Merge branch 'v2'

ropensci · Oct 2, 2017 · c08a6ca · c08a6ca
2 parents e2bb8da + 46a1458
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diff --git a/R/oadoi_fetch.r b/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 = "[email protected]")
@@ -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

diff --git a/R/roadoi-package.r b/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

diff --git a/README.Rmd b/README.Rmd
@@ -36,7 +36,7 @@ roadoi::oadoi_fetch(dois = c("10.1038/ng.3260", "10.1093/nar/gkr1047"),
                     email = "[email protected]")
 ```
 
-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
 

diff --git a/README.md b/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
 

diff --git a/man/oadoi_fetch.Rd b/man/oadoi_fetch.Rd
diff --git a/man/roadoi-package.Rd b/man/roadoi-package.Rd
diff --git a/vignettes/intro.Rmd b/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).