aboutsummaryrefslogtreecommitdiff
path: root/README.md
diff options
context:
space:
mode:
Diffstat (limited to 'README.md')
-rw-r--r--README.md95
1 files changed, 18 insertions, 77 deletions
diff --git a/README.md b/README.md
index 50fc4412..a8d6a11b 100644
--- a/README.md
+++ b/README.md
@@ -36,73 +36,13 @@ detailed guidance and helpful tools have been developed as detailed in
## Usage
-The simplest usage example that I can think of, using model shorthand notation
-(available since mkin 0.9-32) and a built-in dataset is
-
-
-```r
-library(mkin)
-fit <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE)
-plot(fit, show_residuals = TRUE)
-```
-
-![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-1.png)
-
-
-```r
-# Output not shown in this README to avoid distraction
-summary(fit)
-```
-
-A still very simple usage example including the definition of the same data in R
-code would be
-
-
-```r
-example_data = data.frame(
- name = rep("parent", 9),
- time = c(0, 1, 3, 7, 14, 28, 63, 91, 119),
- value = c(85.1, 57.9, 29.9, 14.6, 9.7, 6.6, 4, 3.9, 0.6)
-)
-fit2 <- mkinfit("FOMC", example_data, quiet = TRUE)
-plot(fit2, show_residuals = TRUE)
-```
-
-![plot of chunk unnamed-chunk-5](figure/unnamed-chunk-5-1.png)
-
-A fairly complex usage example using another built-in dataset:
-
-
-
-
-```r
-data <- mkin_wide_to_long(schaefer07_complex_case, time = "time")
-
-model <- mkinmod(
- parent = mkinsub("SFO", c("A1", "B1", "C1"), sink = FALSE),
- A1 = mkinsub("SFO", "A2"),
- B1 = mkinsub("SFO"),
- C1 = mkinsub("SFO"),
- A2 = mkinsub("SFO"), use_of_ff = "max")
-
-fit3 <- mkinfit(model, data, method.modFit = "Port", quiet = TRUE)
-
-plot(fit3, show_residuals = TRUE)
-```
-
-![plot of chunk unnamed-chunk-7](figure/unnamed-chunk-7-1.png)
-
-```r
-#summary(fit3) # Commented out to avoid distraction from README content
-mkinparplot(fit3)
-```
-
-![plot of chunk unnamed-chunk-7](figure/unnamed-chunk-7-2.png)
-
-For more examples and to see results, have a look at the examples provided in the
-[`mkinfit`](http://kinfit.r-forge.r-project.org/mkin_static/mkinfit.html)
-documentation or the package vignettes referenced from the
-[mkin package documentation page](http://kinfit.r-forge.r-project.org/mkin_static/index.html)
+For a start, have a look a the code examples provided for
+[`plot.mkinfit`](http://kinfit.r-forge.r-project.org/mkin_static/plot.mkinfit.html)
+and
+[`plot.mmkin`](http://kinfit.r-forge.r-project.org/mkin_static/plot.mmmkin.html), and
+at the package vignettes
+[`FOCUS L`](http://kinfit.r-forge.r-project.org/mkin_static/vignettes/FOCUS_L.html) and
+[`FOCUS D`](http://kinfit.r-forge.r-project.org/mkin_static/vignettes/FOCUS_D.html).
## Features
@@ -111,18 +51,18 @@ documentation or the package vignettes referenced from the
including equilibrium reactions and using the single first-order
reversible binding (SFORB) model, which will automatically create
two latent state variables for the observed variable.
+* As of version 0.9-39, fitting of several models to several datasets, optionally in
+ parallel, is supported, see for example
+ [`plot.mmkin`](http://kinfit.r-forge.r-project.org/mkin_static/plot.mmkin.html)
* Model solution (forward modelling) in the function
[`mkinpredict`](http://kinfit.r-forge.r-project.org/mkin_static/mkinpredict.html)
is performed either using the analytical solution for the case of
parent only degradation, an eigenvalue based solution if only simple
first-order (SFO) or SFORB kinetics are used in the model, or
using a numeric solver from the `deSolve` package (default is `lsoda`).
- These have decreasing efficiency, and are automatically chosen
- by default.
-* As of mkin 0.9-36, model solution for models with more than one observed
- variable is based on the inline package. This is even faster than eigenvalue
- based solution, at least in the example shown in the
- [vignette `compiled_models`](http://rawgit.com/jranke/mkin/master/vignettes/compiled_models.html).
+* If a C compiler is installed, the kinetic models are compiled from automatically
+ generated C code, see
+ [vignette `compiled_models`](http://kinfit.r-forge.r-project.org/mkin_static/vignettes/compiled_models.html).
The autogeneration of C code was
inspired by the [`ccSolve`](https://github.com/karlines/ccSolve) package. Thanks
to Karline Soetaert for her work on that.
@@ -151,14 +91,15 @@ documentation or the package vignettes referenced from the
approximately reproduce the fit with other tools.
* The chi-squared error level as defined in the FOCUS kinetics guidance
(see below) is calculated for each observed variable.
-* I recently added iteratively reweighted least squares in a similar way
- it is done in KinGUII and CAKE (see below). Simply add the argument
+* Iteratively reweighted least squares fitting is implemented in a similar way
+ as in KinGUII and CAKE (see below). Simply add the argument
`reweight = "obs"` to your call to `mkinfit` and a separate variance
componenent for each of the observed variables will be optimised
in a second stage after the primary optimisation algorithm has converged.
* When a metabolite decline phase is not described well by SFO kinetics,
- either IORE kinetics or SFORB kinetics can be used for the metabolite,
- adding one respectively two parameters to the system.
+ either IORE kinetics (often producing failures of the integration algorithm)
+ or SFORB kinetics (working nicely) can be used for the metabolite, adding one
+ respectively two parameters to the system.
## GUI

Contact - Imprint