Summary method for class

- -

@@ -155,139 +91,137 @@ 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 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
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-    
-    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
+# S3 method for summary.saem.mmkin
+print(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...)

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

The summary function returns a list based on the saemix::SaemixObject -obtained 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 +

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 +
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.
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)
-
#> Warning: argument is not a function
#>  
#> 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
# }
-
-

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

Arguments

Value

Author

Author

Examples

Examples