Summary method for class

+ + +

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.

+ +

# S3 method for saem.mmkin
+summary(object, data = FALSE, verbose = FALSE, distimes = TRUE, ...)
+
+# S3 method for summary.saem.mmkin
+print(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...)

+ +

Arguments

object: an object of class saem.mmkin
data: logical, indicating whether the full data should be included in +the summary.
verbose: Should the summary be verbose?
distimes: logical, indicating whether DT50 and DT90 values should be +included.
...: optional arguments passed to methods like print.
x: an object of class summary.saem.mmkin
digits: Number of digits to use for printing

Value

The summary function returns a list based on the saemix::SaemixObjectobtained in the fit, with at least the following additional components

saemixversion, mkinversion, Rversion: The saemix, mkin and R versions used
date.fit, date.summary: The dates where the fit and the summary were +produced
diffs: The differential equations used in the degradation model
use_of_ff: Was maximum or minimum use made of formation fractions
data: The data
confint_trans: Transformed parameters as used in the optimisation, with confidence intervals
confint_back: Backtransformed parameters, with confidence intervals if available
confint_errmod: Error model parameters with confidence intervals
ff: The estimated formation fractions derived from the fitted +model.
distimes: The DT50 and DT90 values for each observed variable.
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 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)
+#>  
+#> Error in rxModelVars_(obj): Not compatible with STRSXP: [type=NULL].
+summary(f_saem_dfop_sfo, data = TRUE)
+#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'summary': object 'f_saem_dfop_sfo' not found
+# }
+
+

+ +

Summary method for class "saem.mmkin"

Arguments

Value

Author

Examples