Title: USGS INL Project Office Publications
Version: 1.3.0
Description: Contains bibliographic information for the U.S. Geological Survey (USGS) Idaho National Laboratory (INL) Project Office.
Depends: R (≥ 4.1)
Imports: checkmate, stats, tm
Suggests: chromote, connectapi, covr, cyclocomp, graphics, htmltools, htmlwidgets, jsonlite, kableExtra, knitr, lintr, magick, markdown, png, pkgbuild, pkgdown, pkgload, pdftools, reactable, renv, rmarkdown, rsconnect, RWeka, stringi, tesseract, textutils, tinytest, utils, webshot2, wordcloud2
License: CC0
URL: https://rconnect.usgs.gov/INLPO/inlpubs-main/, https://code.usgs.gov/inl/inlpubs
BugReports: https://code.usgs.gov/inl/inlpubs/-/issues
Copyright: This software is in the public domain because it contains materials that originally came from the United States Geological Survey (USGS), an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at https://www.usgs.gov/information-policies-and-instructions/copyrights-and-credits
Encoding: UTF-8
SystemRequirements: Complete functionality necessitates Amazon Corretto (win), and default-jre, pandoc, libxml2-dev, libpoppler-cpp-dev, libmagick++-dev, optipng, libtesseract-dev, libleptonica-dev, tesseract-ocr-eng (deb)
LazyData: true
LazyDataCompression: xz
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2025-06-25 20:39:49 UTC; jfisher
Author: Jason C. Fisher ORCID iD [aut, cre], Kerri C. Treinen ORCID iD [aut], Allison R. Trcka ORCID iD [aut]
Maintainer: Jason C. Fisher <jfisher@usgs.gov>
Repository: CRAN
Date/Publication: 2025-06-25 23:10:02 UTC

Add Content from PDF Documents

Description

Incorporate the text or cover image from a PDF document into the inlpubs package.

Usage

add_content(
  pub_id,
  year,
  type = c("text", "image"),
  ...,
  srcdir = "archive",
  destdir = tempdir(),
  ignore = NULL,
  pubs = inlpubs::pubs,
  overwrite = FALSE
)

Arguments

pub_id

'character' vector. Unique identifier for the publication. May also be specified using the year of publication.

year

'integer' vector. Year of publication.

type

'character' string. Type of content to obtain from the PDF file. Specify as either "text" (the default) or "image".

...

Arguments to be passed to the function used to obtain the context, get_pdf_text for "text" and get_pdf_image for "image".

srcdir

'character' string. The PDF document is located in a subdirectory of the source directory, and this subdirectory is named after the publication year. It is set to default to the 'archive' directory, which is found in the working directory.

destdir

'character' string. Target folder for the cover image that is saved in JPEG format. Defaults to the temporary directory.

ignore

'character' vector. Publication identifier(s) to ignore.

pubs

'pub' table. Publications of the INLPO, see pubs dataset for data format.

overwrite

'logical' flag. Whether to overwrite an existing text or image file.

Value

Returns the path to the saved text or image file, invisibly.

Author(s)

J.C. Fisher, U.S. Geological Survey, Idaho Water Science Center

Contributing Authors to INLPO Publications

Description

Authors who have contributed to the publications by the U.S. Geological Survey (USGS), Idaho Water Science Center, Idaho National Laboratory Project Office (INLPO).

Usage

authors

Format

An object of class 'author' that inherits behavior from the 'data.frame' class and includes the following columns:

author_id

Unique identifier for the author.

name

Name of author, surname first and initials or given name.

person

Information about the person like email address and ORCiD identifier.

pub_id

Identifier(s) of the publication(s) the author has contributed to, referes to the primry key of the pubs data table.

total_pub

Total number of publications.

single_authored

Number of single-authored publications.

multi_authored

Number of multi-authored publications.

first_authored

Number of multi-authored publications where the researcher appears as first author.

first_year

First year author published.

last_year

Last year author published.

