V1.0.5 May 20, 2019
-------------------
- Improved QSP modeling
- QSP functionality documentation in IQR Tools Book included
- Bug fix in addIndivRegressors_IQRdataGENERAL()
- Further improvements
V1.0.4 April 19, 2019
---------------------
- Compatibility R 3.5.2 and R 3.5.3
- Fix in statXY function
- Better support of MacOS Monolix path setup
- Added compatibility with new Monolix 2019R1
V1.0.3 April 3, 2019
--------------------
- Handle not present outputs in data when doing VPC
- Back-transform exp data when doing VPC
- Added getHeader_IQRnlmeProject()
- Allowed definition of SIGL for NONMEM gradient runs
- Stratified GOF plots for ETAs and ETA vs COV plots
- Add residual diagnostic plots to logistic regression
- New function to add covariate relationships to model specification
- QSP SysFit:
- Compatibility with Microsoft Open R
- Profiles for fixed parameters
- Allow additional integrator options in IQRsysProject
- Allow "." in condition names
V1.0.2 March 18, 2019
---------------------
- Improved NCA functionality now also handling SS data
- Improved survival analysis functionality
- Allow removal of confidence interval
- Allow different xticks (equidistant to last data point or max(xlim))
- Add cox regression information for selected strata
- Display cox regression as table and return
- Add Schoenfeldt cox.zph() test results to cox-table! - somehow - do not do plots at this time?!
- Show quantile values
- Improved QSP modeling
- Small additional fixes
V1.0.1 February 23, 2019
------------------------
- Improved QSP modeling functionality
- vpc_IQRnlmeProject parallelized also for Windows
- Fixed CENS information in converted project_pred.csv file when using MONOLIX
- Small fixes
V1.0.0 February 8, 2019
-----------------------
- QSP modeling backend has been exchanged
- Allowing random effects
- Handling BLOQ data
- Improved convergence and profile likelihood computation
- Faster on Windows (parallelized pLL computation)
- Changed syntax to be identical to NLME project setup
- Improved logistic regression modeling
- Small fixes
V0.9.999 January 16, 2019
-------------------------
- Improved logistic regression functionality
- Date/time conversion functions supporting data programming
- IQRoutputRDS available and producing log file for traceability information
- Event table generation functions
- Shiny app for NLME modeling now included in IQR Tools
- Smaller fixes
V0.9.99 December 06, 2018
-------------------------
- Update to PopED 0.4.0
- Providing convenient installers for
- Rtools
- IQReport
- IQRsbml
- Providing installation test functions for
- Rtools, IQReport, IQRsbml
- MONOLIX and NONMEM
V0.9.9 November 27, 2018
------------------------
- Removed support for MONOLIX old version 2016R1
- Bookdown-style full documentation accessed with "doc_IQRtools()"
- Factored NLME project storage
- All plot functions now return ggplot objects with plot data as attributes
- Improved IQRoutputTable handling and modification
- Replaced IQRexportCSVdata with IQRsaveCSVdata. The new function also stores
potential non-standard attributes of a data.frame as an .atr file. The
IQRloadCSVdata function restores these attributes, if present.
- Made following functions for NLME diagnostic plots available to the user:
- plotETA_NLME()
- plotETACOV_NLME()
- plotINDIV_NLME()
- plotGOF_IQRnlmeProject()
- printOutlier_NLME()
- Allowed "comment" argument in IQRnlmeProject() function call to annotate a model
- Added summaryComments_IQRnlmeProjectMulti function showing the AIC, BIC, OBJ, and
the user provided comments by "comment"
- Shrinkage in parameter table for fixed IIVs
- "results_MONOLIX()" function added allowing to generate results for models built
in the GUI, rather than in IQR Tools
V0.9.3 October 25, 2018
-----------------------
- Fixed as_IQRnlmeProjectMulti to work correctly with MONOLIX >2018R1 when using recursion (exclusion of .Internals folders)
- Allow VPC to not show the data points
- Allow VPC to set alpha/transparency for the data points
- Fixed issue in NONMEM and NLMIXR results table with long expressions
- Allow multi-column stratification in bootstrap_IQRnlmeProject function
V0.9.2 October 18, 2018
-----------------------
- Enforced NRCHAINS if below 50 subjects
- IQRoutputPNG/PDF now first close PNG and PDF devices before opening and printing
- VPC: FLAGindivSimtimeMax on TRUE by default
- More informative information text showing license activity, etc.
