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move gif to pass cran checks
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@njahn82
njahn82 committed May 16, 2017
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Expand Up @@ -10,4 +10,3 @@ cran-comments.md
^README\.Rmd$
^README-.*\.png$
^revdep$
oadoi_addin.gif
2 changes: 1 addition & 1 deletion README.Rmd
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Expand Up @@ -37,7 +37,7 @@ There are no API restrictions. However, providing an email address is required a

The dev version comes with a RStudio Addin.

![](oadoi_addin.gif)
![](inst/img/oadoi_addin.gif)

## How do I get it?

Expand Down
241 changes: 120 additions & 121 deletions README.md
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Expand Up @@ -23,17 +23,19 @@ information and full-text links from oaDOI.
```r
roadoi::oadoi_fetch(dois = c("10.1038/ng.3260", "10.1093/nar/gkr1047"),
email = "[email protected]")
#> # A tibble: 2 × 18
#> `_best_open_url` doi
#> <chr> <chr>
#> 1 http://nrs.harvard.edu/urn-3:HUL.InstRepos:25290367 10.1038/ng.3260
#> 2 http://doi.org/10.1093/nar/gkr1047 10.1093/nar/gkr1047
#> # ... with 16 more variables: doi_resolver <chr>, evidence <chr>,
#> # A tibble: 2 × 20
#> `_best_open_url`
#> <chr>
#> 1 https://dash.harvard.edu/bitstream/handle/1/25290367/mallet%202015%20polyte
#> 2 http://doi.org/10.1093/nar/gkr1047
#> # ... with 19 more variables: `_closed_base_ids` <list>,
#> # `_green_base_collections` <list>, `_open_base_ids` <list>,
#> # `_open_urls` <list>, doi <chr>, doi_resolver <chr>, evidence <chr>,
#> # found_green <lgl>, found_hybrid <lgl>, free_fulltext_url <chr>,
#> # green_base_collections <list>, is_boai_license <lgl>,
#> # is_free_to_read <lgl>, is_subscription_journal <lgl>, license <chr>,
#> # oa_color <chr>, open_base_ids <list>, open_urls <list>,
#> # reported_noncompliant_copies <list>, url <chr>, year <int>
#> # is_boai_license <lgl>, is_free_to_read <lgl>,
#> # is_subscription_journal <lgl>, license <chr>, oa_color <chr>,
#> # oa_color_long <chr>, reported_noncompliant_copies <list>, url <chr>,
#> # year <int>
```

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.
Expand All @@ -42,7 +44,7 @@ There are no API restrictions. However, providing an email address is required a

The dev version comes with a RStudio Addin.

![](oadoi_addin.gif)
![](inst/img/oadoi_addin.gif)

