diff options
Diffstat (limited to 'R/endpoints.R')
| -rw-r--r-- | R/endpoints.R | 39 |
1 files changed, 31 insertions, 8 deletions
diff --git a/R/endpoints.R b/R/endpoints.R index f7ee483a..586ef9ff 100644 --- a/R/endpoints.R +++ b/R/endpoints.R @@ -7,9 +7,13 @@ #' are equivalent to the rate constantes of the DFOP model, but with the #' advantage that the SFORB model can also be used for metabolites. #' -#' @param fit An object of class \code{\link{mkinfit}}. +#' @param fit An object of class \code{\link{mkinfit}} or +#' \code{\link{nlme.mmkin}} #' @importFrom stats optimize -#' @return A list with the components mentioned above. +#' @return A list with a matrix of dissipation times named distimes, +#' and, if applicable, a vector of formation fractions named ff +#' and, if the SFORB model was in use, a vector of eigenvalues +#' of these SFORB models, equivalent to DFOP rate constants #' @note The function is used internally by \code{\link{summary.mkinfit}}. #' @author Johannes Ranke #' @keywords manip @@ -17,6 +21,10 @@ #' #' fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) #' endpoints(fit) +#' \dontrun{ +#' fit_2 <- mkinfit("SFORB", FOCUS_2006_C, quiet = TRUE) +#' endpoints(fit_2) +#' } #' #' @export endpoints <- function(fit) { @@ -25,8 +33,22 @@ endpoints <- function(fit) { # Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from # HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models ep <- list() - obs_vars <- fit$obs_vars - parms.all <- c(fit$bparms.optim, fit$bparms.fixed) + if (inherits(fit, "mkinfit")) { + mkinmod <- fit$mkinmod + parms.all <- c(fit$bparms.optim, fit$bparms.fixed) + } else { + if (inherits(fit, "nlme.mmkin")) { + mkinmod <- fit$mmkin_orig[[1]]$mkinmod + bparms.optim <- backtransform_odeparms(fit$coefficients$fixed, + mkinmod, + transform_rates = fit$mmkin_orig[[1]]$transform_rates, + transform_fractions = fit$mmkin_orig[[1]]$transform_fractions) + parms.all <- c(bparms.optim, fit$bparms.fixed) + } else { + stop("Only implemented for mkinfit and nlme.mmkin objects") + } + } + obs_vars <- names(mkinmod$spec) ep$ff <- vector() ep$SFORB <- vector() ep$distimes <- data.frame( @@ -34,7 +56,7 @@ endpoints <- function(fit) { DT90 = rep(NA, length(obs_vars)), row.names = obs_vars) for (obs_var in obs_vars) { - type = names(fit$mkinmod$map[[obs_var]])[1] + type = names(mkinmod$map[[obs_var]])[1] # Get formation fractions if directly fitted, and calculate remaining fraction to sink f_names = grep(paste("^f", obs_var, sep = "_"), names(parms.all), value=TRUE) @@ -56,7 +78,7 @@ endpoints <- function(fit) { k_tot = sum(parms.all[k_names]) DT50 = log(2)/k_tot DT90 = log(10)/k_tot - if (fit$mkinmod$use_of_ff == "min") { + if (mkinmod$use_of_ff == "min" && length(obs_vars) > 1) { for (k_name in k_names) { ep$ff[[sub("k_", "", k_name)]] = parms.all[[k_name]] / k_tot @@ -78,7 +100,7 @@ endpoints <- function(fit) { n = parms.all[paste("N", obs_var, sep = "_")] k = k_tot # Use the initial concentration of the parent compound - source_name = fit$mkinmod$map[[1]][[1]] + source_name = mkinmod$map[[1]][[1]] c0 = parms.all[paste(source_name, "0", sep = "_")] alpha = 1 / (n - 1) beta = (c0^(1 - n))/(k * (n - 1)) @@ -86,7 +108,7 @@ endpoints <- function(fit) { DT90 = beta * (10^(1/alpha) - 1) DT50_back = DT90 / (log(10)/log(2)) # Backcalculated DT50 as recommended in FOCUS 2011 ep$distimes[obs_var, c("DT50back")] = DT50_back - if (fit$mkinmod$use_of_ff == "min") { + if (mkinmod$use_of_ff == "min") { for (k_name in k_names) { ep$ff[[sub("k_", "", k_name)]] = parms.all[[k_name]] / k_tot @@ -196,6 +218,7 @@ endpoints <- function(fit) { } ep$distimes[obs_var, c("DT50", "DT90")] = c(DT50, DT90) } + if (length(ep$ff) == 0) ep$ff <- NULL if (length(ep$SFORB) == 0) ep$SFORB <- NULL return(ep) } |