From 1fb15e8999053801c2c12ae19493fc2fbfe25983 Mon Sep 17 00:00:00 2001 From: Trevor Riley Date: Mon, 8 Jun 2026 13:23:04 -0400 Subject: [PATCH 1/3] chore: finalize CRAN resubmission prep for 0.2.1 Address remaining reviewer comment: Description no longer starts with "Tools for" (reworded to lead with an active verb). Bump DESCRIPTION date. Rewrite cran-comments.md as a new-package resubmission that documents how each reviewer point was addressed. Regenerate plot_source_overlap_upset.Rd. --- DESCRIPTION | 13 ++++--- cran-comments.md | 65 +++++++++++++++++++------------- man/plot_source_overlap_upset.Rd | 2 - 3 files changed, 45 insertions(+), 35 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5c4d1e1d..d74662da 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: CiteSource Title: Data-Driven Search Strategy Development and Evidence Synthesis Reporting Version: 0.2.1 -Date: 2026-06-01 +Date: 2026-06-08 Authors@R: c( person("Trevor", "Riley", , "tnriley@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6834-9802")), @@ -22,11 +22,12 @@ Authors@R: c( person("Kaitlyn", "Hair", role = "cph", comment = "Author of included ASySD deduplication code"), person("CAMARADES Group", role = "cph", comment = "Authors of ASySD (github.com/camaradesuk/ASySD)") ) -Description: Tools for data-driven search strategy development and evidence - synthesis reporting. Researchers can deduplicate references while - maintaining customizable metadata, analyze results using - plots and tables, and import or export data in 'RIS' and 'CSV' formats. - An interactive 'shiny' application is included for exploratory use. +Description: Deduplicates bibliographic citations from multiple sources while + preserving customizable metadata, supporting data-driven search + strategy development and evidence synthesis reporting. Search + results can be analyzed using plots and tables, and imported or + exported in 'RIS' and 'CSV' formats. An interactive 'shiny' + application is included for exploratory use. License: GPL (>= 3) URL: https://eshackathon.github.io/CiteSource/ BugReports: https://github.com/ESHackathon/CiteSource/issues diff --git a/cran-comments.md b/cran-comments.md index 27867e09..2bed6bbc 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,43 +1,54 @@ -## Submission - -This is a minor feature update (0.2.0 -> 0.2.1). - -New in this version: - -* `dedup_citations_add_sources()` adds new citations to a previously - deduplicated set and deduplicates across both, preserving prior merge - decisions and record provenance (incremental deduplication). -* `export_dedup_candidates()` / `reimport_dedup_candidates()`, and a - `manual_dedup_complete` flag in `export_csv()`, support performing automatic - deduplication now and completing manual review later. -* `reimport_csv()` now reads all columns as character so a re-imported set can - re-enter the manual-merge / incremental-deduplication functions without - column-type clashes. -* Documentation and bundled 'shiny' application updates. +## Resubmission + +This is a resubmission of a new package (not yet on CRAN). It addresses all +points raised in the previous review: + +* **Title / Description formatting.** The `Title` no longer begins with + "An R Package for", and the `Description` no longer begins with "Tools for". + The `Description` now opens with an active verb describing what the package + does. All software/package names in the `Title` and `Description` + (`'shiny'`, `'RIS'`, `'CSV'`) are written in single quotes. + +* **Missing `\value` tags.** `@return` documentation was added to all flagged + functions (`export_bib`, `export_ris`, `plot_contributions`, + `plot_source_overlap_upset`, `reimport_ris`) and the `.Rd` files were + regenerated. Functions called for their side effects use the phrasing + "No return value, called for side effects." and state what file is written; + functions that return objects describe the class and meaning of the output. + All exported functions now carry a `\value` tag. + +* **Writing to the home filespace.** Default `filename` values were removed + from `export_csv()`, `export_ris()`, and `export_bib()`, so the caller must + supply an explicit path. The internal `write_refs()` fallback in + `R/import_export_helpers.R` now writes to `tempdir()` instead of `getwd()`. + All examples write to `tempfile()` / `tempdir()`. + +Since the previous review, the package version was incremented from 0.2.0 to +0.2.1 and a few features were added (incremental deduplication via +`dedup_citations_add_sources()`, deferred manual review via +`export_dedup_candidates()` / `reimport_dedup_candidates()`, and a +deduplication provenance log via `dedup_log()`). These are documented in +`NEWS.md`. All newly exported functions include `\value` documentation and +write only to user-supplied paths. ## Test environments * Local: Windows 11, R 4.5.0 -* win-builder: R-release and