V0.9.1 October 07, 2018
-----------------------
- Improved NCA
- Advanced grouping of results
- Allowing non-numeric profile numbers
- Allowed IQRdataNCA to be exported to CSV and imported again as IQRdataNCA object
- Added modelSpec_IQRest function to allow easier definition of a modelSpec argument for the estimation object generation
- Added data_IQRest function to allow easier definition of a data argument for the estimation object generation
- Added dosing_IQRest function to allow easier definition of a dosing argument for the estimation object generation
- Allowed MONOLIX 2018R2
- Fixed interface to work with both NLMIXR 0.9.1.3 and 1.0.0.7 - now also allowing FOCEI
- Updated installer for NLMIXR and RxODE
- Summary function for IQRnlmeProject now provides units for error parameters and improved comments
- Remove min-max range bars from covariate forest-tree plots
V0.9.0 September 03, 2018
-------------------------
- Improved the NCA functionality to better group subjects (e.g. weight-based dosing groups)
- Allow in NONMEM/BAYES interface to provide a vector for the DF of the omegas
- PopED interface improved
- Updated NLMIXR interface
- Small fixes
V0.8.1 August 7, 2018
---------------------
- packageR_IQRtools() function allowing to package a whole R installation for reproducibility purposes
- getRepos() function to facilitate installation of packages from the MRAN time machine
- Improved VPC function
- Initial Interface popED 0.3.2 with IQRtools
- Survival analysis (KM)
- Logistic regression function
- Added info in IQRnlmeProject output tables that omegas are in standard deviation
- Small fixes
V0.8.0 June 25, 2018
--------------------
- BAYES NONMEM estimation
- Selector for NM and MLX versions
- Added unit tests for MONOLIX 2018R1
- Fixed bug with NONMEM 7.4 on Windows when running from R
- Rename NPROCESSORS to ncores and NPROCESSORSpar to Nparallel
- Handle ncores for MONOLIX 2018R1
- Fixed bug in initial guesses covariates in combination with covariance reordering - NONMEM code generation
- Additional tests for covariates and correlations and BAYES method in NONMEM
- Improved stability of NCA
- Allowed to provide individual simtime vectors when doing eventTable simulations
- Allowed VPCs for models without INPUTs
- Improved VPC to consider consider individual time periods
- Added IQRtteProject and associated functions for TTE modeling (MONOLIX only)
- Rename setup_options.R to setup_options_IQRtools.R
- The inference if old (2016R1) or new (2018R1) MONOLIX is used is not anymore
done by the path name but by the list entry name in the setup_options_IQRtools.R file
- A local / user setup_options_IQRtools.R file can be placed in the users home folder
to define settings that should be overridden from the global definition.
- Allowed to set number of simulated individual parameters for MONOLIX runs (2018R1 only)
- Deprecated MONOLIX 2016R1 ... will disappear end of the year
- IQRnlmeProject now allows to set the TOL option for NONMEM ADVAN13
- Better handling and documentation of the RATE/TINF column pair for NONMEM and MONOLIX
MONOLIX only uses the TINF column
NONMEM uses RATE=0 for bolus, RATE=-2 for using TINF or ABSORPTION0 TINF estimation.
- Joint Modelling (Longitudinal / TTE) using MONOLIX 2018R1
- Allow non full covariance matrices for BAYES
- Parallel NLME fits on Windows in addition to Linux
- Better error messages if identifiers are missing in IQRmodel files
- Small fixes
V0.7.2 May 10, 2018
-------------------
- Parallelized IQRsysFit on Windows
- Update the objective function for IQRsysFit to improve performance of optimization
- Improved dose handling for sensitivity calculations
- Fixed bug in sampling initial guesses for logit transformed parameters in IQRnlmeProject
- Small fixes
V0.7.0 April 23, 2018
------------------------
- Fixed issue with more than 9 model outputs
- Added convenience functions for testing, setup, license and examples
- Fix state-parameter sensitivities to 0 when event is fired
- Updated derivative computation in QSP modeling objective function
- Use sensitivity equations instead of CVODE sensitivities by default to allow
estimation of bioavailability in IQRsysFit
- Updated simulation time vector definition in QSP modeling objective function
- NCA data mean plots also shown now for single subjects in a dose group
- Small additional fixes
V0.6.6 April 16, 2018
------------------------
- Added vpc_IQRnlmeProject function ... still limited and should not be used for infusion data yet
- Added regenerate_IQRmodel as exported.
- Added additional NCA functions
- Small fixes
V0.6.4 March 16, 2018
------------------------
- Support of MONOLIX 2018R1
- Removal of pander as a dependency
- Interfacing with new version of IQReport
- Small bug fixes
V0.6.3 March 08, 2018
------------------------
- Added eigenvalue calculation function for IQRnlmeProjects to quickly
assess the terminal elimination half-life
- Allowed NLME projects without dosing inputs
- Export or IQRnlmeEst object as file in NLME project folder
- Added plotGOF_IQRnlmeProject function
- Improved annotation of GOF plots
- Bug fixes
V0.6.2 February 08, 2018
------------------------
- Updated NCA code to result in same results as Phoenix/Winnonlin
- Improved NCA report generation to stratify dose groups
- Updated print and summary functions for IQRnca objects to allow stratification by dose group
V0.6.1 January 26, 2018
-----------------------
- Improved installability across R 3.3.0 -> R 3.4.3
- Removed doParallel and foreach dependencies (result in IQRsysFit not running in parallel on Windows,
but Linux is anyway better for heavy computation ...)
