Package 'refsplitr'

Title: author name disambiguation, author georeferencing, and mapping of coauthorship networks with 'Web of Science' data
Description: Tools to parse and organize reference records downloaded from the 'Web of Science' citation database into an R-friendly format, disambiguate the names of authors, geocode their locations, and generate/visualize coauthorship networks. This package has been peer-reviewed by rOpenSci (v. 1.0).
Authors: Auriel M.V. Fournier [aut], Matthew E. Boone [aut], Forrest R. Stevens [aut], Emilio Bruna [aut, cre], Bianca Kramer [rev] (Kramer reviewed the package (v 1.0) for rOpenSci, see <https://github.com/ropensci/software-review/issues/256>), Najko Jahn [rev] (Jahn reviewed the package (v1.0) for rOpenSci, see <https://github.com/ropensci/software-review/issues/256>)
Maintainer: Emilio Bruna <[email protected]>
License: GPL-3
Version: 1.0
Built: 2024-12-13 05:33:44 UTC
Source: https://github.com/ropensci/refsplitr

Help Index

Seperates author information in references files from references_read

Description

authors_clean This function takes the output from references_read and cleans the author information.

Usage

authors_clean(references)

Arguments

references

output from references_read

Details

Information on addresses, emails, ORCIDs, etc are matched.

It then attempts to match same author entries together into likely author groups based on common full names, addresses, emails, ORCIDs etc.

Records that are not matched this way have a Jaro-Winkler similiarty analysis metric calculated for all possible matching author names.

This calculates the amount of character similarities based on distance of similar character.

Examples

## Load the refsplitr sample dataset "BITR" 
data(BITR) 
BITR_clean <- authors_clean(BITR)

## The output of authors_clean is a list with two elements, 
## which can be assigend to dataframes.
BITR_review_df <- BITR_clean$review
BITR_prelim_df <- BITR_clean$prelim

## Users can save the these dataframes outside of R as .csv files.
## The "review_df.csv" is then used to review the groupID or authorID 
## assignments and make any necessary corrections. 
## The function "authors_refine" is used to load and merge the changes 
## into R and create a dataframe used for analyses.

Extracts the lat and long for each address from authors_clean

Description

authors_georef This function takes the final author list from refine_authors, and calculates the lat long of the addresses. It does this by feeding the addresses into data science toolkit. In order to maximize effectiveness and mitigate errors in parsing addresses We run this multiple times creating addresses in different ways in hopes that the google georeferencing API can recognize an address 1st. University, city, zipcode, country 2nd. City, zipcode, country 3rd. city, country 4th. University, country

Usage

authors_georef(data, address_column = "address")

Arguments

data

dataframe from authors_refine()
address_column

name of column in quotes where the addresses are

Details

The output is a list with three data.frames addresses is a data frame with all information from refine_authors plus new location columns and calculated lat longs. missing addresses is a data frame with all addresses could not be geocoded addresses is a data frame like addresses except the missing addresses are gone.

Examples

## Not run: 
BITR_georef_df <- authors_georef(BITR_refined, address_column='address')

## End(Not run)

Refines the authors code output from authors_clean()

Description

authors_refine This function takes the author list output after the output has been synthesized for incorrect author matches. It contains a similarity score cutoff like read_authors. This however is to further constrain the list. New values ARE NOT created, instead it filters by the sim_score column in the output file.

Usage

authors_refine(review, prelim, sim_score = NULL, confidence = NULL)

Arguments

review

the review element from list output by authors_clean
prelim

the prelim element from list output by authors_clean
sim_score

similarity score cut off point. Number from 0-1.
confidence

confidence score cut off point. Number from 0 - 10.

Examples

## First gather the authors data.frame from authors_clean
data(BITR)
BITR_authors <- authors_clean(BITR)
BITR_review_df <- BITR_authors$review 
BITR_prelim_df <- BITR_authors$prelim

## If accepting the preliminary disambiguation 
## from authors_clean() without review:
refine_df <- authors_refine(BITR_review_df, BITR_prelim_df,
    sim_score = 0.90, confidence = 5)

## Note that 'sim_score' and 'confidence' are optional arguments and are
## only required if changing the default values. 
refine_df <- authors_refine(BITR_review_df, BITR_prelim_df)


## If changes were made to groupID or authorID in the "_review.csv" file: 
## then incorporate those changes in a text editor, save the corrections as
## a new file name, load in to R and run `authors_refine()` with the 
## new corrections as the review arguement.