R-devel ## R CMD check results -0 errors | 0 warnings | 1 note - -* checking CRAN incoming feasibility ... NOTE - Maintainer: 'Trevor Riley ' +0 errors | 0 warnings | 0 notes (local, `R CMD check --as-cran`). - The "New submission" wording appears only because the previous version is not - yet published on CRAN. Any flagged URLs (e.g. the GNU GPL license pages) are - valid and resolve in a browser; the check machine reported transient - connection resets. +On CRAN's incoming checks we expect the standard "New submission" NOTE, since +the package is not yet published. Any URLs flagged (e.g. the GNU GPL license +pages) are valid and resolve in a browser. ## Reverse dependencies -None - CiteSource has no downstream dependents on CRAN. +None — this is a new submission with no downstream dependents. ## Notes -R/asys_dedup.R contains code vendored from the ASySD package +`R/asys_dedup.R` contains code vendored from the ASySD package (GPL >= 3, CAMARADES Group / Kaitlyn Hair) with attribution in the file header. CiteSource is also GPL >= 3, so the licenses are compatible. diff --git a/man/plot_source_overlap_upset.Rd b/man/plot_source_overlap_upset.Rd index 71bef2b1..61d6c5c7 100644 --- a/man/plot_source_overlap_upset.Rd +++ b/man/plot_source_overlap_upset.Rd @@ -44,7 +44,6 @@ will be the specific intersections listed.} \item{\code{main.bar.color}}{Color of the main bar plot} \item{\code{mainbar.y.max}}{The maximum y value of the intersection size bar plot scale. May be useful when aligning multiple UpSet plots horizontally.} \item{\code{sets.bar.color}}{Color of set size bar plot} - \item{\code{plot.title}}{Title of UpSetR plot} \item{\code{point.size}}{Size of points in matrix plot} \item{\code{line.size}}{Width of lines in matrix plot} \item{\code{mb.ratio}}{Ratio between matrix plot and main bar plot (Keep in terms of hundredths)} @@ -54,7 +53,6 @@ will be the specific intersections listed.} \item{\code{decreasing}}{How the variables in order.by should be ordered. "freq" is decreasing (greatest to least) and "degree" is increasing (least to greatest)} \item{\code{show.numbers}}{Show numbers of intersection sizes above bars} \item{\code{number.angles}}{The angle of the numbers atop the intersection size bars} - \item{\code{number.colors}}{The colors of the numbers atop the intersection size bars} \item{\code{group.by}}{How the data should be grouped ("degree" or "sets")} \item{\code{cutoff}}{The number of intersections from each set (to cut off at) when aggregating by sets} \item{\code{queries}}{Unified query of intersections, elements, and custom row functions. Entered as a list that contains a list of From 4ab9fbc063fed1c144cd5e84a7d7848fff5a9431 Mon Sep 17 00:00:00 2001 From: Trevor Riley Date: Mon, 8 Jun 2026 13:33:32 -0400 Subject: [PATCH 2/3] chore: drop unused networkD3 from Suggests --- DESCRIPTION | 1 - 1 file changed, 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d74662da..fc0bcf1e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -56,7 +56,6 @@ Suggests: htmltools, jsonlite, knitr, - networkD3, plotly, progressr, rmarkdown, From 384e5306d8fe893a2235d9859fee163a02150361 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Mon, 8 Jun 2026 17:35:14 +0000 Subject: [PATCH 3/3] Documentation --- man/plot_source_overlap_upset.Rd | 2 ++ 1 file changed, 2 insertions(+) diff --git a/man/plot_source_overlap_upset.Rd b/man/plot_source_overlap_upset.Rd index 61d6c5c7..71bef2b1 100644 --- a/man/plot_source_overlap_upset.Rd +++ b/man/plot_source_overlap_upset.Rd @@ -44,6 +44,7 @@ will be the specific intersections listed.} \item{\code{main.bar.color}}{Color of the main bar plot} \item{\code{mainbar.y.max}}{The maximum y value of the intersection size bar plot scale. May be useful when aligning multiple UpSet plots horizontally.} \item{\code{sets.bar.color}}{Color of set size bar plot} + \item{\code{plot.title}}{Title of UpSetR plot} \item{\code{point.size}}{Size of points in matrix plot} \item{\code{line.size}}{Width of lines in matrix plot} \item{\code{mb.ratio}}{Ratio between matrix plot and main bar plot (Keep in terms of hundredths)} @@ -53,6 +54,7 @@ will be the specific intersections listed.} \item{\code{decreasing}}{How the variables in order.by should be ordered. "freq" is decreasing (greatest to least) and "degree" is increasing (least to greatest)} \item{\code{show.numbers}}{Show numbers of intersection sizes above bars} \item{\code{number.angles}}{The angle of the numbers atop the intersection size bars} + \item{\code{number.colors}}{The colors of the numbers atop the intersection size bars} \item{\code{group.by}}{How the data should be grouped ("degree" or "sets")} \item{\code{cutoff}}{The number of intersections from each set (to cut off at) when aggregating by sets} \item{\code{queries}}{Unified query of intersections, elements, and custom row functions. Entered as a list that contains a list of