rcrossref_erl

Here is a markdown file with all output run.

Connect to the binder at:

Binder

Introduction

The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text.

Azure Notebooks is a free hosted service to develop and run Jupyter notebooks in the cloud with no installation.

We are using these platforms to avoid having to install R and R Studio onto your own computer. Furthermore, by interacting with R in this notebook, you will be able to execute code that I have already written, and see explanations of it first hand. Because this is such a brief session, we cannot go into detail about learning the R language, but I have provided some resources at the end of this document.

I have also created a binder of this project, which will allow you to launch it in RStudio in your browser without having to download anything. Though we will not be using this as the basis of today’s session, it may be of some use to you. Launch it at

launch binder

If you plan on using rcrossref more extensively, I would recommend downloading R and R Studio to your own computer and using it there. Also, the Crossref team encourages requests with appropriate contact information, and will forward you to a dedicated API cluster for improved performance when you share your email with them. We cannot do that in this notebook, but you can do that in R.

For a more detailed walkthrough of this entire lesson, including instructions for downloading R and R Studio, sharing your email with Crossref, and much more, please visit the set of tutorials at https://ciakovx.github.io/fsci_syllabus.html.

Licensing

This walkthrough is distributed under a https://creativecommons.org/licenses/by/4.0/.


Jupyter Notebooks

Jupyter Notebooks have two different keyboard input modes:

A new cell will always start as a Code cell, where you can type in R code and execute it here in your Jupyter notebook. All code in this notebook is R, but in Azure Notebooks you can create Notebooks that are F# or Python.

Please feel free to add your own notes in a Markdown cell during this workshop, or write your own R code!

Useful keyboard shortcurts when you are in Command Mode:

Shortcuts when you are in Edit Mode:

TRY IT YOURSELF

Select the below cell in Edit Mode by double clicking in it, or by clicking it on the margin and pressing Enter. It should have a green border. Notice that this is a Code cell. Press Shift + Enter to execute the code. This will print the output and select the next cell.

Then, when you are in the next cell, press Ctrl + Enter. This will print the output and stay in the same cell.

Then, press the down arrow on your keyboard to to to the next cell. Enter Edit Mode (green border) by pressing Enter. Press Alt (or option on Mac) + Enter. This will print the output and create a new cell.

Then press the down arrow or select the new empty cell. Make sure you are in Command Mode (blue border). Press D twice to delete the new cell.</a>

# press Shift + Enter
print("You just ran the cell and selected the next cell")

[1] "You just ran the cell and selected the next cell"

# press Ctrl + Enter
print("You just ran this cell and the focus stayed here in this cell")

[1] "You just ran this cell and the focus stayed here in this cell"

# press Alt (or option on Mac) + Enter
print("You just ran the cell and inserted a new cell below it")

[1] "You just ran the cell and inserted a new cell below it"

Notice the text in the above cells that starts with a hash # character. The hash indicates a comment. Anything following the hash symbol will not be evaluated.

Install and load rcrossref, dplyr, purrr, stringr, and tidyr

When you download R it already has a number of functions built in: these encompass what is called Base R. However, many R users write their own libraries of functions, package them together in R packages, and provide them to the R community at no charge. This extends the capacity of R and allows us to do much more. In many cases, they improve on the Base R functions by making them easier and more straight-forward to use.

First install rcrossref using the install.packages() function. Notice the package name is in quotation marks.

Click on the left margin of the cell below so it turns blue. Then click the Run button on the top toolbar, or press Ctrl + Enter. This will execute the code, installing the necessary packages into your Jupyter Notebook environment.

This may take a couple minutes. You will see a [*] on the left margins while the package installs. When the asterisk becomes a number, we will be ready.

install.packages('rcrossref')

Installing package into ‘/home/nbuser/R’
(as ‘lib’ is unspecified)

We will also be using the dplyr, purrr, stringr and tidyr packages. These packages are part of the tidyverse, a collection of R packages designed for data science.

Fortunately, these packages are pre-installed in Azure Notebooks, so we don’t need to install them; we just need to load them into our environment. We do this with the library() function. Let’s load all three packages by clicking the left margin of the below cell (so it turns blue) and clicking the Run button on the top toolbar.

Let’s also set an option to see a max number of 100 columns and max 20 rows in our Jupyter Notebooks environment.

# load packages
library(rcrossref)
library(dplyr)
library(purrr)
library(stringr)
library(tidyr)

# increase number of columns and rows displayed when we print a table
options(repr.matrix.max.cols=100, repr.matrix.max.rows=20)

R Basics



R is more of a programming language than a statistics program. It was started by Robert Gentleman and Ross Ihaka from the University of Auckland in 1995. They described it as “a language for data analysis and graphics.”1 You can use R to create, import, and scrape data from the web; clean and reshape it; visualize it; run statistical analysis and modeling operations on it; text and data mine it; and much more.

If you intend on continuing your R journey after this workshop, I recommend installing R and R Studio and doing your scripting there. To install R, go to https://www.r-project.org/. Click on CRAN (Comprehensive R Archive Network) under Download, and scroll down to your country. Select the download link corresponding to the city that is geographically closest to you. Go to https://www.rstudio.com/products/RStudio/#Desktop to download the RStudio desktop software.

We don’t have enough time in today’s workshop to learn much about R. There are many excellent R tutorials at the end of this document. To get help on R functions within Jupyter Notebooks, type help() with the function name in parentheses. For example, help(sum) or help(which). This will provide a description of the function, its usage, and the arguments the function takes.

Writing & Evaluating Expressions

The prompt is the blinking cursor in a Code cell prompting you to take action. We type expressions into the prompt, and press Ctrl + Enter to evaluate those expressions.

Evaluate this expression:

# Press Ctrl + Enter or click the Run button to evaluate 2 + 2
2 + 2

4

Assigning values

The first operator you’re going to come across is the assignment operator. This is the angle bracket (AKA the “less than”” symbol): &lt;, which you’ll get by pressing Shift + comma and the hyphen - which is located next to the zero key. There is no space between them, and it is designed to look like a left pointing arrow &lt;-.

# assign 5 to y
y <- 5

Here I am creating a symbol called y and I’m assigning it the numeric value 5. Some R users would say “y gets 5.” Lowercase y, is now a numeric vector with one element. Or you could say y is a numeric vector, and the first element is the number 5. When you assign something to a symbol, nothing happens in the console, but in the Environment pane in the upper right, you will notice a new object, y.

If you now type y into the console, and press Enter on your keyboard, R will evaluate the expression. In this case, R will print the elements that are assigned to y (the number 5). We can do this easily since y only has one element, but if you do this with a large dataset loaded into R, it will obliterate your console because it will print the entire thing. The [1] indicates that the number 5 is the first element of this vector.

# evaluate y
y

5

As we saw above, you can also use the print() function:

# using print() will do the same thing as just typing the variable in, it just makes it explicit
print(y)

[1] 5

TRY IT YOURSELF

  1. Use the new code cells below. Make sure that 5 is assigned to y by typing in y &lt;- 5
  2. Assign the number 10 to variable x. Add x and y and evaluate the expression.
  3. Assign x + y to variable myTotal.
# assign 5 to y


# assign 10 to x


# assign the sum of x and y to myTotal. Print myTotal to the console.

Tips for assigning values

Calling a function

R is a “functional programming language,” meaning it contains a number of functions you use to do something with your data. Call a function on a variable by entering the function into the console, followed by parentheses and the variables.

# take the square root of the sum of 2 + 2
sum(2, 2)

4

Typing a question mark before a function will pull the help page up in the Navigation Pane in the lower right. Type ?sum to view the help page for the sum function. You can also call help(sum). This will provide the description of the function, how it is to be used, and the arguments.

In the case of sum(), the ellipses . . . represent an unlimited number of numeric elements. sum() also takes the argument na.rm. This is a logical (TRUE/FALSE) argument specifying if NA values (missing data) should be removed when the argument is evaluated.

The function is.function() will check if an argument is a function in R. If it is a function, it will print TRUE to the console.

# confirm that sum is a function
is.function(sum)

TRUE

# sum takes an unlimited number (. . .) of numeric elements
sum(3, 4, 5, 6, 7)

25

# evaluating a sum with missing values will return NA
sum(3, 4, NA)

<NA>

# look at the help file for sum
?sum

# but setting the argument na.rm to TRUE will remove the NA
sum(3, 4, na.rm = TRUE)

7

Functions can be nested within each other. For example, sqrt() takes the square root of the number provided in the function call. Therefore you can run sum(sqrt(9), 4) to take the sum of the square root of 9 (3) and add it to 4. Or you could write the quadratic formula: [(-b) + sqrt((b^2) - 4ac)] / (2*a).

Crossref & rcrossref

Crossref



Crossref is a a not-for-profit membership organization dedicated to interlinking scholarly metadata, including journals, books, conference proceedings, working papers, technical reports, data sets, authors, funders, and more. The Crossref REST API allows anybody to search and reuse members’ metadata in a variety of ways. Read examples of user stories.

rcrossref

rcrossref is a package developed by Scott Chamberlain, Hao Zhu, Najko Jahn, Carl Boettiger, and Karthik Ram, part of the rOpenSci set of packages. rOpenSci is an incredible organization dedicated to open and reproducible research using shared data and reusable software. I strongly recommend you browse their set of packages at https://ropensci.org/packages/.



rcrossref serves as an interface to the Crossref API.

Key links

Getting publications from journals with cr_journals

cr_journals() takes either an ISSN or a general keyword query, and returns metadata for articles published in the journal, including DOI, title, volume, issue, pages, publisher, authors, etc. A full list of publications in Crossref is available on their website.

Getting journal details

Crossref is entirely dependent on publishers to supply the metadata. Some fields are required, while others are optional. You may therefore first be interested in what metadata publishers have submitted to Crossref for a given journal. By using cr_journals with works = FALSE, you can determine who publishes the journal, the total number of articles for the journal in Crossref, whether abstracts are included, if the full text of articles is deposited, if author ORCIDs are provided, and if the publisher supplies author affiliations, author ORCID iDs, article licensing data, funders for the article, article references, and a few other items.

First we will create a new vector plosone_issn with the ISSN for the journal PLoS ONE.

# assign the PLoS ISSN
plosone_issn <- '1932-6203'

We will then run rcrossref::cr_journals(), setting the ISSN equal to the plosone_issn we just created, and print the results.

# get information about the journal
plosone_details <- rcrossref::cr_journals(issn = plosone_issn, works = FALSE)
plosone_details
$meta
NULL
$data
A data.frame: 1 x 53
titlepublisherissnlast_status_check_timedeposits_abstracts_currentdeposits_orcids_currentdepositsdeposits_affiliations_backfiledeposits_update_policies_backfiledeposits_similarity_checking_backfiledeposits_award_numbers_currentdeposits_resource_links_currentdeposits_articlesdeposits_affiliations_currentdeposits_funders_currentdeposits_references_backfiledeposits_abstracts_backfiledeposits_licenses_backfiledeposits_award_numbers_backfiledeposits_open_references_backfiledeposits_open_references_currentdeposits_references_currentdeposits_resource_links_backfiledeposits_orcids_backfiledeposits_funders_backfiledeposits_update_policies_currentdeposits_similarity_checking_currentdeposits_licenses_currentaffiliations_currentsimilarity_checking_currentfunders_backfilelicenses_backfilefunders_currentaffiliations_backfileresource_links_backfileorcids_backfileupdate_policies_currentopen_references_backfileorcids_currentsimilarity_checking_backfilereferences_backfileaward_numbers_backfileupdate_policies_backfilelicenses_currentaward_numbers_currentabstracts_backfileresource_links_currentabstracts_currentopen_references_currentreferences_currenttotal_doiscurrent_doisbackfile_dois
<chr><chr><chr><date><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><int><int><int>
PLoS ONEPublic Library of Science1932-62032020-03-08FALSETRUETRUEFALSETRUETRUETRUEFALSETRUEFALSETRUETRUEFALSETRUETRUETRUETRUETRUEFALSETRUETRUETRUETRUETRUE010.12749880.99175250.5958421000.1001075110.92009420.90550680.90550680.10869780.999963610.51440210001123035037807192543
$facets
NULL

This actually comes back as a list of three items: meta, data, and facets. The good stuff is in data.

We use the pluck() function from the purrr package to pull that data only. We will be using pluck throughout this tutorial; it’s an easy way of indexing deeply and flexibly into lists to extract information.

We don’t have time in this tutorial to discuss list items and purr. For an excellent in-depth tutorial, see Jenny Bryan’s Introduction to map(): extract elements.

# get information about the journal and pluck the data
plosone_details <- rcrossref::cr_journals(issn = plosone_issn, works = FALSE) %>%
  purrr::pluck("data")

The purrr::pluck() function is connected to plosone_details with something called a Pipe Operator %&gt;%, which we will be using throughout the tutorial. A pipe takes the output of one statement and immediately makes it the input of the next statement. It helps so that you don’t have to write every intermediate, processing data to your R environment. You can think of it as “then” in natural language. So the above script first makes the API call with cr_journals(), then it applies pluck() to extract only the list element called "data", and returns it to the plosone_details value.

We now have a data frame including the details Croassref has on file about PLoS ONE. Scroll to the right to see all the columns.

plosone_details
A data.frame: 1 x 53
titlepublisherissnlast_status_check_timedeposits_abstracts_currentdeposits_orcids_currentdepositsdeposits_affiliations_backfiledeposits_update_policies_backfiledeposits_similarity_checking_backfiledeposits_award_numbers_currentdeposits_resource_links_currentdeposits_articlesdeposits_affiliations_currentdeposits_funders_currentdeposits_references_backfiledeposits_abstracts_backfiledeposits_licenses_backfiledeposits_award_numbers_backfiledeposits_open_references_backfiledeposits_open_references_currentdeposits_references_currentdeposits_resource_links_backfiledeposits_orcids_backfiledeposits_funders_backfiledeposits_update_policies_currentdeposits_similarity_checking_currentdeposits_licenses_currentaffiliations_currentsimilarity_checking_currentfunders_backfilelicenses_backfilefunders_currentaffiliations_backfileresource_links_backfileorcids_backfileupdate_policies_currentopen_references_backfileorcids_currentsimilarity_checking_backfilereferences_backfileaward_numbers_backfileupdate_policies_backfilelicenses_currentaward_numbers_currentabstracts_backfileresource_links_currentabstracts_currentopen_references_currentreferences_currenttotal_doiscurrent_doisbackfile_dois
<chr><chr><chr><date><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><lgl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><int><int><int>
PLoS ONEPublic Library of Science1932-62032020-03-08FALSETRUETRUEFALSETRUETRUETRUEFALSETRUEFALSETRUETRUEFALSETRUETRUETRUETRUETRUEFALSETRUETRUETRUETRUETRUE010.12749880.99175250.5958421000.1001075110.92009420.90550680.90550680.10869780.999963610.51440210001123035037807192543

There are a number of ways to explore this data frame:

#display information about the data frame
str(plosone_details)

'data.frame':	1 obs. of  53 variables:
 $ title                                : chr "PLoS ONE"
 $ publisher                            : chr "Public Library of Science"
 $ issn                                 : chr "1932-6203"
 $ last_status_check_time               : Date, format: "2020-03-08"
 $ deposits_abstracts_current           : logi FALSE
 $ deposits_orcids_current              : logi TRUE
 $ deposits                             : logi TRUE
 $ deposits_affiliations_backfile       : logi FALSE
 $ deposits_update_policies_backfile    : logi TRUE
 $ deposits_similarity_checking_backfile: logi TRUE
 $ deposits_award_numbers_current       : logi TRUE
 $ deposits_resource_links_current      : logi FALSE
 $ deposits_articles                    : logi TRUE
 $ deposits_affiliations_current        : logi FALSE
 $ deposits_funders_current             : logi TRUE
 $ deposits_references_backfile         : logi TRUE
 $ deposits_abstracts_backfile          : logi FALSE
 $ deposits_licenses_backfile           : logi TRUE
 $ deposits_award_numbers_backfile      : logi TRUE
 $ deposits_open_references_backfile    : logi TRUE
 $ deposits_open_references_current     : logi TRUE
 $ deposits_references_current          : logi TRUE
 $ deposits_resource_links_backfile     : logi FALSE
 $ deposits_orcids_backfile             : logi TRUE
 $ deposits_funders_backfile            : logi TRUE
 $ deposits_update_policies_current     : logi TRUE
 $ deposits_similarity_checking_current : logi TRUE
 $ deposits_licenses_current            : logi TRUE
 $ affiliations_current                 : num 0
 $ similarity_checking_current          : num 1
 $ funders_backfile                     : num 0.127
 $ licenses_backfile                    : num 0.992
 $ funders_current                      : num 0.596
 $ affiliations_backfile                : num 0
 $ resource_links_backfile              : num 0
 $ orcids_backfile                      : num 0.1
 $ update_policies_current              : num 1
 $ open_references_backfile             : num 1
 $ orcids_current                       : num 0.92
 $ similarity_checking_backfile         : num 0.906
 $ references_backfile                  : num 0.906
 $ award_numbers_backfile               : num 0.109
 $ update_policies_backfile             : num 1
 $ licenses_current                     : num 1
 $ award_numbers_current                : num 0.514
 $ abstracts_backfile                   : num 0
 $ resource_links_current               : num 0
 $ abstracts_current                    : num 0
 $ open_references_current              : num 1
 $ references_current                   : num 1
 $ total_dois                           : int 230350
 $ current_dois                         : int 37807
 $ backfile_dois                        : int 192543

Type ?str into the console to read the description of the str function. You can call str() on an R object to compactly display information about it, including the data type, the number of elements, and a printout of the first few elements.

