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version to be submitted to CRAN
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njahn82 committed May 17, 2017
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Package: roadoi
Type: Package
Title: Find Free Versions of Scholarly Publications via the oaDOI Service
Version: 0.1.9500
Version: 0.2
Authors@R: c(
person("Najko", "Jahn", role = c("aut", "cre"), email = "[email protected]"))
Description: This web client interfaces oaDOI <https://oadoi.org>, a service finding
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15 changes: 15 additions & 0 deletions NEWS
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## roadoi 0.2

### NEW FEATRUES

- Shiny Addin for finding free full-texts in RStudio
- full support of oadoi API version 1.3.0

### Major changes

- requests must now include email address to reflect new oadoi API version

### Minor changes

- improved output documentation

## roadoi 0.1

### NEW FEATRUES
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2 changes: 1 addition & 1 deletion README.Rmd
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Expand Up @@ -35,7 +35,7 @@ There are no API restrictions. However, providing an email address is required a

### RStudio Addin

The dev version comes with a RStudio Addin.
This package also has a RStudio Addin for easily finding free full-texts in RStudio.

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

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125 changes: 61 additions & 64 deletions README.md
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Expand Up @@ -42,7 +42,7 @@ There are no API restrictions. However, providing an email address is required a

### RStudio Addin

The dev version comes with a RStudio Addin.
This package also has a RStudio Addin for easily finding free full-texts in RStudio.

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

Expand Down Expand Up @@ -187,18 +187,18 @@ random_dois <- rcrossref::cr_r(sample = 100) %>%
.$data
random_dois
#> # A tibble: 100 × 35
#> alternative.id
#> <chr>
#> 1
#> 2
#> 3 768
#> 4 9360
#> 5
#> 6 1177
#> 7
#> 8 S1052305715004553
#> 9
#> 10
#> alternative.id
#> <chr>
#> 1
#> 2
#> 3
#> 4 902065,902065
#> 5 10.1111/j.1467-6494.1958.tb01595.x
#> 6 88
#> 7 S0165-2478(97)88690-7
#> 8
#> 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>, issue <chr>, issued <chr>,
Expand All @@ -207,8 +207,8 @@ random_dois
#> # 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>
#> # license_content.version <chr>, abstract <chr>, archive <chr>,
#> # subtitle <chr>, update.policy <chr>
```

Let's see when these random publications were published
Expand All @@ -222,20 +222,20 @@ random_dois %>%
group_by(issued) %>%
summarize(pubs = n()) %>%
arrange(desc(pubs))
#> # A tibble: 45 × 2
#> # A tibble: 47 × 2
#> issued pubs
#> <dbl> <int>
#> 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
#> 1 2011 8
#> 2 NA 7
#> 3 2013 5
#> 4 1993 4
#> 5 1998 4
#> 6 1999 4
#> 7 2005 4
#> 8 2006 4
#> 9 2008 4
#> 10 2002 3
#> # ... with 37 more rows
```

and of what type they are
Expand All @@ -246,16 +246,14 @@ random_dois %>%
group_by(type) %>%
summarize(pubs = n()) %>%
arrange(desc(pubs))
#> # A tibble: 7 × 2
#> # A tibble: 5 × 2
#> type pubs
#> <chr> <int>
#> 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
#> 1 journal-article 83
#> 2 book-chapter 5
#> 3 component 5
#> 4 proceedings-article 4
#> 5 dataset 3
```

#### Calling oaDOI.org
Expand All @@ -274,19 +272,19 @@ 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 × 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:
#> `_best_open_url`
#> <chr>
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 http://doi.org/10.1155/2014/902065
#> 5 <NA>
#> 6 http://psasir.upm.edu.my/24536/1/Quantifying%20the%20effects%20of%20iodine%
#> 7 <NA>
#> 8 <NA>
#> 9 <NA>
#> 10 <NA>
#> # ... with 90 more rows, and 53 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>,
Expand All @@ -301,8 +299,8 @@ my_df
#> # 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>
#> # license_content.version <chr>, abstract <chr>, archive <chr>,
#> # subtitle <chr>, update.policy <chr>
```

#### Reporting
Expand All @@ -325,12 +323,12 @@ my_df %>%

|evidence | Articles| Proportion|
|:-----------------------------------------------------|--------:|----------:|
|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|
|closed | 83| 0.83|
|oa repository (via BASE title and first author match) | 6| 0.06|
|oa repository (via pmcid lookup) | 5| 0.05|
|oa journal (via publisher name) | 4| 0.04|
|oa journal (via journal title in doaj) | 1| 0.01|
|oa repository (via BASE doi match) | 1| 0.01|

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

Expand All @@ -348,10 +346,9 @@ my_df %>%

|oa_color | Articles| Proportion|
|:--------|--------:|----------:|
|NA | 86| 0.86|
|gold | 8| 0.08|
|green | 5| 0.05|
|blue | 1| 0.01|
|NA | 83| 0.83|
|green | 12| 0.12|
|gold | 5| 0.05|

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

Expand All @@ -367,10 +364,10 @@ my_df %>%

|oa_color |type | n|
|:--------|:---------------|--:|
|gold |journal-article | 6|
|green |journal-article | 5|
|gold |component | 2|
|blue |journal-article | 1|
|green |journal-article | 10|
|gold |component | 4|
|green |book-chapter | 2|
|gold |journal-article | 1|


## Meta
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24 changes: 18 additions & 6 deletions cran-comments.md
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# roadoi initial submission v 0.1

## Test environments

* local OS X install, R 3.3.2
* ubuntu 12.04 (on travis-ci), R 3.3.2
* win-builder (devel and release) and appveyor CI
* local OS X install, R 3.4.0
* ubuntu 12.04 (on travis-ci), R 3.4.0
* win-builder (release, devel and oldrelease) and appveyor CI

## R CMD check results

Expand All @@ -24,9 +23,22 @@ and found no problems related to this submission.

Dear CRAN maintainers,

This is a re-submission because the package did not pass the CRAN teams' auto-check service: There was a web API timeout while building the vignettes. This version now waits up to 5 seconds using the httr::timeout function.
This submission implements the most recent API version, and includes new features including a RStudio Addin.

This is my initial submission of roadoi for CRAN.
There is currently one warning on CRAN Package Check Results for roadoi (r-release-osx-x86_64) saying

"Result: WARN
Error in re-building vignettes:
...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 64-65 (intro.Rmd)
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Timeout was reached
Execution halted
"

At least building the vignette should work now.

Thanks!

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