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refresh vignettes; fix bad urls, rbuildignore readme.md, etc
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2 changes: 1 addition & 1 deletion R/plossubject.R
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Expand Up @@ -4,7 +4,7 @@
#' @template plos
#' @return Subject content, in addition to any other fields requested in a
#' data.frame.
#' @details See \url{http://www.plosone.org/taxonomy} for subject areas.
#' @details See \url{https://journals.plos.org/plosone/browse} for subject areas.
#' @examples \dontrun{
#' plossubject('marine ecology', limit = 5)
#' plossubject(q='marine ecology', fl = c('id','journal','title'), limit = 20)
Expand Down
10 changes: 4 additions & 6 deletions README.Rmd
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Expand Up @@ -12,11 +12,11 @@ knitr::opts_chunk$set(
)
```

[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![cran checks](https://cranchecks.info/badges/worst/rplos)](https://cranchecks.info/pkgs/rplos)
[![R-check](https://github.com/ropensci/rplos/workflows/R-check/badge.svg)](https://github.com/ropensci/rplos/actions?query=workflow%3AR-check)
[![codecov.io](https://codecov.io/github/ropensci/rplos/coverage.svg?branch=master)](https://codecov.io/github/ropensci/rplos?branch=master)
[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/rplos)](https://github.com/metacran/cranlogs.app)
[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/rplos)](https://github.com/r-hub/cranlogs.app)
[![cran version](https://www.r-pkg.org/badges/version/rplos)](https://cran.r-project.org/package=rplos)

## Install
Expand Down Expand Up @@ -45,13 +45,13 @@ library("rplos")

You used to need a key to use `rplos` - you no longer do as of 2015-01-13 (or `v0.4.5.999`).

rplos tutorial: <http://ropensci.org/tutorials/rplos_tutorial.html>
rplos vignetttes: <https://docs.ropensci.org/rplos/>

PLOS API documentation: <http://api.plos.org/>

PLOS Solr schema is at <https://gist.github.com/openAccess/9e76aa7fa6135be419968b1372c86957> but is 1.5 years old so may not be up to date.

Crossref API documentation [here](https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md), and [here](http://help.crossref.org/#home). Note that we are working on a new package [rcrossref](https://github.com/ropensci/rcrossref) ([on CRAN](https://cran.r-project.org/package=rcrossref)) with a much fuller implementation of R functions for all Crossref endpoints.
Crossref API documentation can be found at <https://github.com/CrossRef/rest-api-doc>. See also [rcrossref](https://github.com/ropensci/rcrossref) ([on CRAN](https://cran.r-project.org/package=rcrossref)) with a much fuller implementation of R functions for all Crossref endpoints.

## Throttling

Expand Down Expand Up @@ -225,5 +225,3 @@ res <- searchplos(q='*:*', limit = 2000, progress = httr::progress())
This package is part of a richer suite called [fulltext](https://github.com/ropensci/fulltext), along with several other packages, that provides the ability to search for and retrieve full text of open access scholarly articles. We recommend using `fulltext` as the primary R interface to `rplos` unless your needs are limited to this single source.

---

[![rofooter](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)
168 changes: 83 additions & 85 deletions README.md
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Expand Up @@ -3,11 +3,11 @@ rplos



[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![cran checks](https://cranchecks.info/badges/worst/rplos)](https://cranchecks.info/pkgs/rplos)
[![R-check](https://github.com/ropensci/rplos/workflows/R-check/badge.svg)](https://github.com/ropensci/rplos/actions?query=workflow%3AR-check)
[![codecov.io](https://codecov.io/github/ropensci/rplos/coverage.svg?branch=master)](https://codecov.io/github/ropensci/rplos?branch=master)
[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/rplos)](https://github.com/metacran/cranlogs.app)
[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/rplos)](https://github.com/r-hub/cranlogs.app)
[![cran version](https://www.r-pkg.org/badges/version/rplos)](https://cran.r-project.org/package=rplos)

## Install
Expand Down Expand Up @@ -39,13 +39,13 @@ library("rplos")

You used to need a key to use `rplos` - you no longer do as of 2015-01-13 (or `v0.4.5.999`).

rplos tutorial: <http://ropensci.org/tutorials/rplos_tutorial.html>
rplos vignetttes: <https://docs.ropensci.org/rplos/>

PLOS API documentation: <http://api.plos.org/>

PLOS Solr schema is at <https://gist.github.com/openAccess/9e76aa7fa6135be419968b1372c86957> but is 1.5 years old so may not be up to date.