# dimensions: 1 row, 53 columns
dim(plosone_details)
  1. 1
  2. 53
# number of rows
nrow(plosone_details)

1

# number of columns
ncol(plosone_details)

53

# column names
names(plosone_details)
  1. 'title'
  2. 'publisher'
  3. 'issn'
  4. 'last_status_check_time'
  5. 'deposits_abstracts_current'
  6. 'deposits_orcids_current'
  7. 'deposits'
  8. 'deposits_affiliations_backfile'
  9. 'deposits_update_policies_backfile'
  10. 'deposits_similarity_checking_backfile'
  11. 'deposits_award_numbers_current'
  12. 'deposits_resource_links_current'
  13. 'deposits_articles'
  14. 'deposits_affiliations_current'
  15. 'deposits_funders_current'
  16. 'deposits_references_backfile'
  17. 'deposits_abstracts_backfile'
  18. 'deposits_licenses_backfile'
  19. 'deposits_award_numbers_backfile'
  20. 'deposits_open_references_backfile'
  21. 'deposits_open_references_current'
  22. 'deposits_references_current'
  23. 'deposits_resource_links_backfile'
  24. 'deposits_orcids_backfile'
  25. 'deposits_funders_backfile'
  26. 'deposits_update_policies_current'
  27. 'deposits_similarity_checking_current'
  28. 'deposits_licenses_current'
  29. 'affiliations_current'
  30. 'similarity_checking_current'
  31. 'funders_backfile'
  32. 'licenses_backfile'
  33. 'funders_current'
  34. 'affiliations_backfile'
  35. 'resource_links_backfile'
  36. 'orcids_backfile'
  37. 'update_policies_current'
  38. 'open_references_backfile'
  39. 'orcids_current'
  40. 'similarity_checking_backfile'
  41. 'references_backfile'
  42. 'award_numbers_backfile'
  43. 'update_policies_backfile'
  44. 'licenses_current'
  45. 'award_numbers_current'
  46. 'abstracts_backfile'
  47. 'resource_links_current'
  48. 'abstracts_current'
  49. 'open_references_current'
  50. 'references_current'
  51. 'total_dois'
  52. 'current_dois'
  53. 'backfile_dois'

We see this data frame includes one observation of 53 different variables. This includes the total number of DOIs, whether the abstracts, orcids, article references are current; and other information.

You can use the $ symbol to work with particular variables. For example, the publisher column:

# print the publisher variable
plosone_details$publisher

‘Public Library of Science’

The total number of DOIs on file:

# print the total number of DOIs
plosone_details$total_dois

230350

Whether the data publishers provide on funders of articles they publish is current in Crossref (a TRUE/FALSE value–called “logical” in R):

# is funder data current on deposits?
plosone_details$deposits_funders_current

TRUE

TRY IT YOURSELF

  1. Assign an ISSN for a well-known journal to a new variable in R. Name it whatever you like. You can use the Scimago Journal Rank to look up the ISSN. If you need a couple examples, try RUSA or Library Hi Tech. Make sure to put the ISSN in quotes to create a character vector.
  2. Look up the journal details using cr_journals. Make sure to pass the argument works = FALSE.
  3. Print the data to your console by typing in the value name.

Does it matter if the ISSN has a hyphen or not? Try both methods.

# assign an ISSN to a value. Call the value what you want (e.g. plosone_issn)


# look up journal details using the cr_journals function and assign it to a new value (e.g. plosone_details). 
# Remember to include a %>% pipe and call purrr::pluck("data")


# print the journal details to the console by typing in the value name

Getting journal publications by ISSN

To get metadata for the publications themselves rather than data about the journal, we will again use the plosone_issn value in the issn = argument to cr_journals, but we now set works = TRUE.

# get metadata on articles by setting works = TRUE
plosone_publications <- cr_journals(issn = plosone_issn, works = TRUE, limit = 25) %>%
  pluck("data")

Let’s walk through this step by step:

Let’s explore the data frame:

# print dimensions of this data frame
dim(plosone_publications)
  1. 25
  2. 28

When we run dim() (dimensions) on this result, we now see a different number of rows and columns: 25 rows and 28 columns. This is therefore a different dataset than plosone_details. Let’s call names() to see what the column names are:

# print column names
names(plosone_publications)
  1. 'container.title'
  2. 'created'
  3. 'deposited'
  4. 'published.online'
  5. 'doi'
  6. 'indexed'
  7. 'issn'
  8. 'issue'
  9. 'issued'
  10. 'member'
  11. 'page'
  12. 'prefix'
  13. 'publisher'
  14. 'reference.count'
  15. 'score'
  16. 'source'
  17. 'title'
  18. 'type'
  19. 'update.policy'
  20. 'url'
  21. 'volume'
  22. 'author'
  23. 'link'
  24. 'license'
  25. 'reference'
  26. 'subject'
  27. 'funder'
  28. 'clinical-trial-number'

We view the entire data frame below. Because there are some nested lists within the data, we will use the select() function from the dplyr package to select only a few columns. This will make it easier for us to view here in the Azure Notebook environment. You can also use the select() function to rearrange the columns.

# print select columns from the data frame
plosone_publications %>%
  dplyr::select(title, doi, volume, issue, page, issued, url, publisher, reference.count, type, issn)
A tibble: 25 x 11
titledoivolumeissuepageissuedurlpublisherreference.counttypeissn
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>
Extinction-Dependent Alterations in Corticostriatal mGluR2/3 and mGluR7 Receptors following Chronic Methamphetamine Self-Administration in Rats 10.1371/journal.pone.00342997 3 e34299 2012-03-29http://dx.doi.org/10.1371/journal.pone.0034299Public Library of Science (PLoS)77journal-article1932-6203
Pathophysiological Defects and Transcriptional Profiling in the RBM20-/- Rat Model 10.1371/journal.pone.00842818 12e84281 2013-12-19http://dx.doi.org/10.1371/journal.pone.0084281Public Library of Science (PLoS)60journal-article1932-6203
Ab-Externo AAV-Mediated Gene Delivery to the Suprachoroidal Space Using a 250 Micron Flexible Microcatheter 10.1371/journal.pone.00171406 2 e17140 2011-02-11http://dx.doi.org/10.1371/journal.pone.0017140Public Library of Science (PLoS)11journal-article1932-6203
Proteomic and Phospho-Proteomic Profile of Human Platelets in Basal, Resting State: Insights into Integrin Signaling 10.1371/journal.pone.00076274 10e7627 2009-10-27http://dx.doi.org/10.1371/journal.pone.0007627Public Library of Science (PLoS)67journal-article1932-6203
Alterations of Neuromuscular Function after the World's Most Challenging Mountain Ultra-Marathon 10.1371/journal.pone.00655968 6 e65596 2013-06-26http://dx.doi.org/10.1371/journal.pone.0065596Public Library of Science (PLoS)51journal-article1932-6203
Integrated Metagenomic and Physiochemical Analyses to Evaluate the Potential Role of Microbes in the Sand Filter of a Drinking Water Treatment System10.1371/journal.pone.00610118 4 e61011 2013-04-11http://dx.doi.org/10.1371/journal.pone.0061011Public Library of Science (PLoS)43journal-article1932-6203
Major Facilitator Superfamily Domain-Containing Protein 2a (MFSD2A) Has Roles in Body Growth, Motor Function, and Lipid Metabolism 10.1371/journal.pone.00506297 11e50629 2012-11-29http://dx.doi.org/10.1371/journal.pone.0050629Public Library of Science (PLoS)52journal-article1932-6203
Analysis of Autophagy Genes in Microalgae: Chlorella as a Potential Model to Study Mechanism of Autophagy 10.1371/journal.pone.00418267 7 e41826 2012-07-27http://dx.doi.org/10.1371/journal.pone.0041826Public Library of Science (PLoS)0 journal-article1932-6203
Osteoprotegerin Regulates Pancreatic β-Cell Homeostasis upon Microbial Invasion 10.1371/journal.pone.0146544111 e01465442016-01-11http://dx.doi.org/10.1371/journal.pone.0146544Public Library of Science (PLoS)54journal-article1932-6203
Health Behavior and Metabolic Risk Factors Associated with Normal Weight Obesity in Adolescents 10.1371/journal.pone.0161451118 e01614512016-08-25http://dx.doi.org/10.1371/journal.pone.0161451Public Library of Science (PLoS)42journal-article1932-6203
.................................
Cross-Modal Calibration of Vestibular Afference for Human Balance 10.1371/journal.pone.0124532104 e01245322015-04-20http://dx.doi.org/10.1371/journal.pone.0124532Public Library of Science (PLoS)44journal-article1932-6203
Genetic Factors Are Not the Major Causes of Chronic Diseases 10.1371/journal.pone.0154387114 e01543872016-04-22http://dx.doi.org/10.1371/journal.pone.0154387Public Library of Science (PLoS)45journal-article1932-6203
Manipulation of Pre-Target Activity on the Right Frontal Eye Field Enhances Conscious Visual Perception in Humans 10.1371/journal.pone.00362327 5 e36232 2012-05-15http://dx.doi.org/10.1371/journal.pone.0036232Public Library of Science (PLoS)46journal-article1932-6203
Splicing of the rSlo Gene Affects the Molecular Composition and Drug Response of Ca2+-Activated K+ Channels in Skeletal Muscle 10.1371/journal.pone.00402357 7 e40235 2012-07-10http://dx.doi.org/10.1371/journal.pone.0040235Public Library of Science (PLoS)55journal-article1932-6203
5-HT2C Receptors in the Basolateral Amygdala and Dorsal Striatum Are a Novel Target for the Anxiolytic and Antidepressant Effects of Exercise10.1371/journal.pone.00461187 9 e46118 2012-09-25http://dx.doi.org/10.1371/journal.pone.0046118Public Library of Science (PLoS)0 journal-article1932-6203
Task-Level Strategies for Human Sagittal-Plane Running Maneuvers Are Consistent with Robotic Control Policies 10.1371/journal.pone.00518887 12e51888 2012-12-20http://dx.doi.org/10.1371/journal.pone.0051888Public Library of Science (PLoS)49journal-article1932-6203
Fc Gamma Receptor IIb on GM-CSF Macrophages Controls Immune Complex Mediated Inhibition of Inflammatory Signals 10.1371/journal.pone.01109669 10e110966 2014-10-23http://dx.doi.org/10.1371/journal.pone.0110966Public Library of Science (PLoS)37journal-article1932-6203
Does the Clock Make the Poison? Circadian Variation in Response to Pesticides 10.1371/journal.pone.00064694 7 e6469 2009-07-31http://dx.doi.org/10.1371/journal.pone.0006469Public Library of Science (PLoS)52journal-article1932-6203
Sleep Architecture When Sleeping at an Unusual Circadian Time and Associations with Insulin Sensitivity 10.1371/journal.pone.00728778 8 e72877 2013-08-08http://dx.doi.org/10.1371/journal.pone.0072877Public Library of Science (PLoS)34journal-article1932-6203
Tradeoff between Stability and Maneuverability during Whole-Body Movements 10.1371/journal.pone.00218156 7 e21815 2011-07-14http://dx.doi.org/10.1371/journal.pone.0021815Public Library of Science (PLoS)29journal-article1932-6203

Here we are just getting back the last 25 articles that have been indexed in Crossref by PLoS ONE. However, this gives you a taste of how rich the metadata is. We have the dates the article was deposited and published online, the title, DOI, the ISSN, the volume, issue, and page numbers, the number of references, the URL, and for some items, the subjects. The omitted columns include information on licensing, authors, and more. We will deal with those columns further down.

Getting multiple publications by ISSN

You can also pass multiple ISSNs to cr_journals. Here we create 2 new values, jama_issn and jah_issn. These are ISSNs for the Journal of American History and JAMA: The Journal of the American Medical Association. We then pass them to cr_journals by passing them to the c() function, which will combine them (it’s like CONCATENATE in Excel). We set works to TRUE so we’ll get the publications metadata, and we set the limit to 50, so we’ll get 50 publications per journal.

# assign the JAMA and JAH ISSNs
jama_issn <- '1538-3598'
jah_issn <- '0021-8723'

# get the last 10 publications on deposit from each journal. For multiple ISSNs, use c() to combine them
jah_jama_publications <- rcrossref::cr_journals(issn = c(jama_issn, jah_issn), works = T, limit = 10) %>%
  purrr::pluck("data")

Here we used c() to combine jama_issn and jah_issn. c() is used to create a vector in R. A vector is a sequence of elements of the same type. In this case, even though the ISSNs are numbers, we created them as character vectors by surrounding them in quotation marks. You can use single or double quotes. Above, when we assigned 5 to y, we created a numeric vector.

Vectors can only contain “homogenous” data–in other words, all data must be of the same type. The type of a vector determines what kind of analysis you can do on it. For example, you can perform mathematical operations on numeric objects, but not on character objects. You can think of vectors as columns in an Excel spreadsheet: for example, in a name column, you want every value to be a character; in a date column, you want every value to be a date; etc.

Going back to our jah_jama_publications object, we have a dataframe composed of 20 observations of 24 variables. This is a rich set of metadata for the articles in the given publications. The fields are detailed in the Crossref documentation, including the field name, type, description, and whether or not it’s required. Some of these fields are title, DOI, DOI prefix identifer, ISSN, volume, issue, publisher, abstract (if provided), reference count (if provided–i.e., the number of references in the given article), link (if provided), subject (if provided), and other information. The number of citations to the article are not pulled, but these can be gathered separately with cr_citation_count() (see below).

# print column names
names(jah_jama_publications)
  1. 'container.title'
  2. 'created'
  3. 'deposited'
  4. 'published.print'
  5. 'doi'
  6. 'indexed'
  7. 'issn'
  8. 'issue'
  9. 'issued'
  10. 'member'
  11. 'page'
  12. 'prefix'
  13. 'publisher'
  14. 'reference.count'
  15. 'score'
  16. 'source'
  17. 'title'
  18. 'type'
  19. 'url'
  20. 'volume'
  21. 'author'
  22. 'link'
  23. 'reference'
# print data frame with select columns
jah_jama_publications %>%
  dplyr::select(title, doi, volume, issue, page, issued, url, publisher, reference.count, type, issn)
A tibble: 20 x 11
titledoivolumeissuepageissuedurlpublisherreference.counttypeissn
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>
Basics of International Humanitarian Missions; Emergency Relief Operations 10.1001/jama.291.2.249 2912249-250 2004-01-14http://dx.doi.org/10.1001/jama.291.2.249 American Medical Association (AMA)0journal-article0098-7484,1538-3598
Saving Lives and Saving Money: Transforming Health and Healthcare 10.1001/jama.291.2.251-a2912251-251 2004-01-14http://dx.doi.org/10.1001/jama.291.2.251-aAmerican Medical Association (AMA)0journal-article0098-7484,1538-3598
Books, Journals, New Media Received 10.1001/jama.291.2.252 2912252-253 2004-01-14http://dx.doi.org/10.1001/jama.291.2.252 American Medical Association (AMA)0journal-article0098-7484,1538-3598
Affirmative Action in Medicine: Improving Health Care for Everyone 10.1001/jama.291.2.251-b2912251-a-2522004-01-14http://dx.doi.org/10.1001/jama.291.2.251-bAmerican Medical Association (AMA)0journal-article0098-7484,1538-3598
Hemangiomas and Other Congenital Malformations in Infants Exposed to Antiretroviral Therapy In Utero 10.1001/jama.291.3.305 2913305-305 2004-01-21http://dx.doi.org/10.1001/jama.291.3.305 American Medical Association (AMA)0journal-article0098-7484,1538-3598
The Privatization of Health Care Reform: Legal and Regulatory Perspectives 10.1001/jama.291.3.375-a2913375-375 2004-01-21http://dx.doi.org/10.1001/jama.291.3.375-aAmerican Medical Association (AMA)0journal-article0098-7484,1538-3598
Textbook of Gastroenterology, vols 1 & 2; Atlas of Gastroenterology 10.1001/jama.291.3.375-b2913375-a-3762004-01-21http://dx.doi.org/10.1001/jama.291.3.375-bAmerican Medical Association (AMA)0journal-article0098-7484,1538-3598
Silent Injustice: True Stories of Innocent Women 10.1001/jama.291.3.376 2913376-377 2004-01-21http://dx.doi.org/10.1001/jama.291.3.376 American Medical Association (AMA)0journal-article0098-7484,1538-3598
Fitzpatrick's Dermatology in General Medicine, vols 1 & 2 10.1001/jama.291.3.377 2913377-378 2004-01-21http://dx.doi.org/10.1001/jama.291.3.377 American Medical Association (AMA)0journal-article0098-7484,1538-3598
Books, Journals, New Media Received 10.1001/jama.291.3.378-b2913378-a-3792004-01-21http://dx.doi.org/10.1001/jama.291.3.378-bAmerican Medical Association (AMA)0journal-article0098-7484,1538-3598
Outlawing "Treachery": Split Tickets and Ballot Laws in New York and New Jersey, 1880-1910 10.2307/1908893 72 4835 1986-03 http://dx.doi.org/10.2307/1908893 Oxford University Press (OUP) 0journal-article0021-8723
Circulating Race and Empire: Transnational Labor Activism and the Politics of Anti-Asian Agitation in the Anglo-American Pacific World, 1880-191010.1093/jahist/96.3.678 96 3678-701 2009-12-01http://dx.doi.org/10.1093/jahist/96.3.678 Oxford University Press (OUP) 5journal-article0021-8723
Abraham Lincoln: A Constitutional Biography 10.2307/2675150 88 2649 2001-09 http://dx.doi.org/10.2307/2675150 Oxford University Press (OUP) 0journal-article0021-8723
And I Will Dwell in Their Midst: Orthodox Jews in Suburbia 10.2307/2675242 88 2731 2001-09 http://dx.doi.org/10.2307/2675242 Oxford University Press (OUP) 0journal-article0021-8723
International Politics and Civil Rights Policies in the United States, 1941-1960 10.2307/2675236 88 2726 2001-09 http://dx.doi.org/10.2307/2675236 Oxford University Press (OUP) 0journal-article0021-8723
The Cold War American West, 1945-1989 10.2307/2675235 88 2725 2001-09 http://dx.doi.org/10.2307/2675235 Oxford University Press (OUP) 0journal-article0021-8723
America's Instrument: The Banjo in the Nineteenth Century 10.2307/2675168 88 2665 2001-09 http://dx.doi.org/10.2307/2675168 Oxford University Press (OUP) 0journal-article0021-8723
Designs against Charleston: The Trial Record of the Denmark Vesey Slave Conspiracy of 1822 10.2307/2675142 88 2642 2001-09 http://dx.doi.org/10.2307/2675142 Oxford University Press (OUP) 0journal-article0021-8723
Scarlett Doesn't Live Here Anymore: Southern Women in the Civil War Era 10.2307/2675156 88 2654 2001-09 http://dx.doi.org/10.2307/2675156 Oxford University Press (OUP) 0journal-article0021-8723
Skull Wars: Kennewick Man, Archaeology, and the Battle for Native American Identity 10.2307/2675255 88 2742 2001-09 http://dx.doi.org/10.2307/2675255 Oxford University Press (OUP) 0journal-article0021-8723

