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njahn82 committed Sep 15, 2019
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25 changes: 12 additions & 13 deletions README.md
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Expand Up @@ -305,6 +305,7 @@ To display how many full-text links were found and which sources were used in a


```r
if(!is.null(oa_df))
oa_df %>%
group_by(is_oa) %>%
summarise(Articles = n()) %>%
Expand All @@ -317,13 +318,14 @@ oa_df %>%

|is_oa | Articles| Proportion|
|:-----|--------:|----------:|
|FALSE | 35| 0.7|
|TRUE | 15| 0.3|
|FALSE | 33| 0.66|
|TRUE | 17| 0.34|

How did Unpaywall find those Open Access full-texts, which were characterized as best matches, and how are these OA types distributed over publication types?


```r
if(!is.null(oa_df))
oa_df %>%
filter(is_oa == TRUE) %>%
select(best_oa_location, genre) %>%
Expand All @@ -336,17 +338,14 @@ oa_df %>%



|evidence |genre | Articles|
|:--------------------------------------------------------|:---------------|--------:|
|open (via page says license) |journal-article | 4|
|open (via free pdf) |journal-article | 3|
|oa repository (via OAI-PMH title and first author match) |journal-article | 2|
|oa journal (via doaj) |journal-article | 1|
|oa journal (via observed oa rate) |journal-article | 1|
|oa repository (via OAI-PMH title match) |report | 1|
|open (via crossref license) |journal-article | 1|
|open (via free pdf) |book-chapter | 1|
|open (via free pdf) |other | 1|
|evidence |genre | Articles|
|:--------------------------------------------------------|:-------------------|--------:|
|open (via free pdf) |journal-article | 7|
|open (via page says license) |journal-article | 6|
|oa repository (via OAI-PMH doi match) |journal-article | 1|
|oa repository (via OAI-PMH title and first author match) |journal-article | 1|
|open (via free pdf) |book-chapter | 1|
|open (via page says license) |proceedings-article | 1|

#### More examples

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37 changes: 21 additions & 16 deletions codemeta.json
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@@ -1,13 +1,16 @@
{
"@context": ["https://doi.org/10.5063/schema/codemeta-2.0", "http://schema.org"],
"@context": [
"https://doi.org/10.5063/schema/codemeta-2.0",
"http://schema.org"
],
"@type": "SoftwareSourceCode",
"identifier": "roadoi",
"description": "This web client interfaces Unpaywall <https://unpaywall.org/products/api>, formerly\n oaDOI, a service finding free full-texts of academic papers by linking DOIs with \n open access journals and repositories. It provides unified access to various data sources \n for open access full-text links including Crossref and the Directory of Open Access \n Journals (DOAJ). API usage is free and no registration is required.",
"name": "roadoi: Find Free Versions of Scholarly Publications via Unpaywall",
"codeRepository": "https://github.com/ropensci/roadoi",
"issueTracker": "https://github.com/ropensci/roadoi/issues",
"license": "https://spdx.org/licenses/MIT",
"version": "0.5.2",
"version": "0.6",
"programmingLanguage": {
"@type": "ComputerLanguage",
"name": "R",
Expand Down Expand Up @@ -102,18 +105,6 @@
},
"sameAs": "https://CRAN.R-project.org/package=rmarkdown"
},
{
"@type": "SoftwareApplication",
"identifier": "lubridate",
"name": "lubridate",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=lubridate"
},
{
"@type": "SoftwareApplication",
"identifier": "rcrossref",
Expand Down Expand Up @@ -252,11 +243,25 @@
],
"releaseNotes": "https://github.com/ropensci/roadoi/blob/master/NEWS",
"readme": "https://github.com/ropensci/roadoi/blob/master/README.md",
"contIntegration": ["https://travis-ci.org/ropensci/roadoi", "https://ci.appveyor.com/project/ropensci/roadoi", "https://codecov.io/github/ropensci/roadoi?branch=master"],
"contIntegration": [
"https://travis-ci.org/ropensci/roadoi",
"https://ci.appveyor.com/project/ropensci/roadoi",
"https://codecov.io/github/ropensci/roadoi?branch=master"
],
"review": {
"@type": "Review",
"url": "https://github.com/ropensci/onboarding/issues/115",
"provider": "http://ropensci.org"
},
"keywords": ["open-access", "oadoi", "r", "webclient", "code4lib", "altmetrics", "rstats", "r-package", "peer-reviewed"]
"keywords": [
"open-access",
"oadoi",
"r",
"webclient",
"code4lib",
"altmetrics",
"rstats",
"r-package",
"peer-reviewed"
]
}
2 changes: 1 addition & 1 deletion cran-comments.md
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Expand Up @@ -20,7 +20,7 @@ I have run R CMD check on downstream dependencies using revdepcheck::revdep_chec
Dear CRAN maintainers,

This submission fixes the problems shown on
<https://cran.r-project.org/web/checks/check_results_roadoi.html>.
<https://cran.r-project.org/web/checks/check_results_roadoi.html>, and problems encountered in the last submission.