Crossref API documentation [here](https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md), and [here](http://help.crossref.org/#home). Note that we are working on a new package [rcrossref](https://github.com/ropensci/rcrossref) ([on CRAN](https://cran.r-project.org/package=rcrossref)) with a much fuller implementation of R functions for all Crossref endpoints.
Crossref API documentation can be found at <https://github.com/CrossRef/rest-api-doc>. See also [rcrossref](https://github.com/ropensci/rcrossref) ([on CRAN](https://cran.r-project.org/package=rcrossref)) with a much fuller implementation of R functions for all Crossref endpoints.

## Throttling

Expand All @@ -70,7 +70,7 @@ searchplos('ecology', 'id,publication_date', limit = 5)
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 54485 0
#> 1 55873 0
#>
#> $data
#> # A tibble: 5 x 2
Expand All @@ -79,8 +79,8 @@ searchplos('ecology', 'id,publication_date', limit = 5)
#> 1 10.1371/journal.pone.0001248 2007-11-28T00:00:00Z
#> 2 10.1371/journal.pone.0059813 2013-04-24T00:00:00Z
#> 3 10.1371/journal.pone.0080763 2013-12-10T00:00:00Z
#> 4 10.1371/journal.pone.0220747 2019-08-01T00:00:00Z
#> 5 10.1371/journal.pone.0155019 2016-05-11T00:00:00Z
#> 4 10.1371/journal.pone.0246749 2021-02-08T00:00:00Z
#> 5 10.1371/journal.pone.0220747 2019-08-01T00:00:00Z
```

Get DOIs for full article in PLoS One
Expand All @@ -93,17 +93,17 @@ searchplos(q="*:*", fl='id', fq=list('journal_key:PLoSONE',
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 241782 0
#> 1 246927 0
#>
#> $data
#> # A tibble: 5 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0000003
#> 2 10.1371/journal.pone.0000004
#> 3 10.1371/journal.pone.0000012
#> 4 10.1371/journal.pone.0000015
#> 5 10.1371/journal.pone.0000018
#> 1 10.1371/journal.pone.0002399
#> 2 10.1371/journal.pone.0002401
#> 3 10.1371/journal.pone.0002403
#> 4 10.1371/journal.pone.0002405
#> 5 10.1371/journal.pone.0002407
```

Query to get some PLOS article-level metrics, notice difference between two outputs
Expand All @@ -117,22 +117,22 @@ head(out$data)
#> # A tibble: 6 x 3
#> id alm_twitterCount counter_total_all
#> <chr> <int> <int>
#> 1 10.1371/journal.pcbi.0040029 0 5463
#> 2 10.1371/journal.pcbi.0040032 0 5593
#> 3 10.1371/journal.pcbi.0040033 11 70239
#> 4 10.1371/journal.pcbi.0040036 0 7795
#> 5 10.1371/journal.pcbi.0040038 0 7035
#> 6 10.1371/journal.pbio.1000449 0 8816
#> 1 10.1371/journal.pcbi.0020071 0 17862
#> 2 10.1371/journal.pbio.1000152 0 7180
#> 3 10.1371/journal.pbio.1000153 5 27702
#> 4 10.1371/journal.pbio.1000159 0 14256
#> 5 10.1371/journal.pbio.1000165 8 30629
#> 6 10.1371/journal.pbio.1000166 0 6884
head(out_sorted$data)
#> # A tibble: 6 x 3
#> id alm_twitterCount counter_total_all
#> <chr> <int> <int>
#> 1 10.1371/journal.pmed.0020124 3792 3147637
#> 2 10.1371/journal.pone.0133079 308 1877590
#> 3 10.1371/journal.pcbi.1003149 216 1680291
#> 4 10.1371/journal.pmed.1000376 9 1087228
#> 5 10.1371/journal.pone.0141854 3790 989374
#> 6 10.1371/journal.pcbi.0030102 65 973049
#> 1 10.1371/journal.pmed.0020124 3890 3226572
#> 2 10.1371/journal.pone.0133079 312 2481307
#> 3 10.1371/journal.pcbi.1003149 216 1766230
#> 4 10.1371/journal.pmed.1000376 9 1213573
#> 5 10.1371/journal.pone.0141854 3804 996693
#> 6 10.1371/journal.pcbi.0030102 65 986338
```

A list of articles about social networks that are popular on a social network
Expand All @@ -146,22 +146,22 @@ searchplos(q="*:*",fl=c('id','alm_twitterCount'),
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 63 0
#> 1 64 0
#>
#> $data
#> # A tibble: 10 x 2
#> id alm_twitterCount
#> <chr> <int>
