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authorJohannes Ranke <jranke@uni-bremen.de>2020-10-27 15:34:14 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-10-27 15:36:46 +0100
commita5874ab7fce4616e80be69366ff0685332f47bf1 (patch)
tree17f36842de8ff457879be152779f8704f06a4787 /R
parentca1b4c8cdb1de72b44df0ee8cebe11e10814efdf (diff)
Add summary method for nlme.mmkin objects
Improve and update docs
Diffstat (limited to 'R')
-rw-r--r--R/nlme.mmkin.R46
-rw-r--r--R/plot.nlme.mmkin.R6
-rw-r--r--R/sigma_twocomp.R21
-rw-r--r--R/summary.nlme.mmkin.R233
4 files changed, 285 insertions, 21 deletions
diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R
index d3369cf5..6d24a044 100644
--- a/R/nlme.mmkin.R
+++ b/R/nlme.mmkin.R
@@ -42,6 +42,9 @@ get_deg_func <- function() {
#' @importFrom stats na.fail as.formula
#' @return Upon success, a fitted nlme.mmkin object, which is an nlme object
#' with additional elements
+#' @note As the object inherits from [nlme::nlme], there is a wealth of
+#' methods that will automatically work on 'nlme.mmkin' objects, such as
+#' [nlme::intervals()], [nlme::anova.lme()] and [nlme::coef.lme()].
#' @export
#' @seealso \code{\link{nlme_function}}
#' @examples
@@ -141,8 +144,8 @@ nlme.mmkin <- function(model, data = sys.frame(sys.parent()),
thisCall[["model"]] <- this_model
- mean_dp <- mean_degparms(model)
- dp_names <- names(mean_dp)
+ mean_dp_start <- mean_degparms(model)
+ dp_names <- names(mean_dp_start)
thisCall[["data"]] <- nlme_data(model)
@@ -175,10 +178,21 @@ nlme.mmkin <- function(model, data = sys.frame(sys.parent()),
thisCall[["control"]] <- control
}
- val <- do.call("nlme.formula", thisCall)
+ fit_time <- system.time(val <- do.call("nlme.formula", thisCall))
+ val$time <- fit_time
+
+ val$mean_dp_start <- mean_dp_start
val$mmkin_orig <- model
val$data <- thisCall[["data"]]
val$mkinmod <- model[[1]]$mkinmod
+ val$err_mode <- error_model
+ val$transform_rates <- model[[1]]$transform_rates
+ val$transform_fractions <- model[[1]]$transform_fractions
+ val$solution_type <- model[[1]]$solution_type
+ val$date.fit <- date()
+ val$nlmeversion <- as.character(utils::packageVersion("nlme"))
+ val$mkinversion <- as.character(utils::packageVersion("mkin"))
+ val$Rversion <- paste(R.version$major, R.version$minor, sep=".")
class(val) <- c("nlme.mmkin", "nlme", "lme")
return(val)
}
@@ -186,10 +200,30 @@ nlme.mmkin <- function(model, data = sys.frame(sys.parent()),
#' @export
#' @rdname nlme.mmkin
#' @param x An nlme.mmkin object to print
-#' @param ... Further arguments as in the generic
print.nlme.mmkin <- function(x, ...) {
- x$call$data <- "Not shown"
- NextMethod("print", x)
+ cat( "Kinetic nonlinear mixed-effects model fit by " )
+ cat( if(x$method == "REML") "REML\n" else "maximum likelihood\n")
+ cat("\nStructural model:\n")
+ diffs <- x$mmkin_orig[[1]]$mkinmod$diffs
+ nice_diffs <- gsub("^(d.*) =", "\\1/dt =", diffs)
+ writeLines(strwrap(nice_diffs, exdent = 11))
+ cat("\nData:\n")
+ cat(nrow(x$data), "observations of",
+ length(unique(x$data$name)), "variable(s) grouped in",
+ length(unique(x$data$ds)), "datasets\n")
+ cat("\nLog-", if(x$method == "REML") "restricted-" else "",
+ "likelihood: ", format(x$logLik), "\n", sep = "")
+ fixF <- x$call$fixed
+ cat("\nFixed effects:\n",
+ deparse(
+ if(inherits(fixF, "formula") || is.call(fixF) || is.name(fixF))
+ x$call$fixed
+ else
+ lapply(fixF, function(el) as.name(deparse(el)))), "\n")
+ print(fixef(x), ...)
+ cat("\n")
+ print(summary(x$modelStruct), sigma = x$sigma, ...)
+ invisible(x)
}
#' @export
diff --git a/R/plot.nlme.mmkin.R b/R/plot.nlme.mmkin.R
index afb682a7..05a17a22 100644
--- a/R/plot.nlme.mmkin.R
+++ b/R/plot.nlme.mmkin.R
@@ -11,6 +11,8 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds")
#' @param rel.height.legend The relative height of the legend shown on top
#' @param rel.height.bottom The relative height of the bottom plot row
#' @param ymax Vector of maximum y axis values
+#' @param ncol.legend Number of columns to use in the legend
+#' @param nrow.legend Number of rows to use in the legend
#' @param \dots Further arguments passed to \code{\link{plot.mkinfit}} and
#' \code{\link{mkinresplot}}.
