Format the NEWS file in markdown, add Makefile target

5 files changed, 74 insertions, 132 deletions

diff --git a/.Rbuildignore b/.Rbuildignore
index 5ea06f4f..ccde5577 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,4 +1,5 @@
 GNUmakefile
+NEWS.md
 gmkin_screenshot.png
 ^inst/web$
 out$
diff --git a/.gitignore b/.gitignore
index e8678b11..9dc50c23 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
+NEWS
 inst/web*
 vignettes/*.aux
 vignettes/*.bbl
diff --git a/GNUmakefile b/GNUmakefile
index 39143ec3..969b4ff0 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -13,9 +13,6 @@ RBIN ?= $(shell dirname "`which R`")
 # Specify the directory where the static documentation belongs
 SDDIR ?= $(HOME)/svn/kinfit.r-forge/www/mkin_static
 
-#------------------------------------------------------------------------------
-# These must be manually kept up to date 
-#------------------------------------------------------------------------------
 pkgfiles = NEWS \
 	   data/* \
 	   DESCRIPTION \
@@ -28,41 +25,12 @@ pkgfiles = NEWS \
 	   tests/* \
 	   TODO \
 	   vignettes/*
-#------------------------------------------------------------------------------
 
-.PHONY: help vignettes
-
-help:
-	@echo "\nExecute development tasks for $(PKGNAME)\n"
-	@echo "Usage: \`make <task>\` where <task> is one of:"
-	@echo ""
-	@echo "Development Tasks"
-	@echo "-----------------"
-	@echo "  build                   Create the package"
-	@echo "  build-no-vignettes      Create the package without rebuilding vignettes"
-	@echo "  check                   Invoke build and then check the package"
-	@echo "  check-no-vignettes      Invoke build without rebuilding vignettes, and then check"
-	@echo "  install                 Invoke build and then install the result"
-	@echo "  install-no-vignettes    Invoke build without rebuilding vignettes and then install the result"
-	@echo "  test                    Install a new copy of the package without vignette rebuilding"
-	@echo "                          and run it through the testsuite"
-	@echo "  vignettes               Build the vignettes"
-	@echo "  sd                      Build the static documentation"
-	@echo "  move-sd                 Move the static documentation where it belongs"
-	@echo ""
-	@echo "Packaging Tasks"
-	@echo "---------------"
-	@echo "  winbuilder              Check building on Windows using the winbuilder service"
-	@echo "  r-forge                 Give reminders how to sync the r-forge repo"
-	@echo "  submit                  Submit to CRAN"
-	@echo ""
-	@echo "Using R in: $(RBIN)"
-	@echo "Set the RBIN environment variable to change this."
-	@echo ""
+all: NEWS check
 
-#------------------------------------------------------------------------------
-# Development Tasks
-#------------------------------------------------------------------------------
+# convert markdown to R's NEWS format (from knitr package)
+NEWS: NEWS.md
+	sed -e 's/^-/ -/' -e 's/^## *//' -e 's/^#/\t\t/' <NEWS.md | fmt -80 >NEWS
 
 $(TGZ): $(pkgfiles)
 	cd ..;\
@@ -95,6 +63,7 @@ test: install-no-vignettes
 	cd tests;\
 		"$(RBIN)/Rscript" doRUnit.R
 
+.PHONY: vignettes
 vignettes:
 	"$(RBIN)/Rscript" -e "tools::buildVignettes(dir = '.')"
 		
diff --git a/NEWS b/NEWS
deleted file mode 100644
index cb3143a5..00000000
--- a/NEWS
+++ /dev/null
@@ -1,96 +0,0 @@
-CHANGES in mkin 0.9-30 

-

-  * The ChangeLog was renamed to NEWS and the style of its entries is 

-    now adapted to that of a NEWS file. For a detailed list of changes to the

-    mkin source please consult the commit history on

-    http://github.com/jranke/mkin

-

-  * The order of some of the information blocks in print.summary.mkinfit.R()

-    has been ordered in a more logical way

-

-  * The vignette FOCUS_Z has been slightly amended to use the new versions

-    of DT50 values calculated since mkin 0.9-29.

