How does Atlas handle R's dynamic dispatch during a rename?

Atlas leverages the `lsp` tool, which queries the R language server. This server understands R's AST and dynamic nature, providing accurate `findReferences` results that account for how R resolves symbols at runtime, ensuring comprehensive renaming.

Can Atlas rename a symbol that appears in `roxygen2` documentation blocks?

Yes, Atlas uses its `grep` tool to identify occurrences of the old symbol name within `roxygen2` documentation comments in your `R/` files. These textual matches are then included in the rename operation, ensuring your documentation remains consistent.

What if Atlas finds an ambiguous match for an R symbol?

The `edit` tool in Atlas is designed for safety. If it encounters an ambiguous single replacement, it will throw a "Found multiple matches for oldString" error. You would then need to provide more context or explicitly opt into `replaceAll` for that specific file.

How does Atlas ensure my `renv` environment is not broken after a rename?

Atlas focuses on code and documentation changes. While renaming a symbol typically does not directly affect `renv.lock`, Atlas's permission-gated tools and diff review process ensure that any changes to configuration files are explicitly approved, preventing unintended modifications to your `renv` setup.

Does Atlas automatically run `devtools::document()` after renaming R functions?

Atlas can be instructed to regenerate `NAMESPACE` with `roxygen2` and format files with `Air` as part of its post-refactoring steps, behind a permission prompt. This ensures your package documentation and structure remain up-to-date.

How does Atlas handle renaming symbols within `tidyverse` pipelines?

Atlas's `lsp` tool understands R's AST, including `tidyverse` idioms. It accurately identifies symbol references within `dplyr` or `purrr` pipelines, ensuring that all occurrences, even those within chained operations, are correctly identified and renamed.

Can I roll back a symbol rename performed by Atlas in R?

Yes. Atlas snapshots file changes as git patches before writing them. If you need to revert a rename, you can use standard git commands to roll back the changes, providing a robust safety net for your R refactoring.

What R files does Atlas index for symbol declarations?

Atlas indexes R code by AST declarations using tree-sitter. For R projects, this includes all `.R` files within your `R/` directory, `tests/testthat/` files, and it understands `DESCRIPTION`-based package structures and `roxygen2` docblocks.

Rename a symbol across the repo in R with Atlas in 2026

Renaming a symbol across an R repository in 2026 is precise and safe with Atlas, which integrates directly with your R toolchain, including `testthat` for testing, `renv` for package management, and `Air` for formatting. Atlas uses the `lsp` tool's `findReferences` to get authoritative callsite lists, `grep` for non-code occurrences, and `edit` for mechanical replacements, ensuring no R code is missed or wrongly matched.

How Atlas Accurately Renames R Symbols Across a Repository

In 2026, accurately renaming an R symbol like a function or class across a large repository requires more than simple text replacement. Atlas addresses this by first using the `lsp` tool's `findReferences` operation, which queries the R language server to identify all true code references, ensuring 100% accuracy within the type system.

Atlas begins a symbol rename by invoking the `lsp` tool. For an R project, this means Atlas connects to the R language server, which understands the abstract syntax tree (AST) of your R code, including `DESCRIPTION`-based packages and `tidyverse` pipelines. When you ask Atlas to rename a symbol, it executes `lsp findReferences` on the old symbol name. This operation returns a precise list of every location where the symbol is declared or used within your R files, such as `R/my_package_function.R` or `R/my_class_definition.R`. This method is crucial for R, where dynamic dispatch and non-standard evaluation can make static analysis challenging, preventing the common pitfalls of renaming only visible calls or missing indirect references.

Capturing All R Symbol Occurrences Beyond Code with Grep

While the R language server provides precise code references, a complete rename in 2026 must also account for non-code occurrences. Atlas uses its `grep` tool to scan the entire repository for the old symbol name, catching instances in comments, `roxygen2` documentation blocks, string literals, and configuration files that the `lsp` tool might overlook. This ensures a comprehensive refactor.

After gathering authoritative code references via `lsp`, Atlas employs its `grep` tool to find all other instances of the old symbol name. This step is vital for R projects, where symbols often appear in `roxygen2` documentation comments above function definitions in `R/` files, within example code, or as string arguments in functions like `getOption()` or `match.arg()`. `grep` also identifies the symbol in `tests/testthat/` files, `README.md`, or other project documentation. This two-pronged approach,`lsp` for structural code and `grep` for textual occurrences,ensures that every mention of the symbol, whether it is a direct code reference or a descriptive string, is identified for potential renaming, preventing broken documentation or confusing comments.

Applying Mechanical Renames and Ensuring Safety in R Code

Applying mechanical renames in R with Atlas is a controlled process, ensuring safety and preventing unintended changes. Atlas uses its `edit` tool with `replaceAll` to perform the actual text substitutions, but only after a read-only plan agent drafts a strategy. For instance, if 50 files are affected, Atlas computes a unified diff for each, presenting it for your approval before any changes are written to disk.

Once all occurrences are identified, Atlas uses its `edit` tool to perform the mechanical replacements. For the authoritative code references from `lsp` and the textual matches from `grep`, Atlas applies `edit replaceAll` to substitute the old symbol name with the new one. A key safety feature is that `edit` refuses ambiguous single replacements; if an unintended match occurs, it throws an error rather than silently corrupting your R code. Before any file is modified, Atlas drafts a plan in a read-only plan agent and seeks your explicit permission. Every proposed change, whether in `R/` source files, `tests/testthat/` scripts, or `DESCRIPTION` files, is presented as a unified diff. This allows you to review and approve each modification, ensuring that the rename aligns with your intent and that no critical R idioms or configurations are inadvertently altered.

