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2015-06-22Another reorganisation of vignette building by GNUmakefileJohannes Ranke1-18/+0
2015-06-22Vignettes rebuilt by staticdocs::build_site() for r-forgeJohannes Ranke4-52/+48
2015-06-22Version bump, correct benchmark in vignette/compiled_modelsJohannes Ranke9-788/+403
Reorganisation of the vignette generation in the Makefile. Improved YAML header in the R markdown vignettes. Rebuilt vignettes with the package installed.
2015-06-21Rebuild vignettes with the released package installedJohannes Ranke6-59/+63
2015-06-21Vignettes as rebuilt for the static documentation for r-forgeJohannes Ranke4-33/+33
2015-06-21Do the t-test for untransformed parametersv0.9-36Johannes Ranke6-219/+232
2015-06-20Low-level generation of compiled modelsJohannes Ranke2-8/+6
As it is unclear if and when ccSolve will be published on CRAN, the generation, compilation and use of the C version of the system of differential equations was developed for mkin, inspired and guided by the code from the ccSolve package. Many thanks again to Karline Soetaert for all of her work on this and other R packages. Now all model types, including the Hockey-Stick model for the parent compund and the IORE model for parent and/or metabolites can be compiled.
2015-06-05FOCUS D vignette generated from MakefileJohannes Ranke1-83/+248
2015-06-05Add a simple vignette with an evaluation of FOCUS DJohannes Ranke2-0/+352
2015-05-15Merge branch 'master' into compile_odesJohannes Ranke2-0/+0
Conflicts (resolved manually, deleting code that I had integrated into the RUnit tests for testing the compiled version): .gitignore DESCRIPTION inst/unitTests/runit.mkinerrmin.R inst/unitTests/runit.mkinfit.R tests/testthat/test_mkinpredict_SFO_SFO.R vignettes/FOCUS_L.html
2015-05-15Update of vignettes during staticdoc documentationJohannes Ranke3-61/+61
2015-04-18Add a vignette showing the performance of compiled modelsJohannes Ranke3-0/+256
2015-04-16Pending commit of an updated vignetteJohannes Ranke1-77/+76
2014-12-18Updated vignettes during staticdoc generationJohannes Ranke3-30/+30
2014-11-21Update date and static docs for release to CRANv0.9-34Johannes Ranke3-277/+271
2014-11-12Update the FOCUS_Z vignette for default "Port" algorithmJohannes Ranke2-11/+4
2014-11-12Merge branch 'master' into ioreJohannes Ranke5-338/+382
2014-10-15Switch to using the Port algorithm per defaultJohannes Ranke2-62/+73
2014-10-14Further formatting improvement for differential equationsJohannes Ranke2-45/+51
2014-10-11Updated vignettes by building static documentationJohannes Ranke3-97/+111
2014-08-25Bug fix and unit tests for mkinerrminJohannes Ranke2-51/+61
See NEWS.md for details
2014-08-19Improve formatting of differential equations in outputJohannes Ranke2-0/+1
Rebuild of FOCUS_Z vignette with improved formatting
2014-07-24Update vignettes with 0.9-32 just released to CRANJohannes Ranke3-39/+33
2014-07-21Bugfix, model shorthand, state.ini[[1]] from observed dataJohannes Ranke3-209/+200
- The bug occurred when using transform_rates=FALSE for FOMC, DFOP or HS - Make it possible to use mkinfit("SFO", ...) - Take initial mean value at time zero for the variable with the highest value in the observed data - Update of vignette/FOCUS_L - Improve the Makefile to build single vignettes
2014-07-17Handle non-convergence and maximum number of iterationsJohannes Ranke3-51/+67
For details see NEWS.md
2014-07-14Vignettes as just synced to the static documentation on r-forgeJohannes Ranke3-27/+21
2014-07-14Merge bugfix branch 'master' into ioreJohannes Ranke3-0/+1083
Add IORE support to mkinerrmin
2014-07-14Bugfix release version 0.9-31Johannes Ranke3-0/+1090
2014-07-11Improve formatting in FOCUS_L vignette, rebuild vignettesJohannes Ranke28-0/+5
2014-07-02Update of vignettesJohannes Ranke16-0/+0
2014-07-02Update vignettes - working flawlessly now!Johannes Ranke16-0/+0
2014-07-02TypoJohannes Ranke1-1/+1
2014-07-02Support formation fractions without sink pathway, updatesJohannes Ranke1-21/+9
2014-06-27Reorder endpoints in R/endpoints.R, update vignettesJohannes Ranke17-1/+1
2014-06-27Comment using the additional DT50 values at least onceJohannes Ranke1-2/+8
2014-06-27Vignette rebuilds commited to be in sync with static docsJohannes Ranke16-0/+0
2014-06-26Updated vignettes by building static documentationJohannes Ranke16-0/+0
2014-06-26Calculate additional DT50 values for non-SFO modelsJohannes Ranke16-0/+0
2014-05-20Update of the static documentationJohannes Ranke16-0/+0
2014-05-20Step back regarding confidence intervals of formation fractionsJohannes Ranke4-19/+112
- Don't give confidence intervals for formation fractions that belong to a set, only for single formation fractions - Update the vignette with history and background - Correct 'isotropic' into 'isometric' in the ilr documentation, the README and the comments in transform_odeparms - Candidate for release to CRAN
2014-05-08Support building static documentation, build itJohannes Ranke28-931/+0
2014-05-08README update, fix the vignette title for FOCUS ZJohannes Ranke16-1/+1
2014-05-05Another attempt to fix vignette building on windowsJohannes Ranke16-1/+1
2014-05-05Update of vignettesJohannes Ranke18-5/+23
2014-05-02Update of the FOCUS Z vignette, release candidateJohannes Ranke15-13/+44
2013-11-17Conflicts:jranke32-706/+1512
README.md TODO git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@163 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-11Remove vignette PDFs to have them rebuilt on every buildjranke2-0/+0
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@152 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-06Update of the vignettesjranke5-6/+8
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@140 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-04-14- Update the TODO list, setting some requirements for version 1.0jranke4-5/+5
- Check that initial values specified using parms.ini are actually needed for the model, stop otherwise - List all formation fractions in the same place in the summary, also if they were fitted in the model - Include an FOMC model coupled to two metabolites in the unit tests - Some updates needed because of the above - Update of static documentation including the vignettes - Update of the mkin vignettes in the vignettes directory git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@82 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-03-05Update of vignettes and static HTML documentationjranke2-0/+0
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@75 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

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