-

-  * All vignettes have been rebuilt so they reflect all changes

-

-2014-06-26  Johannes Ranke <jranke@uni-bremen.de> for mkin (0.9-29)

-

-	* R/mkinresplot.R: Make it possible to specify xlim

-	* R/geometric_mean.R, man/geometric_mean.Rd: Add geometric mean

-	  function

-	* 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

-

-2014-05-20  Johannes Ranke <jranke@uni-bremen.de> for mkin (0.9-28)

-

-	* 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

-	* Add historical remarks and some background to the main package vignette

-	* Correct 'isotropic' into 'isometric' for the ilr transformation

-

-2014-05-09  Johannes Ranke <jranke@uni-bremen.de> for mkin (0.9-27)

-

-	* Fork the GUI into a separate package gmkin

-	* DESCRIPTION, NAMESPACE, TODO: Adapt and add copyright information

-	* Remove files belonging to the GUI

-	* Possibility to fit without parameter transformations, using bounds

-	  as implemented in FME

-	* Add McCall 2,4,5-T dataset

-	* Enable selection of observed variables in plotting

-	* Add possibility to show residual plot in plot.mkinfit

-	* R/mkinparplot.R, man/mkinparplot.Rd: plot parameters with confidence

-	  intervals

-

-2014-02-27  Johannes Ranke <jranke@uni-bremen.de> for mkin (0.9-25)

-

-	* Change vignette format from Sweave to knitr

-	* Split examples vignette to FOCUS_L and FOCUS_Z

-	* Remove warning about constant formation fractions in mkinmod

-	  as it was based on a misconception

-	* Restrict the unit test with the Schaefer data to parent and primary

-	  metabolites as formation fraction and DT50 for A2 are higly

-	  correlated and passing the test is platform dependent. For example,

-	  the test fails in 1 out of 14 platforms on CRAN as of today.

-	* Add Eurofins Regulatory AG copyright notices

-	* Import FME and deSolve instead of depending on them to have clean startup

-	* Add a starter function for the GUI: gmkin()

-	* Change the format of the workspace files of gmkin so they can be

-	  distributed and documented in the package

-	* Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin

-

-2013-11-06  Johannes Ranke <jranke@uni-bremen.de> for mkin (0.9-24)

-

-	* Bugfix re-enabling the fixing of any combination of initial values

-	  for state variables

-	* Default values for kinetic rate constants are not all 0.1 any more

-	  but are "salted" with a small increment to avoid numeric artefacts

-	  with the eigenvalue based solutions

-

-2013-10-30  Johannes Ranke <jranke@uni-bremen.de> for mkin (0.9-23)

-

-	* Backtransform fixed ODE parameters for the summary

-

-2013-10-21  Johannes Ranke <jranke@uni-bremen.de> for mkin (0.9-22)

-

-	* 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

-	* Fix plot.mkinfit as it passed graphical arguments like main to the solver

-	* Do not use plot=TRUE in mkinfit example

-	* The first successful fits in the not so simple GUI

-	* Fix iteratively reweighted least squares for the case of many metabolites

-	* Unify naming of initial values of state variables

-	* Unify naming in dataframes of optimised and fixed parameters in the summary

-	* Show the weighting method for residuals in the summary

-	* Correct the output of the data in the case of manual weighting

-	* Implement IRLS assuming different variances for observed variables

-	* Do not use 0 values at time zero for chi2 error level calculations.