## How do I get it?

Expand Down Expand Up @@ -89,17 +91,17 @@ library(roadoi)
roadoi::oadoi_fetch(dois = c("10.1186/s12864-016-2566-9",
"10.1016/j.cognition.2014.07.007"),
email = "[email protected]")
#> # A tibble: 2 × 18
#> `_best_open_url`
#> <chr>
#> 1 http://doi.org/10.1186/s12864-016-2566-9
#> 2 http://hdl.handle.net/11858/00-001M-0000-0024-2A9E-8
#> # ... with 17 more variables: doi <chr>, doi_resolver <chr>,
#> # evidence <chr>, found_green <lgl>, found_hybrid <lgl>,
#> # free_fulltext_url <chr>, green_base_collections <list>,
#> # is_boai_license <lgl>, is_free_to_read <lgl>,
#> # is_subscription_journal <lgl>, license <chr>, oa_color <chr>,
#> # open_base_ids <list>, open_urls <list>,
#> # A tibble: 2 × 20
#> `_best_open_url` `_closed_base_ids`
#> <chr> <list>
#> 1 http://doi.org/10.1186/s12864-016-2566-9 <list [0]>
#> 2 http://hdl.handle.net/11858/00-001M-0000-0024-2A9E-8 <chr [1]>
#> # ... with 18 more variables: `_green_base_collections` <list>,
#> # `_open_base_ids` <list>, `_open_urls` <list>, doi <chr>,
#> # doi_resolver <chr>, evidence <chr>, found_green <lgl>,
#> # found_hybrid <lgl>, free_fulltext_url <chr>, is_boai_license <lgl>,
#> # is_free_to_read <lgl>, is_subscription_journal <lgl>, license <chr>,
#> # oa_color <chr>, oa_color_long <chr>,
#> # reported_noncompliant_copies <list>, url <chr>, year <int>
```

Expand Down Expand Up @@ -153,17 +155,17 @@ roadoi::oadoi_fetch(dois = c("10.1186/s12864-016-2566-9",
email = "[email protected]",
.progress = "text")
#> | | | 0% | |================================ | 50% | |=================================================================| 100%
#> # A tibble: 2 × 18
#> `_best_open_url`
#> <chr>
#> 1 http://doi.org/10.1186/s12864-016-2566-9
#> 2 http://hdl.handle.net/11858/00-001M-0000-0024-2A9E-8
#> # ... with 17 more variables: doi <chr>, doi_resolver <chr>,
#> # evidence <chr>, found_green <lgl>, found_hybrid <lgl>,
#> # free_fulltext_url <chr>, green_base_collections <list>,
#> # is_boai_license <lgl>, is_free_to_read <lgl>,
#> # is_subscription_journal <lgl>, license <chr>, oa_color <chr>,
#> # open_base_ids <list>, open_urls <list>,
#> # A tibble: 2 × 20
#> `_best_open_url` `_closed_base_ids`
#> <chr> <list>
#> 1 http://doi.org/10.1186/s12864-016-2566-9 <list [0]>
#> 2 http://hdl.handle.net/11858/00-001M-0000-0024-2A9E-8 <chr [1]>
#> # ... with 18 more variables: `_green_base_collections` <list>,
#> # `_open_base_ids` <list>, `_open_urls` <list>, doi <chr>,
#> # doi_resolver <chr>, evidence <chr>, found_green <lgl>,
#> # found_hybrid <lgl>, free_fulltext_url <chr>, is_boai_license <lgl>,
#> # is_free_to_read <lgl>, is_subscription_journal <lgl>, license <chr>,
#> # oa_color <chr>, oa_color_long <chr>,
#> # reported_noncompliant_copies <list>, url <chr>, year <int>
```

Expand All @@ -184,29 +186,29 @@ random_dois <- rcrossref::cr_r(sample = 100) %>%
rcrossref::cr_works() %>%
.$data
random_dois
#> # A tibble: 100 × 34
#> alternative.id
#> <chr>
#> 1 10.1201/9781420006452.ch23,10.1201/9781420006452
#> 2 10.1177/0890334412459036
#> 3
#> 4 S0010782407002600
#> 5
#> 6 10.1137/1020042
#> 7 10.4135/9781483387833
#> 8 10.1046/j.1365-2249.2000.01160.x
#> 9 0016706169900421
#> 10
#> # ... with 90 more rows, and 33 more variables: container.title <chr>,
#> # A tibble: 100 × 35
#> alternative.id
#> <chr>
#> 1
#> 2
#> 3 768
#> 4 9360
#> 5
#> 6 1177
#> 7
#> 8 S1052305715004553
#> 9
#> 10
#> # ... 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>
#> # 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>, archive <chr>,
#> # subtitle <chr>, abstract <chr>
```

Let's see when these random publications were published
Expand All @@ -220,20 +222,20 @@ random_dois %>%
group_by(issued) %>%
summarize(pubs = n()) %>%
arrange(desc(pubs))
#> # A tibble: 46 × 2
#> # A tibble: 45 × 2
#> issued pubs
#> <dbl> <int>
#> 1 NA 8
#> 2 2012 7
#> 3 2016 7
#> 4 2015 6
#> 5 2011 5
#> 6 1991 4
#> 7 2004 4
#> 8 2005 4
#> 9 1971 3
#> 10 2006 3
#> # ... with 36 more rows
#> 1 NA 10
#> 2 2016 9
#> 3 2015 8
#> 4 2006 5
#> 5 2010 5
#> 6 2011 5
#> 7 2013 4
#> 8 2014 4
#> 9 1979 3
#> 10 2008 3
#> # ... with 35 more rows
```

