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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
2013-03-05- Calculate confidence intervals for parameters based on the t distributionjranke3-62/+79
Thanks to the CAKE developers at Tessella for the call to qt() - Calculate asymetric confidence intervals for backtransformed parameters - Overhaul and recompile vignettes git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@74 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-02-18- Completion of the multicompartment part of the mkin examples vignettejranke5-51/+60
- Fix to chi2 error level calculation by correctly returning backtransformed parameters as bparms.optim and bparms.fixed - Adaptations of unit tests, summary and plot functions git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@67 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-02-18- Some more work on the vignettejranke1-29/+46
- Don't plot a main title in mkinresplot git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@66 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-02-18More work on the examples vignettejranke2-1/+189
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@65 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-02-17- Removed vignette files that are built during generationjranke22-25660/+0
- Updated the staticdoc documentation git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@63 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-02-17- Added the examples vignette to the kinfit packagejranke1-3/+0
- Added calls to utils::globalVariables to make R CMD check pass cleanly without NOTES git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@62 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-02-16- Some maintenance fixesjranke22-0/+2047
- Start of the examples vignette git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@61 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-09-20Some updates of the mkin vignettejranke3-68/+88
Added the kinfit vignette file to the repository git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@57 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-06-28Delete the PDF versions of the vignette to have them rebuilt on r-forge/CRANjranke1-0/+0
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@46 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-06-26- Created an html index instead of a php indexjranke1-0/+0
- Rebuilt the mkin documentation git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@44 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-06-26Some stuff I did not check in yesterday for some reason.jranke1-0/+6
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@43 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-06-25- Document endpoints() functionjranke2-3/+3
- Fix unit tests that were broken by introduction of the endpoints function - Small documentation fixes - Format output of backtransformed parameters - Integrate snippet for making static documentation using staticdocs by Hadley Wickham git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@41 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-04-24- Added the reference fit data for FOCUS 2006 datasets from the kinfit packagejranke1-2/+2
- Used these data in unit tests for parent only models - Fixed SFORB data and calculation of formation fractions along the way - Reintroduced the test for the Schaefer 2007 data - Got rid of the mkinmod unit tests - they are too hard to maintain and the mkinfit tests test the model definitions as well git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@32 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

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