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updated vignette
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sckott committed Jan 22, 2015
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2 changes: 1 addition & 1 deletion inst/vign/rplos_vignette.Rmd
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Expand Up @@ -14,7 +14,7 @@ knitr::opts_chunk$set(
)
```

The `rplos` package interacts with the API services of [PLoS](http://www.plos.org/) (Public Library of Science) Journals. In order to use `rplos`, you need to obtain [your own key](http://api.plos.org/registration/) to their API services. Instruction for obtaining and installing keys so they load automatically when you launch R are on our GitHub Wiki page [Installation and use of API keys](https://github.com/ropensci/rOpenSci/wiki/Installation-and-use-of-API-keys).
The `rplos` package interacts with the API services of [PLoS](http://www.plos.org/) (Public Library of Science) Journals. You used to need an API key to work with this package - that is no longer needed!

This tutorial will go through three use cases to demonstrate the kinds
of things possible in `rplos`.
Expand Down
154 changes: 77 additions & 77 deletions inst/vign/rplos_vignette.md
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Expand Up @@ -8,7 +8,7 @@ rplos tutorial



The `rplos` package interacts with the API services of [PLoS](http://www.plos.org/) (Public Library of Science) Journals. In order to use `rplos`, you need to obtain [your own key](http://api.plos.org/registration/) to their API services. Instruction for obtaining and installing keys so they load automatically when you launch R are on our GitHub Wiki page [Installation and use of API keys](https://github.com/ropensci/rOpenSci/wiki/Installation-and-use-of-API-keys).
The `rplos` package interacts with the API services of [PLoS](http://www.plos.org/) (Public Library of Science) Journals. You used to need an API key to work with this package - that is no longer needed!

This tutorial will go through three use cases to demonstrate the kinds
of things possible in `rplos`.
Expand Down Expand Up @@ -41,8 +41,8 @@ searchplos(q= "Helianthus", fl= "id", limit = 5)

```
#> $meta
#> numFound start maxScore
#> 1 296 0 0.4991457
#> numFound start maxScore
#> 1 300 0 NA
#>
#> $data
#> id
Expand All @@ -63,15 +63,15 @@ searchplos(q="*:*", fl='id', fq='doc_type:full', start=0, limit=5)
```
#> $meta
#> numFound start maxScore
#> 1 1188800 0 1
#> 1 142126 0 NA
#>
#> $data
#> id
#> 1 10.1371/journal.pone.0057487
#> 2 10.1371/journal.ppat.0030138
#> 3 10.1371/journal.pone.0071347
#> 4 10.1371/journal.pone.0043700
#> 5 10.1371/journal.pone.0015651
#> 1 10.1371/journal.pbio.1000156
#> 2 10.1371/journal.pbio.1000106
#> 3 10.1371/journal.pmed.1001197
#> 4 10.1371/journal.pbio.0040294
#> 5 10.1371/journal.pone.0093878
```

Get DOIs for only PLoS One articles
Expand All @@ -84,15 +84,15 @@ searchplos(q="*:*", fl='id', fq='cross_published_journal_key:PLoSONE', start=0,
```
#> $meta
#> numFound start maxScore
#> 1 1188800 0 1
#> 1 1013893 0 NA
#>
#> $data
#> id
#> 1 10.1371/journal.pone.0098523/introduction
#> 2 10.1371/journal.pone.0015652/introduction
#> 3 10.1371/journal.pone.0015652/results_and_discussion
#> 4 10.1371/journal.pone.0015652/materials_and_methods
#> 5 10.1371/journal.pone.0098523/results_and_discussion
#> id
#> 1 10.1371/journal.pone.0094673/body
#> 2 10.1371/journal.pone.0093878
#> 3 10.1371/journal.pone.0093878/title
#> 4 10.1371/journal.pone.0093878/abstract
#> 5 10.1371/journal.pone.0093878/references
```

