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authorJohannes Ranke <jranke@uni-bremen.de>2021-02-06 18:30:32 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-02-06 18:30:32 +0100
commit48c463680b51fa767b4cd7bd62865f192d0354ac (patch)
tree5b66eb08a7fd5e29fb7e6d3a9a8258ccdcaea73e /R/summary.saem.mmkin.R
parent2ee20b257e34210e2d1f044431f3bfe059c9c5e7 (diff)
Reintroduce interface to saemix
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed.
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+#' Summary method for class "saem.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.
+#'
+#' @param object an object of class [saem.mmkin]
+#' @param x an object of class [summary.saem.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 based on the [saemix::SaemixObject]
+#' obtained in the fit, with at least the following additional components
+#' \item{saemixversion, mkinversion, Rversion}{The saemix, 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_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.}
+#' \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
+#' saemix authors for the parts inherited from saemix.
+#' @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 saem
+#' f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo,
+#' quiet = TRUE, error_model = "tc", cores = 5)
+#' f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo)
+#' summary(f_saem_dfop_sfo, data = TRUE)
+#' }
+#'
+#' @export
+summary.saem.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes = TRUE, ...) {
+
+ mod_vars <- names(object$mkinmod$diffs)
+
+ pnames <- names(object$mean_dp_start)
+ np <- length(pnames)
+
+ conf.int <- object$so@results@conf.int
+ rownames(conf.int) <- conf.int$name
+ confint_trans <- as.matrix(conf.int[pnames, c("estimate", "lower", "upper")])
+ colnames(confint_trans)[1] <- "est."
+
+ # In case objects were produced by earlier versions of saem
+ if (is.null(object$transformations)) object$transformations <- "mkin"
+
+ if (object$transformations == "mkin") {
+ bp <- backtransform_odeparms(confint_trans[, "est."], object$mkinmod,
+ object$transform_rates, object$transform_fractions)
+ bpnames <- names(bp)
+
+ # Transform boundaries of CI for one parameter at a time,
+ # with the exception of sets of formation fractions (single fractions are OK).
+ f_names_skip <- character(0)
+ for (box in mod_vars) { # Figure out sets of fractions to skip
+ f_names <- grep(paste("^f", box, sep = "_"), pnames, value = TRUE)
+ n_paths <- length(f_names)
+ if (n_paths > 1) f_names_skip <- c(f_names_skip, f_names)
+ }
+
+ confint_back <- matrix(NA, nrow = length(bp), ncol = 3,
+ dimnames = list(bpnames, colnames(confint_trans)))
+ confint_back[, "est."] <- bp
+
+ for (pname in pnames) {
+ if (!pname %in% f_names_skip) {
+ par.lower <- confint_trans[pname, "lower"]
+ par.upper <- confint_trans[pname, "upper"]
+ names(par.lower) <- names(par.upper) <- pname
+ bpl <- backtransform_odeparms(par.lower, object$mkinmod,
+ object$transform_rates,
+ object$transform_fractions)
+ bpu <- backtransform_odeparms(par.upper, object$mkinmod,
+ object$transform_rates,
+ object$transform_fractions)
+ confint_back[names(bpl), "lower"] <- bpl
+ confint_back[names(bpu), "upper"] <- bpu
+ }
+ }
+ } else {
+ confint_back <- confint_trans
+ }
+
+ # Correlation of fixed effects (inspired by summary.nlme)
+ varFix <- vcov(object$so)[1:np, 1:np]
+ stdFix <- sqrt(diag(varFix))
+ object$corFixed <- array(
+ t(varFix/stdFix)/stdFix,
+ dim(varFix),
+ list(pnames, pnames))
+
+ # Random effects
+ rnames <- paste0("SD.", pnames)
+ confint_ranef <- as.matrix(conf.int[rnames, c("estimate", "lower", "upper")])
+ colnames(confint_ranef)[1] <- "est."
+
+ # Error model
+ enames <- if (object$err_mod == "const") "a.1" else c("a.1", "b.1")
+ confint_errmod <- as.matrix(conf.int[enames, c("estimate", "lower", "upper")])
+ colnames(confint_errmod)[1] <- "est."
+
+
+ object$confint_trans <- confint_trans
+ object$confint_ranef <- confint_ranef
+ object$confint_errmod <- confint_errmod
+ object$confint_back <- confint_back
+
+ object$date.summary = date()
+ object$use_of_ff = object$mkinmod$use_of_ff
+ object$error_model_algorithm = object$mmkin_orig[[1]]$error_model_algorithm
+ err_mod = object$mmkin_orig[[1]]$err_mod
+
+ object$diffs <- object$mkinmod$diffs
+ object$print_data <- data # boolean: Should we print the data?
+ so_pred <- object$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$so, method = "is")
+
+ ep <- endpoints(object)
+ if (length(ep$ff) != 0)
+ object$ff <- ep$ff
+ if (distimes) object$distimes <- ep$distimes
+ if (length(ep$SFORB) != 0) object$SFORB <- ep$SFORB
+ class(object) <- c("summary.saem.mmkin")
+ return(object)
+}
+
+#' @rdname summary.saem.mmkin
+#' @export
+print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...) {
+ cat("saemix version used for fitting: ", x$saemixversion, "\n")
+ cat("mkin version used for pre-fitting: ", x$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("\nModel predictions using solution type", x$solution_type, "\n")
+
+ cat("\nFitted in", x$time[["elapsed"]], "s using", paste(x$so@options$nbiter.saemix, collapse = ", "), "iterations\n")
+
+ cat("\nVariance model: ")
+ cat(switch(x$err_mod,
+ const = "Constant variance",
+ obs = "Variance unique to each observed variable",
+ tc = "Two-component variance function"), "\n")
+
+ cat("\nMean of starting values for individual parameters:\n")
+ print(x$mean_dp_start, digits = digits)
+
+ cat("\nFixed degradation parameter values:\n")
+ if(length(x$fixed$value) == 0) cat("None\n")
+ else print(x$fixed, digits = digits)
+
+ cat("\nResults:\n\n")
+ cat("Likelihood computed by importance sampling\n")
+ print(data.frame(AIC = x$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$corFixed
+ class(corr) <- "correlation"
+ print(corr, title = "\nCorrelation:", ...)
+ }
+
+ cat("\nRandom effects:\n")
+ print(x$confint_ranef, digits = digits)
+
+ cat("\nVariance model:\n")
+ print(x$confint_errmod, digits = digits)
+
+ if (x$transformations == "mkin") {
+ 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)
+}

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