install.packages("prismaid", repos = c("https://open-and-sustainable.r-universe.dev", "https://cloud.r-project.org"))

library(prismaid)

# Run screening on manuscripts
screening_content <- paste(readLines("screening.toml"), collapse = "\n")
Screening(screening_content)  # Note the capitalization


# Download papers from Zotero
zotero_content <- paste(readLines("zotero.toml"), collapse = "\n")
DownloadZotero(zotero_content)

# Download from URL list
DownloadURLList("urls.txt")

# Convert files to text
Convert("./papers", "pdf,docx,html")  # Note the capitalization

# Convert with Tika OCR fallback
Convert("./papers", "pdf", "localhost:9998")

# OCR-only for PDFs
Convert("./papers", "pdf", "localhost:9998", "", TRUE)

# Run a systematic review
toml_content <- paste(readLines("project.toml"), collapse = "\n")
RunReview(toml_content)  # Note the capitalization

# Validate a configuration without executing it
# config type is one of "review", "screening", or "zotero"
ValidateConfig("review", toml_content)

# Check a RevAIse review record against a reporting protocol (returns a JSON string)
report <- CheckConformance(record_json, "prisma-2020")

# Get a protocol's full requirement checklist, to plan a conforming review
guidance <- ProtocolGuidance("prisma-2020")