#' @param resplot Should the residuals plotted against time or against
@@ -28,7 +30,8 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds")
#' names(ds) <- paste0("ds ", 6:10)
#' dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
#' A1 = mkinsub("SFO"), quiet = TRUE)
-#' f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, cores = 1)
+#' \dontrun{
+#' f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE)
#' plot(f[, 3:4], standardized = TRUE)
#'
#' library(nlme)
@@ -36,6 +39,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds")
#' # tolerance in order to speed up the fit for this example evaluation
#' f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3))
#' plot(f_nlme)
+#' }
#' @export
plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig),
obs_vars = names(x$mkinmod$map),
diff --git a/R/sigma_twocomp.R b/R/sigma_twocomp.R
index e8a92ced..e7f4368b 100644
--- a/R/sigma_twocomp.R
+++ b/R/sigma_twocomp.R
@@ -1,16 +1,16 @@
#' Two-component error model
-#'
+#'
#' Function describing the standard deviation of the measurement error in
#' dependence of the measured value \eqn{y}:
-#'
+#'
#' \deqn{\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}} sigma =
#' sqrt(sigma_low^2 + y^2 * rsd_high^2)
-#'
+#'
#' This is the error model used for example by Werner et al. (1978). The model
#' proposed by Rocke and Lorenzato (1995) can be written in this form as well,
#' but assumes approximate lognormal distribution of errors for high values of
#' y.
-#'
+#'
#' @param y The magnitude of the observed value
#' @param sigma_low The asymptotic minimum of the standard deviation for low
#' observed values
@@ -20,7 +20,7 @@
#' @references Werner, Mario, Brooks, Samuel H., and Knott, Lancaster B. (1978)
#' Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry
#' 24(11), 1895-1898.
-#'
+#'
#' Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for
#' measurement error in analytical chemistry. Technometrics 37(2), 176-184.
#' @examples
@@ -36,15 +36,8 @@
#' data = d_syn, na.action = na.omit,
#' start = list(parent_0 = 100, lrc = -3))
#' if (length(findFunction("varConstProp")) > 0) {
-#' f_gnls_tc <- gnls(value ~ SSasymp(time, 0, parent_0, lrc),
-#' data = d_syn, na.action = na.omit,
-#' start = list(parent_0 = 100, lrc = -3),
-#' weights = varConstProp())
-#' f_gnls_tc_sf <- gnls(value ~ SSasymp(time, 0, parent_0, lrc),
-#' data = d_syn, na.action = na.omit,
-#' start = list(parent_0 = 100, lrc = -3),
-#' control = list(sigma = 1),
-#' weights = varConstProp())
+#' f_gnls_tc <- update(f_gnls, weights = varConstProp())
+#' f_gnls_tc_sf <- update(f_gnls_tc, control = list(sigma = 1))
#' }
#' f_mkin <- mkinfit("SFO", d_syn, error_model = "const", quiet = TRUE)
#' f_mkin_tc <- mkinfit("SFO", d_syn, error_model = "tc", quiet = TRUE)
diff --git a/R/summary.nlme.mmkin.R b/R/summary.nlme.mmkin.R
new file mode 100644
index 00000000..9fdd3f73
--- /dev/null
+++ b/R/summary.nlme.mmkin.R
@@ -0,0 +1,233 @@
+#' Summary method for class "nlme.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 [nlme.mmkin]
+#' @param x an object of class [summary.nlme.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 alpha error level for confidence interval estimation from the t
+#' distribution
+#' @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 [nlme] object
+#' obtained in the fit, with at least the following additional components
+#' \item{nlmeversion, mkinversion, Rversion}{The nlme, 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{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
+#' @author Johannes Ranke for the mkin specific parts
+#' José Pinheiro and Douglas Bates for the components inherited from nlme
+#' @examples
+#'
+#' # Generate five datasets following SFO kinetics
+#' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+#' dt50_sfo_in_pop <- 50
+#' k_in_pop <- log(2) / dt50_sfo_in_pop
+#' set.seed(1234)
+#' k_in <- rlnorm(5, log(k_in_pop), 0.5)
+#' SFO <- mkinmod(parent = mkinsub("SFO"))
+#'
+#' pred_sfo <- function(k) {
+#' mkinpredict(SFO,
+#' c(k_parent = k),
+#' c(parent = 100),
+#' sampling_times)
+#' }
+#'
+#' ds_sfo_mean <- lapply(k_in, pred_sfo)
+#' names(ds_sfo_mean) <- paste("ds", 1:5)
+#'
+#' ds_sfo_syn <- lapply(ds_sfo_mean, function(ds) {
+#' add_err(ds,
+#' sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2),
+#' n = 1)[[1]]
+#' })
+#'
+#' # Evaluate using mmkin and nlme
+#' library(nlme)
+#' f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1)
+#' f_nlme <- nlme(f_mmkin)
+#' summary(f_nlme, data = TRUE)
+#'
+#' @export
+summary.nlme.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes = TRUE, alpha = 0.05, ...) {
+
+ mod_vars <- names(object$mkinmod$diffs)
+
+ confint_trans <- intervals(object, which = "fixed", level = 1 - alpha)$fixed
+ attr(confint_trans, "label") <- NULL
+ pnames <- rownames(confint_trans)
+ confint_trans[, "est."]
