From 38f9e15f0c972c1516ae737a2bca8d7789581bbd Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 6 Oct 2016 09:19:21 +0200 Subject: Static documentation rebuilt by pkgdown::build_site() --- docs/reference/add_err.html | 196 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 196 insertions(+) create mode 100644 docs/reference/add_err.html (limited to 'docs/reference/add_err.html') diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html new file mode 100644 index 00000000..cbc925ca --- /dev/null +++ b/docs/reference/add_err.html @@ -0,0 +1,196 @@ + + + + + + + + +add_err. mkin + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+

+

+
+ +
+
+ +

Normally distributed errors are added to data predicted for a specific + degradation model using mkinpredict. The variance of the error + may depend on the predicted value and is specified as a standard deviation.

+ + + 
add_err(prediction, sdfunc,
+          n = 1000, LOD = 0.1, reps = 2,
+          digits = 1, seed = NA)
+ +

Arguments

+
+
prediction
+
+ A prediction from a kinetic model as produced by mkinpredict. +
+
sdfunc
+
+ A function taking the predicted value as its only argument and returning + a standard deviation that should be used for generating the random error + terms for this value. +
+
n
+
+ The number of datasets to be generated. +
+
LOD
+
+ The limit of detection (LOD). Values that are below the LOD after adding + the random error will be set to NA. +
+
reps
+
+ The number of replicates to be generated within the datasets. +
+
digits
+
+ The number of digits to which the values will be rounded. +
+
seed
+
+ The seed used for the generation of random numbers. If NA, the seed + is not set. +
+
+ +
+

Value

+ +

A list of datasets compatible with mmkin, i.e. + the components of the list are datasets compatible with + mkinfit.

+
+ +
+

References

+ +

Ranke J and Lehmann R (2015) To t-test or not to t-test, that is the question. XV Symposium on Pesticide Chemistry 2-4 September 2015, Piacenza, Italy + http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf

+
+ +

Examples

+ 
# The kinetic model
+m_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
+                     M1 = mkinsub("SFO"), use_of_ff = "max")
Successfully compiled differential equation model from auto-generated C code.

+# Generate a prediction for a specific set of parameters
+sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+
+# This is the prediction used for the "Type 2 datasets" on the Piacenza poster
+# from 2015
+d_SFO_SFO <- mkinpredict(m_SFO_SFO,
+                         c(k_parent = 0.1, f_parent_to_M1 = 0.5,
+                           k_M1 = log(2)/1000),
+                         c(parent = 100, M1 = 0),
+                         sampling_times)
+
+# Add an error term with a constant (independent of the value) standard deviation
+# of 10, and generate three datasets
+d_SFO_SFO_err <- add_err(d_SFO_SFO, function(x) 10, n = 3, seed = 123456789 )
+
+# Name the datasets for nicer plotting
+names(d_SFO_SFO_err) <- paste("Dataset", 1:3)
+
+# Name the model in the list of models (with only one member in this case)
+# for nicer plotting later on.
+# Be quiet and use the faster Levenberg-Marquardt algorithm, as the datasets
+# are easy and examples are run often. Use only one core not to offend CRAN
+# checks
+f_SFO_SFO <- mmkin(list("SFO-SFO" = m_SFO_SFO),
+                   d_SFO_SFO_err, cores = 1,
+                   quiet = TRUE, method.modFit = "Marq")
+
+plot(f_SFO_SFO)

+# We would like to inspect the fit for dataset 3 more closely
+# Using double brackets makes the returned object an mkinfit object
+# instead of a list of mkinfit objects, so plot.mkinfit is used
+plot(f_SFO_SFO[[3]], show_residuals = TRUE)

+# If we use single brackets, we should give two indices (model and dataset),
+# and plot.mmkin is used
+plot(f_SFO_SFO[1, 3])

+
+
+
+

Author

+ + Johannes Ranke + +
+
+ + +
+ + + -- cgit v1.2.1