What’s New
Issues Corrected
Known Issues
January 2023
pyDarwin now supports Omega band matrix and Omega sub-matrix in candidate model search (DRWN-333, DRWN-457).
pyDarwin now supports use of the particle swarms optimization (PSO) algorithm to search for global optimal solution in the candidate model search space (DRWN-292).
The following have been implemented to support Darwin searches within Pirana:
– A new Darwin Search properties window provides access to the Darwin settings, grouped into a series of pages. Access the window by Models > New model with drwn chosen from the “filter by extension” menu in the upper right (DRWN-170, DRWN-377). Basic ADVANs are available for search (ADVAN1-ADVAN4, ADVAN10-ADVAN12) within bound covariates chosen.
– All property fields in the Darwin Search properties window are validated and any invalid fields are highlighted in light red (the page name in the tree is also highlighted) (DRWN-396, DRWN-414).
– Search properties can be saved, restored, and edited (DRWN-307, DRWN-379).
– Search execution can occur locally or on a grid (DRWN-378, DRWN-383).
– A Darwin section has been added to Pirana settings window where execution profiles and other settings can be defined (DRWN-354).
Pirana installation qualification of NONMEM output results (DRWN-130, DRWN-132, DRWN-133): The Tools > Installation Qualification menu option provides access to installation qualification scripts that test the parsing, organization, and display of run results for approximately 40 predefined NONMEM models. Custom model sets can also be tested by these scripts. During installation qualification, a comparison of values in the raw output files produced by NONMEM is made with those values shown in Pirana displays. A summary report of the qualification results can also be generated and saved to a specified location.
Installation on Linux is now accomplished with a ‘packed’ version of Pirana (DRWN-426): The packed version of Pirana bundles Perl dependencies in the installation files. Previously, users were required to install necessary Perl modules from the web as part of the Pirana installation on Linux distributions, which could lead to issues if the Perl modules were updated after the Pirana release. The packed version of Pirana prevents such issues from arising.
NLME engine is now installed with GCC version 8.4 on Windows. RHEL8/CentOS8 Linux Distributives are supported (PHX-8048, DRWN-230). RHEL7/CentOS7 distributives are no longer supported. To avoid collision with Phoenix installed, NLMEGCCDir64 environment variable is created during installation pointing to GCC version 8.4 on Windows.
For each observed variable per each replicate, predout (PredCheckAll worksheet) now lists simulated values, population predictions if either OutputPRED is requested or prediction correction is enabled, correction factor and corrected simulated value if predication correction is enabled (PHX-8046). See also the note for DRWN-260 in the “Certara.RsNLME and Certara.NLME8” section.
LLOQ value is now outputted to predcheck0 (Observations data frame) for predictive check mode (vpc() function in RsNLME package) (PHX-8304).
Certara.RsNLME and Certara.NLME8
PRED is now output, when requested, as a separate column (DRWN-260): Previously, it was output in the DV column with REPLICATE =-1. See also the note for DRWN-8046 in the “NLME Engine” section.
RsNLME printing model object now displays the values of modelName and workingDir slots (DRWN-241).
A new wrapper function called hostParams() allows setup of host objects without using the NlmeParallelHost class initializer (DRWN-271).
A new wrapper function called tableParams() allows defining table output instead of using NlmeTableDef-class/NlmeSimTableDef-class initializers (DRWN-316).
The syntax for the colMapping() function now allows for unquoted key-value pairs that may be specified via the ellipses argument (DRWN-281).
The following built-in model functions support unquoted column names: pkmodel(), pklinearmodel(), pkemaxmodel(), pkindirectmodel(), emaxmodel(), linearmodel() (DRWN-290).
A new filesToReturn argument is available for the fitmodel() and sortfit() functions, which allows specification of data tables to return (DRWN-397).
In estimatesUI(), when overlay=TRUE, the number of lines in the resulting plot now reflects the number of unique dose values in the data (DRWN-362).
UNC paths are now supported, allowing RsNLME to be utilized with a shared directory inside a network drive (e.g., \\S01ABCD-EF1.certara.com/UserData$/user/Documents/) (DRWN-335).
A new xposeNlmeModel() function in Certara.Xpose.NLME creates xpdb with the model object (DRWN-423): This function has two arguments – model (object of class NlmePmlModel) and fitmodelOutput (returned value of fitmodel execution).
The model working directory now defaults to the current working directory in an RStudio Session, instead of a temp directory, and can be overridden with a user-defined directory (DRWN-129).
R code generation of table and engine parameters for workflows performed in Model Executor is now supported (DRWN-286, DRWN-323).
Real time convergence plots for simple run mode are now available (DRWN-169): Previously, convergence plots of -2LL and model parameters were only available after execution was finished.
Scenario/Sort fit convergence plots are now produced for simple run mode (with sort column) or scenario run mode (DRWN-399).
Stratification by categorical covariates is now supported for Bootstrap (DRWN-429).
A single host can now be specified without wrapping in “c()” (DRWN-270).
During model execution, the same output that is returned in the R console is now reported in the Progress Text window in Model Executor (DRWN-391).
Font customization options are now formal font names (DRWN-163): Previously, the choices were typefaces (i.e., serif, sans, mono). Now the choices are font names such as Times New Roman, Arial, Courier New, etc.
The binning methods headtails, maximum, and box are now available (DRWN-293).
Font customization options are now formal font names (DRWN-216): Previously, the choices were typefaces (i.e., serif, sans, mono). Now the choices are font names such as Times New Roman, Arial, Courier New, etc.
Customization options for VPC plot legend are now available (DRWN-186).
An issue where using special words like 'dose', 'obs', 'covr', and 'mode' could cause NLME to fail has been resolved (PHX-8024): In the previous version, using such special words as variables in the simulation table or as stratification variables would occasionally cause NLME to fail.
The issue of fraction excreted theta, used in urinecpt, being fixed irrespective of other statements has been resolved (PHX-8015).
An issue where having an overall number of fixed effects (including frozen and not enabled for the current scenario run) exceed the number of thetas + 100 could cause optimization to stop has been resolved (PHX-8020).
For non-time based models with covariate effects, if the When covr set field contains a covariate that is not the last one defined in the Column Definition Text area, NLME no longer generates an incorrect execution error message that the covariate was not set (PHX-8199).
Using a sscol() statement in column definitions no longer creates additional rows in the doses.csv file (PHX-8214).
The QRPEM engine now supports models in which the same thetas are used in different stparm statements (PHX-8168).
In the calculation of steady state when the DelayInfCpt statement is used and reset statements are present, the reset statements are now handled correctly (PHX-8013).
Certara.RsNLME and Certara.NLME8
An issue where stepwise covariate searches with criterion set to AIC could give incorrect results during backward elimination has been resolved (PHX-8226): Previously, for a stepwise covariate search run involving a multicore host and AIC, the package would use “+” instead of “-“ for certain scenarios during the backward elimination.
For shotgun covariate searches, the total number of jobs/scenarios executed is set to 2^n, where n denotes the number of enabled covariate effects (DRWN-447).
January 2023: Pirana 23.1.1 release: added DRWN-545
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
Custom specifications of font type and/or size (other than default) can affect display of UI elements (DRWN-545): Adjusting the font type and/or font size may lead to some buttons being inaccessible. If part of the interface appears to be hidden or missing, select a different type and/or size or try restoring the default font size (10) and font family (Verdana) in Pirana Settings > Appearance.
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.