Filtering the cr_journals query with the filter argument

You can use the filter argument within cr_journals to specify some parameters as the query is executing. This filter is built into the Crossref API query. See the available filters by calling rcrossref::filter_names(), and details by calling rcrossref::filter_details. It’s also in the API documentation.

filter possible values description  
has-funder   metadata which includes one or more funder entry  
funder {funder_id} metadata which include the {funder_id} in FundRef data  
location {country_name} funder records where location = {country name}. Only works on /funders route  
prefix {owner_prefix} metadata belonging to a DOI owner prefix {owner_prefix} (e.g. 10.1016 )  
member {member_id} metadata belonging to a Crossref member  
from-index-date {date} metadata indexed since (inclusive) {date}  
until-index-date {date} metadata indexed before (inclusive) {date}  
from-deposit-date {date} metadata last (re)deposited since (inclusive) {date}  
until-deposit-date {date} metadata last (re)deposited before (inclusive) {date}  
from-update-date {date} Metadata updated since (inclusive) {date}. Currently the same as from-deposit-date.  
until-update-date {date} Metadata updated before (inclusive) {date}. Currently the same as until-deposit-date.  
from-created-date {date} metadata first deposited since (inclusive) {date}  
until-created-date {date} metadata first deposited before (inclusive) {date}  
from-pub-date {date} metadata where published date is since (inclusive) {date}  
until-pub-date {date} metadata where published date is before (inclusive) {date}  
from-online-pub-date {date} metadata where online published date is since (inclusive) {date}  
until-online-pub-date {date} metadata where online published date is before (inclusive) {date}  
from-print-pub-date {date} metadata where print published date is since (inclusive) {date}  
until-print-pub-date {date} metadata where print published date is before (inclusive) {date}  
from-posted-date {date} metadata where posted date is since (inclusive) {date}  
until-posted-date {date} metadata where posted date is before (inclusive) {date}  
from-accepted-date {date} metadata where accepted date is since (inclusive) {date}  
until-accepted-date {date} metadata where accepted date is before (inclusive) {date}  
has-license   metadata that includes any &lt;license_ref&gt; elements.  
license.url {url} metadata where &lt;license_ref&gt; value equals {url}  
license.version {string} metadata where the &lt;license_ref&gt;’s applies_to attribute is {string}  
license.delay {integer} metadata where difference between publication date and the &lt;license_ref&gt;’s start_date attribute is <= {integer} (in days)  
has-full-text   metadata that includes any full text &lt;resource&gt; elements.  
full-text.version {string} metadata where &lt;resource&gt; element’s content_version attribute is {string}.  
full-text.type {mime_type} metadata where &lt;resource&gt; element’s content_type attribute is {mime_type} (e.g. application/pdf).  
full-text.application {string} metadata where &lt;resource&gt; link has one of the following intended applications: text-mining, similarity-checking or unspecified  
has-references   metadata for works that have a list of references  
reference-visibility [open, limited, closed] metadata for works where references are either open, limited (to Metadata Plus subscribers) or closed  
has-archive   metadata which include name of archive partner  
archive {string} metadata which where value of archive partner is {string}  
has-orcid   metadata which includes one or more ORCIDs  
has-authenticated-orcid   metadata which includes one or more ORCIDs where the depositing publisher claims to have witness the ORCID owner authenticate with ORCID  
orcid {orcid} metadata where &lt;orcid&gt; element’s value = {orcid}  
issn {issn} metadata where record has an ISSN = {issn}. Format is xxxx-xxxx.  
isbn {isbn} metadata where record has an ISBN = {issn}.  
type {type} metadata records whose type = {type}. Type must be an ID value from the list of types returned by the /types resource  
directory {directory} metadata records whose article or serial are mentioned in the given {directory}. Currently the only supported value is doaj.  
doi {doi} metadata describing the DOI {doi}  
updates {doi} metadata for records that represent editorial updates to the DOI {doi}  
is-update   metadata for records that represent editorial updates  
has-update-policy   metadata for records that include a link to an editorial update policy  
container-title   metadata for records with a publication title exactly with an exact match  
category-name   metadata for records with an exact matching category label. Category labels come from this list published by Scopus  
type   metadata for records with type matching a type identifier (e.g. journal-article)  
type-name   metadata for records with an exactly matching type label  
award.number {award_number} metadata for records with a matching award nunber. Optionally combine with award.funder  
award.funder {funder doi or id} metadata for records with an award with matching funder. Optionally combine with award.number  
has-assertion   metadata for records with any assertions  
assertion-group   metadata for records with an assertion in a particular group  
assertion   metadata for records with a particular named assertion  
has-affiliation   metadata for records that have any affiliation information  
alternative-id   metadata for records with the given alternative ID, which may be a publisher-specific ID, or any other identifier a publisher may have provided  
article-number   metadata for records with a given article number  
has-abstract   metadata for records which include an abstract  
has-clinical-trial-number   metadata for records which include a clinical trial number  
content-domain   metadata where the publisher records a particular domain name as the location Crossmark content will appear  
has-content-domain   metadata where the publisher records a domain name location for Crossmark content  
has-domain-restriction   metadata where the publisher restricts Crossmark usage to content domains  
has-relation   metadata for records that either assert or are the object of a relation  
relation.type   One of the relation types from the Crossref relations schema (e.g. is-referenced-by, is-parent-of, is-preprint-of)  
relation.object   Relations where the object identifier matches the identifier provided  
relation.object-type   One of the identifier types from the Crossref relations schema (e.g. doi, issn) </orcid></resource></resource></resource></resource></license_ref></license_ref></license_ref></license_ref>

Filtering by publication date with from_pub_date and until_pub_date

For example, you may only want to pull publications from a given year, or within a date range. Remember to increase the limit or use cursor if you need to. Also notice three things about the filter argument:

Here, we will get all articles from the Journal of Librarianship and Scholarly Communication published after January 1, 2019:

# assign the JLSC ISSN
jlsc_issn <- "2162-3309"

# get articles published since January 1, 2019
jlsc_publications_2019 <- rcrossref::cr_journals(issn = jlsc_issn, works = T, 
                                                 filter = c(from_pub_date='2019-01-01')) %>%
  purrr::pluck("data")

# print the dataframe with select column
jlsc_publications_2019 %>%
  dplyr::select(title, doi, volume, issue, page, issued, url, publisher, reference.count, type, issn)
A tibble: 20 x 11
titledoivolumeissuepageissuedurlpublisherreference.counttypeissn
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>
Considering Creative Activity in Institutional Repositories: An Exploration of Faculty Perceptions 10.7710/2162-3309.23128123122020-02-25http://dx.doi.org/10.7710/2162-3309.2312Pacific University Library0journal-article2162-3309
Avoiding the “Axe”: Advancing Affordable and Open Education Resources at a Midsize University 10.7710/2162-3309.225971NA 2019-05-20http://dx.doi.org/10.7710/2162-3309.2259Pacific University Library0journal-article2162-3309
The Development of the Journal Evaluation Tool to Evaluate the Credibility of Publication Venues 10.7710/2162-3309.225071NA 2019-06-04http://dx.doi.org/10.7710/2162-3309.2250Pacific University Library0journal-article2162-3309
Meaningful Metrics: A 21st Century Librarian's Guide to Bibliometrics, Altmetrics, and Research Impact [Book Review] 10.7710/2162-3309.229071NA 2019-01-15http://dx.doi.org/10.7710/2162-3309.2290Pacific University Library0journal-article2162-3309
Bibliometrics and Research Evaluation: Uses and Abuses 10.7710/2162-3309.228671NA 2019-01-10http://dx.doi.org/10.7710/2162-3309.2286Pacific University Library0journal-article2162-3309
Creating a Library Publishing Program: Your Options Are Limited 10.7710/2162-3309.226271NA 2019-01-10http://dx.doi.org/10.7710/2162-3309.2262Pacific University Library0journal-article2162-3309
Online Safety and Academic Scholarship: Exploring Researchers’ Concerns from Ghana 10.7710/2162-3309.226371NA 2019-01-15http://dx.doi.org/10.7710/2162-3309.2263Pacific University Library0journal-article2162-3309
Data Management Practices in Academic Library Learning Analytics: A Critical Review 10.7710/2162-3309.226871NA 2019-02-22http://dx.doi.org/10.7710/2162-3309.2268Pacific University Library0journal-article2162-3309
Strategies for Supporting OER Adoption through Faculty and Instructor Use of a Federated Search Tool 10.7710/2162-3309.227971NA 2019-02-22http://dx.doi.org/10.7710/2162-3309.2279Pacific University Library0journal-article2162-3309
When a Repository Is Not Enough: Redesigning a Digital Ecosystem to Serve Scholarly Communication 10.7710/2162-3309.222571NA 2019-02-26http://dx.doi.org/10.7710/2162-3309.2225Pacific University Library0journal-article2162-3309
Opening Up Open Access Institutional Repositories to Demonstrate Value: Two Universities’ Pilots on Including Metadata-Only Records10.7710/2162-3309.222071NA 2019-03-08http://dx.doi.org/10.7710/2162-3309.2220Pacific University Library0journal-article2162-3309
Dynamic Research Support for Academic Libraries [Book Review] 10.7710/2162-3309.230771NA 2019-04-15http://dx.doi.org/10.7710/2162-3309.2307Pacific University Library0journal-article2162-3309
Course Review: CopyrightX 10.7710/2162-3309.229771NA 2019-04-11http://dx.doi.org/10.7710/2162-3309.2297Pacific University Library0journal-article2162-3309
Whose Research is it Anyway? Academic Social Networks Versus Institutional Repositories 10.7710/2162-3309.224371NA 2019-04-25http://dx.doi.org/10.7710/2162-3309.2243Pacific University Library0journal-article2162-3309
Mapping the Scholarly Literature Found in Scopus on “Research Data Management”: A Bibliometric and Data Visualization Approach 10.7710/2162-3309.226671NA 2019-04-25http://dx.doi.org/10.7710/2162-3309.2266Pacific University Library0journal-article2162-3309
Library Publishers as Educators: Crafting Curriculum for Undergraduate Research Journals 10.7710/2162-3309.229671NA 2019-05-06http://dx.doi.org/10.7710/2162-3309.2296Pacific University Library0journal-article2162-3309
Embracing New Trends in Scholarly Communication: From Competency Requirements in the Workplace to LIS Curriculum Presence 10.7710/2162-3309.229171NA 2019-07-19http://dx.doi.org/10.7710/2162-3309.2291Pacific University Library0journal-article2162-3309
The Five Laws of OER: Observations from Ranganathan 10.7710/2162-3309.229971NA 2019-08-20http://dx.doi.org/10.7710/2162-3309.2299Pacific University Library0journal-article2162-3309
JLSC Board Editorial 2019 10.7710/2162-3309.233471NA 2019-09-12http://dx.doi.org/10.7710/2162-3309.2334Pacific University Library0journal-article2162-3309
We Can Do I.T.: Women in Library Information Technology 10.7710/2162-3309.232071NA 2019-09-16http://dx.doi.org/10.7710/2162-3309.2320Pacific University Library0journal-article2162-3309

Filtering by funder with award.funder

You can also return all articles funded by a specific funder. See the Crossref Funder Registry for a list of funders and their DOIs.

Here, we will combine two filters: award.funder and from_pub_date to return all articles published in PLoS ONE where a) at least one funder is the National Institutes of Health, and b) the article was published after March 1, 2020. Note that we set a limit here of 25 because we are doing a teaching activity and we don’t want to send heavy queries. If you were doing this on your own, you would likely want to remove the limit.

# assign the PLoS ONE ISSN and the NIH Funder DOI
plosone_issn <- '1932-6203'
nih_funder_doi <- '10.13039/100000002'

# get articles published in PLoS since 3/1 funded by NIH
plosone_publications_nih <- rcrossref::cr_journals(issn = plosone_issn, works = T, limit = 25,
                                                 filter = c(award.funder = nih_funder_doi,
                                                           from_pub_date = '2020-03-01')) %>%
  purrr::pluck("data")

We will use unnest() from the tidyr package to view the data frame here. This is described below in Unnesting List Columns.

# print the dataframe, first unnesting the funder column
plosone_publications_nih %>%
    tidyr::unnest(funder)
A tibble: 21 x 32
container.titlecreateddepositedpublished.onlinedoiindexedissnissueissuedmemberpageprefixpublisherreference.countscoresourcesubjecttitletypeupdate.policyurlvolumeDOInamedoi.asserted.byawardaward1award2award3award4award5award6
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02287822020-03-041932-620332020-03-04340e022878210.1371Public Library of Science (PLoS)731CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineLearning about the Ellsberg Paradox reduces, but does not abolish, ambiguity aversion journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.02287821510.13039/100000002 National Institutes of Health publisherR21AG049293 NA NA NA NA NA NA
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02287822020-03-041932-620332020-03-04340e022878210.1371Public Library of Science (PLoS)731CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineLearning about the Ellsberg Paradox reduces, but does not abolish, ambiguity aversion journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.02287821510.13039/100000049 National Institute on Aging publisherR56AG058769 NA NA NA NA NA NA
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02295412020-03-041932-620332020-03-04340e022954110.1371Public Library of Science (PLoS)621CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineAssociation of combination statin and antihypertensive therapy with reduced Alzheimer’s disease and related dementia riskjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.02295411510.13039/100000002 National Institutes of Health publisherNA R01AG055401K01AG042498P01AG026572R01HL130462P30AG043073R01HL126804
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02295412020-03-041932-620332020-03-04340e022954110.1371Public Library of Science (PLoS)621CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineAssociation of combination statin and antihypertensive therapy with reduced Alzheimer’s disease and related dementia riskjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.02295411510.13039/501100000320Alzheimer's Society crossref NA NA NA NA NA NA NA
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02295412020-03-041932-620332020-03-04340e022954110.1371Public Library of Science (PLoS)621CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineAssociation of combination statin and antihypertensive therapy with reduced Alzheimer’s disease and related dementia riskjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.02295411510.13039/100011699 BRACE publisherNA NA NA NA NA NA NA
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02295412020-03-041932-620332020-03-04340e022954110.1371Public Library of Science (PLoS)621CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineAssociation of combination statin and antihypertensive therapy with reduced Alzheimer’s disease and related dementia riskjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.02295411510.13039/501100000274British Heart Foundation crossref NA NA NA NA NA NA NA
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02295412020-03-041932-620332020-03-04340e022954110.1371Public Library of Science (PLoS)621CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineAssociation of combination statin and antihypertensive therapy with reduced Alzheimer’s disease and related dementia riskjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.022954115NA University of Southern California Zumberge Research FundNA 1R34AG049652NA NA NA NA NA NA
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02295412020-03-041932-620332020-03-04340e022954110.1371Public Library of Science (PLoS)621CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineAssociation of combination statin and antihypertensive therapy with reduced Alzheimer’s disease and related dementia riskjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.022954115NA Schaeffer-Amgen Fellowship Program NA NA NA NA NA NA NA NA
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02295412020-03-041932-620332020-03-04340e022954110.1371Public Library of Science (PLoS)621CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineAssociation of combination statin and antihypertensive therapy with reduced Alzheimer’s disease and related dementia riskjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.022954115NA Sigmund Gestetner Foundation NA NA NA NA NA NA NA NA
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02295412020-03-041932-620332020-03-04340e022954110.1371Public Library of Science (PLoS)621CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineAssociation of combination statin and antihypertensive therapy with reduced Alzheimer’s disease and related dementia riskjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.022954115NA NIHR-EME NA NA NA NA NA NA NA NA
................................................................................................
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02295412020-03-041932-620332020-03-04340e022954110.1371Public Library of Science (PLoS)621CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineAssociation of combination statin and antihypertensive therapy with reduced Alzheimer’s disease and related dementia risk journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.022954115NA Medical Research Council NA NA NA NA NA NANANA
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02281632020-03-041932-620332020-03-04340e022816310.1371Public Library of Science (PLoS)411CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineImmunotherapy with DNA vaccine and live attenuated rubella/SIV gag vectors plus early ART can prevent SIVmac251 viral rebound in acutely infected rhesus macaquesjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.02281631510.13039/100000038U.S. Food and Drug Administration publisherNA NA NA NA NANANA
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02281632020-03-041932-620332020-03-04340e022816310.1371Public Library of Science (PLoS)411CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineImmunotherapy with DNA vaccine and live attenuated rubella/SIV gag vectors plus early ART can prevent SIVmac251 viral rebound in acutely infected rhesus macaquesjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.02281631510.13039/100000002National Institutes of Health publisherR01 AI118586 NA NA NA NANANA
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02281632020-03-041932-620332020-03-04340e022816310.1371Public Library of Science (PLoS)411CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineImmunotherapy with DNA vaccine and live attenuated rubella/SIV gag vectors plus early ART can prevent SIVmac251 viral rebound in acutely infected rhesus macaquesjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.02281631510.13039/100000054National Cancer Institute publisherNA NA NA NA NANANA
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02295372020-03-041932-620332020-03-04340e022953710.1371Public Library of Science (PLoS)591CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineCombined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.02295371510.13039/100000002National Institutes of Health publisherRAI092531A NA NA NA NANANA
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02295372020-03-041932-620332020-03-04340e022953710.1371Public Library of Science (PLoS)591CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineCombined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.02295371510.13039/100000912March of Dimes Foundation publisher5-FY10-103 NA NA NA NANANA
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02295372020-03-041932-620332020-03-04340e022953710.1371Public Library of Science (PLoS)591CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineCombined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.02295371510.13039/100005825National Institute of Food and Agriculturepublisher2016-67012-24717NA NA NA NANANA
PLOS ONE2020-03-032020-03-032020-03-0310.1371/journal.pone.02270942020-03-031932-620332020-03-03340e022709410.1371Public Library of Science (PLoS)431CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineShedding and stability of CWD prion seeding activity in cervid feces journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.02270941510.13039/100000002National Institutes of Health publisherNA RO1-NS061902 PO1-AI077774 RO1-NS076894NANANA
PLOS ONE2020-03-022020-03-022020-03-0210.1371/journal.pone.02288712020-03-021932-620332020-03-02340e022887110.1371Public Library of Science (PLoS)531CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineVariability in protein cargo detection in technical and biological replicates of exosome-enriched extracellular vesicles journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.02288711510.13039/100000002National Institutes of Health crossref NA Grant R01 HL132870 (L.S.)Grant R01 HL128228 (L.S.)NA NANANA
PLOS ONE2020-03-062020-03-062020-03-0610.1371/journal.pone.02285572020-03-061932-620332020-03-06340e022855710.1371Public Library of Science (PLoS)291CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineNovel drug combination nanoparticles exhibit enhanced plasma exposure and dose-responsive effects on eliminating breast cancer lung metastasis journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.02285571510.13039/100000002National Institutes of Health publisherNA 1S10OD010652-01 UM1AI120176 NA NANANA

If you scroll all the way to the right, you can see the funder information. Look at the title column and you will notice that some article titles are now duplicated, however you will see different funders in the name column. This is because a single article may have multiple funders, and a new row is created for each funder, with data including the award number.