Verifying R Symbol Renames with testthat and bash

After Atlas applies the renames, verifying the integrity of your R codebase is paramount. Atlas leverages the `bash` tool to execute your project's `testthat` suite, running `devtools::test()` to confirm that all 0 tests pass. This immediate feedback loop ensures that the refactoring has not introduced regressions, a critical step in any R development workflow in 2026.

The final and most critical step in any R refactoring is verification. Atlas uses its `bash` tool to run your R project's test suite. This typically involves executing `devtools::test()` or directly invoking `testthat::test_dir("tests/testthat")` within your R package. Atlas presents the output of these commands directly in the terminal, allowing you to see if all tests pass. If any tests fail, Atlas can help diagnose the issue or roll back the changes using its git patch snapshot capabilities. Furthermore, Atlas performs a final `grep` for the old symbol name across the entire repository. This last check confirms that zero instances of the old name remain, providing absolute proof that the rename is complete and successful across all R source files, documentation, and configuration.

Atlas's Robust Safety and Review Mechanisms for R Refactoring

Atlas incorporates multiple safety and review mechanisms to protect your R codebase during refactoring operations in 2026. Every Atlas tool call, including `lsp`, `grep`, `edit`, and `bash`, is permission-gated against allow, ask, and deny rules. This means you retain full control, approving each step before it executes, especially critical when modifying `renv.lock` or `DESCRIPTION` files.

Atlas is designed with developer control at its core. Before any tool, such as `lsp` to query the R language server or `edit` to modify `R/` files, is executed, it passes through a permission-gating system. You can configure Atlas to `allow`, `ask`, or `deny` specific operations, ensuring that no changes occur without your explicit consent. The agent first drafts a comprehensive plan in a read-only plan agent, detailing the steps it intends to take. This plan is presented for your review. Only after your approval does Atlas switch to a build agent to execute the plan. For every file modification, Atlas computes and displays a unified diff, allowing you to inspect the exact changes before they are written. This granular control, combined with the ability to snapshot file changes as git patches for easy rollback, makes refactoring R code with Atlas exceptionally safe and transparent.

Step by step

01Initialize Atlas in your R package directory, ensuring a `DESCRIPTION` file and `R/` directory are present.
02Ask Atlas to "Rename `old_function_name` to `new_function_name` across the repo."
03Atlas will use the `lsp` tool's `findReferences` to query the R language server for all code occurrences of `old_function_name` in your `R/` files.
04Atlas will then use the `grep` tool to find all textual occurrences of `old_function_name` in comments, `roxygen2` blocks, strings, and `tests/testthat/` files.
05Review Atlas's proposed plan, which includes a list of files to be modified, and approve the transition to the build agent.
06Atlas will use the `edit` tool with `replaceAll` to apply the renames, presenting a unified diff for each affected R file (e.g., `R/my_script.R`, `tests/testthat/test-my_script.R`) for your approval.
07After changes are written, Atlas will use the `bash` tool to run `devtools::test()` to execute your `testthat` suite and verify no regressions.
08Atlas will perform a final `grep` for `old_function_name` across the repository to confirm zero remaining instances.
09Approve Atlas to format changed R files with `Air` and regenerate `NAMESPACE` with `roxygen2` if necessary.
10Review and approve Atlas's proposed git commit, which includes the refactoring changes.

Frequently asked questions

How does Atlas handle R's dynamic dispatch during a rename?: Atlas leverages the `lsp` tool, which queries the R language server. This server understands R's AST and dynamic nature, providing accurate `findReferences` results that account for how R resolves symbols at runtime, ensuring comprehensive renaming.
Can Atlas rename a symbol that appears in `roxygen2` documentation blocks?: Yes, Atlas uses its `grep` tool to identify occurrences of the old symbol name within `roxygen2` documentation comments in your `R/` files. These textual matches are then included in the rename operation, ensuring your documentation remains consistent.
What if Atlas finds an ambiguous match for an R symbol?: The `edit` tool in Atlas is designed for safety. If it encounters an ambiguous single replacement, it will throw a "Found multiple matches for oldString" error. You would then need to provide more context or explicitly opt into `replaceAll` for that specific file.
How does Atlas ensure my `renv` environment is not broken after a rename?: Atlas focuses on code and documentation changes. While renaming a symbol typically does not directly affect `renv.lock`, Atlas's permission-gated tools and diff review process ensure that any changes to configuration files are explicitly approved, preventing unintended modifications to your `renv` setup.
Does Atlas automatically run `devtools::document()` after renaming R functions?: Atlas can be instructed to regenerate `NAMESPACE` with `roxygen2` and format files with `Air` as part of its post-refactoring steps, behind a permission prompt. This ensures your package documentation and structure remain up-to-date.
How does Atlas handle renaming symbols within `tidyverse` pipelines?: Atlas's `lsp` tool understands R's AST, including `tidyverse` idioms. It accurately identifies symbol references within `dplyr` or `purrr` pipelines, ensuring that all occurrences, even those within chained operations, are correctly identified and renamed.
Can I roll back a symbol rename performed by Atlas in R?: Yes. Atlas snapshots file changes as git patches before writing them. If you need to revert a rename, you can use standard git commands to roll back the changes, providing a robust safety net for your R refactoring.
What R files does Atlas index for symbol declarations?: Atlas indexes R code by AST declarations using tree-sitter. For R projects, this includes all `.R` files within your `R/` directory, `tests/testthat/` files, and it understands `DESCRIPTION`-based package structures and `roxygen2` docblocks.

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