1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
|
#' Extract model parameters
#'
#' This function returns degradation model parameters as well as error
#' model parameters per default, in order to avoid working with a fitted model
#' without considering the error structure that was assumed for the fit.
#'
#' @param object A fitted model object.
#' @param \dots Not used
#' @return Depending on the object, a numeric vector of fitted model parameters,
#' a matrix (e.g. for mmkin row objects), or a list of matrices (e.g. for
#' mmkin objects with more than one row).
#' @seealso [saem], [multistart]
#' @examples
#' # mkinfit objects
#' fit <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE)
#' parms(fit)
#' parms(fit, transformed = TRUE)
#'
#' # mmkin objects
#' ds <- lapply(experimental_data_for_UBA_2019[6:10],
#' function(x) subset(x$data[c("name", "time", "value")]))
#' names(ds) <- paste("Dataset", 6:10)
#' \dontrun{
#' fits <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE, cores = 1)
#' parms(fits["SFO", ])
#' parms(fits[, 2])
#' parms(fits)
#' parms(fits, transformed = TRUE)
#' }
#' @export
parms <- function(object, ...)
{
UseMethod("parms", object)
}
#' @param transformed Should the parameters be returned as used internally
#' during the optimisation?
#' @param errparms Should the error model parameters be returned
#' in addition to the degradation parameters?
#' @rdname parms
#' @export
parms.mkinfit <- function(object, transformed = FALSE, errparms = TRUE, ...)
{
res <- if (transformed) object$par
else c(object$bparms.optim, object$errparms)
if (!errparms) {
res[setdiff(names(res), names(object$errparms))]
}
else return(res)
}
#' @rdname parms
#' @export
parms.mmkin <- function(object, transformed = FALSE, errparms = TRUE, ...)
{
if (nrow(object) == 1) {
res <- sapply(object, parms, transformed = transformed,
errparms = errparms, ...)
colnames(res) <- colnames(object)
} else {
res <- list()
for (i in 1:nrow(object)) {
res[[i]] <- parms(object[i, ], transformed = transformed,
errparms = errparms, ...)
}
names(res) <- rownames(object)
}
return(res)
}
#' @param exclude_failed For [multistart] objects, should rows for failed fits
#' be removed from the returned parameter matrix?
#' @rdname parms
#' @export
parms.multistart <- function(object, exclude_failed = TRUE, ...) {
res <- t(sapply(object, parms))
successful <- which(!is.na(res[, 1]))
first_success <- successful[1]
colnames(res) <- names(parms(object[[first_success]]))
if (exclude_failed[1]) res <- res[successful, ]
return(res)
}
|
