diff options
Diffstat (limited to 'R/summary.nlmixr.mmkin.R')
| -rw-r--r-- | R/summary.nlmixr.mmkin.R | 50 |
1 files changed, 25 insertions, 25 deletions
diff --git a/R/summary.nlmixr.mmkin.R b/R/summary.nlmixr.mmkin.R index ae8e32cf..f2d7c607 100644 --- a/R/summary.nlmixr.mmkin.R +++ b/R/summary.nlmixr.mmkin.R @@ -6,8 +6,9 @@ #' endpoints such as formation fractions and DT50 values. Optionally #' (default is FALSE), the data are listed in full. #' -#' @param object an object of class [nlmix.mmkin] -#' @param x an object of class [summary.nlmix.mmkin] +#' @importFrom stats confint sd +#' @param object an object of class [nlmixr.mmkin] +#' @param x an object of class [summary.nlmixr.mmkin] #' @param data logical, indicating whether the full data should be included in #' the summary. #' @param verbose Should the summary be verbose? @@ -23,9 +24,7 @@ #' \item{diffs}{The differential equations used in the degradation model} #' \item{use_of_ff}{Was maximum or minimum use made of formation fractions} #' \item{data}{The data} -#' \item{confint_trans}{Transformed parameters as used in the optimisation, with confidence intervals} #' \item{confint_back}{Backtransformed parameters, with confidence intervals if available} -#' \item{confint_errmod}{Error model parameters with confidence intervals} #' \item{ff}{The estimated formation fractions derived from the fitted #' model.} #' \item{distimes}{The DT50 and DT90 values for each observed variable.} @@ -78,7 +77,7 @@ #' # The following takes a very long time but gives #' f_nlmixr_dfop_sfo_focei <- nlmixr(f_mmkin_dfop_sfo, est = "focei") #' AIC(f_nlmixr_dfop_sfo_saem$nm, f_nlmixr_dfop_sfo_focei$nm) -#' summary(f_nlmixr_dfop_sfo, data = TRUE) +#' summary(f_nlmixr_dfop_sfo_sfo, data = TRUE) #' } #' #' @export @@ -134,6 +133,7 @@ summary.nlmixr.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes dim(varFix), list(pnames, pnames)) + object$confint_trans <- confint_trans object$confint_back <- confint_back object$date.summary = date() @@ -141,31 +141,29 @@ summary.nlmixr.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes object$diffs <- object$mkinmod$diffs object$print_data <- data # boolean: Should we print the data? - predict(object$nm) - so_pred <- object$so@results@predictions names(object$data)[4] <- "observed" # rename value to observed object$verbose <- verbose object$fixed <- object$mmkin_orig[[1]]$fixed - object$AIC = AIC(object$so) - object$BIC = BIC(object$so) - object$logLik = logLik(object$so, method = "is") + object$AIC = AIC(object$nm) + object$BIC = BIC(object$nm) + object$logLik = logLik(object$nm) ep <- endpoints(object) if (length(ep$ff) != 0) object$ff <- ep$ff if (distimes) object$distimes <- ep$distimes if (length(ep$SFORB) != 0) object$SFORB <- ep$SFORB - class(object) <- c("summary.saem.mmkin") + class(object) <- c("summary.nlmixr.mmkin") return(object) } -#' @rdname summary.saem.mmkin +#' @rdname summary.nlmixr.mmkin #' @export -print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...) { - cat("saemix version used for fitting: ", x$saemixversion, "\n") +print.summary.nlmixr.mmkin <- function(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...) { + cat("nlmixr version used for fitting: ", x$nlmixrversion, "\n") cat("mkin version used for pre-fitting: ", x$mkinversion, "\n") cat("R version used for fitting: ", x$Rversion, "\n") @@ -181,25 +179,29 @@ print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3) length(unique(x$data$name)), "variable(s) grouped in", length(unique(x$data$ds)), "datasets\n") - cat("\nModel predictions using solution type", x$solution_type, "\n") + cat("\nDegradation model predictions using RxODE\n") - cat("\nFitted in", x$time[["elapsed"]], "s using", paste(x$so@options$nbiter.saemix, collapse = ", "), "iterations\n") + cat("\nFitted in", x$time[["elapsed"]], "s\n") cat("\nVariance model: ") cat(switch(x$err_mod, const = "Constant variance", obs = "Variance unique to each observed variable", - tc = "Two-component variance function"), "\n") + tc = "Two-component variance function", + obs_tc = "Two-component variance unique to each observed variable"), "\n") cat("\nMean of starting values for individual parameters:\n") print(x$mean_dp_start, digits = digits) + cat("\nMean of starting values for error model parameters:\n") + print(x$mean_ep_start, digits = digits) + cat("\nFixed degradation parameter values:\n") if(length(x$fixed$value) == 0) cat("None\n") else print(x$fixed, digits = digits) cat("\nResults:\n\n") - cat("Likelihood computed by importance sampling\n") + cat("Likelihood calculated by", nlmixr::getOfvType(x$nm), " \n") print(data.frame(AIC = x$AIC, BIC = x$BIC, logLik = x$logLik, row.names = " "), digits = digits) @@ -212,16 +214,14 @@ print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3) print(corr, title = "\nCorrelation:", ...) } - cat("\nRandom effects:\n") - print(x$confint_ranef, digits = digits) + cat("\nRandom effects (omega):\n") + print(x$nm$omega, digits = digits) cat("\nVariance model:\n") - print(x$confint_errmod, digits = digits) + print(x$nm$sigma, digits = digits) - if (x$transformations == "mkin") { - cat("\nBacktransformed parameters:\n") - print(x$confint_back, digits = digits) - } + cat("\nBacktransformed parameters:\n") + print(x$confint_back, digits = digits) printSFORB <- !is.null(x$SFORB) if(printSFORB){ |