Package 'biorecap'

Add prompt to a data frame of preprints

Description

Add prompt to a data frame of preprints

Usage

add_prompt(preprints, ...)

Arguments

preprints	Result from get_preprints().
...	Additional arguments to build_prompt_preprint().

Value

A data frame of preprints with a prompt added.

See Also

build_prompt_preprint()

Examples

preprints <- get_preprints(subject=c("bioinformatics", "genomics"))
preprints <- add_prompt(preprints)
preprints

---

Add prompts for an entire subject

Description

Add prompts for an entire subject

Usage

add_prompt_subject(preprints, ...)

Arguments

preprints	Output from get_preprints() followed by add_prompt() followed by add_summary().
...	Additional arguments to build_prompt_subject().

Value

A tibble with a subject and prompt column.

Examples

subjects <-
  example_preprints |>
  dplyr::group_by(subject) |>
  add_prompt_subject()
subjects

---

Generate a summary from a data frame of prompts

Description

Generate a summary from a data frame of prompts

Usage

add_summary(preprints, model = "llama3.2", host = NULL)

Arguments

preprints	Output from get_preprints() followed by add_prompt().
model	A model available to Ollama (run ollamar::list_models()) to see what's available.
host	The base URL to use. Default is NULL, which uses Ollama's default base URL.

Value

A tibble, with a response column added.

Examples

## Not run: 
# Individual papers
preprints <-
  get_preprints(c("genomics", "bioinformatics")) |>
  add_prompt() |>
  add_summary()
preprints

## End(Not run)

---

Create a report from bioRxiv/medRxiv preprints

Description

Create a report from bioRxiv/medRxiv preprints

Usage

biorecap_report(
  output_dir = ".",
  subject = NULL,
  nsentences = 2L,
  model = "llama3.2",
  host = NULL,
  use_example_preprints = FALSE,
  ...
)

Arguments

output_dir	Directory to save the report.
subject	Character vector of subjects to include in the report.
nsentences	Number of sentences to summarize each paper in.
model	The model to use for generating summaries. See ollamar::list_models().
host	The base URL to use. Default is NULL, which uses Ollama's default base URL.
use_example_preprints	Use the example preprints data included with the package instead of fetching new data from bioRxiv/medRxiv. For diagnostic/testing purposes only.
...	Other arguments passed to rmarkdown::render().

Value

Nothing; called for its side effects to produce a report.

Examples

## Not run: 
output_dir <- tempdir()
biorecap_report(use_example_preprints=TRUE, output_dir=output_dir)
biorecap_report(subject=c("bioinformatics", "genomics", "synthetic_biology"),
                output_dir=output_dir)

## End(Not run)

---

Construct a prompt to summarize a paper

Description

Construct a prompt to summarize a paper

Usage

build_prompt_preprint(
  title,
  abstract,
  nsentences = 2L,
  instructions = c("I am giving you a paper's title and abstract.",
    "Summarize the paper in as many sentences as I instruct.",
    "Do not include any preamble text to the summary",
    "just give me the summary with no preface or intro sentence.")
)

Arguments

title	The title of the paper.
abstract	The abstract of the paper.
nsentences	The number of sentences to summarize the paper in.
instructions	Instructions to the prompt. This can be a character vector that gets collapsed into a single string.

Value

A string containing the prompt.

Examples

build_prompt_preprint(title="A great paper", abstract="This is the abstract.")

---

Construct a prompt to summarize a set of papers from a subject

Description

Construct a prompt to summarize a set of papers from a subject

Usage

build_prompt_subject(
  subject,
  title,
  summary,
  nsentences = 5L,
  instructions = c("I am giving you information about recent bioRxiv/medRxiv preprints.",
    "I'll give you the subject, preprint titles, and short summary of each paper.",
    "Please provide a general summary new advances in this subject/field in general.",
    "Provide this summary of the field in as many sentences as I instruct.",
    "Do not include any preamble text to the summary",
    "just give me the summary with no preface or intro sentence.")
)

Arguments

subject	The name of the subject.
title	A character vector of titles in the subject
summary	A character vector of the summaries of the paper provided by get_preprints() followed by add_prompt() followed by add_summary().
nsentences	The number of sentences to summarize the subject in.
instructions	Instructions to the prompt. This can be a character vector that gets collapsed into a single string.

Value

A string containing the prompt.

Examples

title <- example_preprints |> dplyr::filter(subject=="bioinformatics") |> dplyr::pull(title)
summary <- example_preprints |> dplyr::filter(subject=="bioinformatics") |> dplyr::pull(summary)
build_prompt_subject(subject="bioinformatics", title=title, summary=summary)

---

Example preprints with summaries

Description

Example preprints with summaries from August 6, 2024.

Usage

example_preprints

Format

A tibble returned from get_preprints() followed by add_prompt() followed by add_summary().

Examples

example_preprints

---

Get bioRxiv/medRxiv preprints

Description

Get bioRxiv/medRxiv preprints

Usage

get_preprints(subject = "all", clean = TRUE)

Arguments

subject	A character vector of valid bioRxiv and/or medRxiv subjects. See subjects.
clean	Logical; try to strip out graphical abstract information? If TRUE, this strips away any text between O_FIG and C_FIG, and the words ⁠graphical abstract⁠ from the abstract text in the RSS feed.

Value

A data frame of preprints from bioRxiv and/or medRxiv.

Examples

preprints <- get_preprints(subject=c("bioinformatics", "Public_and_Global_Health"))
preprints

---

Safely query bioRxiv/medRxiv RSS feeds

Description

Safely query bioRxiv/medRxiv RSS feeds

Usage

safely_query_rss(subject, server = c("biorxiv", "medrxiv"))

Arguments

subject	A character vector of valid bioRxiv and/or medRxiv subjects. See subjects.
server	A character vector of either "biorxiv" or "medrxiv".

Value

A data frame of preprints from bioRxiv and/or medRxiv.

---

bioRxiv subjects

Description

Names of subjects with RSS feeds in biorXiv

Usage

subjects

Format

A list of character vectors of subjects, one for bioRxiv, one for medRxiv.

References

https://www.biorxiv.org/alertsrss

Examples

subjects

---

Create a markdown table from prepreprint summaries

Description

Create a markdown table from prepreprint summaries

Usage

tt_preprints(preprints, cols = c("title", "summary"), width = c(1, 3))

Arguments

preprints	Output from get_preprints() followed by add_prompt() followed by add_summary().
cols	Columns to display in the resulting markdown table.
width	Vector of relative widths equal to length(cols).

Value

A tinytable table.

Examples

# Use built-in example data
example_preprints
tt_preprints(example_preprints[1:2,])

---