Data from the journal BioTropica (pulled from Web of Knowledge)

Description

A dataset containing 10 articles taken from the BioTropica journal. This dataset represents the typical formatted output from references_read() in the refsplitr package. It serves as a testbed for commonly miscategorized names

Usage

BITR

Format

A data frame with 10 rows and 32 variables:

filename

the original filename the text was created from

refID

the unique identifier given to each reference article by references_read()

AB

Abstract

AF

Full Names

AU

Abbreviated names

C1

Addresses

EM

emails

RI

Web of Science ID

OI

OrcID

RP

Reprint Address

TI

Title

UT

Web of Knowledge Unique ID

BP

See url below

CR

See url below

DE

See url below

DI

See url below

EP

See url below

FN

See url below

FU

See url below

PD

See url below

PG

See url below

PT

See url below

PU

See url below

PY

See url below

PM

See url below

SC

See url below

SN

See url below

SO

See url below

TC

See url below

VL

See url below

WC

See url below

Z9

See url below

The remaining codes are described on the Web of Knowledge website: https://images.webofknowledge.com/images/help/WOS/hs_wos_fieldtags.html

Georeferenced data from the journal BioTropica (pulled from Web of Science)

Description

A dataset containing 41 authors taken from the BioTropica journal. This dataset represents the typical formatted output from authors_georef() in the refsplitr package. It serves as a useful testing data set for spatial functions and

Usage

BITR_geocode

Format

A data frame with 41 rows and 15 variables:

authorID

ID field populated in authors_clean

university

also can be considered institution for non-universities

postal_code

character, international postcode

country

country name

lat

numeric, latitude populated from authors_georef

lon

numeric, longitude populated from authors_georef

groupID

ID field for what name group the author is identied as from authors_clean()

author_order

numeric, order of author from jounral article

address

address of references pulled from the original raw WOS file

department

department which is nested within university

RP_address

reprint address, pulled from the original raw WOS file

RI

ResearcherID number, identifier given by web of science only, less common than OrcID

OI

OrcID, unique identifier for researcher given by https://orcid.org

UT

unique identifier to each article, given by WOS

refID

unique identifier for each article, given by references_read()

Names of all the countries in the world

Description

#'

Usage

countries

Format

a character vector of country names

countries

a character vector of country names

@export countries @noRd

Plot addresses, the number of which are summed by country_name

Description

This function plots an addresses data.frame object by country name.

Usage

plot_addresses_country(data, mapRegion = "world")

Arguments

data

address element from the output from the authors_georef() function, containing geocoded address latitude and longitude locations.
mapRegion

what portion of the world map to show. possible values include "world", "North America", "South America", "Australia", "Africa", "Antarctica", and "Eurasia"

Examples

## Using the output of authors_georef (e.g., BITR_geocode)
data(BITR_geocode)
## Plots the whole world
plot_addresses_country(BITR_geocode)

## Just select North America
plot_addresses_country(BITR_geocode, mapRegion = 'North America')

Plot address point locations on world map

Description

This function plots an addresses data.frame object by point overlaid on the countries of the world.

Usage

plot_addresses_points(data, mapCountry = NULL)

Arguments

data

the address element from the list output by the 'authors_georef()“ function, containing geocoded address latitude and longitude locations.
mapCountry

What country to map. Possible values include "USA", "Brazil", ⁠"Australia",⁠ and "UK" use data(countries) to see possible names. No value defaults to the world map.

Examples

## Using the output of authors_georef (e.g., BITR_geocode)
data(BITR_geocode)
## Plots the whole world
plot_addresses_points(BITR_geocode)

## mapCountry names can be querried using:
data(countries)

## Plot only Brazil
plot_addresses_points(BITR_geocode, mapCountry = 'Brazil')

Creates a network diagram of coauthors' addresses linked by reference, and with nodes arranged geographically

Description

This function takes an addresses data.frame, links it to an authors__references dataset and plots a network diagram generated for individual points of co-authorship.

Usage

plot_net_address(
  data,
  mapRegion = "world",
  lineResolution = 10,
  lineAlpha = 0.5
)

Arguments

data

the address element from the list outputted from the authors_georef() function, containing geocoded address latitude and longitude locations.
mapRegion

what portion of the world map to show. possible values include "world", "North America", "South America", "Australia", "Africa", "Antarctica", "Eurasia"
lineResolution

the resolution of the lines drawn, higher numbers will make smoother curves default is 10.
lineAlpha

transparency of the lines, fed into ggplots alpha value. Number between 0 - 1.

