What’s New
Issues Corrected
Known Issues
November 2021
The settings database structure has changed in Pirana 21.11.1 and existing databases are automatically migrated to the new structure without the loss of previously saved settings (PRN-502).
Users can now access information on the Pirana Assistance website directly from dialogs and tabs in the Pirana UI:
Press the Help button on a dialog or wizard step (PRN-710, PRN-716).
Press the F1 key when working in the Files, Estimates, Scripts, or Reports tabs on the right side of the Pirana window (PRN-715).
Additional information for Certara R packages that are accessed through Pirana is now available as pkgdown websites (PRN-838):
Certara.ModelResults https://certara.github.io/R-model-results/
Certara.RsNLME https://certara.github.io/R-RsNLME/
Certara.RsNLME.ModelBuilder https://certara.github.io/R-RsNLME-model-builder/
Certara.RsNLME.ModelExecutor https://certara.github.io/R-RsNLME-model-executor/
Certara.VPCResults https://certara.github.io/R-VPCResults/
Certara.Xpose.NLME https://certara.github.io/R-Xpose-NLME/
Pirana now checks if columns and variables defined in statements exist in the input data (PRN-319, PRN-320): Previously, if a column or variable was defined but did not exist, the run would execute with no error. With Pirana 21.11.1, an error message is now displayed if an unknown column or variable is defined.
A new Results Analysis and Reporting Shiny application is available (PRN-744): Certara.ModelResults facilitates submission-ready generation of Lists of Tables and Figures (LTF). This application can be launched from Pirana or from R command-line for both NONMEM and NLME models.
A VPC Shiny application is now available through that Pirana UI to parameterize VPC and customize plot output for NLME models (PRN-724).
Support of the Condor job scheduler has been dropped (PRN-673): SGE and Torque job schedulers are still supported.
Users are now able to select input dataset columns on which to sort the output for population models (PRN-423).
New “Keep source structure” option is available (PRN-424): When adding a table in the Model Executor interface, the original structures can now be included in the output by checking this new option.
Convergence plots are now generated by Model Executor when performing a scenario model fit (PRN-580).
The lower value for defining reset has been changed from “1” to “4” to allow NONMEM data to be used directly (PRN-313).
It is now possible to set up SGE and Torque for local runs using the new Local Host option (PRN-590).
Pirana now considers the NONMEM version when accounting for OFV (PRN-647): Previously, Pirana always assumed OFV to be -2LL for NONMEM models. Depending on the NONMEM version being used, Pirana 21.11.1 does the following:
For NONMEM 7.3 or earlier:
-2LL = reportedOFV + nobs*log(2pi)
For NONMEM 7.4 and later:
If $EST LNTWOPI is specified in the .mod file, -2LL = reported OFV
If LNTWOPI is not specified on the $EST line, -2LL = reportedOFV + nobs*log(2pi)
A dOFV column is now included in the CSV file that is generated by the detailed run records command (PRN-663).
The detailed run records command now works in mmdl mode (PRN-664).
Pirana now tracks not only the active project, but also the most recent project, and the most recent directory and allows the user to specify which of these to open at Pirana startup (PRN-60).
When Pirana settings are saved, validation checks of entered values are now performed (PRN-229): Any values that fail the validation check are highlighted and must be corrected before the settings are able to be saved.
Multiple entities can now be created without exiting the Settings window (PRN-494): Previously, only one entity could be defined at a time and the user would have to exit and re-open the application, then go to the Settings window to create another one.
When an entity is deleted in the Settings window, it persists until the Settings window is closed (PRN-495): Previously, any deleted entity was deleted immediately and could not be undone.
The following options have been added to the Appearance settings tab:
Windows-style button order: Controls the position of the Cancel button with respect to other buttons along the bottom of dialogs. When checked, the Cancel button is positioned on the far right. When unchecked, the Cancel button is displayed as the first button from the left (unless a Help button is present, in which case the Cancel button will be the second button from the left) (PRN-714).
Fixed-width font family: Sets the font used in the Pirana interface when displaying code text (PRN-738).
“Pandoc location” has been added to the Software Integration settings tab (PRN-788): This is a required setting when generating reports inside the VPC Results and Model Results Shiny apps.
