Releases: andrewhooker/PopED
PopED 0.6.0
-
Added the options
allow_replicates=TRUE/FALSE
,allow_replicates_xt=TRUE/FALSE
andallow_replicates_a=TRUE/FALSE
topoped_optim
. This allows the optimization algorithm to avoid replicates (or not) in the design components. Currently only works for discrete variable optimization. Future versions will also handle continuous optimization. -
Exported a function for the computation of the Bayesian Fisher information matrix for individual parameters of a population model based on Maximum A Posteriori (MAP) estimation of the empirical Bayes estimates (EBEs) in a population model. See
?evaluate_fim_map
for more details. -
Allowing for no covariates in the function that automatically builds a PopED parameter function from a model function (
?build_sfg
). -
Updates to documentation and package testing.
-
Minor bug fixes.
PopED 0.5.0
-
Added the ability to incorporate limit of quantification information into FIM calculations (both upper and lower limits). See the new vignette on the webpage https://andrewhooker.github.io/PopED/articles/handling_loq.html
-
Adding functionality to optimize groupsize and total size of the study. See
?optimize_groupsize
, ``?optimize_n_effand
?optimize_n_rse`. This is also implemented in `poped_optim` through the `opt_inds=T` argument. -
Updating Vignettes, including a new one about using other tools to use as simulators for design computations. See https://andrewhooker.github.io/PopED/articles/model_def_other_pkgs.html
-
Simplify RxODE syntax in the above vingette (#47, @mattfidler).
-
Added the ability to predict and plot model prediction intervals by computing the expected variance (using an FO approximation) and then computing a prediction interval based on an assumption of normality. See
?model_prediciton
and?plot_model_prediction
. The computation is faster but less accurate compared to usingDV=TRUE
(andgroupsize_sim = 500
) in the two functions. -
Named parameters are now passed to all calculations so that the FIM and RSE output is more readable with parameter names instead of default names.
-
Allow for parallel computation in
plot_efficiency_of_windows
(#50). -
Make parallelization work with mrgsolve on windows (#37, #45, #46, #51, @Vincent-AC).
-
Updated the function for automatic building of parameter model function (see
build_sfg
). -
Simplify derivative calculations (#34, @martin-gmx).
-
Allow for only simulating model_switch > 1 models.
-
Change the defult Ds calculation to be on log scale.
-
Updated the website at https://andrewhooker.github.io/PopED
-
Remove options for discontinued dplyr commands
rbind_all
andrbind_list
. -
Minor bug fixes in shrinkage calculations (#44, #39, @martin-gmx).
PopED 0.4.0
-
New and improved vignettes (#30, @giulialestini)!
-
Added power evaluation script to test the power of a design to identify a prameter different
than an assumed value. The function also calculates the number of individuals needed in a design to have a specific
power. See?evaluate_power
for more information (#26, @martin-gmx). -
Added function to compute expected shrinkage of a design. See
?shrinkage
for more information. -
Updated and added new example scripts in
system.file("examples", package="PopED")
(). This includes an example describing
how to handle covariate distributions in optimal design, an example on how to incorporate IOV, an example on how to handle shrinkage, an example with a full covariance matrix and an example with a prior FIM (#30, @giulialestini and @martin-gmx). -
Major overhaul in optimization methods used in
poped_optim()
so that generic optimization routines likeoptim()
can be easily used in optimizing PopED designs. -
Update speed of FIM calculations (#20, @martin-gmx).
-
Update RSE calculations so that prior FIM is handled correctly (#22, @martin-gmx).
-
Simplified code and removed duplicated code (#21, #24 and #32, @martin-gmx).
-
New ways of handling inverting matricies, should be faster and work better when the matricies are ill-conditioned. See
?inv
for more information (#19, @martin-gmx). -
Updated functionality of IOV calculations.
-
Updates to
optim_ARS()
for when to stop search. -
Extended functionality of
plot.model.prediction()
(#23, @martin-gmx). -
Bug fixing. See https://github.com/andrewhooker/PopED/commits/master for more information.
