Add tidy-r skill for modern tidyverse R development

.claude-plugin/marketplace.json

@@ -76,6 +76,15 @@
         "./quarto/quarto-authoring",
         "./quarto/quarto-alt-text"
       ]
+    },
+    {
+      "name": "tidyverse",
+      "description": "Collection of skills for tidyverse-style R development",
+      "source": "./",
+      "strict": false,
+      "skills": [
+        "./tidyverse/tidy-r"
+      ]
     }
   ]
 }

tidyverse/README.md

@@ -1,6 +1,10 @@
 # Tidyverse Skills
 
-Skills specific to using tidyverse packages and tidyverse-specific package development patterns.
+Skills for tidyverse-style R development, covering modern patterns, style guidelines, and best practices.
+
+## Skills
+
+- **[tidy-r](./tidy-r/)** - Modern tidyverse patterns, style guide, and migration guidance for R development. Covers native pipe usage, join_by() syntax, .by grouping, pick/across/reframe operations, filter_out/when_any/when_all, recode_values/replace_values/replace_when, tidy selection, stringr patterns, naming conventions, and migration from base R or older tidyverse APIs.
 
 ## Potential Skills
 

tidyverse/tidy-r/SKILL.md

@@ -0,0 +1,119 @@
+---
+name: tidy-r
+description: >
+  Modern tidyverse patterns, style guide, and migration guidance for R development. Use this skill when writing R code, reviewing tidyverse code, updating legacy R code, or enforcing consistent style. Covers native pipe usage, join_by() syntax, .by grouping, pick/across/reframe, filter_out/when_any/when_all, recode_values/replace_values/replace_when, tidyselect helpers, .data/.env pronouns, stringr, naming conventions, and readr.
+metadata:
+  r_version: ">=4.5.0"
+  tidyverse_version: ">=2.0.0"
+  dplyr_version: ">=1.2.0"
+---
+
+# Modern Tidyverse R Reference
+
+Code from blog posts and StackOverflow often uses deprecated APIs, magrittr pipes, or base R patterns where a modern tidyverse function exists. This guide encodes the current recommended approach.
+
+## Reference files
+
+Consult the appropriate reference file for detailed patterns and examples:
+
+| Topic | Reference file | When to consult |
+|-------|---------------|-----------------|
+| **Joins** | [joins.md](references/joins.md) | Merging data, `*_join`, `join_by`, matching rows, lookup tables |
+| **Grouping & columns** | [grouping.md](references/grouping.md) | `.by`, `group_by`, `across`, `pick`, `reframe`, column operations |
+| **Recoding & replacing** | [recode-replace.md](references/recode-replace.md) | `recode_values`, `replace_values`, `replace_when`, `filter_out`, `when_any`, `when_all` |
+| **Strings** | [stringr.md](references/stringr.md) | String manipulation, regex, `str_*` functions, text processing |
+| **Tidy selection** | [tidyselect.md](references/tidyselect.md) | Column selection helpers, `where()`, `all_of()`, `any_of()`, boolean ops, `.data`/`.env` pronouns |
+| **Style** | [tidyverse-style.md](references/tidyverse-style.md) | Naming, formatting, spacing, error messages, `cli::cli_abort` |
+| **Migration** | [migration.md](references/migration.md) | Updating old code, base R conversion, deprecated functions |
+
+For requests that span multiple topics (e.g., "rewrite this old code" touches migration + style), read multiple files.
+
+## Core principles
+
+1. **Use modern tidyverse patterns** -- Prioritize dplyr 1.2+ features, native pipe, and current APIs
+2. **Write readable code first** -- Optimize only when necessary
+3. **Follow tidyverse style guide** -- Consistent naming, spacing, and structure
+
+## Quick reference
+
+### Pipe and lambda
+
+- Always `|>`, never `%>%`
+- Use `_` placeholder for non-first arguments: `x |> f(1, y = _)`. The placeholder must be named and used exactly once.
+- Always `\(x)`, never `function(x)` or `~` in map/keep/etc.
+
+### Code organization
+
+Use newspaper style: high-level logic first, helpers below. Don't define functions inside other functions unless they are very brief.
+
+### Grouping
+
+- Prefer `.by` for per-operation grouping; use `group_by()` when grouping must persist across multiple operations
+- Never add `ungroup()` before or after `.by` -- it always returns ungrouped data
+- Consolidate multiple `mutate(.by = x)` calls into one when they share the same `.by`; keep separate only when `.by` differs or a later column depends on an earlier one
+- Place `.by` on its own line for readability
+
+### Joins
+
+- Use `join_by()`, never `c("a" = "b")`
+- Use `relationship`, `unmatched`, `na_matches` for quality control
+
+### Recoding and replacing (dplyr >=1.2.0)
+
+| Task | Function |
+|------|----------|
+| Recode values (new column) | `recode_values()` |
+| Replace values in place | `replace_values()` |
+| Conditional update in place | `replace_when()` |
+| Complex conditional (new column) | `case_when()` |
+| Drop rows (NA-safe) | `filter_out()` |
+| OR conditions | `when_any()` |
+| AND conditions | `when_all()` |
+
+### Error handling
+
+Use `cli::cli_abort()` with problem statement + bullets, never `stop()`.
+
+### R idioms
+
+- `TRUE`/`FALSE`, never `T`/`F`
+- `message()` for info, never `cat()`
+- `map_*()` over `sapply()` for type stability
+- `set.seed()` with date-time, never 42
+
+## Example
+
+```r
+library(tidyverse)
+
+penguins <- penguins |>
+  filter_out(is.na(sex)) |>
+  mutate(size = case_when(
+    body_mass > 4500 ~ "large",
+    body_mass > 3500 ~ "medium",
+    .default = "small"
+  ))
+
+# Coordinates for spatial join below
+island_coords <- tribble(
+  ~island,      ~latitude,
+  "Biscoe",     -65.5,
+  "Dream",      -64.7,
+  "Torgersen",  -64.8
+)
+
+island_summary <- penguins |>
+  summarise(
+    mean_flipper = mean(flipper_len),
+    mean_mass = mean(body_mass),
+    n = n(),
+    .by = c(species, island)
+  ) |>
+  left_join(
+    island_coords,
+    by = join_by(island),
+    unmatched = "error"
+  ) |>
+  arrange(species, island)
+```
+