Get DOIs for full article in PLoS One
Expand All @@ -107,15 +107,15 @@ searchplos(q="*:*", fl='id',
```
#> $meta
#> numFound start maxScore
#> 1 1188800 0 1
#> 1 118989 0 NA
#>
#> $data
#> id
#> 1 10.1371/journal.pone.0057487
#> 2 10.1371/journal.pone.0071347
#> 3 10.1371/journal.pone.0043700
#> 4 10.1371/journal.pone.0015651
#> 5 10.1371/journal.pone.0029650
#> 1 10.1371/journal.pone.0093878
#> 2 10.1371/journal.pone.0094012
#> 3 10.1371/journal.pone.0094113
#> 4 10.1371/journal.pone.0094154
#> 5 10.1371/journal.pone.0094152
```

Search for many terms
Expand All @@ -129,8 +129,8 @@ lapply(q, function(x) searchplos(x, limit=2))
```
#> [[1]]
#> [[1]]$meta
#> numFound start maxScore
#> 1 24708 0 0.9781508
#> numFound start maxScore
#> 1 24936 0 NA
#>
#> [[1]]$data
#> id
Expand All @@ -140,8 +140,8 @@ lapply(q, function(x) searchplos(x, limit=2))
#>
#> [[2]]
#> [[2]]$meta
#> numFound start maxScore
#> 1 41781 0 0.8152939
#> numFound start maxScore
#> 1 42116 0 NA
#>
#> [[2]]$data
#> id
Expand All @@ -151,8 +151,8 @@ lapply(q, function(x) searchplos(x, limit=2))
#>
#> [[3]]
#> [[3]]$meta
#> numFound start maxScore
#> 1 120601 0 0.6816086
#> numFound start maxScore
#> 1 121700 0 NA
#>
#> [[3]]$data
#> id
Expand Down Expand Up @@ -180,7 +180,7 @@ plosauthor(q = "Eisen", fl = "author", limit = 5)
```
#> $meta
#> numFound start maxScore
#> 1 741 0 4.189553
#> 1 741 0 NA
#>
#> $data
#> author
Expand All @@ -201,21 +201,21 @@ plosabstract(q = 'drosophila', fl='id,title', limit = 5)
```
#> $meta
#> numFound start maxScore
#> 1 2491 0 2.239879
#> 1 2498 0 NA
#>
#> $data
#> id
#> 1 10.1371/journal.pbio.0040198
#> 2 10.1371/journal.pbio.0030246
#> 3 10.1371/journal.pone.0012421
#> 4 10.1371/journal.pone.0002817
#> 5 10.1371/journal.pbio.0030389
#> title
#> 1 All for All
#> 2 School Students as Drosophila Experimenters
#> 3 Host Range and Specificity of the Drosophila C Virus
#> 4 High-Resolution, In Vivo Magnetic Resonance Imaging of Drosophila at 18.8 Tesla
#> 5 New Environments Set the Stage for Changing Tastes in Mates
#> 4 10.1371/journal.pbio.0030389
#> 5 10.1371/journal.pbio.1000342
#> title
#> 1 All for All
#> 2 School Students as Drosophila Experimenters
#> 3 Host Range and Specificity of the Drosophila C Virus
#> 4 New Environments Set the Stage for Changing Tastes in Mates
#> 5 Variable Transcription Factor Binding: A Mechanism of Evolutionary Change
```

`plostitle` searches across titles, and in this case returns the title and journal of the matching papers
Expand All @@ -228,20 +228,20 @@ plostitle(q='drosophila', fl='title,journal', limit=5)
```
#> $meta
#> numFound start maxScore
#> 1 1599 0 3.805348
#> 1 1603 0 NA
#>
#> $data
#> journal
#> 1 PLoS ONE
#> 2 PLoS ONE
#> 3 PLoS Genetics
#> 1 PLoS Biology
#> 2 PLoS Genetics
#> 3 PLoS Biology
#> 4 PLoS ONE
#> 5 PLoS Computational Biology
#> title
#> 1 A Tripartite Synapse Model in Drosophila
#> 2 Quantification of Food Intake in Drosophila
#> 3 Phenotypic Plasticity of the Drosophila Transcriptome
#> 4 A DNA Virus of Drosophila
#> 1 School Students as Drosophila Experimenters
#> 2 Phenotypic Plasticity of the Drosophila Transcriptome
#> 3 Identification of Drosophila MicroRNA Targets
#> 4 Quantification of Food Intake in Drosophila
#> 5 Parametric Alignment of Drosophila Genomes
```

