Static documentation rebuilt by pkgdown::build_site()

1 files changed, 52 insertions, 54 deletions

diff --git a/NEWS.md b/NEWS.md
index fd079897..1b11db30 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,20 +1,18 @@
-# NEWS for package 'mkin'
+# mkin 0.9.45 
 
-## mkin 0.9.45 
-
-### Minor changes
+## Minor changes
 
 - `plot.mkinfit`: Plotting does not fail any more when the compiled model is not available, e.g. because it was removed from the temporary directory. In this case, the uncompiled model is now used for plotting
 
-## mkin 0.9.44 (2016-06-29)
+# mkin 0.9.44 (2016-06-29)
 
-### Bug fixes
+## Bug fixes
 
 - The test `test_FOMC_ill-defined` failed on several architectures, so the test is now skipped
 
-## mkin 0.9.43 (2016-06-28)
+# mkin 0.9.43 (2016-06-28)
 
-### Major changes
+## Major changes
 
 - The title was changed to `Kinetic evaluations of chemical degradation data`
 
@@ -28,7 +26,7 @@
 
 - The function `add_err` was added to the package, making it easy to generate simulated data using an error model based on the normal distribution
 
-### Minor changes
+## Minor changes
 
 - Remove an outdated reference to the inline package in the `compiled_models` vignette
 
@@ -42,7 +40,7 @@
 
 - `mkinfit`: Return the `err` values used on weighted fits as a column named `err`. Also include these inverse weights when the column `value` in the observed data is used, which is returned as `observed` in the data component of the mkinfit object.
 
-### Bug fixes
+## Bug fixes
 
 - `endpoints`: When the name of a substance degrading to a metabolite (e.g. a parent compound) used in the model formulation ended in the letter `f`, some rate parameters could be listed as formation fractions with mixed up names. These would also appear in the summary.
 
@@ -52,13 +50,13 @@
 
 - `plot.mkinfit`: Correct default values for `col_obs`, `pch_obs` and `lty_obs` for the case that `obs_vars` is specified.
 
-## mkin 0.9.42 (2016-03-25)
+# mkin 0.9.42 (2016-03-25)
 
-### Major changes
+## Major changes
 
 - Add the argument `from_max_mean` to `mkinfit`, for fitting only the decline from the maximum observed value for models with a single observed variable
 
-### Minor changes
+## Minor changes
 
 - Add plots to `compiled_models` vignette
 
@@ -66,9 +64,9 @@
 
 - `print.mkinmod()`: Improve formatting when printing mkinmod model definitions
 
-## mkin 0.9-41 (2015-11-09)
+# mkin 0.9-41 (2015-11-09)
 
-### Minor changes
+## Minor changes
 
 - Add an R6 class `mkinds` representing datasets with a printing method
 
@@ -78,47 +76,47 @@
 
 - Use an index.r file to group help topics in static documentation
 
-### Bug fixes
+## Bug fixes
 
 - `print.summary.mkinfit()`: Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36
 
-## mkin 0.9-40 (2015-07-21)
+# mkin 0.9-40 (2015-07-21)
 
-### Bug fixes
+## Bug fixes
 
 - `endpoints()`: For DFOP and SFORB models, where `optimize()` is used, make use of the fact that the DT50 must be between DT50_k1 and DT50_k2 (DFOP) or DT50_b1 and DT50_b2 (SFORB), as `optimize()` sometimes did not find the minimum. Likewise for finding DT90 values. Also fit on the log scale to make the function more efficient.
 
-### Internal changes
+## Internal changes
 
 - `DESCRIPTION`, `NAMESPACE`, `R/*.R`: Import (from) stats, graphics and methods packages, and qualify some function calls for non-base packages installed with R to avoid NOTES made by R CMD check --as-cran with upcoming R versions.
 
-## mkin 0.9-39 (2015-06-26)
+# mkin 0.9-39 (2015-06-26)
 
-### Major changes
+## Major changes
 
 - New function `mmkin()`: This function takes a character vector of model shorthand names, or alternatively a list of mkinmod models, as well as a list of dataset as main arguments. It returns a matrix of mkinfit objects, with a row for each model and a column for each dataset. A subsetting method with single brackets is available. Fitting the models in parallel using the `parallel` package is supported.
 
