## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

## ----setup--------------------------------------------------------------------
library(krt)

## -----------------------------------------------------------------------------
txt <- "We stained with anti-TH (RRID:AB_390204) from Millipore (Cat# AB152)
        and analyzed images in Fiji (RRID:SCR_002285). Data: GEO GSE12345."
scan_identifiers(txt)

## -----------------------------------------------------------------------------
res <- extract_krt(txt)
as.data.frame(res$krt)[, c("resource_type", "display_name", "rrid")]

## -----------------------------------------------------------------------------
jats <- system.file("extdata", "examples", "sample.jats.xml", package = "krt")
res <- extract_krt(jats)
res$existing_krt

## ----eval = FALSE-------------------------------------------------------------
# cfg <- krt_llm("openai", model = "gpt-4o-mini")   # reads OPENAI_API_KEY
# res <- extract_krt("path/to/manuscript.pdf", engine = "llm", llm = cfg)

## ----eval = FALSE-------------------------------------------------------------
# register_llm_provider("local", function(prompt, llm) {
#   # call your local server, return the model's text output
# })
# extract_krt(txt, engine = "llm",
#             llm = structure(list(provider = "local"), class = "krt_llm"))