Fix ggplot2 deprecation warnings (aes_string, size for lines)

[Copilot]

Problem

Calling Superpower::ANOVA_design() and other plotting functions produced ggplot2 lifecycle warnings about deprecated APIs:

1. aes_string() (deprecated since ggplot2 3.0.0)
2. size aesthetic for lines (deprecated since ggplot2 3.4.0; replaced by linewidth)

Example warning:

Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.

Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Solution

1. Replaced aes_string() with aes() using tidy evaluation

Before:

ggplot(dataframe_means, aes_string(y = "mu", x = factornames[1]))

After:

ggplot(dataframe_means, aes(y = .data[["mu"]], x = .data[[factornames[1]]]))

The .data[[]] pronoun is the recommended approach for programmatic column selection with ggplot2's tidy evaluation system.

2. Replaced size with linewidth for line geometries

Before:

geom_errorbar(..., size = .6, ...)
geom_line(size = 1.5)

After:

geom_errorbar(..., linewidth = .6, ...)
geom_line(linewidth = 1.5)

Files Modified

• R/ANOVA_design.R - Fixed aes_string() and geom_errorbar() size
• R/ANOVA_exact.R - Fixed aes_string()
• R/plot_power.R - Fixed geom_line() size
• R/minimize_balance_alpha.R - Fixed geom_line() size

Impact

• ✅ Eliminates all ggplot2 deprecation warnings
• ✅ No behavior changes - plots remain identical
• ✅ Compatible with current and future ggplot2 versions
• ✅ Minimal, surgical changes to codebase

Fixes #[issue_number]

Original prompt

---

This section details on the original issue you should resolve

<issue_title>ANOVA_design() triggers ggplot2 deprecation warnings (aes_string, size for lines)</issue_title>
<issue_description>### Description

Calling Superpower::ANOVA_design() produces ggplot2 lifecycle warnings about use of deprecated APIs:

• aes_string() (deprecated since ggplot2 3.0.0; use tidy-eval with aes()), and

• size aesthetic for lines (deprecated since ggplot2 3.4.0; use linewidth).

The warnings indicate that the deprecated features are used inside Superpower.

Minimal reproducible example

set.seed(123)
library(Superpower)
library(ggplot2)

design_result <- ANOVA_design(
  design      = "2b*2w",
  n           = 20,
  mu          = c(0, 0, 0, 0),
  sd          = 1,
  r           = 0.5,
  labelnames  = c("condition","A","B","time","pre","post")
)

What I expected

No ggplot2 deprecation warnings during design creation/plotting.

What actually happened

1: aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.
ℹ The deprecated feature was likely used in the Superpower package.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings() to see where this warning was generated.```

2: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
ℹ The deprecated feature was likely used in the Superpower package.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.

Lifecycle trace (from lifecycle::last_lifecycle_warnings())

 2.   └─Superpower::ANOVA_design(...) 
 3.     ├─ggplot2::ggplot(...)
 4.     ├─ggplot2:::ggplot.default(...)
 5.     │ └─ggplot2:::validate_mapping(mapping)
 6.     │   └─S7::S7_inherits(mapping)
 7.     └─ggplot2::aes_string(y = "mu", x = factornames[1], colour = factornames[2])
 8.       └─ggplot2:::deprecate_warn0(...)

Environment

> R.version.string
[1] "R version 4.5.1 (2025-06-13 ucrt)"
> packageVersion("Superpower")   
[1] ‘0.2.4.1’
> packageVersion("ggplot2")      
[1] ‘4.0.0’
> packageVersion("lifecycle") 
[1] ‘1.0.4’
> sessioninfo::session_info() 
─ Session info ─────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.5.1 (2025-06-13 ucrt)
 os       Windows 10 x64 (build 19045)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  English_Jamaica.utf8
 ctype    English_Jamaica.utf8
 tz       Africa/Cairo
 date     2025-10-03
 rstudio  2025.09.1+401 Cucumberleaf Sunflower (desktop)
 pandoc   3.2 @ C:\\PROGRA~1\\Pandoc\\pandoc.exe
```</issue_description>

<agent_instructions>check for deprecation issues with ggplot2, in particular the warning related to size aesthetic for lines</agent_instructions>

## Comments on the Issue (you are @copilot in this section)

<comments>
</comments>

Fixes #52

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[Copilot]

Pull Request Overview

This PR fixes ggplot2 deprecation warnings by updating deprecated API usage in the Superpower package. The changes address two main deprecation issues: replacing aes_string() with tidy evaluation using aes() and .data[[]], and replacing the deprecated size parameter with linewidth for line geometries.

• Replaced aes_string() with aes() using .data[[]] pronoun for tidy evaluation
• Updated geom_line() and geom_errorbar() to use linewidth instead of deprecated size parameter

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.

File	Description
R/ANOVA_design.R	Updated aes_string() calls and geom_errorbar() size parameter
R/ANOVA_exact.R	Replaced aes_string() with tidy evaluation syntax
R/plot_power.R	Changed geom_line() size parameter to linewidth
R/minimize_balance_alpha.R	Updated geom_line() size parameter to linewidth

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