 - New function `plot.mmkin()`: Plots single-row or single-column `mmkin` objects including residual plots.
 
-### Bug fixes
+## Bug fixes
 
 - `mkinparplot()`: Fix the x axis scaling for rate constants and formation fractions that got confused by the introduction of the t-values of transformed parameters.
 
-## mkin 0.9-38 (2015-06-24)
+# mkin 0.9-38 (2015-06-24)
 
-### Minor changes
+## Minor changes
 
 - `vignettes/compiled_models.html`: Show the performance improvement factor actually obtained when building the vignette, as well as mkin version, some system info and the CPU model used for building the vignette.
 
 - `GNUMakefile`,`vignettes/*`: Clean up vignette generation and include table of contents in HTML vignettes.
 
-### Bug fixes
+## Bug fixes
 
 - `mkinmod()`: When generating the C code for the derivatives, only declare the time variable when it is needed and remove the '-W-no-unused-variable' compiler flag as the C compiler used in the CRAN checks on Solaris does not know it.
 
-## mkin 0.9-36 (2015-06-21)
+# mkin 0.9-36 (2015-06-21)
 
-### Major changes
+## Major changes
 
 - `summary.mkinfit()`: A one-sided t-test for significant difference of untransformed parameters from zero is now always shown, based on the assumption of normal distribution for estimators of all untransformed parameters. Use with caution, as this assumption is unrealistic e.g. for rate constants in these nonlinear kinetic models.
 
@@ -128,17 +126,17 @@
 
 - `mkinfit()`: Set the default `solution_type` to `deSolve` when a compiled version of the model is present, except when an analytical solution is possible.
 
-### Minor changes
+## Minor changes
 
 - Added a simple showcase vignette with an evaluation of FOCUS example dataset D
 
-## mkin 0.9-35 (2015-05-15)
+# mkin 0.9-35 (2015-05-15)
 
-### Major changes
+## Major changes
 
 - Switch from RUnit to testthat for testing
 
-### Bug fixes
+## Bug fixes
 
 - `mkinparplot()`: Avoid warnings that occurred when not all confidence intervals were available in the summary of the fit
 
@@ -148,7 +146,7 @@
 
 - `mkinparplot()`: Avoid warning in R CMD check about undeclared global variable `Lower`
 
-### New features
+## New features
 
 - `mkinfit()`: Report successful termination when quiet = FALSE. This is helpful for more difficult problems fitted with reweight.method = obs, as no progress is often indicated during the reweighting.
 
@@ -158,9 +156,9 @@
 
 - Add tests based on these datasets
 
-## mkin 0.9-34 (2014-11-22)
+# mkin 0.9-34 (2014-11-22)
 
-### New features
+## New features
 
 - Add the convenience function `mkinsub()` for creating the lists used in `mkinmod()`
 
@@ -168,21 +166,21 @@
 
 - Switch to using the Port algorithm (using a model/trust region approach) per default. While needing more iterations than the Levenberg-Marquardt algorithm previously used per default, it is less sensitive to starting parameters.
 
-### Minor changes
+## Minor changes
 
 - The formatting of differential equations in the summary was further improved
 
 - Always include 0 on y axis when plotting during the fit
 
-## mkin 0.9-33 (2014-10-22)
+# mkin 0.9-33 (2014-10-22)
 
-### New features
+## New features
 
 - The initial value (state.ini) for the observed variable with the highest observed residue is set to 100 in case it has no time zero observation and `state.ini = "auto"`
 
 - A basic unit test for `mkinerrmin()` was written
 
-### Bug fixes
+## Bug fixes
 
 - `mkinfit()`: The internally fitted parameter for `g` was named `g_ilr` even when `transform_fractions=FALSE`
 
@@ -192,7 +190,7 @@
 
 - `plot.mkinfit()`: Avoid a warning message about only using the first component of ylim that occurred when ylim was specified explicitly
 
-### Minor changes
+## Minor changes
 
 - The formatting of differential equations in the summary was improved by wrapping overly long lines
 
@@ -202,9 +200,9 @@
 
 - `mkinfit()`: Avoid a warning that occurred when summarising a fit that was performed with maxitmodFit = 0 as done in gmkin for configuring new fits.
 