PopED version 0.3.2
- Exported the
summary
method for the results ofpoped_optim
in the PopED NAMESPACE, so that the method can actually be used! Just usesummary(output)
. - Fixed some old bugs that used
return
as a varible in functions, a la MATLAB.
PopED version 0.3.1
- Added a vignette to introduce PopED!
- Improved optimization with
poped_optim
, plus all example scripts now running withpoped_optim
. - Update to more easily allow discrete optimization of xt and a variables. See the example scripts.
- Added a summary method for the results of
poped_optim
. Just usesummary(output)
. - changed handling of seed numbers in optimizations.
- more robust handling of non-population models
- more natural handling of NA values in design vectors
- NAMESPACE: removed ggplot2 from "Depends" and added to "Imports"
- Added mean line to efficiency plots.
- Update to computation and error handling for Laplace approximation to ED objective function.
- Added more intuitive cost function input. See examples in
?poped_optim
- Various small changes and bug fixes.
PopED version 0.3.0
- Added new optimization methods and tools, see
?poped_optim()
. This function incorporates the new optimization routinesoptim_ARS()
andoptim_LS
which are optimized versions of previous optimization algorithms used in PopED. Both can be run with parallelization.poped_optim()
also incorporates the genetic algorithm fromGA::ga()
, which can also be run with parallelization, and the "L-BFGS-B" method fromstats::optim()
.poped_optim()
should be more efficient and faster thanpoped_optimize()
. - Changed the default objective function to be the log of the determinant of the FIM.
create.poped.database(ofv_calc_type=4)
- Various small changes and bug fixes.
PopED for R version 0.2.0
- Fixed
plot_efficiency_of_windows()
bug that had wrong headers on each subplot. - Fixed bug in
plot_model_prediction()
that did not plot the optimized design, but instead the initial design - Reorganized the database created from
create.poped.database()
. The output from this function is now a list with 5 sub-lists: design, design_space, model, parameters and settings. Also removed duplicate entries in the database for easier manipulation. This will cause some back compatibility issues when refering to elements in a database. - Added example 10 describing a PKPD design of hepatitis C virus (HCV) kinetics to the
system.file("examples",package="PopED")
directory of the PopED installation.
PopED for R version 0.1.2
- Updated
model_prediction()
to allow for creation of NONMEM datasets. Useful for testing of optimized designs via PsN's (http://psn.sf.net) SSE tool, for example. - Two new functions
create_design()
andcreate_design_space()
that allow for design and design space creation without the need for a model or parameter values. - Updated the
create.poped.database()
function to usecreate_design()
andcreate_design_space()
- Added examples for evaluation and optimization of a one-target quasi-steady-state target mediated drug disposition model (TMDD) to the
system.file("examples", package="PopED")
directory of the PopED installation. - Added a 2-compartment, oral absorption, multiple dose example to the
system.file("examples",package="PopED")
directory of the PopED installation. - Updated
plot_efficiency_of_windows()
to allow for the plotting of the RSE of each parameter on the y-axis. - Updated error handing for the Laplace approximation of the ED OFV.
- Fixed bug when computing FIM with only one BSV term present in model (calculation gave
an error). - Fixed a bug in plot_model_predictions where an error was returned if not all time values in the xt matrix were to be used for the design calculation (
ni
is different fromsize(xt,2)
, see?create_poped_database
). - Various small bug fixes.
PopED for R version 0.1.1
- Updated package author list
- New functionality to compute the ED OFV using the Laplace approximation.
This can be orders of magnitude faster than the standard MC integration approach.
See?ed_laplace_ofv
and?evaluate.e.ofv.fim
- Added a general function to compute the FIM and OFV(FIM) for all avaialbale methods in PopED.
See?calc_ofv_and_fim
. - Added a general optimization algorithm
RS_opt_gen()
that works for both D-family and
E-family optimization. - Added optimization of E-family designs to
poped_optimize()
. - Changed distribution tests for package building
- Fixed bug where correlations between BSV (between subject variability) terms in the model gave an error when creating a PopED database
- Fixed a bug where get_rse failed when a parameter had a value of 3.
Initial PopED release (for R)
PopED has been translated from MATLAB to R and this is the initial release.
For more information about PopED you can go to http://poped.sf.net.