Filtering by license with has_license

You may be interested in licensing information for articles; for instance, gathering publications in a given journal that are licensed under Creative Commons. First run cr_journals with works set to FALSE in order to return journal details so you can check if the publisher even sends article licensing information to Crossref–it’s not required. We will use PLOS ONE again as an example.

# assign the PLoS ONE ISSN and get journal details by setting works = FALSE
plosone_issn <- '1932-6203'
plosone_details <- rcrossref::cr_journals(issn = plosone_issn, works = FALSE) %>%
  purrr::pluck("data")

We can check the deposits_licenses_current variables to see if license data on file is current. If it is TRUE, PLoS ONE does send licensing information and it is current.

# is article licensing data on file current?
plosone_details$deposits_licenses_current

TRUE

We can now rerun the query but set works = TRUE, and set the has_license to TRUE. This will therefore return only articles that have license information. We will set our limit to 25.

# get last 25 articles on file where has_license is TRUE
plosone_license <- rcrossref::cr_journals(issn = plosone_issn, works = T, limit = 25, filter = c(`has_license` = TRUE)) %>% 
  pluck("data")

# print the data with select columns
plosone_license %>%
  dplyr::select(title, doi, volume, issue, page, issued, url, publisher, reference.count, type, issn, license)
A tibble: 25 x 12
titledoivolumeissuepageissuedurlpublisherreference.counttypeissnlicense
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><list>
Extinction-Dependent Alterations in Corticostriatal mGluR2/3 and mGluR7 Receptors following Chronic Methamphetamine Self-Administration in Rats 10.1371/journal.pone.00342997 3 e34299 2012-03-29http://dx.doi.org/10.1371/journal.pone.0034299Public Library of Science (PLoS)77journal-article1932-62032012-03-29 , http://creativecommons.org/licenses/by/4.0/, 0 , unspecified
Pathophysiological Defects and Transcriptional Profiling in the RBM20-/- Rat Model 10.1371/journal.pone.00842818 12e84281 2013-12-19http://dx.doi.org/10.1371/journal.pone.0084281Public Library of Science (PLoS)60journal-article1932-62032013-12-19 , http://creativecommons.org/licenses/by/4.0/, 0 , vor
Ab-Externo AAV-Mediated Gene Delivery to the Suprachoroidal Space Using a 250 Micron Flexible Microcatheter 10.1371/journal.pone.00171406 2 e17140 2011-02-11http://dx.doi.org/10.1371/journal.pone.0017140Public Library of Science (PLoS)11journal-article1932-62032011-02-11 , http://creativecommons.org/licenses/by/4.0/, 0 , unspecified
Proteomic and Phospho-Proteomic Profile of Human Platelets in Basal, Resting State: Insights into Integrin Signaling 10.1371/journal.pone.00076274 10e7627 2009-10-27http://dx.doi.org/10.1371/journal.pone.0007627Public Library of Science (PLoS)67journal-article1932-62032009-10-27 , http://creativecommons.org/licenses/by/4.0/, 0 , unspecified
Alterations of Neuromuscular Function after the World's Most Challenging Mountain Ultra-Marathon 10.1371/journal.pone.00655968 6 e65596 2013-06-26http://dx.doi.org/10.1371/journal.pone.0065596Public Library of Science (PLoS)51journal-article1932-62032013-06-26 , http://creativecommons.org/licenses/by/4.0/, 0 , unspecified
Integrated Metagenomic and Physiochemical Analyses to Evaluate the Potential Role of Microbes in the Sand Filter of a Drinking Water Treatment System10.1371/journal.pone.00610118 4 e61011 2013-04-11http://dx.doi.org/10.1371/journal.pone.0061011Public Library of Science (PLoS)43journal-article1932-62032013-04-11 , http://creativecommons.org/licenses/by/4.0/, 0 , unspecified
Major Facilitator Superfamily Domain-Containing Protein 2a (MFSD2A) Has Roles in Body Growth, Motor Function, and Lipid Metabolism 10.1371/journal.pone.00506297 11e50629 2012-11-29http://dx.doi.org/10.1371/journal.pone.0050629Public Library of Science (PLoS)52journal-article1932-62032012-11-29 , http://creativecommons.org/licenses/by/4.0/, 0 , unspecified
Analysis of Autophagy Genes in Microalgae: Chlorella as a Potential Model to Study Mechanism of Autophagy 10.1371/journal.pone.00418267 7 e41826 2012-07-27http://dx.doi.org/10.1371/journal.pone.0041826Public Library of Science (PLoS)0 journal-article1932-62032012-07-27 , http://creativecommons.org/licenses/by/4.0/, 0 , unspecified
Osteoprotegerin Regulates Pancreatic β-Cell Homeostasis upon Microbial Invasion 10.1371/journal.pone.0146544111 e01465442016-01-11http://dx.doi.org/10.1371/journal.pone.0146544Public Library of Science (PLoS)54journal-article1932-62032016-01-11 , http://creativecommons.org/licenses/by/4.0/, 0 , vor
Health Behavior and Metabolic Risk Factors Associated with Normal Weight Obesity in Adolescents 10.1371/journal.pone.0161451118 e01614512016-08-25http://dx.doi.org/10.1371/journal.pone.0161451Public Library of Science (PLoS)42journal-article1932-62032016-08-25 , http://creativecommons.org/licenses/by/4.0/, 0 , vor
....................................
Cross-Modal Calibration of Vestibular Afference for Human Balance 10.1371/journal.pone.0124532104 e01245322015-04-20http://dx.doi.org/10.1371/journal.pone.0124532Public Library of Science (PLoS)44journal-article1932-62032015-04-20 , http://creativecommons.org/licenses/by/4.0/, 0 , vor
Genetic Factors Are Not the Major Causes of Chronic Diseases 10.1371/journal.pone.0154387114 e01543872016-04-22http://dx.doi.org/10.1371/journal.pone.0154387Public Library of Science (PLoS)45journal-article1932-62032016-04-22 , http://creativecommons.org/licenses/by/4.0/, 0 , vor
Manipulation of Pre-Target Activity on the Right Frontal Eye Field Enhances Conscious Visual Perception in Humans 10.1371/journal.pone.00362327 5 e36232 2012-05-15http://dx.doi.org/10.1371/journal.pone.0036232Public Library of Science (PLoS)46journal-article1932-62032012-05-15 , http://creativecommons.org/licenses/by/4.0/, 0 , unspecified
Splicing of the rSlo Gene Affects the Molecular Composition and Drug Response of Ca2+-Activated K+ Channels in Skeletal Muscle 10.1371/journal.pone.00402357 7 e40235 2012-07-10http://dx.doi.org/10.1371/journal.pone.0040235Public Library of Science (PLoS)55journal-article1932-62032012-07-10 , http://creativecommons.org/licenses/by/4.0/, 0 , unspecified
5-HT2C Receptors in the Basolateral Amygdala and Dorsal Striatum Are a Novel Target for the Anxiolytic and Antidepressant Effects of Exercise10.1371/journal.pone.00461187 9 e46118 2012-09-25http://dx.doi.org/10.1371/journal.pone.0046118Public Library of Science (PLoS)0 journal-article1932-62032012-09-25 , http://creativecommons.org/licenses/by/4.0/, 0 , unspecified
Task-Level Strategies for Human Sagittal-Plane Running Maneuvers Are Consistent with Robotic Control Policies 10.1371/journal.pone.00518887 12e51888 2012-12-20http://dx.doi.org/10.1371/journal.pone.0051888Public Library of Science (PLoS)49journal-article1932-62032012-12-20 , http://creativecommons.org/licenses/by/4.0/, 0 , unspecified
Fc Gamma Receptor IIb on GM-CSF Macrophages Controls Immune Complex Mediated Inhibition of Inflammatory Signals 10.1371/journal.pone.01109669 10e110966 2014-10-23http://dx.doi.org/10.1371/journal.pone.0110966Public Library of Science (PLoS)37journal-article1932-62032014-10-23 , http://creativecommons.org/licenses/by/4.0/, 0 , unspecified
Does the Clock Make the Poison? Circadian Variation in Response to Pesticides 10.1371/journal.pone.00064694 7 e6469 2009-07-31http://dx.doi.org/10.1371/journal.pone.0006469Public Library of Science (PLoS)52journal-article1932-62032009-07-31 , http://creativecommons.org/licenses/by/4.0/, 0 , unspecified
Sleep Architecture When Sleeping at an Unusual Circadian Time and Associations with Insulin Sensitivity 10.1371/journal.pone.00728778 8 e72877 2013-08-08http://dx.doi.org/10.1371/journal.pone.0072877Public Library of Science (PLoS)34journal-article1932-62032013-08-08 , http://creativecommons.org/licenses/by/4.0/, 0 , unspecified
Tradeoff between Stability and Maneuverability during Whole-Body Movements 10.1371/journal.pone.00218156 7 e21815 2011-07-14http://dx.doi.org/10.1371/journal.pone.0021815Public Library of Science (PLoS)29journal-article1932-62032011-07-14 , http://creativecommons.org/licenses/by/4.0/, 0 , unspecified

The license data comes in as a nested column. We can unnest it using tidyr::unnest, which we used above with funders and will be discussed more below.

# print the data frame with license unnested. The .drop argument will drop all other list columns.
plosone_license %>%
  tidyr::unnest(license, .drop = TRUE)
A tibble: 25 x 26
container.titlecreateddepositedpublished.onlinedoiindexedissnissueissuedmemberpageprefixpublisherreference.countscoresourcetitletypeupdate.policyurlvolumesubjectdateURLdelay.in.dayscontent.version
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><int><chr>
PLoS ONE2012-03-292019-06-262012-03-2910.1371/journal.pone.00342992020-02-051932-62033 2012-03-29340e34299 10.1371Public Library of Science (PLoS)771CrossrefExtinction-Dependent Alterations in Corticostriatal mGluR2/3 and mGluR7 Receptors following Chronic Methamphetamine Self-Administration in Rats journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.00342997 NA 2012-03-29http://creativecommons.org/licenses/by/4.0/0unspecified
PLoS ONE2013-12-192019-08-052013-12-1910.1371/journal.pone.00842812020-02-051932-6203122013-12-19340e84281 10.1371Public Library of Science (PLoS)601CrossrefPathophysiological Defects and Transcriptional Profiling in the RBM20-/- Rat Model journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.00842818 General Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General Medicine2013-12-19http://creativecommons.org/licenses/by/4.0/0vor
PLoS ONE2011-02-112018-10-232011-02-1110.1371/journal.pone.00171402020-02-051932-62032 2011-02-11340e17140 10.1371Public Library of Science (PLoS)111CrossrefAb-Externo AAV-Mediated Gene Delivery to the Suprachoroidal Space Using a 250 Micron Flexible Microcatheter journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.00171406 NA 2011-02-11http://creativecommons.org/licenses/by/4.0/0unspecified
PLoS ONE2009-10-262018-10-232009-10-2710.1371/journal.pone.00076272020-02-051932-6203102009-10-27340e7627 10.1371Public Library of Science (PLoS)671CrossrefProteomic and Phospho-Proteomic Profile of Human Platelets in Basal, Resting State: Insights into Integrin Signaling journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.00076274 NA 2009-10-27http://creativecommons.org/licenses/by/4.0/0unspecified
PLoS ONE2013-06-262019-07-162013-06-2610.1371/journal.pone.00655962020-02-051932-62036 2013-06-26340e65596 10.1371Public Library of Science (PLoS)511CrossrefAlterations of Neuromuscular Function after the World's Most Challenging Mountain Ultra-Marathon journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.00655968 General Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General Medicine2013-06-26http://creativecommons.org/licenses/by/4.0/0unspecified
PLoS ONE2013-04-112019-07-122013-04-1110.1371/journal.pone.00610112020-02-051932-62034 2013-04-11340e61011 10.1371Public Library of Science (PLoS)431CrossrefIntegrated Metagenomic and Physiochemical Analyses to Evaluate the Potential Role of Microbes in the Sand Filter of a Drinking Water Treatment Systemjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.00610118 General Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General Medicine2013-04-11http://creativecommons.org/licenses/by/4.0/0unspecified
PLoS ONE2012-11-292019-07-062012-11-2910.1371/journal.pone.00506292020-02-051932-6203112012-11-29340e50629 10.1371Public Library of Science (PLoS)521CrossrefMajor Facilitator Superfamily Domain-Containing Protein 2a (MFSD2A) Has Roles in Body Growth, Motor Function, and Lipid Metabolism journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.00506297 NA 2012-11-29http://creativecommons.org/licenses/by/4.0/0unspecified
PLoS ONE2012-07-282016-04-202012-07-2710.1371/journal.pone.00418262020-02-051932-62037 2012-07-27340e41826 10.1371Public Library of Science (PLoS)0 1CrossrefAnalysis of Autophagy Genes in Microalgae: Chlorella as a Potential Model to Study Mechanism of Autophagy journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.00418267 NA 2012-07-27http://creativecommons.org/licenses/by/4.0/0unspecified
PLOS ONE2016-01-112019-09-032016-01-1110.1371/journal.pone.01465442020-02-051932-62031 2016-01-11340e014654410.1371Public Library of Science (PLoS)541CrossrefOsteoprotegerin Regulates Pancreatic β-Cell Homeostasis upon Microbial Invasion journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.014654411NA 2016-01-11http://creativecommons.org/licenses/by/4.0/0vor
PLOS ONE2016-08-252019-09-122016-08-2510.1371/journal.pone.01614512020-02-051932-62038 2016-08-25340e016145110.1371Public Library of Science (PLoS)421CrossrefHealth Behavior and Metabolic Risk Factors Associated with Normal Weight Obesity in Adolescents journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.016145111NA 2016-08-25http://creativecommons.org/licenses/by/4.0/0vor
..............................................................................
PLOS ONE2015-04-202019-08-232015-04-2010.1371/journal.pone.01245322020-02-041932-62034 2015-04-20340e012453210.1371Public Library of Science (PLoS)441CrossrefCross-Modal Calibration of Vestibular Afference for Human Balance journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.012453210NA 2015-04-20http://creativecommons.org/licenses/by/4.0/0vor
PLOS ONE2016-04-222019-09-062016-04-2210.1371/journal.pone.01543872020-02-041932-62034 2016-04-22340e015438710.1371Public Library of Science (PLoS)451CrossrefGenetic Factors Are Not the Major Causes of Chronic Diseases journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.015438711NA 2016-04-22http://creativecommons.org/licenses/by/4.0/0vor
PLoS ONE2012-05-152018-10-242012-05-1510.1371/journal.pone.00362322020-02-041932-62035 2012-05-15340e36232 10.1371Public Library of Science (PLoS)461CrossrefManipulation of Pre-Target Activity on the Right Frontal Eye Field Enhances Conscious Visual Perception in Humans journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.00362327 NA 2012-05-15http://creativecommons.org/licenses/by/4.0/0unspecified
PLoS ONE2012-07-102019-06-302012-07-1010.1371/journal.pone.00402352020-02-041932-62037 2012-07-10340e40235 10.1371Public Library of Science (PLoS)551CrossrefSplicing of the rSlo Gene Affects the Molecular Composition and Drug Response of Ca2+-Activated K+ Channels in Skeletal Muscle journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.00402357 NA 2012-07-10http://creativecommons.org/licenses/by/4.0/0unspecified
PLoS ONE2012-09-262016-04-202012-09-2510.1371/journal.pone.00461182020-02-041932-62039 2012-09-25340e46118 10.1371Public Library of Science (PLoS)0 1Crossref5-HT2C Receptors in the Basolateral Amygdala and Dorsal Striatum Are a Novel Target for the Anxiolytic and Antidepressant Effects of Exercisejournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.00461187 NA 2012-09-25http://creativecommons.org/licenses/by/4.0/0unspecified
PLoS ONE2012-12-202019-07-072012-12-2010.1371/journal.pone.00518882020-02-041932-6203122012-12-20340e51888 10.1371Public Library of Science (PLoS)491CrossrefTask-Level Strategies for Human Sagittal-Plane Running Maneuvers Are Consistent with Robotic Control Policies journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.00518887 NA 2012-12-20http://creativecommons.org/licenses/by/4.0/0unspecified
PLoS ONE2014-10-232019-08-162014-10-2310.1371/journal.pone.01109662020-02-041932-6203102014-10-23340e110966 10.1371Public Library of Science (PLoS)371CrossrefFc Gamma Receptor IIb on GM-CSF Macrophages Controls Immune Complex Mediated Inhibition of Inflammatory Signals journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.01109669 NA 2014-10-23http://creativecommons.org/licenses/by/4.0/0unspecified
PLoS ONE2009-07-302019-05-212009-07-3110.1371/journal.pone.00064692020-02-041932-62037 2009-07-31340e6469 10.1371Public Library of Science (PLoS)521CrossrefDoes the Clock Make the Poison? Circadian Variation in Response to Pesticides journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.00064694 NA 2009-07-31http://creativecommons.org/licenses/by/4.0/0unspecified
PLoS ONE2013-08-082019-07-202013-08-0810.1371/journal.pone.00728772020-02-041932-62038 2013-08-08340e72877 10.1371Public Library of Science (PLoS)341CrossrefSleep Architecture When Sleeping at an Unusual Circadian Time and Associations with Insulin Sensitivity journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.00728778 General Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General Medicine2013-08-08http://creativecommons.org/licenses/by/4.0/0unspecified
PLoS ONE2011-07-142019-06-132011-07-1410.1371/journal.pone.00218152020-02-041932-62037 2011-07-14340e21815 10.1371Public Library of Science (PLoS)291CrossrefTradeoff between Stability and Maneuverability during Whole-Body Movements journal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.00218156 NA 2011-07-14http://creativecommons.org/licenses/by/4.0/0unspecified

This adds four columns all the way to the right:

Browsing the rows, we see all are CC BY 4.0, which stands to reason given PLOS ONE is an open access publisher and applies the CC BY license to the articles they publish.