The “Open folder” option in the Tools menu is now labeled “Show in Explorer” and any model/folder selection in the Pirana is also selected in Explorer (PRN-372).
Large and small values are now reported using scientific notation to avoid rounding issues (PRN-418): A situation was reported where a small number was rounded to zero when the model was duplicated. Using scientific notation for such numbers prevents this problem from occurring.
Project information is now saved for projects that do not contain models PRN-446): Previously, if a project was created using a folder that did not contain any models, any information that was added later via the Project Information dialog would not be saved. With Pirana 21.11.1, information entered and saved using the Project Information dialog is saved with the project, regardless of the presence of models.
License for Pirana for Linux can now be successfully applied (PRN-654): Previously, Pirana on Linux would not accept the license file if the installed version of one or more Pirana dependencies are incompatible. This issue has been resolved with Pirana 21.11.1.
When exporting and/or compressing project items, checking the “Attached folders” box now includes attached folders in the output (PRN-802, PRN-803): Previously, attached folders would not be included in the output, even though the Attached folders box was checked.
Individual plot legends now properly display the line type and color (PRN-307).
Pirana now parses omega and sigma info from mmdl correctly (PRN-474): Inconsistencies were noticed between the AIC and BIC calculations in Pirana and those reported in the overall.csv file for a model. The differences stemmed from Pirana's incorrect parsing of omega and sigma information from mmdl, which has been fixed.
When a model involves discontinuous observed variables, the generated cols1.txt file now includes the mapping statements for the observed variables (PRN-314).
##MAP and ##COLDEF can now successfully be used to implement infusion for a one-compartment model (PRN-315).
Defining ADDL or SS using ##COLDEF now works for bolus cases and for infusion cases (PRN-326, PRN-327).
Non-parametric estimation now generates all of the expected non-parametric-related csv files (PRN-329): Previously, only nparsupport.asc was being generated. Pirana 21.11.1, in addition to the usual parameter csv files, generates nonParSupportResult, nonParOverallResult, nonParStackedResult, and nonParEtaResult csv files.
A reported issue involving the display of an error message when metamodel has IV infusion and ##COLDEF containing both “s” and “addl” statements could not be reproduced and has been closed (PRN-334).
Trailing spaces in mmdl block headers no longer prevent duplication of the model (PRN-498/QC 65).
Pirana now calculates dOFV correctly when multiple estimation steps, both including the LAPLACIAN option, are executed within a run (PRN-419).
An issue where the “New MSF file” field in the “Restart using MSF” dialog was not taking entries correctly could not be reproduced and has been closed (PRN-435).
Ability to execute multi-model nmfe runs has returned in Pirana 21.11.1 (PRN-753): Prior to Pirana 3.0, it was possible to run multiple models using nmfe. The UI in Pirana 3.0, however, only accepted a single model for execution. In Pirana 21.11.1, selection of multiple models is supported and the new Run multiple models in parallel checkbox, when checked, will run the models in parallel upon execution. When unchecked, the models will run sequentially.
Previous input selections for an execution are now cleared when setting up a subsequent Model Executor run (PRN-446): Previously, when a user successfully ran an execution and then switched to a different algorithm for a subsequent execution, the input selections applied to the first run would be applied to the second run as well. In some cases, the input options for one algorithm are not applicable to another algorithm and can cause issues during the execution. With Pirana 21.11.1, previous input selections are always cleared when setting up an execution.
R code that is displayed when “Simulate in R” is selected for a Covariance Matrix Simulation has been corrected (PRN-465).
November 2021: Pirana 21.11.1 release: added PRN-844 and PRN-887, removed QC 65 (fixed in Pirana 3.0) and PRN-344 (fixed in Pirana 21.11.1)
February 2021: Pirana 3.0 release
In the Model Builder, elimination input can become disabled (PRN-844): There is a rare situation where changing the Parameterization from Micro to Clearance, with the Closed Form box unchecked can result in the Elimination menu not being accessible. If this should occur, click on any other available input in the window and Elimination will become active.
Unable to create R script for a covariance matrix (PRN-887): In cases where the pirana_temp subfolder is not created in the current folder, the Simulate in R option will not work. If this problem is encountered, open any R script in R Studio using any model in the current folder before using the Simulate in R option. This will create the pirana_temp folder needed to successfully create the R script for the matrix.