Merge branch 'v2'

R/oadoi_fetch.r

@@ -7,7 +7,7 @@
 #'
 #' @param dois character vector, search by a single DOI or many DOIs.
 #' A rate limit of 100k requests per day is suggested. If you need to access
-#' more data, use the data dump \url{https://oadoi.org/api#dataset} instead.
+#' more data, request the data dump \url{https://oadoi.org/api} instead.
 #' @param email character vector, mandatory! oaDOI requires your email address,
 #' so that they can track usage and notify you when something breaks.
 #' Set email address in your `.Rprofile` file with
@@ -17,9 +17,8 @@
 #' See \code{\link[plyr]{create_progress_bar}} for details
 #' of each. By default, no progress bar is displayed.
 #'
-#' @return The result is a tibble with each row representing a publication and
-#' and the following columns. Here are some fields returned by the API.
-#' However, other fields can be added by oaDOI over time.
+#' @return The result is a tibble with each row representing a publication.
+#' Here are the returned columns and descriptions according to the API docu:
 #'
 #'
 #' \tabular{ll}{
@@ -65,7 +64,7 @@
 #'
 #'
 #' To unnest list-columns, you want to use tidyr's unnest function
-#' \code{\link[tidyr]{unnest}} makes each element of the list its own row.
+#' \code{\link[tidyr]{unnest}}.
 
 #' @examples \dontrun{
 #' oadoi_fetch("10.1038/nature12373", email = "name@example.com")
@@ -84,8 +83,8 @@ oadoi_fetch <-
  if (length(dois) > api_limit)
  stop(
  "A rate limit of 100k requests per day is suggested.
- If you need to access tomore data, use the data dump
- https://oadoi.org/api#dataset instead",
+ If you need to access more data, request the data dump
+ https://oadoi.org/api instead",
  .call = FALSE
  )
  # Call API for every DOI, and return results as tbl_df

R/roadoi-package.r

@@ -9,9 +9,8 @@
 #' information and full-text links from oaDOI.
 #'
 #' @section Contribute:
-#' I would be very happy for people willing to contribute to this package.
-#' It is important to keep in mind that oaDOI is still in early development,
-#' which could affect the API and this client.
+#' I would be very happy for people willing to contribute to this package. Use
+#' GitHubs issue tracker for bug reporting and feature requests.
 #'
 #' @importFrom httr GET content modify_url user_agent add_headers status_code timeout
 #' @importFrom jsonlite fromJSON

README.Rmd

@@ -36,7 +36,7 @@ roadoi::oadoi_fetch(dois = c("10.1038/ng.3260", "10.1093/nar/gkr1047"),
  email = "name@example.com")
 ```
 
-There are no API restrictions. However, providing an email address is required and a rate limit of 100k is implemented If you need to access more data, use the data dump <https://oadoi.org/api#dataset> instead.
+There are no API restrictions. However, providing an email address is required and a rate limit of 100k is suggested. If you need to access more data, ask for the data dump <https://oadoi.org/api> instead.
 
 ### RStudio Addin
 

README.md

@@ -38,7 +38,7 @@ roadoi::oadoi_fetch(dois = c("10.1038/ng.3260", "10.1093/nar/gkr1047"),
 #> # year <chr>, updated <chr>, non_compliant <list>
 ```
 
-There are no API restrictions. However, providing an email address is required and a rate limit of 100k is implemented If you need to access more data, use the data dump <https://oadoi.org/api#dataset> instead.
+There are no API restrictions. However, providing an email address is required and a rate limit of 100k is suggested. If you need to access more data, ask for the data dump <https://oadoi.org/api> instead.
 
 ### RStudio Addin
 
@@ -129,11 +129,11 @@ that contain useful metadata about the OA sources found by oaDOI. These are
 
 **Column**|**Description**
 |:------------|:----------------------------------------------
-evidence`|How the OA location was found and is characterized by oaDOI?
-host_type`|OA full-text provided by `publisher` or `repository`. 
-license`|The license under which this copy is published
-url`|The URL where you can find this OA copy.
-versions`|The content version accessible at this location following the DRIVER 2.0 Guidelines evidence (<https://wiki.surfnet.nl/display/DRIVERguidelines/DRIVER-VERSION+Mappings>)
+`evidence`|How the OA location was found and is characterized by oaDOI?
+`host_type`|OA full-text provided by `publisher` or `repository`. 
+`license`|The license under which this copy is published
+`url`|The URL where you can find this OA copy.
+`versions`|The content version accessible at this location following the DRIVER 2.0 Guidelines (<https://wiki.surfnet.nl/display/DRIVERguidelines/DRIVER-VERSION+Mappings>)
 
 You can [simplify these list-columns in at least two ways](http://r4ds.had.co.nz/many-models.html#simplifying-list-columns).
 
