grouping to be used when multiple nested levels of grouping are present.
`subset`	an optional expression indicating the subset of the rows of `data` that should be used in the fit. This can be a logical vector, or a numeric vector indicating which observation numbers are to be included, or a character vector of the row names to be included. All observations are included by default.
`na.action`	a function that indicates what should happen when the data contain `NA`s. The default action (`na.fail`) causes `nlsList` to print an error message and terminate if there are any incomplete observations.
`pool`	an optional logical value that is preserved as an attribute of the returned value. This will be used as the default for `pool` in calculations of standard deviations or standard errors for summaries.
`warn.nls`	`logical` indicating if `nls()` errors (all of which are caught by `tryCatch`) should be signalled as a “summarizing” `warning`.
`...`	some methods for this generic require additional arguments. None are used in this method.
`evaluate`	If `TRUE` evaluate the new call else return the call.

Details

As nls(.) is called on each sub group, and convergence of these may be problematic, these calls happen with error catching.

Since nlme version 3.1-127 (2016-04), all the errors are caught (via tryCatch) and if present, a “summarizing” warning is stored as attribute of the resulting "nlsList" object and signalled unless suppressed by warn.nls = FALSE or currently also when warn.nls = NA (default) and getOption("show.error.messages") is false.

nlsList() originally had used try(*) (with its default silent=FALSE) and hence all errors were printed to the console unless the global option show.error.messages was set to true. This still works, but has been deprecated.

Value

a list of nls objects with as many components as the number of groups defined by the grouping factor. Generic functions such as coef, fixed.effects, lme, pairs, plot, predict, random.effects, summary, and update have methods that can be applied to an nlsList object.

References

Pinheiro, J.C., and Bates, D.M. (2000), Mixed-Effects Models in S and S-PLUS, Springer.

Examples

fm1 <- nlsList(uptake ~ SSasympOff(conc, Asym, lrc, c0),
   data = CO2, start = c(Asym = 30, lrc = -4.5, c0 = 52))
summary(fm1)
cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*
mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4.0.0;  ("matrix" in older R)
i.ok <- which(vapply(cfm1,
                function(r) identical(class(r), mat.class), NA))
stopifnot(length(i.ok) > 0, !anyNA(match(c(2:4, 6:9, 12), i.ok)))
## where as (some of) the others gave errors during profile re-fitting :
str(cfm1[- i.ok])

nlme

Linear and Nonlinear Mixed Effects Models

v3.1-152

GPL (>= 2) | file LICENCE

Authors

José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), Johannes Ranke [ctb] (varConstProp()), R-core [aut, cre]

Initial release

2021-02-03