diff --git a/.Rbuildignore b/.Rbuildignore index 0028191..b201ac0 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -10,4 +10,3 @@ cran-comments.md ^README\.Rmd$ ^README-.*\.png$ ^revdep$ -oadoi_addin.gif diff --git a/README.Rmd b/README.Rmd index 500da17..bc6ea6a 100644 --- a/README.Rmd +++ b/README.Rmd @@ -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? diff --git a/README.md b/README.md index dcd5021..e2d0bf3 100644 --- a/README.md +++ b/README.md @@ -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 = "name@example.com") -#> # A tibble: 2 × 18 -#> `_best_open_url` doi -#> -#> 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 , evidence , +#> # A tibble: 2 × 20 +#> `_best_open_url` +#> +#> 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` , +#> # `_green_base_collections` , `_open_base_ids` , +#> # `_open_urls` , doi , doi_resolver , evidence , #> # found_green , found_hybrid , free_fulltext_url , -#> # green_base_collections , is_boai_license , -#> # is_free_to_read , is_subscription_journal , license , -#> # oa_color , open_base_ids , open_urls , -#> # reported_noncompliant_copies , url , year +#> # is_boai_license , is_free_to_read , +#> # is_subscription_journal , license , oa_color , +#> # oa_color_long , reported_noncompliant_copies , url , +#> # year ``` 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 instead. @@ -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? @@ -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 = "name@example.com") -#> # A tibble: 2 × 18 -#> `_best_open_url` -#> -#> 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 , doi_resolver , -#> # evidence , found_green , found_hybrid , -#> # free_fulltext_url , green_base_collections , -#> # is_boai_license , is_free_to_read , -#> # is_subscription_journal , license , oa_color , -#> # open_base_ids , open_urls , +#> # A tibble: 2 × 20 +#> `_best_open_url` `_closed_base_ids` +#> +#> 1 http://doi.org/10.1186/s12864-016-2566-9 +#> 2 http://hdl.handle.net/11858/00-001M-0000-0024-2A9E-8 +#> # ... with 18 more variables: `_green_base_collections` , +#> # `_open_base_ids` , `_open_urls` , doi , +#> # doi_resolver , evidence , found_green , +#> # found_hybrid , free_fulltext_url , is_boai_license , +#> # is_free_to_read , is_subscription_journal , license , +#> # oa_color , oa_color_long , #> # reported_noncompliant_copies , url , year ``` @@ -153,17 +155,17 @@ roadoi::oadoi_fetch(dois = c("10.1186/s12864-016-2566-9", email = "name@example.com", .progress = "text") #> | | | 0% | |================================ | 50% | |=================================================================| 100% -#> # A tibble: 2 × 18 -#> `_best_open_url` -#> -#> 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 , doi_resolver , -#> # evidence , found_green , found_hybrid , -#> # free_fulltext_url , green_base_collections , -#> # is_boai_license , is_free_to_read , -#> # is_subscription_journal , license , oa_color , -#> # open_base_ids , open_urls , +#> # A tibble: 2 × 20 +#> `_best_open_url` `_closed_base_ids` +#> +#> 1 http://doi.org/10.1186/s12864-016-2566-9 +#> 2 http://hdl.handle.net/11858/00-001M-0000-0024-2A9E-8 +#> # ... with 18 more variables: `_green_base_collections` , +#> # `_open_base_ids` , `_open_urls` , doi , +#> # doi_resolver , evidence , found_green , +#> # found_hybrid , free_fulltext_url , is_boai_license , +#> # is_free_to_read , is_subscription_journal , license , +#> # oa_color , oa_color_long , #> # reported_noncompliant_copies , url , year ``` @@ -184,29 +186,29 @@ random_dois <- rcrossref::cr_r(sample = 100) %>% rcrossref::cr_works() %>% .$data random_dois -#> # A tibble: 100 × 34 -#> alternative.id -#> -#> 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 , +#> # A tibble: 100 × 35 +#> alternative.id +#> +#> 1 +#> 2 +#> 3 768 +#> 4 9360 +#> 5 +#> 6 1177 +#> 7 +#> 8 S1052305715004553 +#> 9 +#> 10 +#> # ... with 90 more rows, and 34 more variables: container.title , #> # created , deposited , DOI , funder , -#> # indexed , ISBN , ISSN , issued , link , -#> # member , page , prefix , publisher , +#> # indexed , ISBN , ISSN , issue , issued , +#> # link , member , page , prefix , publisher , #> # reference.count , score , source , subject , -#> # title , type , URL , assertion , author , -#> # `clinical-trial-number` , issue , volume , -#> # license_date , license_URL , license_delay.in.days , -#> # license_content.version , update.policy , subtitle , -#> # abstract +#> # title , type , URL , volume , assertion , +#> # author , `clinical-trial-number` , license_date , +#> # license_URL , license_delay.in.days , +#> # license_content.version , update.policy , archive , +#> # subtitle , abstract ``` Let's see when these random publications were published @@ -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 #> -#> 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 @@ -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 #> -#> 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 @@ -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` -#> -#> 1 -#> 2 -#> 3 http://www.biodiversitylibrary.org/item/67873 -#> 4 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2697852/pdf -#> 5 -#> 6 -#> 7 -#> 8 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1905606 -#> 9 -#> 10 http://repository.tue.nl/665171 -#> # ... with 90 more rows, and 50 more variables: doi , -#> # doi_resolver , evidence , found_green , -#> # found_hybrid , free_fulltext_url , -#> # green_base_collections , is_boai_license , -#> # is_free_to_read , is_subscription_journal , license , -#> # oa_color , open_base_ids , open_urls , -#> # reported_noncompliant_copies , url , year , -#> # alternative.id , container.title , created , -#> # deposited , funder , indexed , ISBN , ISSN , -#> # issued , link , member , page , prefix , -#> # publisher , reference.count , score , source , -#> # subject , title , type , URL , assertion , -#> # author , `clinical-trial-number` , issue , -#> # volume , license_date , license_URL , -#> # license_delay.in.days , license_content.version , -#> # update.policy , subtitle , abstract +#> # A tibble: 100 × 54 +#> `_best_open_url` `_closed_base_ids` +#> +#> 1 +#> 2 +#> 3 +#> 4 +#> 5 http://doi.org/10.1371/journal.pone.0078558 +#> 6 +#> 7 +#> 8 +#> 9 +#> 10 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766215 +#> # ... with 90 more rows, and 52 more variables: +#> # `_green_base_collections` , `_open_base_ids` , +#> # `_open_urls` , doi , doi_resolver , evidence , +#> # found_green , found_hybrid , free_fulltext_url , +#> # is_boai_license , is_free_to_read , +#> # is_subscription_journal , license , oa_color , +#> # oa_color_long , reported_noncompliant_copies , url , +#> # year , alternative.id , container.title , +#> # created , deposited , funder , indexed , +#> # ISBN , ISSN , issue , issued , link , +#> # member , page , prefix , publisher , +#> # reference.count , score , source , subject , +#> # title , type , URL , volume , assertion , +#> # author , `clinical-trial-number` , license_date , +#> # license_URL , license_delay.in.days , +#> # license_content.version , update.policy , archive , +#> # subtitle , abstract ``` #### Reporting @@ -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| @@ -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? @@ -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 diff --git a/oadoi_addin.gif b/inst/img/oadoi_addin.gif similarity index 100% rename from oadoi_addin.gif rename to inst/img/oadoi_addin.gif