Render a HTML Report for GlySmith Results — polish

Generate a self-contained HTML report for a glysmith_result object. The report is rendered via rmarkdown::render() using an internal R Markdown template. If use_ai is TRUE, the report text will be polished, organized into sections, paired with plot descriptions, and summarized using the configured ellmer provider. DeepSeek is used by default for backward compatibility.

Usage

polish_report(
  x,
  output_file,
  title = "GlySmith report",
  open = interactive(),
  use_ai = FALSE,
  ai_provider = getOption("glysmith.ai_provider", "deepseek"),
  ai_model = getOption("glysmith.ai_model", NULL),
  ai_api_key = getOption("glysmith.ai_api_key", NULL),
  ai_base_url = getOption("glysmith.ai_base_url", NULL)
)

Arguments

x: A glysmith_result object.
output_file: Path to the output HTML file.
title: Report title.
open: Whether to open the report in a browser after rendering.
use_ai: Whether to polish the report text, organize sections, generate plot descriptions, and add a summary using AI with the configured ellmer provider. Default is FALSE.
ai_provider: AI provider passed to ellmer when use_ai = TRUE. One of "deepseek", "openai", "anthropic", "gemini", "openrouter", or "openai_compatible". Defaults to getOption("glysmith.ai_provider", "deepseek").
ai_model: AI model to use when use_ai = TRUE. Defaults to getOption("glysmith.ai_model"), or "deepseek-chat" for DeepSeek and the provider default for other providers.
ai_api_key: API key for the selected provider. If NULL, the provider specific environment variable is used. Defaults to getOption("glysmith.ai_api_key").
ai_base_url: Optional base URL for custom or OpenAI-compatible endpoints. Defaults to getOption("glysmith.ai_base_url").

Value

The normalized path to the generated HTML file.

Examples

if (FALSE) { # \dontrun{
library(glyexp)
exp <- real_experiment2
result <- forge_analysis(exp)
polish_report(result, tempfile(fileext = ".html"), open = FALSE)
} # }