Interactive Web Applications

The interactive Pumas web applications can be accessed via the PumasApps module which can be loaded with

julia> using PumasApps

Once loaded we can access the default application by evaluating

julia> PumasApps.Workspace.default()

which will display a URL that links to the web app running the default workspace. This workspace is always available, but you can also create separate workspaces by evaluating

julia> ws1 = PumasApps.Workspace.new()

which will create a new workspace application that will be accessible from a different URL, which will have been printed to the REPL when evaluating the previous code. Always assign these workspaces to a variable, here we have used ws1, since this allows us to easily close workspaces that we do not require anymore. Workspaces that you do not require anymore can be closed by calling

julia> close(ws1)

where ws1 is the variable name you provided when creating a particular workspace using PumasApps.Workspace.new().

Navigating the Web Application

When clicking on the printed URL for any of the web applications a browser tab will open onto the "Home" screen of the web app. From there you have several options.

We're presented with several elements on this page.

• A collection of tile links in the main body of the screen that link to the individual single-purpose apps available from within the web interface, along with short descriptions of their purposes.

• A left sidebar containing quick links to these same single-purpose apps.

• A top appbar that contains a ? link and, when the application is running tasks, a loading indicator.

The ? link at the top right should be your first stop when initially exploring what the application has to offer. When you click it, it will open up an overlay navigation system that explains the different elements on the screen and their functionality.

Spend some time reading through the "tour" since it will explain in much more detail the individual parts of the application than we can within this standalone documentation.

Screens Overview

We provide a brief overview of the individual screens available in the application and what they are used for, but note that the detailed information regarding how to use each single-purpose app is available from the ? in the top right corner of each screen and should be your main reference for usage information.

Session Explorer

This screen provides a summary of the available Pumas "objects" that are currently defined within your Julia REPL, as well as those available for use in your workspace that the web app has access to.

Objects can be imported and exported between the REPL and the workspace. You can also "delete" objects from either to reclaim memory should you need to do so.

The Session Explorer application can also be accessed via the list_models() function.

julia> lm1 = list_models()

This will provide a URL direct to the Session Explorer screen where you can then select a collection of objects from the "Session" table. After this you can use the selected_models function to extract and pack those objects into a single NamedTuple that can be passed on to other functions.

julia> selected_models(lm1)

list_models()

Data Loader

This app allows you to load a CSV data file from a folder called data in your present working directory (pwd()) into a DataFrame object. This is the first step towards creating Pumas Population objects for use in simulations.

You can also select data to load from the range of data files provided by the PharmaDatasets package.

Model Builder

You can create Pumas models, usually creating via the @model macro in the coding interface for Pumas, from this application screen. This app lets you select from a collection of dropdown menus the characteristics that you would like your model to have.

The automatically generated code for the model, or the mathematical representation of the model can be viewed below the model inputs.

Population Builder

This application can take the outputs from the Data Loader application to create Pumas Population objects for use in simulations. It also allows you to view some basic diagnostics plots of the generated populations.

Estimates

The estimates application lets you perform simobs interactively while seeing the plotted results in real-time.

This Estimates screen can also be accessed via the explore_estimates function which will, given a model, population, and parameters, pre-import those objects into the workspace from the REPL and provide a URL that will pre-select those names when opened.

julia> ee1 = explore_estimates(model, population, parameters)

After adjusting the parameter values interactively inside the application you can then access those values programmatically via the coef and DataFrame functions:

julia> coef(ee1)

and

julia> DataFrame(ee1)

explore_estimates(model, population | subject)

Diagnostics

This application allows for interactively viewing numerous diagnostics plots and tables of Pumas objects, as well as comparing the outputs between different objects side-by-side.

You can also make use of this interface to generate standardized PDF reports based on the compared objects as well as launch interactive notebooks that allow you to write and export your own documents based on the selected objects.

The evaluate_diagnostics function can be used to help you programmatically import Pumas objects into the workspace from the REPL.

evaluate_diagnostics([app,] objects; inspect, infer)

Interactive Pluto Notebooks

The PumasUtilities package provides access to several functions for launching and interacting with Pluto notebooks which you can use to author content for reports.

julia> using PumasUtilities

Loading PumasUtilities makes the following documented functions available.

notebook(file::String)

notebooks()

send_to_notebook(file; objects...)

fetch_from_notebook(file, vars...)