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2015-04-17Make compiled FOMC and DFOP models workJohannes Ranke1-5/+4
- Many thanks @karlines for the hint in ccSolve#1 how to declare the time variable and for writing the ccSolve package in the first place - Add tests for the compiled versions of the FOMC and DFOP models
2015-04-16Order of parameters needs to be right for compiled modelsJohannes Ranke1-1/+1
2015-04-16Update copyright header, improve documentation of solution_typeJohannes Ranke3-14/+19
2015-04-16Check compiled mkinmod versions in examples and testsJohannes Ranke2-1/+5
Tests all pass (Linux)
2015-04-14Compile differential equation models with ccSolve packageJohannes Ranke2-9/+47
If the ccSolve package is available, and time is not in the right hand side of the equations (i.e. if only SFO and SFORB models are used), the differential equation model is compiled from auto-generated C code. Currently, one test (FOCUS 2006 D SFO_SFO) fails
2015-02-21Avoid NOTES in R CMD checkJohannes Ranke1-1/+1
- Export S3 methods - Avoid using undeclared variable names
2015-02-20Add termination message to mkinfit, prepare releaseJohannes Ranke1-1/+9
2015-02-20Fix printing the summary if iterations are not availableJohannes Ranke1-1/+4
This was broken for using method.modFit = "SANN"
2014-11-23Simply get rid of the warnings when drawing arrowsJohannes Ranke1-8/+7
2014-11-23Avoid spurious warning in mkinparplot, bump versionJohannes Ranke1-4/+10
2014-11-12Fix for IORE in mkinmodJohannes Ranke1-4/+4
2014-11-12IORE working for parent and metabolites, introduce mkinsubJohannes Ranke3-4/+33
2014-11-12Merge branch 'master' into ioreJohannes Ranke5-66/+167
2014-11-12Fix a typo in the list of possible argumentsJohannes Ranke1-1/+1
Thanks to Michael Brauer for the hint
2014-10-22Always include 0 on y axis when plotting during the fitJohannes Ranke1-1/+1
2014-10-15Switch to using the Port algorithm per defaultJohannes Ranke1-1/+1
2014-10-14Further formatting improvement for differential equationsJohannes Ranke1-1/+1
2014-10-06Avoid a warning produced by initial fits in gmkinJohannes Ranke1-7/+9
2014-08-29Avoid an unnecessary warningJohannes Ranke1-1/+1
2014-08-25Bug fix and unit tests for mkinerrminJohannes Ranke1-4/+5
See NEWS.md for details
2014-08-20Fix mkinfit for a special situationJohannes Ranke1-7/+7
See NEWS.md: When the parent was not the (only) variable with the highest value out of all variables in the observed data, it could happen that the initial value (state.ini) was not initialised.
2014-08-19Improve formatting of differential equations in outputJohannes Ranke1-1/+1
Rebuild of FOCUS_Z vignette with improved formatting
2014-07-25Fix internal naming of g for transform_fractions=FALSEJohannes Ranke1-2/+13
2014-07-24Bump version, better default for state.iniJohannes Ranke1-2/+8
2014-07-24Avoid artificial zero residual in mkinresplotJohannes Ranke1-1/+2
2014-07-23Parallel metabolite formation with formation fractions in mkinerrminJohannes Ranke1-3/+4
2014-07-21Bugfix, model shorthand, state.ini[[1]] from observed dataJohannes Ranke2-10/+39
- 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
2014-07-17Return complete list of initial states after fittingJohannes Ranke1-1/+4
This is useful for specifying state.ini in a subsequent call to mkinfit
2014-07-17Handle non-convergence and maximum number of iterationsJohannes Ranke1-35/+82
For details see NEWS.md
2014-07-14Merge bugfix branch 'master' into ioreJohannes Ranke2-104/+117
Add IORE support to mkinerrmin
2014-07-14Nearly complete support for IORE, pending mkinerrminJohannes Ranke5-18/+56
2014-07-14Bugfix release version 0.9-31Johannes Ranke2-28/+37
2014-07-12First working fits with IORE modelJohannes Ranke5-8/+48
2014-07-07Coefficient matrix for formation fractions, no sink and one pathwayJohannes Ranke1-22/+26
2014-07-02Do not introduce formation fractions for singular pathwaysJohannes Ranke2-27/+29
- As a consequence, we do not need implicit formation fractions in mkinfit
2014-07-02Warning -> message, and only if initial parameter was not 1Johannes Ranke1-2/+4
2014-07-02Set implicit formation fraction to 1 even if set otherwise in parms.iniJohannes Ranke1-6/+8
2014-07-02Move handling of implicitly fixed formation fractions to mkinfitJohannes Ranke2-19/+11
2014-07-02Support formation fractions without sink pathway, updatesJohannes Ranke4-102/+215
2014-07-01One more source code commentJohannes Ranke1-0/+2
2014-07-01One more check, update source code commentJohannes Ranke1-2/+3
2014-06-27Reorder endpoints in R/endpoints.R, update vignettesJohannes Ranke1-2/+2
2014-06-27Reorganize the summary in a more logical orderJohannes Ranke1-19/+19
2014-06-26Avoid calculation of formation fractions if fittedJohannes Ranke1-3/+5
2014-06-26Fix naming of SFORB DT50_bx values, fix docsJohannes Ranke1-2/+2
2014-06-26Calculate additional DT50 values for non-SFO modelsJohannes Ranke1-2/+20
2014-06-26Add function for geometric meanJohannes Ranke1-0/+4
2014-06-26Start new version, add xlim to mkinresplotJohannes Ranke1-2/+3
2014-06-25Remove old ID tag, improve commentJohannes Ranke2-4/+3
2014-05-20Step back regarding confidence intervals of formation fractionsJohannes Ranke2-5/+17
- 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

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