Thanks for alerting me!

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3 changes: 2 additions & 1 deletion vignettes/intro.Rmd
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Expand Up @@ -149,7 +149,6 @@ my_data <- purrr::map(random_dois,
purrr::map_df(my_data, "result")
#show errors
purrr::map(my_data, "error")
```

### Use Case: Studying the compliance with open access policies
Expand Down Expand Up @@ -186,6 +185,7 @@ After obtaining the data, reporting with R is straightforward. You can even gene
To display how many full-text links were found and which sources were used in a nicely formatted markdown-table using the [`knitr`](https://yihui.name/knitr/)-package:

```{r, results='asis'}
if(!is.null(oa_df))
oa_df %>%
group_by(is_oa) %>%
summarise(Articles = n()) %>%
Expand All @@ -197,6 +197,7 @@ oa_df %>%
How did Unpaywall find those Open Access full-texts, which were characterized as best matches, and how are these OA types distributed over publication types?

```{r, results='asis'}
if(!is.null(oa_df))
oa_df %>%
filter(is_oa == TRUE) %>%
select(best_oa_location, genre) %>%
Expand Down

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R/oadoi_fetch.r:11:1: style: Lines should not be more than 80 characters.

​#'   more data, request the data dump \url{https://unpaywall.org/dataset} instead.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/oadoi_fetch.r:12:1: style: Lines should not be more than 80 characters.

​#' @param email character vector, mandatory! Unpaywall requires your email address,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/oadoi_fetch.r:15:1: style: Lines should not be more than 80 characters.

​#'   the option `roadoi_email` \code{options(roadoi_email = "[email protected]")}.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/oadoi_fetch.r:37:1: style: Lines should not be more than 80 characters.

​#'  for this resource. \code{1} mostly uses Crossref for hybrid detection. \code{2}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/oadoi_fetch.r:41:1: style: Lines should not be more than 80 characters.

​#'  \code{oa_status}        \tab Classifies OA resources by location and license terms as one of: gold, hybrid, bronze, green or closed. See here for more information \url{https://support.unpaywall.org/support/solutions/articles/44001777288-what-do-the-types-of-oa-status-green-gold-hybrid-and-bronze-mean-}. \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/oadoi_fetch.r:42:1: style: Lines should not be more than 80 characters.

​#'  \code{has_repository_copy} \tab Is a full-text available in a repository? \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/oadoi_fetch.r:43:1: style: Lines should not be more than 80 characters.

​#'  \code{journal_is_oa}    \tab Is the article published in a fully OA journal? \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/oadoi_fetch.r:54:1: style: Lines should not be more than 80 characters.

​#'  \code{updated}          \tab Time when the data for this resource was last updated. \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/oadoi_fetch.r:58:1: style: Lines should not be more than 80 characters.

​#' The columns  \code{best_oa_location} and  \code{oa_locations} are list-columns
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/oadoi_fetch.r:64:1: style: Lines should not be more than 80 characters.

​#'  \code{evidence}        \tab How the OA location was found and is characterized
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/oadoi_fetch.r:73:1: style: Lines should not be more than 80 characters.

​#'  (\url{https://wiki.surfnet.nl/display/DRIVERguidelines/DRIVER-VERSION+Mappings}\cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/oadoi_fetch.r:120:1: style: Lines should not be more than 80 characters.

​#' @param email character vector, mandatory! Unpaywall requires your email address,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/oadoi_fetch.r:123:1: style: Lines should not be more than 80 characters.

​#'   the option `roadoi_email` \code{options(roadoi_email = "[email protected]")}.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/roadoi-package.r:4:1: style: Lines should not be more than 80 characters.

​#' roadoi interacts with the Unpaywall data service, which links DOIs representing
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/roadoi-package.r:8:1: style: Lines should not be more than 80 characters.

​#' Use the \code{oadoi_fetch()} function in this package to get open access status
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/roadoi-package.r:15:1: style: Lines should not be more than 80 characters.

​#' @importFrom httr GET content modify_url user_agent add_headers status_code timeout RETRY http_type
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/roadoi-package.r:20:1: style: Lines should not be more than 80 characters.

​#' @importFrom shiny dialogViewer runGadget renderTable reactive observeEvent tableOutput actionButton textAreaInput tags stopApp
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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