Introduction

bllflow uses seven steps to create a model. There is an emphasis on a pre-specified approach to analyses. Pre-specified means a model is described prior to examining the relationship between predictors (also known as variables, risk factors or features) and the outcome (target). All analyses are logged, allowing transparent reporting.

bllflow uses general utility functions for data cleaning and variable transformation. Also included are functions for analyses logs and managing variable labels and other metadata. The utility functions can be used by themselves – even if you don’t want to follow bllflow’s prespecified approach. When you are ready, you can use the Model Specification Workbook to describe the your data cleaning and transformation steps – additional bllflow ‘wrapper’ functions execute the utility functions according the Model Specification Workbook.

Step 1 - Pre-specifying your model

Model specifications are recorded within a series of four CVS worksheets that together form the Model Specification Workbook (MSW). The most important sheets is the variables worksheets – a CSV file with a row for each variable in your model. Included are columns for variable labels, data cleaning, variable transformations and other instructions (Step 4).

We’ve found that people starting a new project like using the MSW even if they don’t use any other part of bllflow. The MSW worksheet helps you organize your thoughts about what variables to include in your model. The worksheets are also helpful when working in teams. We get everyone invovled in the MSW: analysts, methodologist and content experts. Graduate students have a team too – you can use the MSW to review your modelling plans with your supervisor and thesis committee.

Step 2 - Describing the study cohort

Research studies tyipically include a “Table 1” that describe the study cohort or population and additional tables and figures. With bllflow, you specify what variables are required for each table and then use functions to create the tables.

Step 3 - Data cleaning and variable transformation

Data cleaning and varible transformation is the most time consuming step of model development – and also a step that poorly communicated and difficult to reproduce. bllflow strives to reduce the effort required in this step as much as possible, while also improving transparency and reproduciblity.

Step 4 - Developing a predicitve model

This step is short and breif for bllflow. bllflow doesn’t contain any functions for actual statistical or machine learning models. Rather, bllflow is a wrapper around the model model derivation, by providing help prior to and following actual model development.

A challenge when using different modelling packages and software programs are different approaches to variable transformation that occurres within model generation. For example, dummy variables are created in different packages during function call and then exported, but using different naming conventions. In bllflow, dummy variables and other transformations are generated prior to function call.

Step 5 - Reporting the performance of a model

This section generates performance reports for predictive algorithms – and much of this section will not be helpful if are performing other types of studies. We add onto popular packages such as Hmisc in three ways. First, we modify a few functions for competing risk algorithms, since these functions are underdeveloped. Second, bllflow have versions of calibration plots and other visualizations. Third, plots are designed to replication on many subgroups, using information from the aggregatedResults data frame.

Step 6 - Describing a model

bllflow creates a consistent structure for descdribing models. The same as other steps, a structured data frame, model-description is created to facilitate export as a CSV file or other document format. Critically, the model description is translated to Predictive Model Modelling Language (PMML) for deployment in various settings. PMML can be imported into Tensor Flow deployment engines (with future plans for export to Tensor Flow Graph). model-description is also used for manuscript-ready exhibits.

Reference files - Variable types, labels and metadata

bllflow uses consistent labels and metadata throughout the workflow. bllflow metadata is alligned with two documentation initiatives: the Data Documentaiton Initiative (DDI) and PMML. The variable-metadata file is a table that identifies all variable types used. For example, mean refers to the mean value of an exposure. All variable types are defined to ensure consistent, understandable and machine-actionable across software libraries.

Helper and utility functions

Helpter and utility functions to support your workflow. For example, metadata utility functions help maintain variable labels and build from hmsic and labelled and codebook packages.