diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/twa.R | 26 |
1 files changed, 16 insertions, 10 deletions
@@ -18,15 +18,20 @@ #' Create a time series of decline data #' -#' The time series starts with the amount specified for the first application. -#' This does not create objects of type \code{\link{ts}}. -#' #' @param x When numeric, this is the half-life to be used for an exponential -#' decline. If x is an mkinfit object, the decline is calculated from this object -#' @param ini The initial amount for each compound +#' decline. When a character string specifying a parent decline model is given +#' e.g. \code{FOMC}, \code{parms} must contain the corresponding paramters. +#' If x is an \code{\link{mkinfit}} object, the decline is calculated from this +#' object. +#' @param ini The initial amount for the parent compound. If x is an +#' \code{\link{mkinfit}} object, and ini is 'model', the fitted initial +#' concentrations are used. Otherwise, ini must be numeric. If it has +#' length one, it is used for the parent and initial values of metabolites +#' are zero, otherwise, it must give values for all observed variables. #' @param t_end End of the time series #' @param res Resolution of the time series #' @param ... Further arguments passed to methods +#' @return An object of class \code{one_box}, inheriting from \code{\link{ts}}. #' @importFrom stats filter frequency time ts #' @export #' @examples @@ -59,7 +64,7 @@ one_box.numeric <- function(x, ini = 1, ..., half_life = x k = log(2)/half_life t_out <- seq(0, t_end, by = res) - raw <- matrix(exp( - k * t_out), ncol = 1) + raw <- matrix(ini * exp( - k * t_out), ncol = 1) dimnames(raw) <- list(NULL, "parent") result <- ts(raw, 0, t_end, frequency = 1/res) class(result) <- c("one_box", "ts") @@ -87,7 +92,7 @@ one_box.character <- function(x, ini = 1, parms, ..., } t_out <- seq(0, t_end, by = res) - pred <- mkinpredict(m, odeparms = parms, odeini = c(parent = 1), + pred <- mkinpredict(m, odeparms = parms, odeini = c(parent = ini), outtimes = t_out, solution_type = "analytical")[-1] result <- ts(pred, 0, t_end, frequency = 1/res) class(result) <- c("one_box", "ts") @@ -97,13 +102,14 @@ one_box.character <- function(x, ini = 1, parms, ..., #' @rdname one_box #' @importFrom mkin mkinpredict #' @export -one_box.mkinfit <- function(x, ini = c("model", 1), ..., t_end = 100, res = 0.01) { +one_box.mkinfit <- function(x, ini = "model", ..., t_end = 100, res = 0.01) { fit <- x if (ini[1] == "model") { odeini = x$bparms.state } else { - if (ini[1] != 1) stop ("Argument ini can only be 'model' or 1") - odeini <- c(1, rep(0, length(fit$mkinmod$spec) - 1)) + if (!is.numeric(ini[1])) stop ("Argument ini can only be 'model' or numeric") + if (length(ini) == 1) odeini <- c(ini[1], rep(0, length(fit$mkinmod$spec) - 1)) + else odeini = ini names(odeini) <- names(fit$mkinmod$spec) } |