Filtering rows and selecting columns with dplyr

You can use the filter() and select() functions from the dplyr package if you want to get subsets of this data after you have made the query. Note that this is a completely different filter than the one used above inside the cr_journals() function. That one was an argument sent with the API call that filtered the results before they were returned. This is a separate function that is part of dplyr to help you filter a data frame in R.

To learn more about the dplyr package, read the “Data Transformation” chapter in R For Data Science.

Above, we retrieved all articles from the Journal of Librarianship & Scholarly Communication published after January 1, 2019. Let’s say you want only volume 8, issue 1:

# assign the JLSC ISSN and get all publications after January 1, 2019
jlsc_issn <- "2162-3309"
jlsc_publications_2019 <- rcrossref::cr_journals(issn = jlsc_issn, works = T, limit = 25,
                                                 filter = c(from_pub_date='2019-01-01')) %>%
  purrr::pluck("data")

# print the data frame with select columns
jlsc_publications_2019 %>%
  dplyr::select(title, doi, volume, issue, page, issued, url, publisher, reference.count, type, issn)
A tibble: 25 x 11
titledoivolumeissuepageissuedurlpublisherreference.counttypeissn
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>
Considering Creative Activity in Institutional Repositories: An Exploration of Faculty Perceptions 10.7710/2162-3309.23128123122020-02-25http://dx.doi.org/10.7710/2162-3309.2312Pacific University Library0journal-article2162-3309
Avoiding the “Axe”: Advancing Affordable and Open Education Resources at a Midsize University 10.7710/2162-3309.225971NA 2019-05-20http://dx.doi.org/10.7710/2162-3309.2259Pacific University Library0journal-article2162-3309
The Development of the Journal Evaluation Tool to Evaluate the Credibility of Publication Venues 10.7710/2162-3309.225071NA 2019-06-04http://dx.doi.org/10.7710/2162-3309.2250Pacific University Library0journal-article2162-3309
Meaningful Metrics: A 21st Century Librarian's Guide to Bibliometrics, Altmetrics, and Research Impact [Book Review]10.7710/2162-3309.229071NA 2019-01-15http://dx.doi.org/10.7710/2162-3309.2290Pacific University Library0journal-article2162-3309
Bibliometrics and Research Evaluation: Uses and Abuses 10.7710/2162-3309.228671NA 2019-01-10http://dx.doi.org/10.7710/2162-3309.2286Pacific University Library0journal-article2162-3309
Creating a Library Publishing Program: Your Options Are Limited 10.7710/2162-3309.226271NA 2019-01-10http://dx.doi.org/10.7710/2162-3309.2262Pacific University Library0journal-article2162-3309
Online Safety and Academic Scholarship: Exploring Researchers’ Concerns from Ghana 10.7710/2162-3309.226371NA 2019-01-15http://dx.doi.org/10.7710/2162-3309.2263Pacific University Library0journal-article2162-3309
Data Management Practices in Academic Library Learning Analytics: A Critical Review 10.7710/2162-3309.226871NA 2019-02-22http://dx.doi.org/10.7710/2162-3309.2268Pacific University Library0journal-article2162-3309
Strategies for Supporting OER Adoption through Faculty and Instructor Use of a Federated Search Tool 10.7710/2162-3309.227971NA 2019-02-22http://dx.doi.org/10.7710/2162-3309.2279Pacific University Library0journal-article2162-3309
When a Repository Is Not Enough: Redesigning a Digital Ecosystem to Serve Scholarly Communication 10.7710/2162-3309.222571NA 2019-02-26http://dx.doi.org/10.7710/2162-3309.2225Pacific University Library0journal-article2162-3309
.................................
Library Publishers as Educators: Crafting Curriculum for Undergraduate Research Journals 10.7710/2162-3309.229671NA2019-05-06http://dx.doi.org/10.7710/2162-3309.2296Pacific University Library0journal-article2162-3309
Embracing New Trends in Scholarly Communication: From Competency Requirements in the Workplace to LIS Curriculum Presence10.7710/2162-3309.229171NA2019-07-19http://dx.doi.org/10.7710/2162-3309.2291Pacific University Library0journal-article2162-3309
The Five Laws of OER: Observations from Ranganathan 10.7710/2162-3309.229971NA2019-08-20http://dx.doi.org/10.7710/2162-3309.2299Pacific University Library0journal-article2162-3309
JLSC Board Editorial 2019 10.7710/2162-3309.233471NA2019-09-12http://dx.doi.org/10.7710/2162-3309.2334Pacific University Library0journal-article2162-3309
We Can Do I.T.: Women in Library Information Technology 10.7710/2162-3309.232071NA2019-09-16http://dx.doi.org/10.7710/2162-3309.2320Pacific University Library0journal-article2162-3309
A Team Approach: Library Publishing Partnerships with Scholarly Societies 10.7710/2162-3309.232671NA2019-11-21http://dx.doi.org/10.7710/2162-3309.2326Pacific University Library0journal-article2162-3309
Volume 7 Masthead 10.7710/2162-3309.235171NA2019-12-04http://dx.doi.org/10.7710/2162-3309.2351Pacific University Library0journal-article2162-3309
Scholarly Publishing Literacy at the University of South Florida Libraries: From Advising to Active Involvement 10.7710/2162-3309.231071NA2019-12-04http://dx.doi.org/10.7710/2162-3309.2310Pacific University Library0journal-article2162-3309
From Meow to ROAR: Expanding Open Access Repository Services at the University of Houston Libraries 10.7710/2162-3309.230971NA2019-12-13http://dx.doi.org/10.7710/2162-3309.2309Pacific University Library0journal-article2162-3309
Grey Literature: Use, Creation, and Citation Habits of Faculty Researchers across Disciplines 10.7710/2162-3309.231471NA2019-12-18http://dx.doi.org/10.7710/2162-3309.2314Pacific University Library0journal-article2162-3309
 
# use filter from dplyr to get only volume 8, issue 1
jlsc_8_1 <- jlsc_publications_2019 %>%
  dplyr::filter(volume == "8",
         issue == "1") 

# print the data frame with select columns
jlsc_8_1 %>%
  dplyr::select(title, doi, volume, issue, page, issued, url, publisher, reference.count, type, issn)
A tibble: 1 x 11
titledoivolumeissuepageissuedurlpublisherreference.counttypeissn
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>
Considering Creative Activity in Institutional Repositories: An Exploration of Faculty Perceptions10.7710/2162-3309.23128123122020-02-25http://dx.doi.org/10.7710/2162-3309.2312Pacific University Library0journal-article2162-3309

filter() will go through each row of your existing jlsc_publications_2019 data frame, and keep only those rows with values matching the filters you input. Note: be careful of filtering by ISSN. If a journal has multiple ISSNs they’ll be combined in a single cell with a comma and the filter() will fail, as with JAMA above. In this case it may be wiser to use str_detect(), as described a couple code chunks down.

jah_jama_publications$issn[1]

‘0098-7484,1538-3598’

We can use filter() to get a single article from within this data frame if we need, either by DOI:

# filter to get "The Five Laws of OER" article by DOI
jlsc_article <- jlsc_publications_2019 %>%
  dplyr::filter(doi == "10.7710/2162-3309.2299") 

# print data frame with select columns
jlsc_article %>%
  dplyr::select(title, doi, volume, issue, page, issued, url, publisher, reference.count, type, issn)
A tibble: 1 x 11
titledoivolumeissuepageissuedurlpublisherreference.counttypeissn
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>
The Five Laws of OER: Observations from Ranganathan10.7710/2162-3309.229971NA2019-08-20http://dx.doi.org/10.7710/2162-3309.2299Pacific University Library0journal-article2162-3309

Or by title:

# use str_detect to search the title column for articles that include the term OER
jlsc_article <- jlsc_publications_2019 %>%
  dplyr::filter(stringr::str_detect(title, "OER"))

# print the data frame with select column
jlsc_article %>%
  dplyr::select(title, doi, volume, issue, page, issued, url, publisher, reference.count, type, issn)
A tibble: 2 x 11
titledoivolumeissuepageissuedurlpublisherreference.counttypeissn
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>
Strategies for Supporting OER Adoption through Faculty and Instructor Use of a Federated Search Tool10.7710/2162-3309.227971NA2019-02-22http://dx.doi.org/10.7710/2162-3309.2279Pacific University Library0journal-article2162-3309
The Five Laws of OER: Observations from Ranganathan 10.7710/2162-3309.229971NA2019-08-20http://dx.doi.org/10.7710/2162-3309.2299Pacific University Library0journal-article2162-3309

Here, we use the str_detect() function from the stringr package, which is loaded as part of the tidyverse, in order to find a single term (OER) in the title.

Remember that these dplyr and stringr functions are searching through our existing data frame jlsc_publications_2019, not issuing new API calls.

Field queries

There is yet another way of making your query more precise, and that is to use a field query (flq) argument to cr_journals(). This allows you to search in specific bibliographic fields such as author, editor, titles, ISSNs, and author affiliation (not widely available). These are listed in the Crossref documentation and reproduced below. You must provide an ISSN–in other words, you can’t run a field query for authors across all journals.

Field query parameter Description
query.container-title Query container-title aka. publication name
query.author Query author given and family names
query.editor Query editor given and family names
query.chair Query chair given and family names
query.translator Query translator given and family names
query.contributor Query author, editor, chair and translator given and family names
query.bibliographic Query bibliographic information, useful for citation look up. Includes titles, authors, ISSNs and publication years
query.affiliation Query contributor affiliations

Field query by title

Here, we get all publications from the Journal of Librarianship and Scholarly Communication with the term “open access” in the title.

# assign JLSC ISSN and query the bibliographic field for terms mentioning open access. 
jlsc_issn <- "2162-3309"
jlsc_publications_oa <- rcrossref::cr_journals(issn = jlsc_issn, works = T, limit = 25,
                                            flq = c(`query.bibliographic` = 'open access')) %>%
  purrr::pluck("data")

# print the data frame with select columns
jlsc_publications_oa %>%
  dplyr::select(title, doi, volume, issue, page, issued, issn, author)
A tibble: 25 x 8
titledoivolumeissuepageissuedissnauthor
<chr><chr><chr><chr><chr><chr><chr><list>
Campus Open Access Funds: Experiences of the KU “One University” Open Access Author Fund 10.7710/2162-3309.125231 12522015-09-182162-3309Rachel , Allison C. , Crystal , Deborah , Ada , Gyore , Reeve , Cameron-Vedros, Ludwig , Emmett , first , additional , additional , additional , additional
Open Access and the Author-Pays Problem: Assuring Access for Readers and Authors in the Global Academic Community 10.7710/2162-3309.106413 10642013-02-282162-3309A Townsend, Ada , Marc L , Peterson , Emmett , Greenberg , first , additional, additional
“Open Don’t Mean Free”: A Reflection on the Potential Advantages and Disadvantages of Publishing Research via Open Access10.7710/2162-3309.104912 10492012-09-282162-3309Frank C, Manista, first
Open Data, [Open] Access: Linking Data Sharing and Article Sharing in the Earth Sciences 10.7710/2162-3309.21505General IssueNA 2017 2162-3309Samantha , Teplitzky, first
Innovation Fair Abstracts, SPARC 2012 Open Access Meeting 10.7710/2162-3309.104211 10422012-05-152162-3309Abstract, Authors , first
Point & Counterpoint Is CC BY the Best Open Access License? 10.7710/2162-3309.104311 10432012-05-152162-3309Klaus , Sanford , Graf , Thatcher , first , additional
Developing Open Access Journals: A Practical Guide 10.7710/2162-3309.102811 10282012-05-152162-3309Caitlin, Bakker , first
Up from Under the “Open Access” Bus 10.7710/2162-3309.104512 10452012-09-282162-3309Paul , Royster, first
Response to “Is CC BY the Best Open Access License?” 10.7710/2162-3309.105512 10552012-09-282162-3309Andras, Holl , first
“Free to All”: Library Publishing and the Challenge of Open Access 10.7710/2162-3309.118124 11812014-12-112162-3309Micah , Josh , Vandegrift, Bolick , first , additional
........................
The Accessibility Quotient: A New Measure of Open Access 10.7710/2162-3309.102511 10252012-05-152162-3309Mathew A , Katharine H , Ellen Finnie, Willmott , Dunn , Duranceau , first , additional , additional
All That Glisters: Investigating Collective Funding Mechanisms for Gold Open Access in Humanities Disciplines 10.7710/2162-3309.113123 11312014-08-012162-3309Martin Paul, Eve , first
Foxes Propose New Guidelines for Henhouse Design: Comments on NISO’s Proposed Open Access Metadata Standards 10.7710/2162-3309.117023 11702014-08-012162-3309Paul , Royster, first
Counting the Cost: A Report on APC-Supported Open Access Publishing in a Research Library 10.7710/2162-3309.118424 11842014-12-112162-3309Mark P , Eva T , Kerri , Newton , Cunningham, O'Connell , first , additional, additional
University Faculty Awareness and Attitudes towards Open Access Publishing and the Institutional Repository: A Case Study 10.7710/2162-3309.121031 12102015-05-062162-3309Zheng Y (Lan), Yu , Yang , Li , first , additional
Better Sharing Through Licenses? Measuring the Influence of Creative Commons Licenses on the Usage of Open Access Monographs 10.7710/2162-3309.118731 11872015-03-102162-3309Ronald , Snijder, first
Open Access Status of Nano ELSI Research: Determining Availability of a Core Collection of Research for a Disciplinary Repository10.7710/2162-3309.119031 11902015-06-052162-3309Rebecca , Jessica , Reznik-Zellen, Adamick , first , additional
From Concerned to Cautiously Optimistic: Assessing Faculty Perceptions and Knowledge of Open Access in a Campus-Wide Study 10.7710/2162-3309.121231 12122015-06-222162-3309Annie M, Gaines , first
A Resonant Message: Aligning Scholar Values and Open Access Objectives in OA Policy Outreach to Faculty and Graduate Students 10.7710/2162-3309.21524General IssueNA 2016 2162-3309Jane , Johnson Otto, first
Open Access Policies and Academic Freedom: Understanding and Addressing Conflicts 10.7710/2162-3309.21045General IssueNA 2017 2162-3309David James, Johnston , first

Field query by author, contributor, or editor

The flq argument can also be used for authors, contributors, or editors. Here we search the same journal for authors with the name Salo (looking for all articles written by Dorothea Salo).

# Use the query.author field query to find JLSC articles with author name Salo
jlsc_publications_auth <- rcrossref::cr_journals(issn = jlsc_issn, works = T, limit = 25,
                                            flq = c(`query.author` = 'salo')) %>%
  purrr::pluck("data")

# print the data frame with select columns
jlsc_publications_auth %>%
  dplyr::select(title, doi, volume, issue, page, issued, url, publisher, reference.count, type, issn)
A tibble: 2 x 11
titledoivolumeissuepageissuedurlpublisherreference.counttypeissn
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>
How to Scuttle a Scholarly Communication Initiative10.7710/2162-3309.10751410752013-08-15http://dx.doi.org/10.7710/2162-3309.1075Pacific University Library0journal-article2162-3309
On the Mark? Responses to a Sting 10.7710/2162-3309.11162111162013-12-09http://dx.doi.org/10.7710/2162-3309.1116Pacific University Library0journal-article2162-3309

TRY IT YOURSELF

  1. Assign the ISSN for College & Research Libraries to a value - 2150-6701
  2. Use the query.author field query (flq) to find all articles written by Lisa Janicke Hinchliffe
# assign the C&RL ISSN 2150-6701


# use the query.author field query to search for articles written by Lisa Hinchliffe.

Viewing the JSON file

You can view these files in a JSON viewer using the toJSON() function from the jsonlite package.

# assign the PLOS ISSN and get the last 25 articles on deposit
plosone_issn <- '1932-6203'
plosone_publications <- cr_journals(issn = plosone_issn, works = TRUE, limit = 5) %>%
  pluck("data")

# use the toJSON function to convert the output to JSON
plosone_publications_json <- jsonlite::toJSON(plosone_publications)

Print the JSON, triple click inside the box to highlight the text, and copy it to the clipboard.

