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re-submission CRAN
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@njahn82
njahn82 committed Jul 17, 2017
2 parents d80828d + c61bc36 commit 4e705f5
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1 change: 1 addition & 0 deletions README.Rmd
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Expand Up @@ -17,6 +17,7 @@ knitr::opts_chunk$set(
[![rstudio mirror downloads](http://cranlogs.r-pkg.org/badges/roadoi)](https://github.com/metacran/cranlogs.app)
[![review](https://ropensci.org/badges/115_status.svg)](https://github.com/ropensci/onboarding/issues/115)


roadoi interacts with the [oaDOI API](http://oadoi.org/), a simple interface which links DOIs
and open access versions of scholarly works. oaDOI powers [unpaywall](http://unpaywall.org/).

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146 changes: 76 additions & 70 deletions README.md
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Expand Up @@ -10,6 +10,7 @@
[![rstudio mirror downloads](http://cranlogs.r-pkg.org/badges/roadoi)](https://github.com/metacran/cranlogs.app)
[![review](https://ropensci.org/badges/115_status.svg)](https://github.com/ropensci/onboarding/issues/115)


roadoi interacts with the [oaDOI API](http://oadoi.org/), a simple interface which links DOIs
and open access versions of scholarly works. oaDOI powers [unpaywall](http://unpaywall.org/).

Expand Down Expand Up @@ -219,28 +220,28 @@ random_dois <- rcrossref::cr_r(sample = 100) %>%
.$data
random_dois
#> # A tibble: 100 x 35
#> alternative.id
#> <chr>
#> 1
#> 2 5088422
#> 3
#> 4 10.1111/j.1478-1913.1971.tb03042.x
#> 5
#> 6 10.1021/j100789a044
#> 7 10.1080/00107530.1989.10746306
#> 8
#> 9 2758
#> 10 10.1201/9781420063561.ch8,10.1201/9781420063561
#> alternative.id
#> <chr>
#> 1 10.1080/02533950903561353
#> 2 10.1177/000348940601700416
#> 3
#> 4
#> 5
#> 6 1532-429X-14-S1-P37
#> 7 10.1176/ajp.153.3.355
#> 8
#> 9 10.4014/jmb.1511.11068
#> 10 10.1142/S0219030310000637
#> # ... 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>, issued <chr>, link <list>,
#> # member <chr>, page <chr>, prefix <chr>, publisher <chr>,
#> # 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>, issue <chr>, volume <chr>,
#> # license_date <chr>, license_URL <chr>, license_delay.in.days <chr>,
#> # license_content.version <chr>, update.policy <chr>, subtitle <chr>,
#> # abstract <chr>, archive <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>, subtitle <chr>, update.policy <chr>,
#> # archive <chr>, abstract <chr>
```

Let's see when these random publications were published
Expand All @@ -254,20 +255,20 @@ random_dois %>%
group_by(issued) %>%
summarize(pubs = n()) %>%
arrange(desc(pubs))
#> # A tibble: 52 x 2
#> # A tibble: 40 x 2
#> issued pubs
#> <dbl> <int>
#> 1 NA 7
#> 2 2012 6
#> 3 2001 5
#> 4 1992 4
#> 5 2016 4
#> 6 1993 3
#> 7 2005 3
#> 8 2006 3
#> 9 2009 3
#> 10 2010 3
#> # ... with 42 more rows
#> 1 2010 7
#> 2 2016 7
#> 3 NA 7
#> 4 2002 5
#> 5 2011 5
#> 6 2012 5
#> 7 2013 5
#> 8 2015 5
#> 9 1985 3
#> 10 1988 3
#> # ... with 30 more rows
```