Source

Curated by INLPO staff.

Examples

# Subset Jason Fisher's information and display structure:
author <- authors["jfisher", ]
str(author, max.level = 3, width = 75, strict.width = "cut")

# Print author's given name:
author$person |> format(include = "given")

Filter Data List Column

Description

Create a data list column filter for a React Table. Requires that the htmltools packages is available.

Usage

filter_data_list(table_id, style = "width: 100%; height: 28px;")

Arguments

table_id

'character' string. Unique table identifier.

style

'character' string. CSS style applied to input HTML tag.

Value

Returns a function to perform filtering.

Examples

f <- filter_data_list("table-id")

Obtain Image from a PDF Document

Description

Obtain an image from any PDF document. Requires that the pdftools and magick packages are available.

Usage

get_pdf_image(
  input,
  output = tempfile(fileext = ".jpg"),
  page = 1,
  width = 300,
  depth = 8,
  quality = 70
)

Arguments

input

'character' string. File path to PDF document.

output

'character' string. Location to write the JPEG image file.

page

'integer' number. Page number in the document. Defaults to page 1.

width

'integer' number. Image width in pixels.

depth

'integer' number. Image color depth (either 8 or 16). Defaults to 8.

quality

'integer' number. JPEG quality, a number between 0 and 100. Defaults to 70.

Value

Returns the path to the image file.

Author(s)

J.C. Fisher, U.S. Geological Survey, Idaho Water Science Center

See Also

add_content function to add cover images to the inlpubs package.

Examples

input <- system.file("extdata", "test.pdf", package = "inlpubs")
path <- get_pdf_image(input)

unlink(path)

Obtain Text from a PDF Document

Description

Obtain text from any PDF document. Requires that the pdftools and tesseract packages are available.

Usage

get_pdf_text(input, output = tempfile(fileext = ".txt"), dpi = 600, psm = 1)

Arguments

input

'character' string. File path to PDF document.

output

'character' string. Location to write the text file.

dpi

'integer' number between 100 and 1200. Dots per inch (DPI). The resolution of an image, specifically the number of pixels per inch. For optimal optical character recognition (OCR) accuracy, 600 DPI (the default) is recommended.

psm

integer number between 0 and 13. Page Segmentation Mode (PSM). Describes the layout of the text you are trying to extract. For processing two columns of text you should use the page segmentation mode 1 (default). PSM 1 (default) is used to automatically segment the page into different text areas and also detect the orientation and script of the text.

Value

Returns the path to the text file. Each page from the PDF is transcribed as a separate line in the file.

Author(s)

J.C. Fisher, U.S. Geological Survey, Idaho Water Science Center

See Also

add_content function to add texts to the inlpubs-package corpus.

Examples

## Not run: 
  input <- system.file("extdata", "test.pdf", package = "inlpubs")
  path <- get_pdf_text(input)

  unlink(path)

## End(Not run)

Get Person(s)

Description

Filter a list of individuals based on their distinct identifiers.

Usage

get_person(x, persons)

Arguments

x

'character' vector. Identifier for one or more persons.

persons

'person' named list. Information about an arbitrary number of persons. Each element in the list is assigned a name, which uniquely identifies a person.

Value

A subset of persons.

Author(s)

J.C. Fisher, U.S. Geological Survey, Idaho Water Science Center

Examples

get_person("jfisher", persons = inlpubs::authors$person)

Create Author and Publication Webpages

Description

Creates a webpage for each author, listing their publications. Each webpage is saved as an R Markdown file.

Usage

make_webpages(authors = NULL, pubs = NULL, destdir = tempdir(), quiet = FALSE)

Arguments

authors

'author' data frame. Contributing authors to the INLPO publications, see authors dataset for data format.

pubs

'pub' data frame. Publications of the INLPO, see pubs dataset for data format.

destdir

'character' string. Destination directory to write files, with tilde-expansion performed. Defaults to a temporary directory.

quiet

'logical' flag. Whether to suppress printing of debugging information.