Examples

## Using the output of authors_georef (e.g., BITR_geocode)
data(BITR_geocode)
## Plots the whole world
output <- plot_net_address(BITR_geocode)

## Just select North America
output <- plot_net_address(BITR_geocode, mapRegion = 'North America')

## Change the transparency of lines by modifying the lineAlpha parameter
output <- plot_net_address(BITR_geocode, lineAlpha = 0.2)
                 
## Change the curvature of lines by modifying the lineResolution paramater
output <- plot_net_address(BITR_geocode, lineResolution = 30 )
                 
output <- plot_net_address(BITR_geocode, mapRegion = 'North America', lineAlpha = 0.2,
                 lineResolution = 30)

Creates a network diagram of coauthors' countries linked by reference This function takes an addresses data.frame, links it to an authors_references dataset and plots a network diagram generated for co-authorship.

Description

Creates a network diagram of coauthors' countries linked by reference This function takes an addresses data.frame, links it to an authors_references dataset and plots a network diagram generated for co-authorship.

Usage

plot_net_coauthor(data)

Arguments

data

the address element from the list outputted from the 'authors_georef()“ function, containing geocoded address latitude and longitude locations.

Examples

## Using the output of authors_georef (e.g., BITR_geocode)
data(BITR_geocode)
plot_net_coauthor(BITR_geocode)

Creates a network diagram of coauthors' countries linked by reference, #and with nodes arranged geographically

Description

This function takes an addresses data.frame, links it to an authors_references dataset and plots a network diagram generated for countries of co-authorship.

Usage

plot_net_country(
  data,
  lineResolution = 10,
  mapRegion = "world",
  lineAlpha = 0.5
)

Arguments

data

the address element from the list outputted from the authors_georef() function, containing geocoded address latitude and longitude locations.
lineResolution

the resolution of the lines drawn, higher numbers will make smoother curves default is 10.
mapRegion

what portion of the world map to show. possible values include "world", "North America", "South America", "Australia", "Africa", "Antarctica", and "Eurasia"
lineAlpha

transparency of the lines, fed into ggplots alpha value. Number between 0 - 1.

Examples

## Using the output of authors_georef (e.g., BITR_geocode)
data(BITR_geocode)
## Plots the whole world
output <- plot_net_country(BITR_geocode)

## Mapping only North America
output <- plot_net_country(BITR_geocode, mapRegion = 'North America')

## Change the transparency of lines by modifying the lineAlpha parameter
output <- plot_net_country(BITR_geocode, lineAlpha = 0.2)
                 
## Change the curvature of lines by modifying the lineResolution paramater
output <- plot_net_country(BITR_geocode, lineResolution = 30 )
                 
## With all arguments: 
output <- plot_net_country(BITR_geocode, mapRegion = 'North America', lineAlpha = 0.2,
                 lineResolution = 30)

Reads Thomson Reuters Web of Knowledge/Science and ISI reference export files (both .txt or .ciw format accepted)

Description

references_read This function reads Thomson Reuters Web of Knowledge and ISI format reference data files into an R-friendly data format. The resulting dataframe is the argument for the refplitr function authors_clean().

Usage

references_read(data = ".", dir = FALSE, include_all = FALSE)

Arguments

data

the location of the file or files to be imported. This can be either the absolute or relative name of the file (for a single file) or folder (for multiple files stored in the same folder; used in conjuction with 'dir = TRUE“). If left blank it is assumed the location is the working directory.
dir

if FALSE it is assumed a single file is to be imported. Set to TRUE if importing multiple files (the path to the folder in which files are stored is set with 'data=“; all files in the folder will be imported). Defaults to FALSE.
include_all

if FALSE only a subset of commonly used fields from references records are imported. If TRUE then all fields from the reference records are imported. Defaults to FALSE. The additional data fields included if include_all=TRUE: CC, CH, CL, CT, CY, DT, FX, GA, GE, ID, IS, J9, JI, LA, LT, MC, MI, NR, PA, PI, PN, PS, RID, SU, TA, VR.

Examples

## If a single files is being imported from a folder called "data" located in an RStudio Project: 
## imported_refs<-references_read(data = './data/refs.txt', dir = FALSE, include_all=FALSE)

## If multiple files are being imported from a folder named "heliconia" nested within a folder
## called "data" located in an RStudio Project: 
## heliconia_refs<-references_read(data = './data/heliconia', dir = TRUE, include_all=FALSE)

## To load the Web of Science records used in the examples in the documentation  
BITR_data_example <- system.file('extdata', 'BITR_test.txt', package = 'refsplitr')
BITR <- references_read(BITR_data_example)