PKfit v1.2.6
 A Data Analysis Tool for Pharmacokinetics

Update logs (v1.2.5)
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02/17/2014
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 1. added citation into output files;
 2. removed CITATION file;
 3. fixed finfu2() and thanks llan for reporting this error;
 4. changed the name of 'mymodel.R' to 'fitmodel.R';
 5. fixed sinfu2() and sinfu(); removed events from both to avoid
    double doses; one from defun() and the other from events().
 6. fixed output info;
 7. fixed 'Description' content in DESCRIPTION.
 
 
Update logs (v1.2.4)
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10/22/2014
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 1. starting to switch to optimx() since this release; seemed
    more stable than optim() with different weighting schemes;
 2. fixed iv.bolus.demo() for no-stopping plotting;
 3. fixed plotting.xxx() by adding par(ask = FALSE);
 4. fixed weighting schemes for nlsLM() with Cp = 0.;
 5. added CITATION file in the folder of inst;
  
Update logs (v1.2.3)
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08/21/2014
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 1. fixed DESCRIPTION content;
 2. fixed output files of monte-carlo sim for szero.nolag();
 3. added err_types() to simplified all simulation codes;
 4. added UserDefinedModels directory for users required to define
    their own models;
 5. fixed iv.bolus.demo();
 6. added mymodel.R in UserDefinedModels;
 7. added simModle.R in UserDefinedModels;
 

06/24/2014 (v1.2.2)
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 1. fixed return back to PK.fit() after each fitting job; not the
    top menu (run()); don't need to load data file again;
 2. added "fbolus3.mm()" model;
 3. fixed 'Press Enter to continue...' for each model file; this
    can save mouse click from graphic window back to R console;
 4. added optim(...,control=list(maxit=5000)) for each fitting 
    algorithm;
 5. for macroconstant-term model, using equal weighting scheme may
    cause error with messages something like "... Error in 
    nlsModel(formula, mf, start, wts) : singular gradient matrix 
    at initial parameter estimates.."; using '1/Cp' or '1/Cp^2' 
    is fine; don't know why yet; same as nls();
 6. added PK.sim() after each simulation run; no need to go back to
    the top menu;
 7. added logo for normal fitting outputs;
 8. fixed the menu flow, i.e., after finishing loading/editing 
    the data file, then go next to 'model selection' menu;
 9. fixed arguments of nlsLM(...);
10. fixed output formatting;
11. re-fined plotting curve (calculated conc.);
12. fixed iv.bolus.demo() & mmpk.demo() with nlsLM();
13. added output files for simulation runs simultaneously with
    screen outputs;
14. fixed plotting.lin() and plotting.non();
15. added automatic output file names generated to avoid overwriting
    the existed output files;
16. added the time points for simulation run can be saved as a .csv 
    in the working path now; this file will be checked automatically,
    if existed, it will be loaded back to PKfit next time without 
    entering the time point again;
17. added autoload of initial values from a previous run saved as *.csv;
18. added autoload of pk parameters setting from a previous run
    saved as *.csv;
19. started to add multiple-dose simulation now; first one is sbolus2_md();
    seemed looking ok.
20. fixed ffirst2() again for monte-carlo sim (output problem);
21. tried to set argument of "lower=c(...)" in nlsLM; with '1e-06' seems ok;
    but not for fbolus3.mm().
22. added all multiple-dose simulation except 3-compartment iv bolus;
23. changed dose input in lsoda(); using dose event to add dose; seems more
    reasonable with simulated conc..
24. szero.nolag() still cannot be coded with event() in lsoda()...
25. fixed output data set for simulation codes with ODEs; 
    ### dump this subj's data to subj i; all simulations with macroconstants
    are not changed since they still use *.out() routines.


Update logs (v1.2.1)
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04/20/2014
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 1. fixed all Machalis-Menton models; e.g., 
    dCp(t)/dt = - Vmax*Cp(t)/(Km + Cp(t)), C(0) = Dose/Vd
    for all fitting and simulation codes.
 2. fixed demo(mmpk);
 3. fixed read.csv(...,Header=TRUE,...) in data.manipulate() 
    to correctly import simulated dataset (savefile()); after
    read.csv() re-assign col.names = cname = 
    c("Subject", "time", "conc");
 4. added the list of input data & initial values for 
    pk parameters;
 5. fixed fzero.nolag();
 6. included 'Dose' input in parameter initial values;
 7. rearranged output formats;
 8. added display the output file directory at final step;
 9. added a 3-compartment, iv bolus pk model with 1st-ordered elim.
10. added "Variance-Covariance Matrix" in the output
11. switched nls() to nlsLM() from package minpack.lm from this
    release; the default method 'LM' (the Levenberg-Marquardt 
    algorithm) is used in PKfit; nlsLM(...,"weight=NULL",...) as 
    default; we used external setup for weighting scheme to make 
    the minimum code change;
12. fixed simulation for iv bolus with 2-compartment, 1st-ordered
    pk model;
13. fixed smacro.one(), smacro.two() and smacro.three(); removed
    'Dose' from the arguments of smacro.one.out(...), etc.; no 
    Dose is req.;
14. fixed szero.nolag() with Monte-Carlo sim.;
15. added the function of input data file could be saved as a .csv
    format too (with write.csv(...,col.names=TRUE,,,).

04/04/2013 (v1.2.0)
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1. Remove genetic algorithm from PKfit; it still keep
   Nelder-Mead Simplex (optim) and nls() for Guass_newton.
2. fixed some settings for methods used in model-fitting.
   most difficult in this part.
3. If you get error message something like 'minFactors...',
   please check your model, check your data and check your
   initial values.
4. A .txt output and a .pdf file generated for fitting
   results and plots, respectively.

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