Sensitivity analysis ex consultation0 - #74
Merged
Merged
Conversation
Contributor
There was a problem hiding this comment.
🟡 Changes recommended
Critical issues remain in dataset filtering and sensitivity-output handling.
Get a fresh assessment by requesting another Copilot review.
Pull request overview
Adds consultation-rate sensitivity datasets, flow tables, and sensitivity versions of Tables 1 and 2 across cohorts.
Changes:
- Adds sensitivity filtering and flow tracking.
- Generates main and sensitivity table outputs.
- Registers expanded datasets, outputs, and pipeline actions.
File summaries
| File | Summary |
|---|---|
project.yaml |
Registers new outputs and actions. |
analysis/table2/table2.R |
Supports main and sensitivity inputs. |
analysis/table1/table1.R |
Supports main and sensitivity inputs. |
analysis/dataset_clean/fn-inex_practice.R |
Adds consultation-rate sensitivity filtering and flow tracking. |
analysis/dataset_clean/dataset_clean.R |
Produces flow and sensitivity datasets. |
analysis/create_project_actions.R |
Generates expanded project actions. |
Review details
- Files reviewed: 6/6 changed files
- Comments generated: 4
- Review effort level: Lite
💡 Add a code-review agent skill or configure MCP servers for context-aware, tailored reviews. Learn more in the docs.
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Contributor
There was a problem hiding this comment.
Copilot review overview
🔵 Needs a closer look
The new missing-practice_region exclusion changes the main cohort beyond the stated sensitivity analysis and must be documented or disabled.
Review effort: Lite
Findings: None
Resolved since last review (4)
inputis still the output ofpreprocess_measure()/redact(), where the…trajectory_outcomes.R's^icc_input-.*\\.dta$glob, so…FALSEexplicitly skips the existinglist_size >= 1000exclusion, so the main…^icc_input-.*\\.dta$glob in `analysis/graphs/trajectory_outcomes.R:…
rdenholm
approved these changes
Sep 21, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Hi Rachel,
We have now excluded practices with zero consultation rates and recorded the exclusions in a flow table. I have also generated Tables 1 and 2 and the inputs for the outcome trajectory graphs using the sensitivity dataset, so we can assess how the exclusion affects the descriptive results.
The updated pipeline has now run successfully locally.
Best wishes,
Zoe