+ bp <- backtransform_odeparms(confint_trans[, "est."], object$mkinmod,
+ object$transform_rates, object$transform_fractions)
+ bpnames <- names(bp)
+
+ # variance-covariance estimates for fixed effects (from summary.lme)
+ fixed <- fixef(object)
+ stdFixed <- sqrt(diag(as.matrix(object$varFix)))
+ object$corFixed <- array(
+ t(object$varFix/stdFixed)/stdFixed,
+ dim(object$varFix),
+ list(names(fixed), names(fixed)))
+
+ # Transform boundaries of CI for one parameter at a time,
+ # with the exception of sets of formation fractions (single fractions are OK).
+ f_names_skip <- character(0)
+ for (box in mod_vars) { # Figure out sets of fractions to skip
+ f_names <- grep(paste("^f", box, sep = "_"), pnames, value = TRUE)
+ n_paths <- length(f_names)
+ if (n_paths > 1) f_names_skip <- c(f_names_skip, f_names)
+ }
+
+ confint_back <- matrix(NA, nrow = length(bp), ncol = 3,
+ dimnames = list(bpnames, colnames(confint_trans)))
+ confint_back[, "est."] <- bp
+
+ for (pname in pnames) {
+ if (!pname %in% f_names_skip) {
+ par.lower <- confint_trans[pname, "lower"]
+ par.upper <- confint_trans[pname, "upper"]
+ names(par.lower) <- names(par.upper) <- pname
+ bpl <- backtransform_odeparms(par.lower, object$mkinmod,
+ object$transform_rates,
+ object$transform_fractions)
+ bpu <- backtransform_odeparms(par.upper, object$mkinmod,
+ object$transform_rates,
+ object$transform_fractions)
+ confint_back[names(bpl), "lower"] <- bpl
+ confint_back[names(bpu), "upper"] <- bpu
+ }
+ }
+
+ object$confint_trans <- confint_trans
+ 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
+ if (data) {
+ object$data[["observed"]] <- object$data[["value"]]
+ object$data[["value"]] <- NULL
+ object$data[["predicted"]] <- predict(object)
+ object$data[["residual"]] <- residuals(object, type = "response")
+ object$data[["std"]] <- object$sigma <- 1/attr(object$modelStruct$varStruct, "weights")
+ object$data[["standardized"]] <- residuals(object, type = "pearson")
+ }
+ object$verbose <- verbose
+
+ object$fixed <- object$mmkin_orig[[1]]$fixed
+ object$AIC = AIC(object)
+ object$BIC = BIC(object)
+ object$logLik = logLik(object)
+
+ ep <- endpoints(object)
+ if (length(ep$ff) != 0)
+ object$ff <- ep$ff
+ if (distimes) object$distimes <- ep$distimes
+ if (length(ep$SFORB) != 0) object$SFORB <- ep$SFORB
+ class(object) <- c("summary.nlme.mmkin", "nlme.mmkin", "nlme", "lme")
+ return(object)
+}
+
+#' @rdname summary.nlme.mmkin
+#' @export
+print.summary.nlme.mmkin <- function(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...) {
+ cat("nlme version used for fitting: ", x$nlmeversion, "\n")
+ cat("mkin version used for pre-fitting: ", x$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", x$numIter, "iterations\n")
+
+ cat("\nVariance model: ")
+ cat(switch(x$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$mean_dp_start)
+
+ cat("\nFixed degradation parameter values:\n")
+ if(length(x$fixed$value) == 0) cat("None\n")
+ else print(x$fixed)
+
+ cat("\nResults:\n\n")
+ print(data.frame(AIC = x$AIC, BIC = x$BIC, logLik = x$logLik,
+ row.names = " "))
+
+ cat("\nOptimised, transformed parameters with symmetric confidence intervals:\n")
+ print(x$confint_trans)
+
+ if (nrow(x$confint_trans) > 1) {
+ corr <- x$corFixed
+ class(corr) <- "correlation"
+ print(corr, title = "\nCorrelation:", ...)
+ }
+
+ cat("\nBacktransformed parameters with asymmetric confidence intervals:\n")
+ print(x$confint_back)
+
+ print(summary(x$modelStruct), sigma = x$sigma,
+ reEstimates = x$coef$random, verbose = verbose, ...)
+
+ printSFORB <- !is.null(x$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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