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+#' Summary method for class "mkinfit"
+#'
+#' Lists model equations, initial parameter values, optimised parameters with
+#' some uncertainty statistics, the chi2 error levels calculated according to
+#' FOCUS guidance (2006) as defined therein, formation fractions, DT50 values
+#' and optionally the data, consisting of observed, predicted and residual
+#' values.
+#'
+#' @param object an object of class \code{\link{mkinfit}}.
+#' @param x an object of class \code{summary.mkinfit}.
+#' @param data logical, indicating whether the data should be included in the
+#' summary.
+#' @param distimes logical, indicating whether DT50 and DT90 values should be
+#' included.
+#' @param alpha error level for confidence interval estimation from t
+#' distribution
+#' @param digits Number of digits to use for printing
+#' @param \dots optional arguments passed to methods like \code{print}.
+#' @importFrom stats qt pt cov2cor
+#' @return The summary function returns a list with components, among others
+#' \item{version, Rversion}{The mkin and R versions used}
+#' \item{date.fit, date.summary}{The dates where the fit and the summary were
+#' produced}
+#' \item{diffs}{The differential equations used in the model}
+#' \item{use_of_ff}{Was maximum or minimum use made of formation fractions}
+#' \item{bpar}{Optimised and backtransformed
+#' parameters}
+#' \item{data}{The data (see Description above).}
+#' \item{start}{The starting values and bounds, if applicable, for optimised
+#' parameters.}
+#' \item{fixed}{The values of fixed parameters.}
+#' \item{errmin }{The chi2 error levels for
+#' each observed variable.}
+#' \item{bparms.ode}{All backtransformed ODE
+#' parameters, for use as starting parameters for related models.}
+#' \item{errparms}{Error model parameters.}
+#' \item{ff}{The estimated formation fractions derived from the fitted
+#' model.}
+#' \item{distimes}{The DT50 and DT90 values for each observed variable.}
+#' \item{SFORB}{If applicable, eigenvalues of SFORB components of the model.}
+#' The print method is called for its side effect, i.e. printing the summary.
+#' @author Johannes Ranke
+#' @references FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence
+#' and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+#' EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+#' EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+#' \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+#' @examples
+#'
+#' summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
+#'
+#' @export
+summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, alpha = 0.05, ...) {
+ param <- object$par
+ pnames <- names(param)
+ bpnames <- names(object$bparms.optim)
+ epnames <- names(object$errparms)
+ p <- length(param)
+ mod_vars <- names(object$mkinmod$diffs)
+ covar <- try(solve(object$hessian), silent = TRUE)
+ covar_notrans <- try(solve(object$hessian_notrans), silent = TRUE)
+ rdf <- object$df.residual
+
+ if (!is.numeric(covar) | is.na(covar[1])) {
+ covar <- NULL
+ se <- lci <- uci <- rep(NA, p)
+ } else {
+ rownames(covar) <- colnames(covar) <- pnames
+ se <- sqrt(diag(covar))
+ lci <- param + qt(alpha/2, rdf) * se
+ uci <- param + qt(1-alpha/2, rdf) * se
+ }
+
+ beparms.optim <- c(object$bparms.optim, object$par[epnames])
+ if (!is.numeric(covar_notrans) | is.na(covar_notrans[1])) {
+ covar_notrans <- NULL
+ se_notrans <- tval <- pval <- rep(NA, p)
+ } else {
+ rownames(covar_notrans) <- colnames(covar_notrans) <- c(bpnames, epnames)
+ se_notrans <- sqrt(diag(covar_notrans))
+ tval <- beparms.optim / se_notrans
+ pval <- pt(abs(tval), rdf, lower.tail = FALSE)
+ }
+
+ names(se) <- pnames
+
+ param <- cbind(param, se, lci, uci)
+ dimnames(param) <- list(pnames, c("Estimate", "Std. Error", "Lower", "Upper"))
+
+ bparam <- cbind(Estimate = beparms.optim, se_notrans,
+ "t value" = tval, "Pr(>t)" = pval, Lower = NA, Upper = NA)
+
+ # Transform boundaries of CI for one parameter at a time,
+ # with the exception of sets of formation fractions (single fractions are OK).