#> 1 10.1371/journal.pmed.1000316 1194
#> 1 10.1371/journal.pmed.1000316 1199
#> 2 10.1371/journal.pone.0069841 896
#> 3 10.1371/journal.pone.0073791 1884
#> 4 10.1371/journal.pcbi.1005399 604
#> 5 10.1371/journal.pone.0090315 464
#> 6 10.1371/journal.pone.0118093 133
#> 7 10.1371/journal.pone.0150989 245
#> 8 10.1371/journal.pbio.1002195 778
#> 9 10.1371/journal.pone.0162678 172
#> 10 10.1371/journal.pbio.1001535 2144
#> 5 10.1371/journal.pcbi.1007513 122
#> 6 10.1371/journal.pone.0236517 123
#> 7 10.1371/journal.pbio.1002195 778
#> 8 10.1371/journal.pone.0118093 133
#> 9 10.1371/journal.pone.0155923 200
#> 10 10.1371/journal.pone.0162678 172
```

Show all articles that have these two words less then about 15 words apart
Expand All @@ -173,7 +173,7 @@ searchplos(q='everything:"sports alcohol"~15', fl='title', fq='doc_type:full', l
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 157 0
#> 1 163 0
#>
#> $data
#> # A tibble: 3 x 1
Expand All @@ -193,7 +193,7 @@ searchplos(q='everything:"sports alcohol"~7', fl='title', fq='doc_type:full', li
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 87 0
#> 1 91 0
#>
#> $data
#> # A tibble: 3 x 1
Expand All @@ -214,17 +214,17 @@ searchplos(q='*:*', fl=c('id','article_type'),
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 2389062 0
#> 1 2434439 0
#>
#> $data
#> # A tibble: 5 x 2
#> id article_type
#> <chr> <chr>
#> 1 10.1371/journal.pbio.1000436/title Research Article
#> 2 10.1371/journal.pbio.1000436/abstract Research Article
#> 3 10.1371/journal.pbio.1000436/references Research Article
#> 4 10.1371/journal.pbio.1000436/body Research Article
#> 5 10.1371/journal.pbio.1000436/introduction Research Article
#> id article_type
#> <chr> <chr>
#> 1 10.1371/journal.pbio.1000146/title Unsolved Mystery
#> 2 10.1371/journal.pbio.1000146/abstract Unsolved Mystery
#> 3 10.1371/journal.pbio.1000146/references Unsolved Mystery
#> 4 10.1371/journal.pbio.1000146/body Unsolved Mystery
#> 5 10.1371/journal.pbio.1000146/supporting_information Unsolved Mystery
```

### Faceted search
Expand All @@ -242,21 +242,21 @@ facetplos(q='alcohol', facet.field=c('journal','subject'), facet.limit=5)
#> # A tibble: 5 x 2
#> term value
#> <chr> <chr>
#> 1 plos one 30838
#> 2 plos genetics 688
#> 3 plos medicine 678
#> 4 plos neglected tropical diseases 607
#> 5 plos pathogens 446
#> 1 plos one 31656
#> 2 plos genetics 702
#> 3 plos medicine 699
#> 4 plos neglected tropical diseases 637
#> 5 plos pathogens 459
#>
#> $facet_fields$subject
#> # A tibble: 5 x 2
#> term value
#> <chr> <chr>
#> 1 biology and life sciences 32440
#> 2 medicine and health sciences 29475
#> 3 research and analysis methods 16985
#> 4 biochemistry 14343
#> 5 physical sciences 12192
#> 1 biology and life sciences 33275
#> 2 medicine and health sciences 30309
#> 3 research and analysis methods 17340
#> 4 biochemistry 14587
#> 5 physical sciences 12502
#>
#>
#> $facet_pivot
Expand Down Expand Up @@ -292,16 +292,16 @@ facetplos(q='*:*', url=url, facet.range='counter_total_all',
#> # A tibble: 10 x 2
#> term value
#> <chr> <chr>
#> 1 5 24
#> 2 15 5
#> 3 25 15
#> 4 35 34
#> 5 45 38
#> 1 5 39
#> 2 15 12
#> 3 25 33
#> 4 35 47
#> 5 45 47
#> 6 55 44
#> 7 65 70
#> 8 75 109
#> 9 85 120
#> 10 95 160
#> 7 65 59
#> 8 75 80
#> 9 85 114
#> 10 95 136
```

### Highlight searches
Expand Down Expand Up @@ -385,22 +385,22 @@ plossubject(q='marine ecology', fl = c('id','journal'), limit = 10)
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 2226 0
#> 1 2287 0
#>
#> $data
#> # A tibble: 10 x 2
#> id journal
#> <chr> <chr>
#> 1 10.1371/journal.pone.0092590/title PLoS ONE
