1 files changed, 250 insertions, 0 deletions
diff --git a/R/summary.nlmixr.mmkin.R b/R/summary.nlmixr.mmkin.R
new file mode 100644
index 00000000..a023f319
--- /dev/null
+++ b/R/summary.nlmixr.mmkin.R
@@ -0,0 +1,250 @@
+#' Summary method for class "nlmixr.mmkin"
+#'
+#' Lists model equations, initial parameter values, optimised parameters
+#' for fixed effects (population), random effects (deviations from the
+#' population mean) and residual error model, as well as the resulting
+#' endpoints such as formation fractions and DT50 values. Optionally
+#' (default is FALSE), the data are listed in full.
+#'
+#' @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?
+#' @param distimes logical, indicating whether DT50 and DT90 values should be
+#'   included.
+#' @param digits Number of digits to use for printing
+#' @param \dots optional arguments passed to methods like \code{print}.
+#' @return The summary function returns a list obtained in the fit, with at
+#'   least the following additional components
+#'   \item{nlmixrversion, mkinversion, Rversion}{The nlmixr, 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 degradation model}
+#'   \item{use_of_ff}{Was maximum or minimum use made of formation fractions}
+#'   \item{data}{The data}
+#'   \item{confint_back}{Backtransformed parameters, with confidence intervals if available}
+#'   \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.
+#' @importFrom stats predict vcov
+#' @author Johannes Ranke for the mkin specific parts
+#'   nlmixr authors for the parts inherited from nlmixr.
+#' @examples
+#' # Generate five datasets following DFOP-SFO kinetics
+#' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+#' dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "m1"),
+#'  m1 = mkinsub("SFO"), quiet = TRUE)
+#' set.seed(1234)
+#' k1_in <- rlnorm(5, log(0.1), 0.3)
+#' k2_in <- rlnorm(5, log(0.02), 0.3)
+#' g_in <- plogis(rnorm(5, qlogis(0.5), 0.3))
+#' f_parent_to_m1_in <- plogis(rnorm(5, qlogis(0.3), 0.3))
+#' k_m1_in <- rlnorm(5, log(0.02), 0.3)
+#'
+#' pred_dfop_sfo <- function(k1, k2, g, f_parent_to_m1, k_m1) {
+#'   mkinpredict(dfop_sfo,
+#'     c(k1 = k1, k2 = k2, g = g, f_parent_to_m1 = f_parent_to_m1, k_m1 = k_m1),
+#'     c(parent = 100, m1 = 0),
+#'     sampling_times)
+#' }
+#'
+#' ds_mean_dfop_sfo <- lapply(1:5, function(i) {
+#'   mkinpredict(dfop_sfo,
+#'     c(k1 = k1_in[i], k2 = k2_in[i], g = g_in[i],
+#'       f_parent_to_m1 = f_parent_to_m1_in[i], k_m1 = k_m1_in[i]),
+#'     c(parent = 100, m1 = 0),
+#'     sampling_times)
+#' })
+#' names(ds_mean_dfop_sfo) <- paste("ds", 1:5)
+#'
+#' ds_syn_dfop_sfo <- lapply(ds_mean_dfop_sfo, function(ds) {
+#'   add_err(ds,
+#'     sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2),
+#'     n = 1)[[1]]
+#' })
+#'
+#' \dontrun{
+#' # Evaluate using mmkin and nlmixr
+#' f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo,
+#'   quiet = TRUE, error_model = "tc", cores = 5)
+#' f_saemix_dfop_sfo <- mkin::saem(f_mmkin_dfop_sfo)
+#' f_nlme_dfop_sfo <- mkin::nlme(f_mmkin_dfop_sfo)
+#' f_nlmixr_dfop_sfo_saem <- nlmixr(f_mmkin_dfop_sfo, est = "saem")
+#' # 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_sfo, data = TRUE)
+#' }
+#'
+#' @export
+summary.nlmixr.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes = TRUE, ...) {
+
+  mod_vars <- names(object$mkinmod$diffs)
+
+  conf.int <- confint(object$nm)
+  dpnames <- setdiff(rownames(conf.int), names(object$mean_ep_start))
+  ndp <- length(dpnames)
+
+  confint_trans <- as.matrix(conf.int[dpnames, c(1, 3, 4)])
+  colnames(confint_trans) <- c("est.", "lower", "upper")
+
+  bp <- backtransform_odeparms(confint_trans[, "est."], object$mkinmod,
+    object$transform_rates, object$transform_fractions)
+  bpnames <- names(bp)
+
+  # Transform boundaries of CI for one parameter at a time,
+  # with the exception of sets of formation fractions (single fractions are OK).