# print the JSON
plosone_publications_json

[{"container.title":"PLoS ONE","created":"2012-03-29","deposited":"2019-06-26","published.online":"2012-03-29","doi":"10.1371/journal.pone.0034299","indexed":"2020-02-05","issn":"1932-6203","issue":"3","issued":"2012-03-29","member":"340","page":"e34299","prefix":"10.1371","publisher":"Public Library of Science (PLoS)","reference.count":"77","score":"1","source":"Crossref","title":"Extinction-Dependent Alterations in Corticostriatal mGluR2/3 and mGluR7 Receptors following Chronic Methamphetamine Self-Administration in Rats","type":"journal-article","update.policy":"http://dx.doi.org/10.1371/journal.pone.corrections_policy","url":"http://dx.doi.org/10.1371/journal.pone.0034299","volume":"7","author":[{"given":"Marek","family":"Schwendt","sequence":"first"},{"given":"Carmela M.","family":"Reichel","sequence":"additional"},{"given":"Ronald E.","family":"See","sequence":"additional"}],"link":[{"URL":"http://dx.plos.org/10.1371/journal.pone.0034299","content.type":"unspecified","content.version":"vor","intended.application":"similarity-checking"}],"license":[{"date":"2012-03-29","URL":"http://creativecommons.org/licenses/by/4.0/","delay.in.days":0,"content.version":"unspecified"}],"reference":[{"key":"ref1","doi.asserted.by":"crossref","first.page":"1847","DOI":"10.1038/sj.npp.1301578","article.title":"Acute physiological and behavioral effects of intranasal methamphetamine in humans.","volume":"33","author":"CL Hart","year":"2008","journal.title":"Neuropsychopharmacology: official publication of the American College of Neuropsychopharmacology"},{"key":"ref2","doi.asserted.by":"crossref","first.page":"317","DOI":"10.1176/jnp.15.3.317","article.title":"Neuropsychological effects of chronic methamphetamine use on neurotransmitters and cognition: a review.","volume":"15","author":"TE Nordahl","year":"2003","journal.title":"J Neuropsychiatry Clin Neurosci"},{"key":"ref3","doi.asserted.by":"crossref","first.page":"141","DOI":"10.1080/10673220591003605","article.title":"Implications of chronic methamphetamine use: a literature review.","volume":"13","author":"CW Meredith","year":"2005","journal.title":"Harv Rev Psychiatry"},{"key":"ref4","first.page":"301","article.title":"The need for speed: an update on methamphetamine addiction.","volume":"31","author":"AM Barr","year":"2006","journal.title":"J Psychiatry Neurosci"},{"key":"ref5","doi.asserted.by":"crossref","first.page":"77","DOI":"10.4065/81.1.77","article.title":"Methamphetamine abuse: a perfect storm of complications.","volume":"81","author":"TW Lineberry","year":"2006","journal.title":"Mayo Clin Proc"},{"key":"ref6","doi.asserted.by":"crossref","first.page":"1272","DOI":"10.1016/j.biopsych.2006.07.031","article.title":"Attentional control and brain metabolite levels in methamphetamine abusers.","volume":"61","author":"R Salo","year":"2007","journal.title":"Biol Psychiatry"},{"key":"ref7","doi.asserted.by":"crossref","first.page":"1581","DOI":"10.1016/j.addbeh.2008.07.024","article.title":"Comparing the dynamic course of heroin, cocaine, and methamphetamine use over 10 years.","volume":"33","author":"YI Hser","year":"2008","journal.title":"Addict Behav"},{"key":"ref8","doi.asserted.by":"crossref","first.page":"345","DOI":"10.1007/s11920-006-0035-x","article.title":"Management of methamphetamine abuse and dependence.","volume":"8","author":"W Ling","year":"2006","journal.title":"Curr Psychiatry Rep"},{"key":"ref9","doi.asserted.by":"crossref","first.page":"309","DOI":"10.1080/09595230801919494","article.title":"A systematic review of cognitive and behavioural therapies for methamphetamine dependence.","volume":"27","author":"NK Lee","year":"2008","journal.title":"Drug Alcohol Rev"},{"key":"ref10","doi.asserted.by":"crossref","first.page":"31","DOI":"10.1080/08897070802218554","article.title":"Pharmacotherapy of methamphetamine addiction: an update.","volume":"29","author":"A Elkashef","year":"2008","journal.title":"Subst Abus"},{"key":"ref11","doi.asserted.by":"crossref","first.page":"48","DOI":"10.1007/s00213-006-0353-z","article.title":"Escalation of methamphetamine self-administration in rats: a dose-effect function.","volume":"186","author":"O Kitamura","year":"2006","journal.title":"Psychopharmacology (Berl)"},{"key":"ref12","doi.asserted.by":"crossref","first.page":"615","DOI":"10.1007/s00213-008-1187-7","article.title":"Extended methamphetamine self-administration enhances reinstatement of drug seeking and impairs novel object recognition in rats.","volume":"199","author":"JL Rogers","year":"2008","journal.title":"Psychopharmacology 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physiology"},{"key":"ref29","doi.asserted.by":"crossref","first.page":"334","DOI":"10.1111/j.1440-1681.2008.05021.x","article.title":"Mechanisms of fatigue induced by isometric contractions in exercising humans and in mouse isolated single muscle fibres","volume":"36","author":"N Place","year":"2009","journal.title":"Clinical and experimental pharmacology & physiology"},{"key":"ref30","doi.asserted.by":"crossref","first.page":"2198","DOI":"10.1073/pnas.0711074105","article.title":"Remodeling of ryanodine receptor complex causes “aky”channels: a molecular mechanism for decreased exercise capacity","volume":"105","author":"AM Bellinger","year":"2008","journal.title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref31","doi.asserted.by":"crossref","first.page":"82","DOI":"10.3389/fphys.2012.00082","article.title":"Fatigue is a Brain-Derived Emotion that Regulates the Exercise Behavior to Ensure the Protection of Whole Body Homeostasis","volume":"3","author":"TD Noakes","year":"2012","journal.title":"Frontiers in physiology"},{"key":"ref32","doi.asserted.by":"crossref","first.page":"2005","DOI":"10.1016/j.jbiomech.2005.06.019","article.title":"Differences in muscle function during walking and running at the same speed","volume":"39","author":"K Sasaki","year":"2006","journal.title":"Journal of biomechanics"},{"key":"ref33","doi.asserted.by":"crossref","first.page":"2283","DOI":"10.1242/jeb.066332","article.title":"The role of elastic energy storage and recovery in downhill and uphill running","volume":"215","author":"KL Snyder","year":"2012","journal.title":"The Journal of experimental biology"},{"key":"ref34","doi.asserted.by":"crossref","first.page":"274","DOI":"10.1080/15438627.2012.697084","article.title":"The effects of a downhill running bout on running economy","volume":"20","author":"WA Braun","year":"2012","journal.title":"Research in sports medicine"},{"key":"ref35","doi.asserted.by":"crossref","first.page":"591","DOI":"10.1055/s-2005-865920","article.title":"Greater muscle damage induced by fast versus slow velocity eccentric exercise","volume":"27","author":"D Chapman","year":"2006","journal.title":"International journal of sports medicine"},{"key":"ref36","doi.asserted.by":"crossref","first.page":"1039","DOI":"10.1152/japplphysiol.01177.2001","article.title":"Energy cost of walking and running at extreme uphill and downhill slopes","volume":"93","author":"AE Minetti","year":"2002","journal.title":"Journal of applied physiology"},{"key":"ref37","doi.asserted.by":"crossref","first.page":"686","DOI":"10.1152/japplphysiol.00642.2012","article.title":"Economy is not sacrificed in ultramarathon runners","volume":"113","author":"GP Millet","year":"2012","journal.title":"Journal of Applied Physiology"},{"key":"ref38","doi.asserted.by":"crossref","first.page":"507","DOI":"10.1152/japplphysiol.00016.2012","article.title":"Sacrificing economy to improve running performance – a reality in the ultramarathon?","volume":"113","author":"GY Millet","year":"2012","journal.title":"Journal of Applied Physiology"},{"key":"ref39","doi.asserted.by":"crossref","first.page":"345","DOI":"10.1007/BF02332962","article.title":"Effect of sleep deprivation on tolerance of prolonged exercise","volume":"47","author":"BJ Martin","year":"1981","journal.title":"European journal of applied physiology and occupational physiology"},{"key":"ref40","doi.asserted.by":"crossref","first.page":"155","DOI":"10.1007/s00421-009-1103-9","article.title":"One night of sleep deprivation decreases treadmill endurance performance","volume":"107","author":"SJ Oliver","year":"2009","journal.title":"European journal of applied physiology"},{"key":"ref41","doi.asserted.by":"crossref","first.page":"580","DOI":"10.1249/00005768-198510000-00011","article.title":"Sleep deprivation, physical fatigue, and the perception of exercise intensity","volume":"17","author":"WS Myles","year":"1985","journal.title":"Medicine and science in sports and exercise"},{"key":"ref42","doi.asserted.by":"crossref","first.page":"983","DOI":"10.1113/jphysiol.2003.056598","article.title":"Leukocytes, cytokines, growth factors and hormones in human skeletal muscle and blood after uphill or downhill running","volume":"556","author":"C Malm","year":"2004","journal.title":"The Journal of physiology"},{"key":"ref43","doi.asserted.by":"crossref","first.page":"89","DOI":"10.1136/bjsm.29.2.89","article.title":"Eccentric activation and muscle damage: biomechanical and physiological considerations during downhill running","volume":"29","author":"RG Eston","year":"1995","journal.title":"British Journal of Sports Medicine"},{"key":"ref44","doi.asserted.by":"crossref","first.page":"264","DOI":"10.1136/bjsm.33.4.264","article.title":"The biochemistry of runners in a 1600 km ultramarathon","volume":"33","author":"KE Fallon","year":"1999","journal.title":"British Journal of Sports Medicine"},{"key":"ref45","doi.asserted.by":"crossref","first.page":"75","DOI":"10.1097/00005768-200301000-00013","article.title":"Human albumin synthesis is increased by an ultra-endurance trial","volume":"35","author":"I Mischler","year":"2003","journal.title":"Medicine and science in sports and exercise"},{"key":"ref46","doi.asserted.by":"crossref","first.page":"477","DOI":"10.1080/02640410701552872","article.title":"Intensity and physiological strain of competitive ultra-endurance exercise in humans","volume":"26","author":"SJ Lucas","year":"2008","journal.title":"Journal of sports sciences"},{"key":"ref47","doi.asserted.by":"crossref","first.page":"457","DOI":"10.1113/jphysiol.1993.sp019645","article.title":"Mechanical factors in the initiation of eccentric contraction-induced injury in rat soleus muscle","volume":"464","author":"GL Warren","year":"1993","journal.title":"The Journal of physiology"},{"key":"ref48","doi.asserted.by":"crossref","first.page":"288","DOI":"10.1080/02640414.2012.729135","article.title":"The effects of eccentric exercise-induced muscle damage on running kinematics at different speeds","volume":"31","author":"T Tsatalas","year":"2013","journal.title":"Journal of sports sciences"},{"key":"ref49","doi.asserted.by":"crossref","first.page":"1565","DOI":"10.1152/japplphysiol.00578.2007","article.title":"Influence of concentric and eccentric resistance training on architectural adaptation in human quadriceps muscles","volume":"103","author":"AJ Blazevich","year":"2007","journal.title":"J Appl Physiol"},{"key":"ref50","doi.asserted.by":"crossref","first.page":"2723","DOI":"10.1007/s00421-011-1894-3","article.title":"Muscle architecture and EMG activity changes during isotonic and isokinetic eccentric exercises","volume":"111","author":"G Guilhem","year":"2011","journal.title":"Eur J Appl Physiol"},{"key":"ref51","doi.asserted.by":"crossref","first.page":"34","DOI":"10.1007/s004210100430","article.title":"The repeated bout effect of reduced-load eccentric exercise on elbow flexor muscle damage","volume":"85","author":"K Nosaka","year":"2001","journal.title":"Eur J Appl Physiol"}],"subject":"General Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General Medicine"}]

Go to Code Beautify and paste the JSON on the left side. Click Tree Viewer to view the data. Open the first item to view the metadata. Note especially the last few variables. These are nested lists, as a single article can have multiple authors, and each author has a given name, family name, and sequence of authorship.

To write to JSON, use jsonlite::write_json()

# write a JSON file
jsonlite::write_json(plosone_publications_json, "plosone_publications.json")

Using cr_works() to get data on articles

cr_works() allows you to search by DOI or a general query in order to return the Crossref metadata.

It is important to note, as Crossref does in the documentation:

> Crossref does not use “works” in the FRBR sense of the word. In Crossref parlance, a “work” is just a thing identified by a DOI. In practice, Crossref DOIs are used as citation identifiers. So, in FRBR terms, this means, that a Crossref DOI tends to refer to one expression which might include multiple manifestations. So, for example, the ePub, HTML and PDF version of an article will share a Crossref DOI because the differences between them should not effect the interpretation or crediting of the content. In short, they can be cited interchangeably. The same is true of the “accepted manuscript” and the “version-of-record” of that accepted manuscript.

Searching by DOI

You can pass a DOI directly to cr_works() using the dois argument:

# Get metadata for a single article by DOI
jlsc_ku_oa <- cr_works(dois = '10.7710/2162-3309.1252') %>%
  purrr::pluck("data")

# print the data frame with select columns
jlsc_ku_oa %>%
  dplyr::select(title, doi, volume, issue, page, issued, url, publisher, reference.count, type, issn)
A tibble: 1 x 11
titledoivolumeissuepageissuedurlpublisherreference.counttypeissn
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>
Campus Open Access Funds: Experiences of the KU “One University” Open Access Author Fund10.7710/2162-3309.12523112522015-09-18http://dx.doi.org/10.7710/2162-3309.1252Pacific University Library0journal-article2162-3309

You can also pass more than one DOI. Here we start by assigning our DOIs to a variable my_dois, then pass it to cr_works() in the doi argument:

# Use c() to create a vector of DOIs
my_dois <- c("10.2139/ssrn.2697412", 
                        "10.1016/j.joi.2016.08.002", 
                        "10.1371/journal.pone.0020961", 
                        "10.3389/fpsyg.2018.01487", 
                        "10.1038/d41586-018-00104-7", 
                        "10.12688/f1000research.8460.2", 
                        "10.7551/mitpress/9286.001.0001")

# pass the my_dois vector to cr_works()
my_dois_works <- rcrossref::cr_works(dois = my_dois) %>%
  pluck("data")

# print the data frame with select columns
my_dois_works %>%
  dplyr::select(title, doi, volume, issue, page, issued, url, publisher, reference.count, type, issn)
A tibble: 7 x 11
titledoivolumeissuepageissuedurlpublisherreference.counttypeissn
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>
Open Access Publishing: A Literature Review 10.2139/ssrn.2697412 NA NA NA 2014 http://dx.doi.org/10.2139/ssrn.2697412 Elsevier BV 0 journal-article1556-5068
Hybrid open access—A longitudinal study 10.1016/j.joi.2016.08.002 10 4 919-9322016-11 http://dx.doi.org/10.1016/j.joi.2016.08.002 Elsevier BV 33 journal-article1751-1577
The Development of Open Access Journal Publishing from 1993 to 2009 10.1371/journal.pone.0020961 6 6 e20961 2011-06-13http://dx.doi.org/10.1371/journal.pone.0020961 Public Library of Science (PLoS) 31 journal-article1932-6203
The Impact Factor Fallacy 10.3389/fpsyg.2018.01487 9 NA NA 2018-08-20http://dx.doi.org/10.3389/fpsyg.2018.01487 Frontiers Media SA 52 journal-article1664-1078
Funders should mandate open citations 10.1038/d41586-018-00104-7 5537687129-1292018-01 http://dx.doi.org/10.1038/d41586-018-00104-7 Springer Science and Business Media LLC0 journal-article0028-0836,1476-4687
The academic, economic and societal impacts of Open Access: an evidence-based review10.12688/f1000research.8460.2 5 NA 632 2016-06-09http://dx.doi.org/10.12688/f1000research.8460.2 F1000 Research Ltd 184journal-article2046-1402
Open Access 10.7551/mitpress/9286.001.0001NA NA NA 2012 http://dx.doi.org/10.7551/mitpress/9286.001.0001The MIT Press 0 book NA

Unnesting list columns

Authors, links, licenses, funders, and some other values can appear in nested lists when you call cr_journals because there can be, and often are, multiple of each of these items per article. You can check the data classes on all variables by running typeof() across all columns using the map_chr() function from purrr:

# query to get data on a specific PLOS article
plos_article <- cr_works(dois = '10.1371/journal.pone.0228782') %>%
  purrr::pluck("data")

# print the type of each column (e.g. character, numeric, logical, list)
purrr::map_chr(plos_article, typeof)
container.title
'character'
created
'character'
deposited
'character'
published.online
'character'
doi
'character'
indexed
'character'
issn
'character'
issue
'character'
issued
'character'
member
'character'
page
'character'
prefix
'character'
publisher
'character'
reference.count
'character'
score
'character'
source
'character'
subject
'character'
title
'character'
type
'character'
update.policy
'character'
url
'character'
volume
'character'
author
'list'
funder
'list'
link
'list'
license
'list'
reference
'list'

Our plos_article data frame has a nested list for author. We can unnest this column using unnest() from the tidyr package. The .drop = TRUE argument will drop any other list columns.

# unnest author column
plos_article %>%
    tidyr::unnest(author, .drop = TRUE)
A tibble: 5 x 27
container.titlecreateddepositedpublished.onlinedoiindexedissnissueissuedmemberpageprefixpublisherreference.countscoresourcesubjecttitletypeupdate.policyurlvolumeORCIDauthenticated.orcidgivenfamilysequence
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><lgl><chr><chr><chr>
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02287822020-03-041932-620332020-03-04340e022878210.1371Public Library of Science (PLoS)731CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineLearning about the Ellsberg Paradox reduces, but does not abolish, ambiguity aversionjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.022878215http://orcid.org/0000-0001-5870-9336TRUERuonan Jia first
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02287822020-03-041932-620332020-03-04340e022878210.1371Public Library of Science (PLoS)731CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineLearning about the Ellsberg Paradox reduces, but does not abolish, ambiguity aversionjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.022878215NA NAEllen Furlongadditional
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02287822020-03-041932-620332020-03-04340e022878210.1371Public Library of Science (PLoS)731CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineLearning about the Ellsberg Paradox reduces, but does not abolish, ambiguity aversionjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.022878215NA NASean Gao additional
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02287822020-03-041932-620332020-03-04340e022878210.1371Public Library of Science (PLoS)731CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineLearning about the Ellsberg Paradox reduces, but does not abolish, ambiguity aversionjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.022878215NA NALaurie R.Santos additional
PLOS ONE2020-03-042020-03-042020-03-0410.1371/journal.pone.02287822020-03-041932-620332020-03-04340e022878210.1371Public Library of Science (PLoS)731CrossrefGeneral Biochemistry, Genetics and Molecular Biology,General Agricultural and Biological Sciences,General MedicineLearning about the Ellsberg Paradox reduces, but does not abolish, ambiguity aversionjournal-articlehttp://dx.doi.org/10.1371/journal.pone.corrections_policyhttp://dx.doi.org/10.1371/journal.pone.022878215NA NAIfat Levy additional

We can see this has added 5 rows and 3 new columns: given (first name), family (last name), and sequence (order in which they appeared).