-## mkin 0.9-32 (2014-07-24)
+# mkin 0.9-32 (2014-07-24)
 
-### New features
+## New features
 
 - The number of degrees of freedom is difficult to define in the case of ilr transformation of formation fractions. Now for each source compartment the number of ilr parameters (=number of optimised parameters) is divided by the number of pathways to metabolites (=number of affected data series) which leads to fractional degrees of freedom in some cases.
 
@@ -218,7 +216,7 @@
 
 - mkinfit gives a warning when the fit does not converge (does not apply to SANN method). This warning is included in the summary.
 
-### Bug fixes
+## Bug fixes
 
 - Avoid plotting an artifical 0 residual at time zero in `mkinresplot`
 
@@ -230,7 +228,7 @@
 
 - No warning was given when the fit did not converge when a method other than the default Levenberg-Marquardt method `Marq` was used.
 
-### Minor changes
+## Minor changes
 
 - Vignettes were rebuilt to reflect the changes in the summary method.
 
@@ -238,25 +236,25 @@
 
 - Algorithm `Newton` was excluded because of its different way to specify the maximum number of iterations and because it does not appear to provide additional benefits.
 
-## mkin 0.9-31 (2014-07-14)
+# mkin 0.9-31 (2014-07-14)
 
-### Bug fixes
+## Bug fixes
 
 - The internal renaming of optimised parameters in Version 0.9-30 led to errors in the determination of the degrees of freedom for the chi2 error level calulations in `mkinerrmin()` used by the summary function.
 
-## mkin 0.9-30 (2014-07-11)
+# mkin 0.9-30 (2014-07-11)
 
-### New features
+## New features
 
 - It is now possible to use formation fractions in combination with turning off the sink in `mkinmod()`.
 
-### Major changes
+## Major changes
 
 - The original and the transformed parameters now have different names (e.g. `k_parent` and `log_k_parent`. They also differ in how many they are when we have formation fractions but no pathway to sink.
 
 - The order of some of the information blocks in `print.summary.mkinfit.R()` has been ordered in a more logical way.
 
-### Minor changes
+## Minor changes
 
 - The vignette FOCUS_Z has been simplified to use formation fractions with turning off the sink, and slightly amended to use the new versions of DT50 values calculated since mkin 0.9-29.
 
@@ -270,7 +268,7 @@
 
 - Some more checks were introduced to `mkinfit()`, leading to warnings or stopping execution if unsupported combinations of methods and parameters are requested.
 
-## mkin 0.9-29 (2014-06-27)
+# mkin 0.9-29 (2014-06-27)
 
 - R/mkinresplot.R: Make it possible to specify `xlim`
 
@@ -278,7 +276,7 @@
 
 - R/endpoints.R, man/endpoints.Rd: Calculate additional (pseudo)-DT50 values for FOMC, DFOP, HS and SFORB. Avoid calculation of formation fractions from rate constants when they are directly fitted
 
-## mkin 0.9-28 (2014-05-20)
+# mkin 0.9-28 (2014-05-20)
 
 - Do not backtransform confidence intervals for formation fractions if more than one compound is formed, as such parameters only define the pathways as a set
 
@@ -286,7 +284,7 @@
 
 - Correct 'isotropic' into 'isometric' for the ilr transformation
 
-## mkin 0.9-27 (2014-05-10)
+# mkin 0.9-27 (2014-05-10)
 
 - Fork the GUI into a separate package [gmkin](http://github.com/jranke/gmkin)
 
@@ -322,7 +320,7 @@
 
 - Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin
 
-## mkin 0.9-24 (2013-11-06)
+# mkin 0.9-24 (2013-11-06)
 
 - Bugfix re-enabling the fixing of any combination of initial values for state variables
 
@@ -330,7 +328,7 @@
 
 - Backtransform fixed ODE parameters for the summary
 
-## mkin 0.9-22 (2013-10-26)
+# mkin 0.9-22 (2013-10-26)
 
 - Get rid of the optimisation step in `mkinerrmin` - this was unnecessary. Thanks to KinGUII for the inspiration - actually this is equation 6-2 in FOCUS kinetics p. 91 that I had overlooked originally