From e18d1c7a740cb96704f14afc5d703e1ae0e84329 Mon Sep 17 00:00:00 2001 From: Najko Jahn Date: Wed, 17 May 2017 12:55:02 +0200 Subject: [PATCH] version to be submitted to CRAN --- DESCRIPTION | 2 +- NEWS | 15 ++++++ README.Rmd | 2 +- README.md | 125 +++++++++++++++++++++++------------------------ cran-comments.md | 24 ++++++--- 5 files changed, 96 insertions(+), 72 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index cb9c590..399e3d5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ 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 = "najko.jahn@gmail.com")) Description: This web client interfaces oaDOI , a service finding diff --git a/NEWS b/NEWS index 1e0e641..f662481 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,18 @@ +## 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 diff --git a/README.Rmd b/README.Rmd index bc6ea6a..3ac8fe9 100644 --- a/README.Rmd +++ b/README.Rmd @@ -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) diff --git a/README.md b/README.md index e2d0bf3..fe7aaa6 100644 --- a/README.md +++ b/README.md @@ -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) @@ -187,18 +187,18 @@ random_dois <- rcrossref::cr_r(sample = 100) %>% .$data random_dois #> # A tibble: 100 × 35 -#> alternative.id -#> -#> 1 -#> 2 -#> 3 768 -#> 4 9360 -#> 5 -#> 6 1177 -#> 7 -#> 8 S1052305715004553 -#> 9 -#> 10 +#> alternative.id +#> +#> 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 , #> # created , deposited , DOI , funder , #> # indexed , ISBN , ISSN , issue , issued , @@ -207,8 +207,8 @@ random_dois #> # 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 +#> # license_content.version , abstract , archive , +#> # subtitle , update.policy ``` Let's see when these random publications were published @@ -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 #> -#> 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 @@ -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 #> -#> 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 @@ -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` -#> -#> 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: +#> `_best_open_url` +#> +#> 1 +#> 2 +#> 3 +#> 4 http://doi.org/10.1155/2014/902065 +#> 5 +#> 6 http://psasir.upm.edu.my/24536/1/Quantifying%20the%20effects%20of%20iodine% +#> 7 +#> 8 +#> 9 +#> 10 +#> # ... with 90 more rows, and 53 more variables: `_closed_base_ids` , #> # `_green_base_collections` , `_open_base_ids` , #> # `_open_urls` , doi , doi_resolver , evidence , #> # found_green , found_hybrid , free_fulltext_url , @@ -301,8 +299,8 @@ my_df #> # 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 +#> # license_content.version , abstract , archive , +#> # subtitle , update.policy ``` #### Reporting @@ -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? @@ -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? @@ -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 diff --git a/cran-comments.md b/cran-comments.md index 2f8aed8..02e484b 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,10 +1,9 @@ -# 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 @@ -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!