Value

NULL invisibly.

Author(s)

J.C. Fisher, U.S. Geological Survey, Idaho Water Science Center

Examples

destdir <- tempfile("")
make_webpages(
  authors = inlpubs::authors,
  pubs = inlpubs::pubs,
  destdir = destdir,
  quiet = TRUE
)

unlink(destdir, recursive = TRUE)

Create Word Cloud

Description

Create a word cloud from a frequency table of words, and save to a PNG file. Requires R-packages htmltools, htmlwidgets, magick, webshot2, and wordcloud2 are available. System dependencies include the the following: ImageMagick for displaying the PNG image, OptiPNG for PNG file compression, and Chrome- or a Chromium-based browser with support for the Chrome DevTools protocol. Use find_chromate function to find the path to the Chrome browser.

Usage

make_wordcloud(
  x,
  max_terms = 200,
  size = 1,
  shape = "circle",
  ellipticity = 0.65,
  ...,
  width = 910,
  output = NULL,
  display = FALSE
)

Arguments

x

'data.frame'. A frequency table of terms that includes "term" and "freq" in each column.

max_terms

'integer' number. Maximum number of terms to include in the word cloud.

size

'numeric' number. Font size.

shape

'character' string. Shape of the “cloud” to draw. Possible shapes include a "circle", "cardioid", "diamond", "triangle-forward", "triangle", "pentagon", and "star".

ellipticity

'numeric' number. Degree of “flatness” of the shape to draw, a value between 0 and 1.

...

Additional arguments to be passed to the wordcloud2 function.

width

'integer' number. Desired image width in pixels.

output

'character' string. Path to the output file, by default the word cloud is copied to a temporary file.

display

'logical' flag. Whether to display the saved PNG file in a graphics window. Requires access to the magick package.

Value

File path to the word cloud plot in PNG format.

Author(s)

J.C. Fisher, U.S. Geological Survey, Idaho Water Science Center

See Also

mine_text function to perform a term frequency text analysis.

Examples

## Not run: 
  d <- wordcloud2::demoFreq |> head(n = 10)
  colnames(d) <- c("term", "freq")
  file <- make_wordcloud(d, display = interactive())

  unlink(file)

## End(Not run)

Mine Text

Description

Performs a term frequency text analysis. A term is defined as a word or group of words.

Usage

mine_text(docs, ngmin = 1, ngmax = ngmin, sparse = NULL)

Arguments

docs

'list' or 'character' vector. Document text to analyze. Each list item contains the extracted text from a single document.

ngmin, ngmax

integer number. Splits strings into n-grams with given minimal and maximal numbers of grams. An n-gram is an ordered sequence of n words taken from the body of a text. Requires the RWeka package is available and that the environment variable JAVA_HOME points to where the Java software is located. Recommended for single text compoents only.

sparse

'numeric' number that is greater than 0 and less than 1. A threshold of relative document frequency for a term. It specifies the proportion of documents in which a term must appear to be retained. For example if you specify sparse equal to 0.99, it removes terms that are more sparse than 0.99. Conversely, at 0.01, only terms appearing in nearly every document will be retained.

Details

HTML entities are decoded when the textutils package is available.

Value

A term-frequency data table giving the number of times each word occurs in the text. A column in the table represents a single component in the docs argument, and each row provides frequency counts for a particular word (also known as a 'term').

Author(s)

J.C. Fisher, U.S. Geological Survey, Idaho Water Science Center

See Also

search_terms function to search for terms within the resulting term-frequency data table.

make_wordcloud function to create a word cloud.

Examples

d <- c(
  "The quick brown fox jumps over the lazy lazy dog.",
  "Pack my brown box.",
  "Jazz fly brown dog."
) |>
  mine_text()

d <- list(
  "A" = "The quick brown fox jumps over the lazy lazy dog.",
  "B" = c("Pack my brown box.", NA, "Jazz fly brown dog."),
  "C" = NA_character_
) |>
  mine_text()

Publications of the INLPO

Description

Bibliographic information for reports, articles, maps, and theses related to scientific monitoring and research conducted by the U.S. Geological Survey (USGS), Idaho Water Science Center, Idaho National Laboratory Project Office (INLPO).