See https://ciakovx.github.io/rcrossref.html#unnesting_list_columns for more detailed strategies in unnesting nested lists in Crossref. For more details, call ?unnest and read the R for Data Science section on Unnesting.

TRY IT YOURSELF

  1. Refer back to the type of each column above. Try unnesting one of the other list columns. Scroll all the way to the right. What new columns have appeared? Have any rows been duplicated?

Getting more than 1000 results with the cursor argument to cr_journals

If our result will have more than 1000 results, we have to use the cursor argument. We will not be covering this in this class, but see https://ciakovx.github.io/rcrossref.html#getting_more_than_1000_results_with_the_cursor_argument_to_cr_journals for instructions on how to do it.

Running general queries on cr_works()

You can also use cr_works() to run a query based on very simple text keywords. For example, you can run oa_works &lt;- rcrossref::cr_works(query = "open+access"). Paul Oldham gives a great example of this, but does make the comment:

> CrossRef is not a text based search engine and the ability to conduct text based searches is presently crude. Furthermore, we can only search a very limited number of fields and this will inevitably result in lower returns than commercial databases such as Web of Science (where abstracts and author keywords are available). Unfortunately there is no boolean AND for Crossref queries (see https://github.com/CrossRef/rest-api-doc/issues/135 and https://twitter.com/CrossrefSupport/status/1073601263659610113). However, as discussed above, the Crossref API assigns a score to each item returned giving a measure of the API’s confidence in the match, and if you connect words using + the Crossref API will give items with those terms a higher score.

Specifying field queries to cr_works() with flq

As with cr_journals, you can use flq to pass field queries on to cr_works(), such as author.

Here we search for the book Open Access by Peter Suber by doing a general keyword search for “open access” and an author search for “suber”:

# do a general query for the term open access and a field query to return results where the author name includes Suber
suber_oa <- cr_works(query = 'open+access', flq = c(`query.author` = 'suber')) %>%
  pluck("data")

# print the data frame with select columns
suber_oa %>%
  dplyr::select(title, doi, volume, issue, page, issued, url, publisher, reference.count, type, issn)
A tibble: 20 x 11
titledoivolumeissuepageissuedurlpublisherreference.counttypeissn
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>
Open access in the USA 10.1016/b978-1-84334-203-8.50015-7NA NA 149-160 2006 http://dx.doi.org/10.1016/b978-1-84334-203-8.50015-7Elsevier 0book-chapter NA
Gratis Open Access 10.32388/878441 NA NA NA 2019-07-22http://dx.doi.org/10.32388/878441 Qeios 1reference-entryNA
Open Access 10.32388/499151 NA NA NA 2019-07-19http://dx.doi.org/10.32388/499151 Qeios 1reference-entryNA
Open Access 10.7551/mitpress/9286.001.0001 NA NA NA 2012 http://dx.doi.org/10.7551/mitpress/9286.001.0001 The MIT Press 0book NA
Open Access in 2007 10.3998/3336451.0011.110 11 1 NA 2008-01-30http://dx.doi.org/10.3998/3336451.0011.110 University of Michigan Library 0journal-article1080-2711
Knowledge Unbound 10.7551/mitpress/8479.001.0001 NA NA NA 2016 http://dx.doi.org/10.7551/mitpress/8479.001.0001 The MIT Press 0book NA
Open Access in 2008 10.3998/3336451.0012.104 12 1 NA 2009-02-15http://dx.doi.org/10.3998/3336451.0012.104 University of Michigan Library 0journal-article1080-2711
Ensuring open access for publicly funded research 10.1136/bmj.e5184 345aug08 1e5184-e51842012-08-08http://dx.doi.org/10.1136/bmj.e5184 BMJ 0journal-article1756-1833
Promoting Open Access in the Humanities 10.1353/syl.2005.0001 16 1 231-246 2005 http://dx.doi.org/10.1353/syl.2005.0001 Project Muse 0journal-article2160-5157
Open access: other ways 10.1038/426015b 4266962 15-15 2003-11 http://dx.doi.org/10.1038/426015b Springer Science and Business Media LLC 0journal-article0028-0836,1476-4687
Open access? 10.1038/ngeo450 2 3 155-155 2009-03 http://dx.doi.org/10.1038/ngeo450 Springer Science and Business Media LLC 1journal-article1752-0894,1752-0908
Thoughts on prestige, quality, and open access 10.1163/095796510x546959 21 1-2 115-128 2010 http://dx.doi.org/10.1163/095796510x546959 Brill 0journal-article0957-9656,1878-4712
Open Access to Electronic Theses and Dissertations 10.14429/djlit.28.1.149 28 1 25-34 2008-01-01http://dx.doi.org/10.14429/djlit.28.1.149 Defence Scientific Information and Documentation Centre 0journal-article0974-0643,0976-4658
Open Access and Quality 10.14429/djlit.28.1.152 28 1 49-56 2008-01-01http://dx.doi.org/10.14429/djlit.28.1.152 Defence Scientific Information and Documentation Centre 0journal-article0974-0643,0976-4658
Open access, impact, and demand 10.1136/bmj.330.7500.1097 3307500 1097-1098 2005-05-12http://dx.doi.org/10.1136/bmj.330.7500.1097 BMJ 0journal-article0959-8138,1468-5833
SCHOLARLY COMMUNICATION: Removing barriers to research: An introduction to open access for librarians10.5860/crln.64.2.92 64 2 92-113 2003-02-01http://dx.doi.org/10.5860/crln.64.2.92 American Library Association 0journal-article2150-6698,0099-0086
A living open book 10.5334/bal.l NA NA 113-117 2014-11-28http://dx.doi.org/10.5334/bal.l Ubiquity Press 0book-chapter NA
Public access to federally funded research: The Cornyn-Lieberman and CURES bills 10.5860/crln.67.6.7637 67 6 362-365 2006-06-01http://dx.doi.org/10.5860/crln.67.6.7637 American Library Association 0journal-article2150-6698,0099-0086
Support for the NIH Public Access Policy 10.1126/science.313.5793.1572a 3135793 1572a-1572a2006-09-15http://dx.doi.org/10.1126/science.313.5793.1572a American Association for the Advancement of Science (AAAS)0journal-article0036-8075,1095-9203
NSF 19-501 AccelNet Proposal: Community of Open Scholarship Grassroots Networks (COSGN) 10.31222/osf.io/d7mwk NA NA NA 2020-01-30http://dx.doi.org/10.31222/osf.io/d7mwk Center for Open Science 0posted-content NA

Dr. Suber has written lots of materials that includes the term “open access.” We can use the filter() function from dplyr to look only at books, from the type column:

# use filter() from dplyr to filter that result to include only books
suber_oa_books <- suber_oa %>%
  filter(type == "book")

# print the data frame with select columns
suber_oa_books %>%
  dplyr::select(title, doi, volume, issue, page, issued, url, publisher, reference.count, type, issn)
A tibble: 2 x 11
titledoivolumeissuepageissuedurlpublisherreference.counttypeissn
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>
Open Access 10.7551/mitpress/9286.001.0001NANANA2012http://dx.doi.org/10.7551/mitpress/9286.001.0001The MIT Press0bookNA
Knowledge Unbound10.7551/mitpress/8479.001.0001NANANA2016http://dx.doi.org/10.7551/mitpress/8479.001.0001The MIT Press0bookNA

One is the book from MIT Press that we’re looking for; the other is Knowledge Unbound, which is a collection of his writings.

We could be more specific from the outset by adding bibliographic information in query.bibliographic, such as ISBN (or ISSN, if it’s a journal):

# run a different cr_works() query with author set to Suber and his book's ISBN passed to query.bibliographic
suber_isbn <- cr_works(flq = c(`query.author` = 'suber',
                           `query.bibliographic` = '9780262301732')) %>%
  pluck("data")

# print the data frame with select columns
suber_isbn %>%
  dplyr::select(title, doi, issued, url, publisher, type, author)
A tibble: 1 x 7
titledoiissuedurlpublishertypeauthor
<chr><chr><chr><chr><chr><chr><list>
Open Access10.7551/mitpress/9286.001.00012012http://dx.doi.org/10.7551/mitpress/9286.001.0001The MIT PressbookPeter, Suber, first

You can combine the filter argument with flq to return only items of type book published in 2012.

Getting formatted references in a text file

We can use the cr_cn() function from the rcrossref package to get the citations to those articles in text form in the style you specify. We’ll put it into Chicago. The cr_cn() function returns each citation into a list element. We can use the map_chr and the pluck functions from purrr to instead assign them to a character vector.

# Use c() to create a vector of DOIs
my_dois <- c("10.2139/ssrn.2697412", 
                        "10.1016/j.joi.2016.08.002", 
                        "10.1371/journal.pone.0020961", 
                        "10.3389/fpsyg.2018.01487", 
                        "10.1038/d41586-018-00104-7", 
                        "10.12688/f1000research.8460.2", 
                        "10.7551/mitpress/9286.001.0001")

# Use cr_cn to get back citations formatted in Chicago for those DOIs
my_citations <- rcrossref::cr_cn(my_dois,
                                 format = "text",
                                 style = "chicago-note-bibliography") %>% 
  purrr::map_chr(., purrr::pluck, 1)

# print the formatted citations
my_citations
  1. 'Frosio, Giancarlo F. “Open Access Publishing: A Literature Review.” SSRN Electronic Journal (2014). doi:10.2139/ssrn.2697412.'
  2. 'Laakso, Mikael, and Bo-Christer Björk. “Hybrid Open access—A Longitudinal Study.” Journal of Informetrics 10, no. 4 (November 2016): 919–932. doi:10.1016/j.joi.2016.08.002.'
  3. 'Laakso, Mikael, Patrik Welling, Helena Bukvova, Linus Nyman, Bo-Christer Björk, and Turid Hedlund. “The Development of Open Access Journal Publishing from 1993 to 2009.” Edited by Marcelo Hermes-Lima. PLoS ONE 6, no. 6 (June 13, 2011): e20961. doi:10.1371/journal.pone.0020961.'
  4. 'Paulus, Frieder M., Nicole Cruz, and Sören Krach. “The Impact Factor Fallacy.” Frontiers in Psychology 9 (August 20, 2018). doi:10.3389/fpsyg.2018.01487.'
  5. 'Shotton, David. “Funders Should Mandate Open Citations.” Nature 553, no. 7687 (January 2018): 129–129. doi:10.1038/d41586-018-00104-7.'
  6. 'Tennant, Jonathan P., François Waldner, Damien C. Jacques, Paola Masuzzo, Lauren B. Collister, and Chris. H. J. Hartgerink. “The Academic, Economic and Societal Impacts of Open Access: An Evidence-Based Review.” F1000Research 5 (June 9, 2016): 632. doi:10.12688/f1000research.8460.2.'
  7. 'Suber, Peter. “Open Access” (2012). doi:10.7551/mitpress/9286.001.0001.'

Beautiful formatted citations from simply a list of DOIs! You can then write this to a text file using writeLines.

# write the formatted citations to a text file
writeLines(my_citations, "my_citations_text.txt")

The above is helpful if you need to paste the references somewhere, and there are loads of other citation styles included in rcrossref–view them by calling rcrossref::get_styles() and it will print a vector of these styles to your console. I’ll just print the first 15 below:

# look at the first 15 styles Crossref offers
rcrossref::get_styles()[1:15]
  1. 'academy-of-management-review'
  2. 'accident-analysis-and-prevention'
  3. 'aci-materials-journal'
  4. 'acm-sig-proceedings-long-author-list'
  5. 'acm-sig-proceedings'
  6. 'acm-sigchi-proceedings-extended-abstract-format'
  7. 'acm-sigchi-proceedings'
  8. 'acm-siggraph'
  9. 'acme-an-international-journal-for-critical-geographies'
  10. 'acta-amazonica'
  11. 'acta-anaesthesiologica-scandinavica'
  12. 'acta-anaesthesiologica-taiwanica'
  13. 'acta-botanica-croatica'
  14. 'acta-chiropterologica'
  15. 'acta-chirurgiae-orthopaedicae-et-traumatologiae-cechoslovaca'

Getting formatted references in a BibTeX or RIS file

In addition to a text file, you can also write it to BibTeX or RIS:

# Use cr_cn() to get BibTeX files for my DOIs
my_citations_bibtex <- rcrossref::cr_cn(my_dois, format = "bibtex") %>%
  purrr::map_chr(., purrr::pluck, 1)

Write it to a .bib file using writeLines():

# write to bibtex file
writeLines(my_citations_bibtex, "my_citations_bibtex.bib")

Getting works from a typed citation in a Word document/text file

This can be helpful if you have a bibliography in a Word document or text file that you want to get into a reference management tool like Zotero. For instance, you may have written the citations in APA style and need to change to Chicago, but don’t want to rekey it all out. Or perhaps you jotted down your citations hastily and left out volume, issue, or page numbers, and you need a nice, fully-formatted citation.

If each citation is on its own line in your document’s bibliography, then you can probably paste the whole bibliography into an Excel spreadsheet. If it goes as planned, each citation will be in its own cell. You can then save it to a CSV file, which can then be read into R.

# read in a CSV file of citations
my_references <- read.csv("references.txt", stringsAsFactors = FALSE, fileEncoding = "ISO 8859-1")

# print the file
my_references
A data.frame: 8 x 1
reference
<chr>
Frosio, G. F. (2014). Open Access Publishing: A Literature Review. SSRN Electronic Journal. https://doi.org/10.2139/ssrn.2697412
Laakso, M., & Bjork, B.-C. (2016). Hybrid open access: A longitudinal study. Journal of Informetrics, 10(4), 919-932. https://doi.org/10.1016/j.joi.2016.08.002
Laakso, M., Welling, P., Bukvova, H., Nyman, L., Bjork, B.-C., & Hedlund, T. (2011). The Development of Open Access Journal Publishing from 1993 to 2009. PLoS ONE, 6(6), e20961. https://doi.org/10.1371/journal.pone.0020961
Paulus, F. M., Cruz, N., & Krach, S. (2018). The Impact Factor Fallacy. Frontiers in Psychology, 9. https://doi.org/10.3389/fpsyg.2018.01487
Science, Digital; Hook, Daniel; Hahnel, Mark; Calvert, Ian (2019): The Ascent of Open Access. figshare. Journal contribution. https://doi.org/10.6084/m9.figshare.7618751
Shotton, D. (2018). Funders should mandate open citations. Nature, 553(7687), 129-129. https://doi.org/10.1038/d41586-018-00104-7
Suber, P. (2012). Open access. Cambridge, Mass: MIT Press.
Tennant, J. P., Waldner, F., Jacques, D. C., Masuzzo, P., Collister, L. B., & Hartgerink, C. H. J. (2016). The academic, economic and societal impacts of Open Access: an evidence-based review. F1000Research, 5, 632. https://doi.org/10.12688/f1000research.8460.2

As you can see, these are just raw citations, not divided into variables by their metadata elements (that is, with title in one column, author in another, etc.). But, we can now run a query to get precisely that from Crossref using cr_works. Because cr_works is not vectorized, we will need to build a loop using map() from the purrr package.

Don’t mind the technical details–it is basically saying to take each row and look it up in the Crossref search engine. Basically, this is the equivalent of copy/pasting the whole reference into the Crossref search engine. The loop will print() the citation before searching for it so we can keep track of where it is. We set the limit to 5 because if Crossref didn’t find it in the first 5 results, it’s not likely to be there at all.

