Use autoplot for curve params in methodology vignette

[Copilot]

Thank you for taking the time to submit a pull request!

To maximize the chances of acceptance:

• The title of your PR should briefly describe the change.
• Commit/merge messages to be included in NEWS.md should begin with -.
• Code should follow the tidyverse style guide.
• Documentation should use roxygen2, with Markdown syntax.
• Contributions should include unit tests (using testthat).

For more information see Contributing.

The methodology vignette example relied on a deprecated plotting helper, resulting in missing curves in the rendered figure. This switches the example to the curve_params autoplot method and records the documentation update with a version bump.

• Vignette update
  • Replace plot_curve_params_one_ab() with autoplot() for curve params and keep the same plot composition.
• Metadata
  • Bump development version and add a Documentation entry in NEWS.

curve1 |>
  autoplot(
    quantiles = NULL,
    log_y = FALSE,
    n_curves = 1
  ) +
  xlim(0, 100) +
  theme_minimal()

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• https://storage.googleapis.com/cos-osf-prod-files-us-east1/eb679c16124f859a9a715a4b48babdcaad12c23a1e82b8a21f0e471aaa4b216d
  • Triggering command: /opt/R/4.5.3/lib/R/bin/exec/R /opt/R/4.5.3/lib/R/bin/exec/R -e library(serocalculator);~+~library(dplyr);~+~library(ggplot2);~+~cur_ai~+~<-~+~'HlyE_IgG';~+~curves~+~<-~+~'REDACTED'~+~|>~+~load_sr_params()~+~|>~+~filter(iter~+~<~+~50);~+~curve1~+~<-~+~curves~+~|>~+~filter(iter~+~==~+~5,~+~antigen o -e /R/include ges=datasets,utils,grDevices,graphics,stats,methods -e 'tryCatch(parallel:::.workRSOCK,error=fun-c de (http block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

---

⌨️ Start Copilot coding agent tasks without leaving your editor — available in VS Code, Visual Studio, JetBrains IDEs and Eclipse.

[kristinawlai]

@copilot That still didn't fix the issue in this code in methodology.qmd. The plot is created, but the curve is completely missing on the plot: library(serocalculator)
library(dplyr)

Import longitudinal antibody parameters from OSF

curves <-
"https://osf.io/download/rtw5k/" %>%
load_sr_params() %>%
filter(iter < 50)

curve1 <-
curves %>%
filter(
iter == 5,
antigen_iso == cur_ai
)
library(ggplot2)

curve1 |>
serocalculator:::plot_curve_params_one_ab(
log_y = FALSE
) +
xlim(0, 100) +
theme_minimal() +
geom_vline(
aes(
xintercept = curve1$t1,
col = "t1"
)
) +

geom_hline(
aes(
yintercept = curve1$y0,
col = "y0"
)
) +

geom_hline(
aes(
yintercept = curve1$y1,
col = "y1"
)
) +
geom_point(
data = curve1,
aes(
x = t1,
y = y1,
col = "(t1,y1)"
)
) +
theme(legend.position = "bottom") +
labs(col = "")

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ All tests successful. No failed tests found.

Files with missing lines	Coverage Δ
R/plot_curve_params_one_ab.R	93.75% <100.00%> (ø)

[kristinawlai]

@copilot plot_curve_params_one_ab() is an older function. Please replace with an autoplot method for curve params in the methodology.qmd.

[Copilot]

@kristinawlai The model claude-sonnet-4.6 is not available for your account. This can happen if the model was disabled by your organization's policy or if your Copilot plan doesn't include access to it.

You can try again without specifying a model (just @copilot) to use the default, or choose a different model from the model picker.

If you want to contact GitHub about this error, please mention the following identifier so they can better serve you: 02f103ff-ee32-404e-ae63-0576213ad7d5

[Copilot]

@kristinawlai The model claude-sonnet-4.6 is not available for your account. This can happen if the model was disabled by your organization's policy or if your Copilot plan doesn't include access to it.

You can try again without specifying a model (just @copilot) to use the default, or choose a different model from the model picker.

If you want to contact GitHub about this error, please mention the following identifier so they can better serve you: 02f103ff-ee32-404e-ae63-0576213ad7d5

[Copilot]

@kristinawlai The model claude-sonnet-4.6 is not available for your account. This can happen if the model was disabled by your organization's policy or if your Copilot plan doesn't include access to it.

You can try again without specifying a model (just @copilot) to use the default, or choose a different model from the model picker.

If you want to contact GitHub about this error, please mention the following identifier so they can better serve you: 02f103ff-ee32-404e-ae63-0576213ad7d5

[kristinawlai]

@copilot plot_curve_params_one_ab() is an older function. Please replace with an autoplot method for curve params in the methodology.qmd.

[github-actions]

📖 https://UCD-SERG.github.io/serocalculator/preview/pr511/
Preview documentation for this PR (at commit 3ef1b3f)