Expand All @@ -261,15 +261,15 @@ facetplos(q='*:*', facet.field='journal')
#> $facet_fields
#> $facet_fields$journal
#> X1 X2
#> 1 plos one 946507
#> 2 plos genetics 41277
#> 3 plos pathogens 35950
#> 4 plos computational biology 30312
#> 5 plos biology 26292
#> 6 plos neglected tropical diseases 25694
#> 7 plos medicine 18601
#> 1 plos one 955046
#> 2 plos genetics 41615
#> 3 plos pathogens 36230
#> 4 plos computational biology 30535
#> 5 plos biology 26456
#> 6 plos neglected tropical diseases 26120
#> 7 plos medicine 18672
#> 8 plos clinical trials 521
#> 9 plos collections 10
#> 9 plos collections 15
#> 10 plos medicin 9
#>
#>
Expand All @@ -295,15 +295,15 @@ facetplos(q='*:*', facet.field='journal', facet.query='cell,bird')
#> $facet_fields
#> $facet_fields$journal
#> X1 X2
#> 1 plos one 946507
#> 2 plos genetics 41277
#> 3 plos pathogens 35950
#> 4 plos computational biology 30312
#> 5 plos biology 26292
#> 6 plos neglected tropical diseases 25694
#> 7 plos medicine 18601
#> 1 plos one 955046
#> 2 plos genetics 41615
#> 3 plos pathogens 36230
#> 4 plos computational biology 30535
#> 5 plos biology 26456
#> 6 plos neglected tropical diseases 26120
#> 7 plos medicine 18672
#> 8 plos clinical trials 521
#> 9 plos collections 10
#> 9 plos collections 15
#> 10 plos medicin 9
#>
#>
Expand Down Expand Up @@ -332,12 +332,12 @@ facetplos(q='*:*', url=url, facet.date='publication_date',
#> $facet_dates
#> $facet_dates$publication_date
#> date value
#> 1 2014-12-17T00:00:00Z 1712
#> 2 2014-12-18T00:00:00Z 1569
#> 3 2014-12-19T00:00:00Z 536
#> 4 2014-12-20T00:00:00Z 0
#> 5 2014-12-21T00:00:00Z 0
#> 6 2014-12-22T00:00:00Z 0
#> 1 2015-01-17T00:00:00Z 0
#> 2 2015-01-18T00:00:00Z 0
#> 3 2015-01-19T00:00:00Z 406
#> 4 2015-01-20T00:00:00Z 930
#> 5 2015-01-21T00:00:00Z 745
#> 6 2015-01-22T00:00:00Z 221
#>
#>
#> $facet_ranges
Expand Down Expand Up @@ -396,9 +396,9 @@ highplos(q='everything:"experiment"', fl='id,title', fq='doc_type:full',
#> [1] " Selection of Transcriptomics <em>Experiments</em> Improves Guilt-by-Association Analyses Transcriptomics <em>Experiment</em>"
#>
#>
#> $`10.1371/journal.pone.0108803`
#> $`10.1371/journal.pone.0108803`$everything
#> [1] " PONE-D-14-40021 10.1371/journal.pone.0108803 Correction Correction: Partner <em>Experiences</em>"
#> $`10.1371/annotation/9b8741e2-0f5f-49f9-9eaa-1b0cb9b8d25f`
#> $`10.1371/annotation/9b8741e2-0f5f-49f9-9eaa-1b0cb9b8d25f`$everything
#> [1] " in the labels under the bars. The labels should read <em>Experiment</em> 3 / <em>Experiment</em> 4 instead of <em>Experiment</em>"
```

### Search for terms and visualize results as a histogram OR as a plot through time
Expand All @@ -415,11 +415,11 @@ out$table

```
#> No_Articles Term
#> 1 8274 monkey
#> 2 296 Helianthus
#> 3 809 sunflower
#> 4 91291 protein
#> 5 1014 whale
#> 1 8335 monkey
#> 2 300 Helianthus
#> 3 818 sunflower
#> 4 91971 protein
#> 5 1023 whale
```


Expand All @@ -438,7 +438,7 @@ plosword('Helianthus', callopts=list(verbose=TRUE))

```
#> Number of articles with search term
#> 296
#> 300
```

### Visualize terms
Expand Down
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