-	  This is the way it is done in KinGUII and it makes sense. It does

-	  impact the chi2 error levels in the output. Generally they seem to be

-	  lower for metabolites now, presumably because the mean of the observed

-	  values is higher

-

-Changes performed in earlier versions are documented in the subversion log

-files on R-Forge http://www.r-forge.r-project.org/scm/?group_id=615

diff --git a/NEWS.md b/NEWS.md
new file mode 100644
index 00000000..d1b631e9
--- /dev/null
+++ b/NEWS.md
@@ -0,0 +1,67 @@
+# CHANGES in mkin VERSION 0.9-30 
+
+- The ChangeLog was renamed to NEWS.md and the entries were converted to markdown syntax compatible with the `tools::news()` function built into R. For a detailed list of changes to the mkin source please consult the commit history on http://github.com/jranke/mkin
+
+- The order of some of the information blocks in `print.summary.mkinfit.R()` has been ordered in a more logical way
+
+- The vignette FOCUS_Z has been slightly amended to use the new versions of DT50 values calculated since mkin 0.9-29.
+
+- All vignettes have been rebuilt so they reflect all changes
+
+# CHANGES in mkin VERSION 0.9-29
+
+- R/mkinresplot.R: Make it possible to specify `xlim`
+- R/geometric_mean.R, man/geometric_mean.Rd: Add geometric mean function
+- 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
+
+# CHANGES in mkin VERSION 0.9-28
+
+- 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
+- Add historical remarks and some background to the main package vignette
+- Correct 'isotropic' into 'isometric' for the ilr transformation
+
+# CHANGES in mkin VERSION 0.9-27
+
+- Fork the GUI into a separate package gmkin
+- DESCRIPTION, NAMESPACE, TODO: Adapt and add copyright information
+- Remove files belonging to the GUI
+- Possibility to fit without parameter transformations, using bounds as implemented in FME
+- Add McCall 2,4,5-T dataset
+- Enable selection of observed variables in plotting
+- Add possibility to show residual plot in `plot.mkinfit`
+- R/mkinparplot.R, man/mkinparplot.Rd: plot parameters with confidence intervals
+
+# CHANGES in mkin VERSION 0.9-25
+
+- Change vignette format from Sweave to knitr
+- Split examples vignette to FOCUS_L and FOCUS_Z
+- Remove warning about constant formation fractions in mkinmod as it was based on a misconception
+- Restrict the unit test with the Schaefer data to parent and primary metabolites as formation fraction and DT50 for A2 are higly correlated and passing the test is platform dependent. For example, the test fails in 1 out of 14 platforms on CRAN as of today.
+- Add Eurofins Regulatory AG copyright notices
+- Import FME and deSolve instead of depending on them to have clean startup
+- Add a starter function for the GUI: `gmkin()`
+- Change the format of the workspace files of gmkin so they can be distributed and documented in the package
+- Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin
+
+# CHANGES in mkin VERSION 0.9-24
+
+- Bugfix re-enabling the fixing of any combination of initial values for state variables
+- Default values for kinetic rate constants are not all 0.1 any more but are "salted" with a small increment to avoid numeric artefacts with the eigenvalue based solutions
+
+# CHANGES in mkin VERSION 0.9-23
+
+- Backtransform fixed ODE parameters for the summary
+
+# CHANGES in mkin VERSION 0.9-22
+
+- 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
+- Fix `plot.mkinfit` as it passed graphical arguments like main to the solver
+- Do not use `plot=TRUE` in `mkinfit()` example
+- The first successful fits in the not so simple GUI
+- Fix iteratively reweighted least squares for the case of many metabolites
+- Unify naming of initial values of state variables
+- Unify naming in dataframes of optimised and fixed parameters in the summary
+- Show the weighting method for residuals in the summary
+- Correct the output of the data in the case of manual weighting
+- Implement IRLS assuming different variances for observed variables
+- Do not use 0 values at time zero for chi2 error level calculations. This is the way it is done in KinGUII and it makes sense. It does impact the chi2 error levels in the output. Generally they seem to be lower for metabolites now, presumably because the mean of the observed values is higher