+ f_names_skip <- character(0)
+ for (box in mod_vars) { # Figure out sets of fractions to skip
+ f_names <- grep(paste("^f", box, sep = "_"), pnames, value = TRUE)
+ n_paths <- length(f_names)
+ if (n_paths > 1) f_names_skip <- c(f_names_skip, f_names)
+ }
+
+ for (pname in pnames) {
+ if (!pname %in% f_names_skip) {
+ par.lower <- param[pname, "Lower"]
+ par.upper <- param[pname, "Upper"]
+ names(par.lower) <- names(par.upper) <- pname
+ bpl <- backtransform_odeparms(par.lower, object$mkinmod,
+ object$transform_rates,
+ object$transform_fractions)
+ bpu <- backtransform_odeparms(par.upper, object$mkinmod,
+ object$transform_rates,
+ object$transform_fractions)
+ bparam[names(bpl), "Lower"] <- bpl
+ bparam[names(bpu), "Upper"] <- bpu
+ }
+ }
+ bparam[epnames, c("Lower", "Upper")] <- param[epnames, c("Lower", "Upper")]
+
+ ans <- list(
+ version = as.character(utils::packageVersion("mkin")),
+ Rversion = paste(R.version$major, R.version$minor, sep="."),
+ date.fit = object$date,
+ date.summary = date(),
+ solution_type = object$solution_type,
+ warning = object$warning,
+ use_of_ff = object$mkinmod$use_of_ff,
+ error_model_algorithm = object$error_model_algorithm,
+ df = c(p, rdf),
+ covar = covar,
+ covar_notrans = covar_notrans,
+ err_mod = object$err_mod,
+ niter = object$iterations,
+ calls = object$calls,
+ time = object$time,
+ par = param,
+ bpar = bparam)
+
+ if (!is.null(object$version)) {
+ ans$fit_version <- object$version
+ ans$fit_Rversion <- object$Rversion
+ }
+
+ ans$diffs <- object$mkinmod$diffs
+ if(data) ans$data <- object$data
+ ans$start <- object$start
+ ans$start_transformed <- object$start_transformed
+
+ ans$fixed <- object$fixed
+
+ ans$errmin <- mkinerrmin(object, alpha = 0.05)
+
+ if (object$calls > 0) {
+ if (!is.null(ans$covar)){
+ Corr <- cov2cor(ans$covar)
+ rownames(Corr) <- colnames(Corr) <- rownames(ans$par)
+ ans$Corr <- Corr
+ } else {
+ warning("Could not calculate correlation; no covariance matrix")
+ }
+ }
+
+ ans$bparms.ode <- object$bparms.ode
+ ep <- endpoints(object)
+ if (length(ep$ff) != 0)
+ ans$ff <- ep$ff
+ if (distimes) ans$distimes <- ep$distimes
+ if (length(ep$SFORB) != 0) ans$SFORB <- ep$SFORB
+ if (!is.null(object$d_3_message)) ans$d_3_message <- object$d_3_message
+ class(ans) <- c("summary.mkinfit", "summary.modFit")
+ return(ans)
+}
+
+#' @rdname summary.mkinfit
+#' @export
+print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), ...) {
+ if (is.null(x$fit_version)) {
+ cat("mkin version: ", x$version, "\n")
+ cat("R version: ", x$Rversion, "\n")
+ } else {
+ cat("mkin version used for fitting: ", x$fit_version, "\n")
+ cat("R version used for fitting: ", x$fit_Rversion, "\n")
+ }
+
+ cat("Date of fit: ", x$date.fit, "\n")
+ cat("Date of summary:", x$date.summary, "\n")
+
+ if (!is.null(x$warning)) cat("\n\nWarning:", x$warning, "\n\n")
+
+ cat("\nEquations:\n")
+ nice_diffs <- gsub("^(d.*) =", "\\1/dt =", x[["diffs"]])
+ writeLines(strwrap(nice_diffs, exdent = 11))
+ df <- x$df
+ rdf <- df[2]
+
+ cat("\nModel predictions using solution type", x$solution_type, "\n")
+
+ cat("\nFitted using", x$calls, "model solutions performed in", x$time[["elapsed"]], "s\n")
+
+ if (!is.null(x$err_mod)) {
+ cat("\nError model: ")
+ cat(switch(x$err_mod,
+ const = "Constant variance",
+ obs = "Variance unique to each observed variable",
+ tc = "Two-component variance function"), "\n")
+
+ cat("\nError model algorithm:", x$error_model_algorithm, "\n")
+ if (!is.null(x$d_3_message)) cat(x$d_3_message, "\n")
+ }
+
+ cat("\nStarting values for parameters to be optimised:\n")
+ print(x$start)
+
+ cat("\nStarting values for the transformed parameters actually optimised:\n")
+ print(x$start_transformed)
+
+ cat("\nFixed parameter values:\n")
+ if(length(x$fixed$value) == 0) cat("None\n")
+ else print(x$fixed)
+
+ cat("\nOptimised, transformed parameters with symmetric confidence intervals:\n")
+ print(signif(x$par, digits = digits))
+
+ if (x$calls > 0) {
+ cat("\nParameter correlation:\n")
+ if (!is.null(x$covar)){
+ print(x$Corr, digits = digits, ...)
+ } else {
+ cat("No covariance matrix")
+ }
+ }
+
+ cat("\nBacktransformed parameters:\n")
+ cat("Confidence intervals for internally transformed parameters are asymmetric.\n")
+ if ((x$version) < "0.9-36") {
+ cat("To get the usual (questionable) t-test, upgrade mkin and repeat the fit.\n")
+ print(signif(x$bpar, digits = digits))
+ } else {
+ cat("t-test (unrealistically) based on the assumption of normal distribution\n")
+ cat("for estimators of untransformed parameters.\n")
+ print(signif(x$bpar[, c(1, 3, 4, 5, 6)], digits = digits))
+ }
+
+ cat("\nFOCUS Chi2 error levels in percent:\n")
+ x$errmin$err.min <- 100 * x$errmin$err.min
+ print(x$errmin, digits=digits,...)
+
+ printSFORB <- !is.null(x$SFORB)
+ if(printSFORB){
+ cat("\nEstimated Eigenvalues of SFORB model(s):\n")
+ print(x$SFORB, digits=digits,...)
+ }
+
+ printff <- !is.null(x$ff)
+ if(printff){
+ cat("\nResulting formation fractions:\n")
+ print(data.frame(ff = x$ff), digits=digits,...)
+ }
+
+ printdistimes <- !is.null(x$distimes)
+ if(printdistimes){
+ cat("\nEstimated disappearance times:\n")
+ print(x$distimes, digits=digits,...)
+ }
+
+ printdata <- !is.null(x$data)
+ if (printdata){
+ cat("\nData:\n")
+ print(format(x$data, digits = digits, ...), row.names = FALSE)
+ }
+
+ invisible(x)
+}

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