gmptk/rvis

Open access PBPK modelling platform

RVis

RVis is a modeller's tool for loading and exercising simulation code written in R or MCSim.

Prerequisites

RVis is a desktop application for Microsoft Windows. You will need:

• Microsoft Windows 10 (April 2018 Update or later)
• R v3.1 or later

RVis depends on various R packages to provide functionality:

• To use the sensitivity analysis feature in RVis, you will need to install the R sensitivity package
• The MCMC feature in RVis can provide diagnostics, for which you will need to install the coda package
• To use all of the features of the sampling module, you will need to install the dicedesign and mc2d packages.

Installation

Visit the releases page and download the zip archive containing the latest RVis.

[more instructions]

Getting Started

[basics]

[links]

Funding and Development

RVis was funded by CEFIC and developed by HSE.

rvis's Issues

Setting R directory through config file

Add an option through configuration file to specify the location of the R installation directory for R.NET.

Useful for security settings that limit program access to registry files or for non-standard R installations.

Default limits in LHS

When configuring LHS the parameter distributions default to uniform. The default lower and upper ranges appear reasonable for most parameters except Qliv, liver blood flow rate. This defaults to 0.1 - 1. This gives values as high as 0.99 or 99% cardiac output. This causes faulty simulations for any given output.

sliders - negative values

Provide a zero lower bound limit for sliders to prevent biologically implausible values

Parameter estimation with 4 data sets

Imported 4 urinary metabolite excretion data sets for use in parameter estimation module. Set target accept rate to 0.4. Click on "Iterate" and the the "Stop" button is momentarily enabled before returning to Iterate. Simulation does not initiate.

Enhancement: Batch execution of an input file

At present RVis can create a design prior to executing a batch run (Monte Carlo and Latin Hypercube options) but it does not have an option of reading in an externally created design and batch running. This would be pretty useful for post processing of MCMC output and would link in with our other software tools (PopGen).

LHS

Define/select a range of acceptable simulations from the LHS output from which the upper and lower limits of parameter distributions can be set.

Fails to load if FIPS compliant algorithms are enforced

No response from program, will not load when the following Windows 10 STIG is applied.
https://www.stigviewer.com/stig/windows_10/2019-01-04/finding/V-63811

Solution:
The software should support FIPS compliant algos. Unless it's something stronger, then the workaround should be sufficient for now.

Workaround:
Powershell
Set-ItemProperty -Path "HKLM:\SYSTEM\CurrentControlSet\Control\Lsa\FipsAlgorithmPolicy" -Name "Enabled" -Value "0" -Force
And/Or Disable the GPO:
Configure the policy value for Computer Configuration >> Windows Settings >> Security Settings
>> Local Policies >> Security Options >> "System cryptography: Use FIPS compliant algorithms for encryption, hashing, and signing" to "Disabled".

NAN when ranking parameters in eFAST

In eFAST, the ranking of parameters fails if the range starts at 0 min. The parameters are assigned NAN. Setting the lower range to a >0 avoids this fault.

Monte Carlo Sampling

Return mean or median and display bounds of simulations with +/- 1-3 * standard deviation

Access information about executive function and template from question mark

Reinstating access by clicking question mark (help) on Import page to the information about executive functions and templates available here:
https://r-vis.github.io/doc/home/simulation-code/#executive-function

LHS-Provide row numbers

Provide row numbers in the Samples field to match simulation line number in chart in Outputs. This should aid user to quickly identify suspect parameter(s).

Identify faulty parameter values in LHS

User should be able to click on a spurious simulation in the LHS chart and identify the suspect line of parameters in the design. These parameter values can then be tested as inputs in the plotter module to test whether the fault can be reproduced and the spurious parameter(s) values identified.

BD MCSim in file realted error for Rvis 0.10

Line 5 of .in file produces an error that Expected ,model-variable> before 'BDW"
line 16: Bad definition of experiment 1.
butadiene.template.in.txt
mcsim.butadiene.model.R.txt
Please note that the attachments are for the .in and .exe Butadiene files

Sampling Plots Slow

Fix: plot subset of data; provide chart control to adjust.

White screen on simulation (.NET CAS problems)

Test on Installed: .NET Framework 4.8, or 4.7.2

Symptom:
When running a simulation, a blank white screen appears (No graph displayed).

Fix?
The possible call to 'file:///C:' May be escalating security on this path due to it's potential to be a hyperlink. Is it possible to call C:\ directly without the File:///?

I don't understand the .NET sandbox security fully, but i believe the least priv approach is safest. This may be a better key to the fix:
https://docs.microsoft.com/en-us/previous-versions/dotnet/netframework-4.0/bb763046(v=vs.100)?redirectedfrom=MSDN

Workaround:
Edit RVisUI.exe.config
Below <runtime>
Paste: <loadFromRemoteSources enabled="true"/>

Logfile Error:
10:58:31 Failed to load module in C:\Apps\RVis_v0.8.11068.1\module\sensitivity System.IO.FileLoadException: Could not load file or assembly 'file:///C:\Apps\RVis_v0.8.11068.1\module\sensitivity\Sensitivity.dll' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) File name: 'file:///C:\Apps\RVis_v0.8.11068.1\module\sensitivity\Sensitivity.dll' ---> System.NotSupportedException: An attempt was made to load an assembly from a network location which would have caused the assembly to be sandboxed in previous versions of the .NET Framework. This release of the .NET Framework does not enable CAS policy by default, so this load may be dangerous. If this load is not intended to sandbox the assembly, please enable the loadFromRemoteSources switch. See http://go.microsoft.com/fwlink/?LinkId=155569 for more information.

at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
at System.Reflection.RuntimeAssembly.nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
at System.Reflection.RuntimeAssembly.InternalLoadFrom(String assemblyFile, Evidence securityEvidence, Byte[] hashValue, AssemblyHashAlgorithm hashAlgorithm, Boolean forIntrospection, Boolean suppressSecurityChecks, StackCrawlMark& stackMark)
at System.Reflection.Assembly.LoadFrom(String assemblyFile)
at Ninject.Modules.AssemblyNameRetriever.AssemblyChecker.GetAssemblyNames(IEnumerable1 filenames, Predicate1 filter)
at Ninject.Modules.AssemblyNameRetriever.AssemblyChecker.GetAssemblyNames(IEnumerable1 filenames, Predicate1 filter)
at Ninject.Modules.AssemblyNameRetriever.GetAssemblyNames(IEnumerable1 filenames, Predicate1 filter)
at Ninject.Extensions.Conventions.BindingBuilder.AssemblyFinder.FindAssemblies(IEnumerable1 assemblies, Predicate1 filter)
at Ninject.Extensions.Conventions.BindingBuilder.ConventionSyntax.FromAssembliesInPath(String path)
at RVisUI.Ioc.AppState.<>c__DisplayClass68_0.b__0(IFromSyntax x)
at Ninject.Extensions.Conventions.ExtensionsForIKernel.Bind(IBindingRoot kernel, Action1 configure) at RVisUI.Ioc.AppState.DoDirectoryBind(String directory)

Morris Test Ranking calculation

Calculation for ranking parameters in Morris test is not correct.

Delete Sim Slow

Fix: move to temp and delete dir on worker thread.