Usage

pubs

Format

An object of class 'pub' that inherits behavior from the 'data.frame' class and includes the following columns:

pub_id

Unique identifier for the publication.

institution

Name of the institution that published and/or sponsored the report.

type

Type of publication.

text_ref

Text reference (also known as the in-text citation) that excludes the year of publication.

year

Year of publication.

author_id

Identifier(s) of the author(s), referes to the primry key of the authors data table.

title

Title of publication.

bibentry

Bibliographic entry of class bibentry.

abstract

Abstract of publication.

annotation

Annotation of publication.

annotation_src

Identifier for the annotation source publication (Knobel and others, 2005; Bartholomay, 2022).

files

File names associated with the publication.

Source

Many of these publications are available through the USGS Publications Warehouse.

References

Bartholomay, R.C., 2022, Historical development of the U.S. Geological Survey hydrological monitoring and investigative programs at the Idaho National Laboratory, Idaho, 2002-2020: U.S. Geological Survey Open-File Report 2022-1027 (DOE/ID-22256), 54 p., doi:10.3133/ofr20221027.

Knobel, L.L., Bartholomay, R.C., and Rousseau, J.P., 2005, Historical development of the U.S. Geological Survey hydrologic monitoring and investigative programs at the Idaho National Engineering and Environmental Laboratory, Idaho, 1949 to 2001: U.S. Geological Survey Open-File Report 2005–1223 (DOE/ID–22195), 93 p., doi:10.3133/ofr20051223.

Examples

# Subset Fisher and others (2012) and display structure:
id <- "FisherOthers2012"
pub <- pubs[id, ]
str(pub, max.level = 3, width = 75, strict.width = "cut")

# Print suggested citation:
attr(unclass(pub$bibentry[[1]])[[1]], which = "textVersion")

# Print authors full name:
format(pub$bibentry[[1]]$author, include = c("given", "family"))

# Print abstract:
pub$abstract

Search Terms

Description

Pattern matches a search term within the term-frequency data table.

Usage

search_terms(
  x,
  data = inlpubs::terms,
  ignore_case = TRUE,
  ...,
  low_freq = 1,
  high_freq = Inf,
  simplify = TRUE
)

Arguments

x

'character' string. Term searched for in the term-frequency data table.

data

'term' and 'data.frame' class. Term-frequency data table. Defaults to using the term frequencies from the INLPO publications, see terms dataset for details.

ignore_case

'logical' flag. Whether to ignore character case during pattern matching.

...

Additional arguments passed to the grep function.

low_freq

'numeric' number. Lower frequency bound.

high_freq

'numeric' number. Upper frequency bound.

simplify

'logical' flag. Whether to return only the unique publication identifiers.

Value

A subset of the data table sorted by decreasing frequency.

Author(s)

J.C. Fisher, U.S. Geological Survey, Idaho Water Science Center

See Also

mine_text function to perform a term frequency text analysis.

Examples

search_terms("mlms")

out <- search_terms("mlms", simplify = FALSE)
head(out)

Term Frequency from INLPO Publications

Description

Term frequency from publications by the U.S. Geological Survey (USGS), Idaho Water Science Center, Idaho National Laboratory Project Office (INLPO).

Usage

terms

Format

An object of class 'term' that inherits behavior from the 'data.frame' class and includes the following columns:

term

Term, a word or group of words, represented by an ASCII character string in lowercase.

pub_id

Identifier for a publication, referes to the primry key of the pubs data table.

freq

Frequency count from text analysis.

Source

The publication text was sourced from the original PDF documents using the get_pdf_text function, and term frequencies were extracted from the text using the mine_text function.

Examples

str(terms, max.level = 3, width = 75, strict.width = "cut")