and of what type they are
Expand All @@ -244,15 +246,16 @@ random_dois %>%
group_by(type) %>%
summarize(pubs = n()) %>%
arrange(desc(pubs))
#> # A tibble: 6 × 2
#> # A tibble: 7 × 2
#> type pubs
#> <chr> <int>
#> 1 journal-article 74
#> 2 book-chapter 15
#> 3 proceedings-article 4
#> 4 component 3
#> 5 monograph 3
#> 6 reference-entry 1
#> 1 journal-article 75
#> 2 book-chapter 8
#> 3 proceedings-article 8
#> 4 dataset 5
#> 5 component 2
#> 6 book 1
#> 7 journal-issue 1
```

#### Calling oaDOI.org
Expand All @@ -270,35 +273,36 @@ and merge the resulting information about open access full-text links with our C
```r
my_df <- dplyr::left_join(oa_df, random_dois, by = c("doi" = "DOI"))
my_df
#> # A tibble: 100 × 51
#> `_best_open_url`
#> <chr>
#> 1 <NA>
#> 2 <NA>
#> 3 http://www.biodiversitylibrary.org/item/67873
#> 4 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2697852/pdf
#> 5 <NA>
#> 6 <NA>
#> 7 <NA>
#> 8 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1905606
#> 9 <NA>
#> 10 http://repository.tue.nl/665171
#> # ... with 90 more rows, and 50 more variables: doi <chr>,
#> # doi_resolver <chr>, evidence <chr>, found_green <lgl>,
#> # found_hybrid <lgl>, free_fulltext_url <chr>,
#> # green_base_collections <list>, is_boai_license <lgl>,
#> # is_free_to_read <lgl>, is_subscription_journal <lgl>, license <chr>,
#> # oa_color <chr>, open_base_ids <list>, open_urls <list>,
#> # reported_noncompliant_copies <list>, url <chr>, 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>, 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>
#> # A tibble: 100 × 54
#> `_best_open_url` `_closed_base_ids`
#> <chr> <list>
#> 1 <NA> <chr [1]>
#> 2 <NA> <list [0]>
#> 3 <NA> <list [0]>
#> 4 <NA> <list [0]>
#> 5 http://doi.org/10.1371/journal.pone.0078558 <list [0]>
#> 6 <NA> <list [0]>
#> 7 <NA> <list [0]>
#> 8 <NA> <list [0]>
#> 9 <NA> <list [0]>
#> 10 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766215 <list [0]>
#> # ... with 90 more rows, and 52 more variables:
#> # `_green_base_collections` <list>, `_open_base_ids` <list>,
#> # `_open_urls` <list>, doi <chr>, doi_resolver <chr>, evidence <chr>,
#> # found_green <lgl>, found_hybrid <lgl>, free_fulltext_url <chr>,
#> # is_boai_license <lgl>, is_free_to_read <lgl>,
#> # is_subscription_journal <lgl>, license <chr>, oa_color <chr>,
#> # oa_color_long <chr>, reported_noncompliant_copies <list>, url <chr>,
#> # year <int>, alternative.id <chr>, container.title <chr>,
#> # created <chr>, deposited <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>, 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>, archive <chr>,
#> # subtitle <chr>, abstract <chr>
```

#### Reporting
Expand All @@ -321,11 +325,10 @@ my_df %>%

|evidence | Articles| Proportion|
|:-----------------------------------------------------|--------:|----------:|
|closed | 80| 0.80|
|oa repository (via BASE title and first author match) | 10| 0.10|
|oa journal (via publisher name) | 3| 0.03|
|oa journal (via journal title in doaj) | 2| 0.02|
|oa repository (via BASE doi match) | 2| 0.02|
|closed | 86| 0.86|
|oa journal (via journal title in doaj) | 6| 0.06|
|oa repository (via BASE title and first author match) | 3| 0.03|
|oa journal (via publisher name) | 2| 0.02|
|oa repository (via pmcid lookup) | 2| 0.02|
|oa repository (via BASE title match) | 1| 0.01|

Expand All @@ -345,10 +348,10 @@ my_df %>%

|oa_color | Articles| Proportion|
|:--------|--------:|----------:|
|NA | 80| 0.80|
|green | 13| 0.13|
|gold | 5| 0.05|
|blue | 2| 0.02|
|NA | 86| 0.86|
|gold | 8| 0.08|
|green | 5| 0.05|
|blue | 1| 0.01|

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

Expand All @@ -362,16 +365,12 @@ my_df %>%



|oa_color |type | n|
|:--------|:-------------------|--:|
|green |journal-article | 10|
|gold |component | 3|
|gold |journal-article | 2|
|blue |book-chapter | 1|
|blue |journal-article | 1|
|green |book-chapter | 1|
|green |monograph | 1|
|green |proceedings-article | 1|
|oa_color |type | n|
|:--------|:---------------|--:|
|gold |journal-article | 6|
|green |journal-article | 5|
|gold |component | 2|
|blue |journal-article | 1|


## Meta
Expand Down
0 oadoi_addin.gif → inst/img/oadoi_addin.gif
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