Fix dplyr::as_tibble and dplyr::tbl_df references to use tibble package#197
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….R and Run_Mod.R Agent-Logs-Url: https://github.com/ucdavis/serodynamics/sessions/212b7544-cbf9-4137-a367-61fd31be832d Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com>
Agent-Logs-Url: https://github.com/ucdavis/serodynamics/sessions/212b7544-cbf9-4137-a367-61fd31be832d Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com>
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[WIP] Fix dplyr tibble references for as_tibble
Fix dplyr::as_tibble and dplyr::tbl_df references to use tibble package
Apr 14, 2026
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📕 Preview documentation for this PR has been cleaned up. |
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Pull request overview
This PR cleans up namespace usage and documentation links by switching as_tibble() and tbl_df references from dplyr re-exports/defunct topics to the canonical tibble package, keeping the package’s code and docs aligned with current tidyverse exports.
Changes:
- Updated code to call
tibble::as_tibble()instead ofdplyr::as_tibble()in key post-processing paths. - Updated roxygen links from
[dplyr::tbl_df]to[tibble::tbl_df](and regenerated.Rdoutput accordingly). - Bumped package development version and added a NEWS entry describing the change.
Reviewed changes
Copilot reviewed 11 out of 11 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
R/post_summ.R |
Switches tibble conversion to tibble::as_tibble() for correct namespacing. |
R/Run_Mod.R |
Switches tibble conversion to tibble::as_tibble() and updates roxygen link for sr_model return type. |
R/plot_predicted_curve.R |
Updates roxygen link for dataset parameter type to tibble::tbl_df. |
R/nepal_sees_jags_output.R |
Updates roxygen link in dataset format documentation to tibble::tbl_df. |
R/use_att_names.R |
Updates roxygen link for run_mod() output type to tibble::tbl_df. |
man/run_mod.Rd |
Regenerated docs reflecting tibble::tbl_df link target. |
man/plot_predicted_curve.Rd |
Regenerated docs reflecting tibble::tbl_df link target. |
man/nepal_sees_jags_output.Rd |
Regenerated docs reflecting tibble::tbl_df link target. |
man/use_att_names.Rd |
Regenerated docs reflecting tibble::tbl_df link target. |
NEWS.md |
Documents the namespace correction for as_tibble(). |
DESCRIPTION |
Bumps development version. |
Kwan-Jenny
reviewed
May 3, 2026
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- Typo on line 183 ("restructing" → "restructuring") that the
Copilot bot also noticed earlier — could we fix it here? - Merge order with #195 and #199 — these PRs touch the same
.Rdfiles. I think merging this one first is easiest since
it's smallest. What do you think? - Overlap with #193 — quick question about whether some of
these fixes are also in #193, to avoid duplicate work.
Looks good overall. Once the typo is corrected and the merge order is finalized, it should be ready to go.
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Merge commit '144cdd68a93c565dd7427fe3b9c01eb57ea10005' #Conflicts: # NEWS.md
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #197 +/- ##
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Coverage 81.42% 81.42%
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Files 25 25
Lines 915 915
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Hits 745 745
Misses 170 170 ☔ View full report in Codecov by Sentry. |
Collaborator
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@d-morrison, I just requested your review. This PR is basically changing all tbl_df references from dplyr to tibble. Thank you! |
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as_tibble()andtbl_dfare exported fromtibble, notdplyr. References todplyr::as_tibble()still work via re-export but are incorrect, and[dplyr::tbl_df]roxygen links now resolve todplyr:defunct.Code
R/post_summ.R,R/Run_Mod.R:dplyr::as_tibble()→tibble::as_tibble()Documentation
R/Run_Mod.R,R/plot_predicted_curve.R,R/nepal_sees_jags_output.R,R/use_att_names.R:[dplyr::tbl_df]→[tibble::tbl_df]in roxygen2 commentstibblewas already inDESCRIPTIONImports; no dependency changes needed.R/as_case_data.R,R/sim_case_data.R, andR/postprocess_jags_output.Ralready used the correcttibble::namespace.