#> 2 10.1371/journal.pone.0092590/abstract PLoS ONE
#> 3 10.1371/journal.pone.0092590/references PLoS ONE
#> 4 10.1371/journal.pone.0092590/body PLoS ONE
#> 5 10.1371/journal.pone.0092590/introduction PLoS ONE
#> 6 10.1371/journal.pone.0092590/results_and_discussion PLoS ONE
#> 7 10.1371/journal.pone.0092590/materials_and_methods PLoS ONE
#> 8 10.1371/journal.pone.0092590/conclusions PLoS ONE
#> 9 10.1371/journal.pone.0092590 PLoS ONE
#> 10 10.1371/journal.pone.0149852/body PLOS ONE
#> 1 10.1371/journal.pone.0092590 PLoS ONE
#> 2 10.1371/journal.pone.0092590/title PLoS ONE
#> 3 10.1371/journal.pone.0092590/abstract PLoS ONE
#> 4 10.1371/journal.pone.0092590/references PLoS ONE
#> 5 10.1371/journal.pone.0092590/body PLoS ONE
#> 6 10.1371/journal.pone.0092590/introduction PLoS ONE
#> 7 10.1371/journal.pone.0092590/results_and_discussion PLoS ONE
#> 8 10.1371/journal.pone.0092590/materials_and_methods PLoS ONE
#> 9 10.1371/journal.pone.0092590/conclusions PLoS ONE
#> 10 10.1371/journal.pone.0149852 PLOS ONE
```

However, you can always just do this in `searchplos()` like `searchplos(q = "subject:science")`. See also the `fq` parameter. The above convenience functions are simply wrappers around `searchplos`, so take all the same parameters.
Expand All @@ -413,11 +413,11 @@ Search with term _marine ecology_, by field _subject_, and limit to 5 results
```r
plosviews(search='marine ecology', byfield='subject', limit=5)
#> id counter_total_all
#> 3 10.1371/journal.pone.0167128 5057
#> 4 10.1371/journal.pone.0012946 5259
#> 1 10.1371/journal.pone.0092590 12601
#> 2 10.1371/journal.pone.0149852 18139
#> 5 10.1371/journal.pone.0011372 27681
#> 5 10.1371/journal.pone.0012946 5309
#> 3 10.1371/journal.pone.0167128 5423
#> 1 10.1371/journal.pone.0092590 12839
#> 2 10.1371/journal.pone.0149852 18954
#> 4 10.1371/journal.pone.0011372 28244
```

### Visualize
Expand All @@ -429,11 +429,11 @@ Visualize word use across articles
plosword(list('monkey','Helianthus','sunflower','protein','whale'), vis = 'TRUE')
#> $table
#> No_Articles Term
#> 1 14310 monkey
#> 2 634 Helianthus
#> 3 1845 sunflower
#> 4 162008 protein
#> 5 2093 whale
#> 1 14528 monkey
#> 2 646 Helianthus
#> 3 1876 sunflower
#> 4 164537 protein
#> 5 2142 whale
#>
#> $plot
```
Expand Down Expand Up @@ -463,5 +463,3 @@ res <- searchplos(q='*:*', limit = 2000, progress = httr::progress())
This package is part of a richer suite called [fulltext](https://github.com/ropensci/fulltext), along with several other packages, that provides the ability to search for and retrieve full text of open access scholarly articles. We recommend using `fulltext` as the primary R interface to `rplos` unless your needs are limited to this single source.

---

[![rofooter](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)
2 changes: 1 addition & 1 deletion man-roxygen/high.r
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Expand Up @@ -25,7 +25,7 @@
#' @param hl.fragsize The size, in characters, of the snippets (aka fragments) created by
#' the highlighter. In the original Highlighter, "0" indicates that the whole field value
#' should be used with no fragmenting. See
#' \url{http://wiki.apache.org/solr/HighlightingParameters} for more info.
#' https://cwiki.apache.org/confluence/display/solr/HighlightingParameters for more info
#' @param hl.mergeContiguous Collapse contiguous fragments into a single fragment. "true"
#' indicates contiguous fragments will be collapsed into single fragment. This parameter
#' accepts per-field overrides. This parameter makes sense for the original Highlighter
Expand Down
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