# loop through the references column, using cr_works() to look the item up and return the top 5 hits
my_references_works_list <- purrr::map(
  my_references$reference,
  function(x) {
    print(x)
    my_works <- rcrossref::cr_works(query = x, limit = 5) %>%
      purrr::pluck("data")
  })

[1] "Frosio, G. F. (2014). Open Access Publishing: A Literature Review. SSRN Electronic Journal. https://doi.org/10.2139/ssrn.2697412"
[1] "Laakso, M., & Bjork, B.-C. (2016). Hybrid open access: A longitudinal study. Journal of Informetrics, 10(4), 919-932. https://doi.org/10.1016/j.joi.2016.08.002"
[1] "Laakso, M., Welling, P., Bukvova, H., Nyman, L., Bjork, B.-C., & Hedlund, T. (2011). The Development of Open Access Journal Publishing from 1993 to 2009. PLoS ONE, 6(6), e20961. https://doi.org/10.1371/journal.pone.0020961"
[1] "Paulus, F. M., Cruz, N., & Krach, S. (2018). The Impact Factor Fallacy. Frontiers in Psychology, 9. https://doi.org/10.3389/fpsyg.2018.01487"
[1] "Science, Digital; Hook, Daniel; Hahnel, Mark; Calvert, Ian (2019): The Ascent of Open Access. figshare. Journal contribution. https://doi.org/10.6084/m9.figshare.7618751"
[1] "Shotton, D. (2018). Funders should mandate open citations. Nature, 553(7687), 129-129. https://doi.org/10.1038/d41586-018-00104-7"
[1] "Suber, P. (2012). Open access. Cambridge, Mass: MIT Press."
[1] "Tennant, J. P., Waldner, F., Jacques, D. C., Masuzzo, P., Collister, L. B., & Hartgerink, C. H. J. (2016). The academic, economic and societal impacts of Open Access: an evidence-based review. F1000Research, 5, 632. https://doi.org/10.12688/f1000research.8460.2"

The Crossref API assigns a score to each item returned within each query, giving a measure of the API’s confidence in the match. The item with the highest score is returned first in the datasets. We can return the first result in each item in the my_references_works_list by using map_dfr(), which is like map() except it returns the results into a data frame rather than a list:

# for each reference looked up, get back the first result
my_references_works_df <- my_references_works_list %>%
  purrr::map_dfr(., function(x) {
    x[1, ]
  })

# print the data frame with select columns
my_references_works_df %>%
  dplyr::select(title, doi, volume, issue, page, issued, url, publisher, reference.count, type, issn)
A tibble: 8 x 11
titledoivolumeissuepageissuedurlpublisherreference.counttypeissn
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>
Open Access Publishing: A Literature Review 10.2139/ssrn.2697412 NA NA NA 2014 http://dx.doi.org/10.2139/ssrn.2697412 Elsevier BV 0 journal-article1556-5068
Hybrid open access—A longitudinal study 10.1016/j.joi.2016.08.002 10 4 919-9322016-11 http://dx.doi.org/10.1016/j.joi.2016.08.002 Elsevier BV 33 journal-article1751-1577
The Development of Open Access Journal Publishing from 1993 to 2009 10.1371/journal.pone.0020961 6 6 e20961 2011-06-13http://dx.doi.org/10.1371/journal.pone.0020961 Public Library of Science (PLoS) 31 journal-article1932-6203
The Impact Factor Fallacy 10.3389/fpsyg.2018.01487 9 NA NA 2018-08-20http://dx.doi.org/10.3389/fpsyg.2018.01487 Frontiers Media SA 52 journal-article1664-1078
Table S1: Digital copies of visualizations, alignments, and phylogenetic trees deposited at Figshare (also accessible under Figshare Collection doi:10.6084/m9.figshare.c.3521787)10.7717/peerj.2951/supp-3 NA NA NA NA http://dx.doi.org/10.7717/peerj.2951/supp-3 PeerJ 0 component NA
Funders should mandate open citations 10.1038/d41586-018-00104-7 5537687129-1292018-01 http://dx.doi.org/10.1038/d41586-018-00104-7 Springer Science and Business Media LLC0 journal-article0028-0836,1476-4687
Open Access by Peter Suber. MIT Press, Cambridge, MA, U.S.A., 2012. 230 pp. ISBN: 978-0- 262-51763-8 10.1162/leon_r_00535 46 2 180-1812013-04 http://dx.doi.org/10.1162/leon_r_00535 MIT Press - Journals 3 journal-article0024-094X,1530-9282
The academic, economic and societal impacts of Open Access: an evidence-based review 10.12688/f1000research.8460.15 NA 632 2016-04-11http://dx.doi.org/10.12688/f1000research.8460.1F1000 Research Ltd 137journal-article2046-1402

We can print just the titles to quickly see how well they match with the titles of the works we requested:

# print the title column
my_references_works_df$title
  1. 'Open Access Publishing: A Literature Review'
  2. 'Hybrid open access—A longitudinal study'
  3. 'The Development of Open Access Journal Publishing from 1993 to 2009'
  4. 'The Impact Factor Fallacy'
  5. 'Table S1: Digital copies of visualizations, alignments, and phylogenetic trees deposited at Figshare (also accessible under Figshare Collection doi:10.6084/m9.figshare.c.3521787)'
  6. 'Funders should mandate open citations'
  7. 'Open Access by Peter Suber. MIT Press, Cambridge, MA, U.S.A., 2012. 230 pp. ISBN: 978-0- 262-51763-8'
  8. 'The academic, economic and societal impacts of Open Access: an evidence-based review'

Not bad! Looks like we got 6 out of 8, with problems on number 5 and 7. To see more about how to troubleshoot those two, go to https://ciakovx.github.io/rcrossref.html#getting_works_from_a_typed_citation_in_a_word_documenttext_file

Writing publications to CSV

We will use the write.csv() function to write our data to disk as a CSV file.

# Use c() to create a vector of DOIs
my_dois <- c("10.2139/ssrn.2697412", 
                        "10.1016/j.joi.2016.08.002", 
                        "10.1371/journal.pone.0020961", 
                        "10.3389/fpsyg.2018.01487", 
                        "10.1038/d41586-018-00104-7", 
                        "10.12688/f1000research.8460.2", 
                        "10.7551/mitpress/9286.001.0001")

# pass the my_dois vector to cr_works()
my_dois_works <- rcrossref::cr_works(dois = my_dois) %>%
  pluck("data")

Unfortunately, you cannot simply write the plosone_publications data frame to a CSV, due to the nested lists. It will throw an error: "Error in stream_delim_(df, path, ...) : Don't know how to handle vector of type list."

I run through three solutions at https://ciakovx.github.io/rcrossref.html#writing_publications_to_disk

Here, we will use solution 3: You can use mutate() from dplyr to coerce the list columns into character vectors with as.character().

First, identify the list vectors:

# use map_chr to print the column types
purrr::map_chr(my_dois_works, typeof)
container.title
'character'
created
'character'
deposited
'character'
doi
'character'
indexed
'character'
issn
'character'
issued
'character'
member
'character'
prefix
'character'
publisher
'character'
reference.count
'character'
score
'character'
source
'character'
title
'character'
type
'character'
url
'character'
author
'list'
alternative.id
'character'
published.print
'character'
issue
'character'
page
'character'
update.policy
'character'
volume
'character'
assertion
'list'
link
'list'
license
'list'
published.online
'character'
reference
'list'
subject
'character'
abstract
'character'
isbn
'character'

For any variables that are type list, coerce those columns to character:

# use mutate() to coerce list columns to character vectors
my_dois_mutated <- my_dois_works %>%
  dplyr::mutate(author = as.character(author)) %>%
  dplyr::mutate(assertion = as.character(assertion)) %>%
  dplyr::mutate(link = as.character(link)) %>%
  dplyr::mutate(license = as.character(license)) %>%
  dplyr::mutate(reference = as.character(reference))
write.csv(my_dois_mutated, "my_dois_mutated.csv")

Again, this is not an ideal solution, but if you need to move the data into CSV to view in Excel, it can do the trick.

Using roadoi to check for open access

roadoi was developed by Najko Jahn, with reviews from Tuija Sonkkila and Ross Mounce. It interfaces with Unpaywall (which used to be called oaDOI), an important tool developed by ImpactStory (Heather Piwowar and Jason Priem) for locating open access versions of scholarship–read more in this Nature article. See here for the roadoi documentation.

This incredible Introduction to roadoi by Najko Jahn provides much of what you need to know to use the tool, as well as an interesting use case. Also see his recently published article Open Access Evidence in Unpaywall, running deep analysis on Unpaywall data.

First install the package and load it.

# install the roadoi package
install.packages("roadoi")

Installing package into ‘/home/nbuser/R’
(as ‘lib’ is unspecified)

# load the roadoi package
library(roadoi)

Setting up roadoi

Your API calls to Unpaywall must include a valid email address where you can be reached in order to keep the service open and free for everyone.

Checking OA status with oadoi_fetch

We then create DOI vector and use the oadoi_fetch() function from roadoi.

Be sure to replace the email below with your own

# Use c() to create a vector of DOIs
my_dois <- c("10.2139/ssrn.2697412", 
                        "10.1016/j.joi.2016.08.002", 
                        "10.1371/journal.pone.0020961", 
                        "10.3389/fpsyg.2018.01487", 
                        "10.1038/d41586-018-00104-7", 
                        "10.12688/f1000research.8460.2", 
                        "10.7551/mitpress/9286.001.0001")

# use oadoi_fetch() to get Unpaywall data on those DOIs
my_dois_oa <- roadoi::oadoi_fetch(dois = my_dois,
                                 email = "name@example.edu")

Look at the column names.

# print column names
names(my_dois_oa)
  1. 'doi'
  2. 'best_oa_location'
  3. 'oa_locations'
  4. 'data_standard'
  5. 'is_oa'
  6. 'genre'
  7. 'oa_status'
  8. 'has_repository_copy'
  9. 'journal_is_oa'
  10. 'journal_is_in_doaj'
  11. 'journal_issns'
  12. 'journal_issn_l'
  13. 'journal_name'
  14. 'publisher'
  15. 'title'
  16. 'year'
  17. 'updated'
  18. 'authors'

The returned variables are described on the Unpaywall Data Format page.

We can see that Unpaywall could not find OA versions for two of the seven of these, so we will filter them out:

# use filter() to overwrite the data frame and keep only items that are available OA
my_dois_oa <- my_dois_oa %>%
  dplyr::filter(is_oa == TRUE)

As above, it is easier to use unnest() to more closely view one of the variables:

# print the data frame with best open access location unnested
my_dois_oa %>%
    tidyr::unnest(best_oa_location)
A tibble: 6 x 29
doioa_locationsdata_standardis_oagenreoa_statushas_repository_copyjournal_is_oajournal_is_in_doajjournal_issnsjournal_issn_ljournal_namepublishertitleyearupdatedauthorsendpoint_idevidencehost_typeis_bestlicensepmh_idrepository_institutionupdated1urlurl_for_landing_pageurl_for_pdfversion
<chr><list><int><lgl><chr><chr><lgl><lgl><lgl><chr><chr><chr><chr><chr><chr><chr><list><chr><chr><chr><lgl><chr><chr><chr><chr><chr><chr><chr><chr>
10.2139/ssrn.2697412 kmlgamtfmx4w6tf78ykl , NA , oa repository (via OAI-PMH title and first author match) , oa repository (semantic scholar lookup) , repository , repository , TRUE , FALSE , cc-by , NA , oai:zenodo.org:8381 , NA , CERN European Organization for Nuclear Research - Zenodo , NA , 2019-11-21T02:00:14.479076 , 2019-10-01T00:00:00 , https://zenodo.org/record/8381/files/CREATe-Working-Paper-2014-01.pdf , http://pdfs.semanticscholar.org/a26e/76b34730effa24dab8fa278465553c0cdf98.pdf, https://zenodo.org/record/8381 , https://semanticscholar.org/paper/a26e76b34730effa24dab8fa278465553c0cdf98 , https://zenodo.org/record/8381/files/CREATe-Working-Paper-2014-01.pdf , http://pdfs.semanticscholar.org/a26e/76b34730effa24dab8fa278465553c0cdf98.pdf, publishedVersion , submittedVersion 2TRUEjournal-articlegreen TRUEFALSEFALSE1556-5068 1556-5068SSRN Electronic JournalElsevier BV Open Access Publishing: A Literature Review 20142020-02-06T10:15:13.003631Frosio , Giancarlo F.kmlgamtfmx4w6tf78ykloa repository (via OAI-PMH title and first author match)repositoryTRUEcc-byoai:zenodo.org:8381CERN European Organization for Nuclear Research - Zenodo2019-11-21T02:00:14.479076https://zenodo.org/record/8381/files/CREATe-Working-Paper-2014-01.pdf https://zenodo.org/record/8381 https://zenodo.org/record/8381/files/CREATe-Working-Paper-2014-01.pdf publishedVersion
10.1016/j.joi.2016.08.002 NA , open (via crossref license) , publisher , TRUE , cc-by , NA , NA , 2020-03-08T17:25:36.368594 , https://doi.org/10.1016/j.joi.2016.08.002, https://doi.org/10.1016/j.joi.2016.08.002, NA , publishedVersion 2TRUEjournal-articlehybridFALSEFALSEFALSE1751-1577 1751-1577Journal of InformetricsElsevier BV Hybrid open access—A longitudinal study 20162020-02-07T21:11:02.775326http://orcid.org/0000-0003-3951-7990, http://orcid.org/0000-0003-1545-9642, FALSE , FALSE , Laakso , Björk , Mikael , Bo-Christer NA open (via crossref license) publisher TRUEcc-byNA NA 2020-03-08T17:25:36.368594https://doi.org/10.1016/j.joi.2016.08.002 https://doi.org/10.1016/j.joi.2016.08.002 NA publishedVersion
10.1371/journal.pone.0020961 NA , NA , pubmedcentral.nih.gov , NA , NA , open (via page says license) , oa journal (via doaj) , oa repository (via OAI-PMH doi match) , oa repository (via pmcid lookup) , oa repository (semantic scholar lookup) , publisher , publisher , repository , repository , repository , TRUE , FALSE , FALSE , FALSE , FALSE , cc-by , cc-by , implied-oa , NA , NA , NA , NA , oai:pubmedcentral.nih.gov:3113847 , NA , NA , NA , NA , pubmedcentral.nih.gov , NA , NA , 2018-09-26T18:32:55.188635 , 2020-03-08T17:25:36.653131 , 2017-10-22T12:50:17.733660 , 2020-03-08T17:25:36.653256 , 2019-10-01T00:00:00 , https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0020961&type=printable, https://doi.org/10.1371/journal.pone.0020961 , http://europepmc.org/articles/pmc3113847?pdf=render , https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113847 , http://pdfs.semanticscholar.org/066e/b2ec4d41fb27ac7a0403f3a86b098c3e8238.pdf , https://doi.org/10.1371/journal.pone.0020961 , https://doi.org/10.1371/journal.pone.0020961 , http://europepmc.org/articles/pmc3113847 , https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113847 , https://semanticscholar.org/paper/066eb2ec4d41fb27ac7a0403f3a86b098c3e8238 , https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0020961&type=printable, NA , http://europepmc.org/articles/pmc3113847?pdf=render , NA , http://pdfs.semanticscholar.org/066e/b2ec4d41fb27ac7a0403f3a86b098c3e8238.pdf , publishedVersion , publishedVersion , publishedVersion , publishedVersion , submittedVersion 2TRUEjournal-articlegold TRUE TRUE TRUE1932-6203 1932-6203PLoS ONE Public Library of Science (PLoS) The Development of Open Access Journal Publishing from 1993 to 2009 20112020-02-04T16:37:55.660994Laakso , Welling , Bukvova , Nyman , Björk , Hedlund , Mikael , Patrik , Helena , Linus , Bo-Christer, Turid , first , additional , additional , additional , additional , additional NA open (via page says license) publisher TRUEcc-byNA NA 2018-09-26T18:32:55.188635https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0020961&type=printablehttps://doi.org/10.1371/journal.pone.0020961 https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0020961&type=printablepublishedVersion
10.3389/fpsyg.2018.01487 NA , NA , NA , 319be07214511446630 , NA , open (via page says license) , oa journal (via doaj) , oa repository (via pmcid lookup) , oa repository (via OAI-PMH doi match) , oa repository (semantic scholar lookup) , publisher , publisher , repository , repository , repository , TRUE , FALSE , FALSE , FALSE , FALSE , cc-by , cc-by , NA , cc-by , NA , NA , NA , NA , oai:eprints.bbk.ac.uk.oai2:23967 , NA , NA , NA , NA , Birkbeck, University of London - BIROn - Birkbeck Institutional Research Online, NA , 2019-11-09T20:20:21.096918 , 2020-03-08T17:25:36.922865 , 2020-03-08T17:25:36.922996 , 2020-03-02T03:24:49.468453 , 2019-10-01T00:00:00 , https://www.frontiersin.org/articles/10.3389/fpsyg.2018.01487/pdf , https://doi.org/10.3389/fpsyg.2018.01487 , https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6109637 , https://eprints.bbk.ac.uk/23967/1/23967.pdf , http://pdfs.semanticscholar.org/fc82/2399aa6a22352085179b6505db893be13820.pdf , https://doi.org/10.3389/fpsyg.2018.01487 , https://doi.org/10.3389/fpsyg.2018.01487 , https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6109637 , https://eprints.bbk.ac.uk/23967/1/23967.pdf , https://semanticscholar.org/paper/fc822399aa6a22352085179b6505db893be13820 , https://www.frontiersin.org/articles/10.3389/fpsyg.2018.01487/pdf , NA , NA , https://eprints.bbk.ac.uk/23967/1/23967.pdf , http://pdfs.semanticscholar.org/fc82/2399aa6a22352085179b6505db893be13820.pdf , publishedVersion , publishedVersion , publishedVersion , acceptedVersion , submittedVersion 2TRUEjournal-articlegold TRUE TRUE TRUE1664-1078 1664-1078Frontiers in PsychologyFrontiers Media SA The Impact Factor Fallacy 20182020-02-04T08:31:45.023735Paulus , Cruz , Krach , Frieder M., Nicole , Sören , first , additional, additionalNA open (via page says license) publisher TRUEcc-byNA NA 2019-11-09T20:20:21.096918https://www.frontiersin.org/articles/10.3389/fpsyg.2018.01487/pdf https://doi.org/10.3389/fpsyg.2018.01487 https://www.frontiersin.org/articles/10.3389/fpsyg.2018.01487/pdf publishedVersion
10.1038/d41586-018-00104-7 NA , open (via free pdf) , publisher , TRUE , pd , NA , NA , 2019-12-23T19:38:29.249435 , https://www.nature.com/magazine-assets/d41586-018-00104-7/d41586-018-00104-7.pdf, https://doi.org/10.1038/d41586-018-00104-7 , https://www.nature.com/magazine-assets/d41586-018-00104-7/d41586-018-00104-7.pdf, publishedVersion 2TRUEjournal-articlehybridFALSEFALSEFALSE0028-0836,1476-46870028-0836Nature Springer Science and Business Media LLCFunders should mandate open citations 20182020-02-27T21:47:08.667168Shotton, David , first NA open (via free pdf) publisher TRUEpd NA NA 2019-12-23T19:38:29.249435https://www.nature.com/magazine-assets/d41586-018-00104-7/d41586-018-00104-7.pdf https://doi.org/10.1038/d41586-018-00104-7 https://www.nature.com/magazine-assets/d41586-018-00104-7/d41586-018-00104-7.pdf publishedVersion
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Next steps

There are several other excellent R packages that interface with publication metadata that can be used in conjunction with this package. Examples:

R Resources

Learning R

  1. swirl is a package you can install in R to learn about R and data science interactively. Just type install.packages("swirl") into your R console, load the package by typing library("swirl"), and then type swirl(). Read more at <http: swirlstats.com=”“>.

  2. Try R is a browser-based interactive tutorial developed by Code School.

  3. Anthony Damico’s twotorials are a series of 2 minute videos demonstrating several basic tasks in R.

  4. Cookbook for R by Winston Change provides solutions to common tasks and problems in analyzing data

  5. If you’re up for a challenge, try the free R Programming MOOC in Coursera by Roger Peng.

  6. Books:

Data

If you need some data to play with, type data() in the console for a list of data sets. To load a dataset, type it like this: data(mtcars). Type help(mtcars) to learn more about it. You can then perform operations, e.g. {r dataloading, comment=NA, eval=F} head(mtcars) nrow(mtcars) mean(mtcars$mpg) sixCylinder &lt;- mtcars[mtcars$cyl == 6, ]

See also rdatamining.com’s list of free datasets.

Cheat Sheets

Style guides

Use these resources to write cleaner code, according to established style conventions