PKfit v1.2.4
A Data Analysis Tool for Pharmacokinetics
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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