and of what type they are
Expand All @@ -278,17 +279,18 @@ random_dois %>%
group_by(type) %>%
summarize(pubs = n()) %>%
arrange(desc(pubs))
#> # A tibble: 8 x 2
#> # A tibble: 9 x 2
#> type pubs
#> <chr> <int>
#> 1 journal-article 70
#> 2 book-chapter 17
#> 3 component 4
#> 4 proceedings-article 4
#> 5 book 2
#> 6 dataset 1
#> 7 journal-issue 1
#> 8 reference-entry 1
#> 1 journal-article 79
#> 2 book-chapter 9
#> 3 proceedings-article 5
#> 4 component 2
#> 5 dataset 1
#> 6 journal-issue 1
#> 7 monograph 1
#> 8 proceedings 1
#> 9 report 1
```

#### Calling oaDOI.org
Expand All @@ -307,18 +309,18 @@ and merge the resulting information about open access full-text links with our C
my_df <- dplyr::left_join(oa_df, random_dois, by = c("doi" = "DOI"))
my_df
#> # A tibble: 100 x 56
#> `_best_open_url` `_closed_base_ids`
#> <chr> <list>
#> 1 <NA> <list [0]>
#> 2 <NA> <list [0]>
#> 3 <NA> <list [0]>
#> 4 <NA> <list [0]>
#> 5 <NA> <list [0]>
#> 6 <NA> <list [0]>
#> 7 <NA> <list [0]>
#> 8 http://doi.org/10.1371/journal.pone.0125302.g001 <list [0]>
#> 9 <NA> <list [0]>
#> 10 <NA> <list [0]>
#> `_best_open_url` `_closed_base_ids`
#> <chr> <list>
#> 1 <NA> <list [0]>
#> 2 <NA> <list [0]>
#> 3 <NA> <list [0]>
#> 4 <NA> <list [0]>
#> 5 <NA> <list [0]>
#> 6 http://doi.org/10.1186/1532-429x-14-s1-p37 <list [0]>
#> 7 <NA> <list [0]>
#> 8 <NA> <list [0]>
#> 9 <NA> <list [0]>
#> 10 <NA> <list [0]>
#> # ... with 90 more rows, and 54 more variables: `_closed_urls` <list>,
#> # `_green_base_collections` <list>, `_open_base_ids` <list>,
#> # `_open_urls` <list>, doi <chr>, doi_resolver <chr>, evidence <chr>,
Expand All @@ -328,14 +330,14 @@ my_df
#> # oa_color_long <chr>, reported_noncompliant_copies <list>, url <chr>,
#> # version <lgl>, year <int>, alternative.id <chr>,
#> # container.title <chr>, created <chr>, deposited <chr>, funder <list>,
#> # indexed <chr>, ISBN <chr>, ISSN <chr>, issued <chr>, link <list>,
#> # member <chr>, page <chr>, prefix <chr>, publisher <chr>,
#> # 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>, issue <chr>, volume <chr>,
#> # license_date <chr>, license_URL <chr>, license_delay.in.days <chr>,
#> # license_content.version <chr>, update.policy <chr>, subtitle <chr>,
#> # abstract <chr>, archive <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>, subtitle <chr>, update.policy <chr>,
#> # archive <chr>, abstract <chr>
```

#### Reporting
Expand All @@ -358,10 +360,12 @@ my_df %>%

|evidence | Articles| Proportion|
|:--------------------------------------|--------:|----------:|
|closed | 93| 0.93|
|oa journal (via publisher name) | 3| 0.03|
|oa repository (via BASE) | 3| 0.03|
|oa journal (via journal title in doaj) | 1| 0.01|
|closed | 86| 0.86|
|oa journal (via journal title in doaj) | 5| 0.05|
|oa repository (via BASE) | 4| 0.04|
|oa journal (via publisher name) | 2| 0.02|
|oa repository (via pmcid lookup) | 2| 0.02|
|hybrid (via free pdf) | 1| 0.01|

How many of them are provided as green or gold open access?

Expand All @@ -379,9 +383,10 @@ my_df %>%

|oa_color | Articles| Proportion|
|:--------|--------:|----------:|
|NA | 93| 0.93|
|gold | 4| 0.04|
|green | 3| 0.03|
|NA | 86| 0.86|
|gold | 7| 0.07|
|green | 6| 0.06|
|blue | 1| 0.01|

Let's take a closer look and assess how green and gold is distributed over publication types?

Expand All @@ -397,10 +402,11 @@ my_df %>%

|oa_color |type | n|
|:--------|:---------------|--:|
|gold |component | 3|
|green |journal-article | 2|
|gold |journal-article | 1|
|green |book-chapter | 1|
|gold |journal-article | 5|
|green |journal-article | 5|
|gold |component | 2|
|blue |journal-article | 1|
|green |monograph | 1|


## Meta
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