@@ -244,27 +244,28 @@ random_dois <- rcrossref::cr_r(sample = 100) %>%
  .$data
 random_dois
 #> # A tibble: 100 x 35
-#> alternative.id container.title
-#> <chr> <chr>
-#> 1 Southern Medical Journal
-#> 2 10.1021/cm000092r Chemistry of Materials
-#> 3 Overcoming Anxiety for Dummies®
-#> 4 S0006291X72800251 Biochemical and Biophysical Research Communications
-#> 5 Acta Theriologica
-#> 6 Virginia Law Review
-#> 7 0378475489900542 Mathematics and Computers in Simulation
-#> 8 S0169433212014869 Applied Surface Science
-#> 9 S0922156500002120 Leiden Journal of International Law
-#> 10 S000299041934058166 Bulletin of the American Mathematical Society
-#> # ... with 90 more rows, and 33 more variables: created <chr>,
-#> # deposited <chr>, DOI <chr>, funder <list>, indexed <chr>, ISBN <chr>,
-#> # ISSN <chr>, issue <chr>, issued <chr>, link <list>, member <chr>,
-#> # page <chr>, prefix <chr>, publisher <chr>, reference.count <chr>,
-#> # score <chr>, source <chr>, subject <chr>, subtitle <chr>, title <chr>,
-#> # type <chr>, URL <chr>, volume <chr>, assertion <list>, author <list>,
-#> # `clinical-trial-number` <list>, license_date <chr>, license_URL <chr>,
-#> # license_delay.in.days <chr>, license_content.version <chr>,
-#> # update.policy <chr>, abstract <chr>, archive <chr>
+#> alternative.id
+#> <chr>
+#> 1 
+#> 2 
+#> 3 
+#> 4 10.1080/10739149908085828
+#> 5 
+#> 6 
+#> 7 
+#> 8 S0266462300004918
+#> 9 
+#> 10 BF00202270
+#> # ... with 90 more rows, and 34 more variables: container.title <chr>,
+#> # created <chr>, deposited <chr>, DOI <chr>, funder <list>,
+#> # indexed <chr>, ISBN <chr>, ISSN <chr>, issue <chr>, issued <chr>,
+#> # link <list>, member <chr>, page <chr>, prefix <chr>, publisher <chr>,
+#> # reference.count <chr>, score <chr>, source <chr>, subject <chr>,
+#> # title <chr>, type <chr>, URL <chr>, assertion <list>, author <list>,
+#> # `clinical-trial-number` <list>, volume <chr>, archive <chr>,
+#> # license_date <chr>, license_URL <chr>, license_delay.in.days <chr>,
+#> # license_content.version <chr>, subtitle <chr>, abstract <chr>,
+#> # update.policy <chr>
 ```
 
 Let's see when these random publications were published
@@ -281,16 +282,16 @@ random_dois %>%
 #> # A tibble: 49 x 2
 #> issued pubs
 #> <dbl> <int>
-#> 1 2010  5
-#> 2 2013 5
-#> 3  NA  5
-#> 4 1999 4
-#> 5 2004 4
-#> 6 2006 4
-#> 7 2007 4
-#> 8 2009 4
-#> 9 2011 4
-#> 10 2014 4
+#> 1  NA  12
+#> 2 2003 5
+#> 3 2006  4
+#> 4 2012 4
+#> 5 2014 4
+#> 6 1985 3
+#> 7 1993 3
+#> 8 1994 3
+#> 9 1998 3
+#> 10 2007 3
 #> # ... with 39 more rows
 ```
 
@@ -305,13 +306,13 @@ random_dois %>%
 #> # A tibble: 7 x 2
 #> type pubs
 #> <chr> <int>
-#> 1 journal-article 78
+#> 1 journal-article 72
 #> 2 book-chapter 8
-#> 3 proceedings-article 7
-#> 4  component 3
-#> 5 journal-issue 2
-#> 6  monograph 1
-#> 7  other 1
+#> 3  component 7
+#> 4 proceedings-article 7
+#> 5  dataset 3
+#> 6 reference-entry 2
+#> 7 journal-issue 1
 ```
 
 #### Calling oaDOI.org
@@ -352,8 +353,8 @@ my_df %>%
 
 |is_oa | Articles| Proportion|
 |:-----|--------:|----------:|
-|FALSE | 82| 0.82|
-|TRUE | 18| 0.18|
+|FALSE | 80|  0.8|
+|TRUE | 20|  0.2|
 
 How did oaDOI find those Open Access full-texts, which were characterized as best matches, and how are these OA types distributed over publication types?
 
@@ -372,11 +373,12 @@ my_df %>%
 
 |evidence |type | Articles|
 |:-------------------------------|:-------------------|--------:|
-|hybrid (via free pdf) |journal-article | 7|
-|oa repository (via BASE) |journal-article | 7|
-|oa repository (via BASE) |proceedings-article | 2|
-|hybrid (via crossref license) |journal-article | 1|
-|oa journal (via publisher name) |component | 1|
+|hybrid (via free pdf) |journal-article | 8|
+|oa journal (via publisher name) |component | 5|
+|oa repository (via BASE) |journal-article | 3|
+|hybrid (via crossref license) |journal-article | 2|
+|oa journal (via publisher name) |journal-article | 1|
+|oa repository (via BASE) |proceedings-article | 1|
 
 #### More examples
 

vignettes/intro.Rmd

@@ -59,11 +59,11 @@ that contain useful metadata about the OA sources found by oaDOI. These are
 
 **Column**|**Description**
 |:------------|:----------------------------------------------
-evidence`|How the OA location was found and is characterized by oaDOI?
-host_type`|OA full-text provided by `publisher` or `repository`. 
-license`|The license under which this copy is published
-url`|The URL where you can find this OA copy.
-versions`|The content version accessible at this location following the DRIVER 2.0 Guidelines evidence (<https://wiki.surfnet.nl/display/DRIVERguidelines/DRIVER-VERSION+Mappings>)
+`evidence`|How the OA location was found and is characterized by oaDOI?
+`host_type`|OA full-text provided by `publisher` or `repository`. 
+`license`|The license under which this copy is published
+`url`|The URL where you can find this OA copy.
+`versions`|The content version accessible at this location following the DRIVER 2.0 Guidelines (<https://wiki.surfnet.nl/display/DRIVERguidelines/DRIVER-VERSION+Mappings>)
 
 You can [simplify these list-columns in at least two ways](http://r4ds.had.co.nz/many-models.html#simplifying-list-columns).