+  f_names_skip <- character(0)
+  for (box in mod_vars) { # Figure out sets of fractions to skip
+    f_names <- grep(paste("^f", box, sep = "_"), dpnames, value = TRUE)
+    n_paths <- length(f_names)
+    if (n_paths > 1) f_names_skip <- c(f_names_skip, f_names)
+  }
+
+  confint_back <- matrix(NA, nrow = length(bp), ncol = 3,
+    dimnames = list(bpnames, colnames(confint_trans)))
+  confint_back[, "est."] <- bp
+
+  for (pname in dpnames) {
+    if (!pname %in% f_names_skip) {
+      par.lower <- confint_trans[pname, "lower"]
+      par.upper <- confint_trans[pname, "upper"]
+      names(par.lower) <- names(par.upper) <- pname
+      bpl <- backtransform_odeparms(par.lower, object$mkinmod,
+                                            object$transform_rates,
+                                            object$transform_fractions)
+      bpu <- backtransform_odeparms(par.upper, object$mkinmod,
+                                            object$transform_rates,
+                                            object$transform_fractions)
+      confint_back[names(bpl), "lower"] <- bpl
+      confint_back[names(bpu), "upper"] <- bpu
+    }
+  }
+
+  #  Correlation of fixed effects (inspired by summary.nlme)
+  varFix <- vcov(object$nm)
+  stdFix <- sqrt(diag(varFix))
+  object$corFixed <- array(
+    t(varFix/stdFix)/stdFix,
+    dim(varFix),
+    list(dpnames, dpnames))
+
+  object$confint_trans <- confint_trans
+  object$confint_back <- confint_back
+
+  object$date.summary = date()
+  object$use_of_ff = object$mkinmod$use_of_ff
+
+  object$diffs <- object$mkinmod$diffs
+  object$print_data <- data # boolean: Should we print the data?
+
+  names(object$data)[4] <- "observed" # rename value to observed
+
+  object$verbose <- verbose
+
+  object$fixed <- object$mmkin_orig[[1]]$fixed
+  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.nlmixr.mmkin")
+  return(object)
+}
+
+#' @rdname summary.nlmixr.mmkin
+#' @export
+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")
+
+  cat("Date of fit:    ", x$date.fit, "\n")
+  cat("Date of summary:", x$date.summary, "\n")
+
+  cat("\nEquations:\n")
+  nice_diffs <- gsub("^(d.*) =", "\\1/dt =", x[["diffs"]])
+  writeLines(strwrap(nice_diffs, exdent = 11))
+
+  cat("\nData:\n")
+  cat(nrow(x$data), "observations of",
+    length(unique(x$data$name)), "variable(s) grouped in",
+    length(unique(x$data$ds)), "datasets\n")
+
+  cat("\nDegradation model predictions using RxODE\n")
+
+  cat("\nFitted in", x$time[["elapsed"]],  "s\n")
+
+  cat("\nVariance model: ")
+  cat(switch(x$err_mod,
+    const = "Constant variance",
+    obs = "Variance unique to each observed variable",
+    tc = "Two-component variance function",
+    obs_tc = "Two-component variance unique to each observed variable"), "\n")
+
+  cat("\nMean of starting values for individual parameters:\n")
+  print(x$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 calculated by", nlmixr::getOfvType(x$nm), " \n")
+  print(data.frame(AIC = x$AIC, BIC = x$BIC, logLik = x$logLik,
+      row.names = " "), digits = digits)
+
+  cat("\nOptimised parameters:\n")
+  print(x$confint_trans, digits = digits)
+
+  if (nrow(x$confint_trans) > 1) {
+    corr <- x$corFixed
+    class(corr) <- "correlation"
+    print(corr, title = "\nCorrelation:", ...)
+  }
+
+  cat("\nRandom effects (omega):\n")
+  print(x$nm$omega, digits = digits)
+
+  cat("\nVariance model:\n")
+  print(x$nm$sigma, digits = digits)
+
+  cat("\nBacktransformed parameters:\n")
+  print(x$confint_back, 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,...)
+  }
+
+  if (x$print_data){
+    cat("\nData:\n")
+    print(format(x$data, digits = digits, ...), row.names = FALSE)
+  }
+
+  invisible(x)
+}