- Changed gather() -> gather_() where needed to ensure its working for some time around R 3.4.1 where the
tidyr package seems to have changed
V0.6.0 January 24, 2018
-----------------------
- Finalized NCA functions including documentation, testing, and examples
- Added function getParameters_IQRnlmeProject()
V0.5.8 January 19, 2018
-----------------------
- Added NCA functions (still without examples)
- Removed need for the MASS package
- Fixed a bug in regression parameter adding to datasets (made this new version necessary)
V0.5.7 January 16, 2018
-----------------------
- IQRdataGENERAL: non-task events taken out by default
- Fixed issue in MONOLIX project generation that was not allowing ADDL/II
- Small bug fixes
V0.5.6 December 14, 2017
-----------------------
- Allowed for bioavailability terms in NONMEM infusion/absorption0 models
- Smaller improvements (e.g. showing ID in addition to USUBJID in individual PK plots)
- Added clustering function for binning and function to generate binned statistics
- Small bug fixes
V0.5.5 December 04, 2017
-----------------------
- Handling NONMEM 7.4 bug by automatically setting the MUM=N(...) option when needed
- Allow to provide simulatiokn time vector for plot.IQRsysData
- Add convergence info steps to trust and IQRsysPharm
- Add function setparameters_IQRmodel
- Allow not to provide doseNAMES and obsNAMES in IQRdataGENERAL - Handled by identifying doses by !is.na(ROUTE) and the rest as observations.
- Addition of a number of graphical data exploration functions
- Adding optional columns PROFTIME and PROFNR in the general dataset format
- subset_IQRdataGENERAL function
- Access to IQRdataGENERAL attributes via "convenience" functions
- ETA correlation plots were changed to allow for reasonable formatting when a larger number of parameters available in model
- Bug fix and improvement in ETA plots
V0.5.1 October 14, 2017
-----------------------
- ACoP version
- Mainly fixing some documentation
V0.5.0 October 10, 2017
-----------------------
- Exchanged "." in all non-S3 methods to "_"
- Added functions for generation of graphical exploration plots for IQRdataGENERAL objects
- Improved determination of estimated parameters for display purposes
- Display selected order metric in summary IQRnlmeProjectMulti tables
- Improved test-suite for validation of IQRtools
- Minor bug fixed that displayed in print.IQRnlmeEst function the wrong initial guesses for random effects
- Fixed all Notes that were important to fix.
- Improved ETA and ETA vs. COV plots by adding better titles for plots
- Added comparison based on t-test to ETA vs. categorical covariates
V0.4.2 September 21, 2017
-------------------------
- Added function to generate an observation summary table for IQRdataGENERAL objects
- Added function rmDosePostLastObs.IQRdataGENERAL
- Optional removal of doses post last observation in clean.IQRdataGENERAL
- Bootstrap function updated to work with NLMIXR
- Simple NLMIXR Test functions
- Improved annotation of covariateEffect.IQRnlmeProject
- Sampling from uncertainty for MONOLIX results now ensures parameters in correct range (log, logit)
without the user needing to take care of it
- Minor bug fixes
V0.4.1 September 14, 2017
-------------------------
- NLMIXR has been interfaced with IQRtools ... it is experimental still
- Demographics tables generated for IQRdataGENERAL objects
- Exported auxiliary functions
- Small fixes
- Added log for project_model.txt in MONOLIX export and also the graphics.xml one
- Removed the ADM=2 for IV by default if single ROUTE ... for single admin ADM=1 will be default if single ROUTE
- Write out which covariates are not in the data when importing general dataset
- Fixed covariate forest plot if covariate centering was chosen
- Added residuals over TAD to GoF plots
- Removed required dose names from IQRdataGENERAL
- Minor bug fixes where needed
V0.3.0 August 14, 2017
--------------------
- Support of NONMEM ADVAN 1,3, and 11
- Improvement of IQRnlmeProjectMulti summary tables to be fit for reporting
- Improvement of IQRnlmeProject summary table for reporting purposes
- Small bug fixes
V0.2.0 July 14, 2017
--------------------
- Small improvements
- Diagram representation of model via plot() function
- IQRsysPharm Shiny App provided separately which works with V0.2.0
V0.1.0 June 5, 2017
-------------------
- First release of Windows 64bit binary version