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prepare CRAN submission and bump version.
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3 changes: 2 additions & 1 deletion DESCRIPTION
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Package: europepmc
Title: R Interface to the Europe PubMed Central RESTful Web Service
Version: 0.1.2
Version: 0.1.3
Authors@R: c(
person("Najko", "Jahn", email = "[email protected]",
role = c("aut", "cre", "cph")))
License: GPL-3
Date: 2017-02-22
URL: http://github.com/ropensci/europepmc/
BugReports: http://github.com/ropensci/europepmc/issues
Description: An R Client for the Europe PubMed Central RESTful Web Service. It
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8 changes: 8 additions & 0 deletions NEWS.md
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# europepmc 0.1.3

## Minor changes

- [removed explicit API versioning, so that the client now always supports the most recent API version #13](https://github.com/ropensci/europepmc/issues/13)
- set user agent to "ropensci/europepmc"
- `epmc_db()`, `epmc_db_count()`: add PRIDE archive as external database

# europepmc 0.1.2

- cache HTTP 500 errors which sometimes occur and re-try up to five times. It is based on [googlesheet's approach](https://github.com/jennybc/googlesheets/commit/a91403ecb8ab5d8059bf14a9f9878ab68a829f0a)
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178 changes: 90 additions & 88 deletions README.md
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Expand Up @@ -141,27 +141,27 @@ Use [ORCID](http://orcid.org/) to search for personal publications:

```r
epmc_search(query = 'AUTHORID:"0000-0002-7635-3473"', limit = 1000)
#> # A tibble: 131 × 27
#> id source pmid pmcid doi
#> <chr> <chr> <chr> <chr> <chr>
#> 1 27711162 MED 27711162 PMC5053417 10.1371/journal.pone.0164321
#> 2 27230558 MED 27230558 PMC4881148 10.1186/s12870-016-0805-5
#> 3 27214749 MED 27214749 <NA> 10.1111/nph.14008
#> 4 26980001 MED 26980001 PMC4791833 10.1186/s12864-016-2566-9
#> 5 27557761 MED 27557761 <NA> 10.1007/978-1-4939-6396-6_5
#> 6 26676716 MED 26676716 <NA> 10.1111/tpj.13103
#> 7 26343971 MED 26343971 <NA> 10.1016/j.molp.2015.08.011
#> 8 26328666 MED 26328666 PMC4556409 10.1186/s13059-015-0729-7
#> 9 27660776 MED 27660776 PMC5034127 10.1128/genomea.00975-16
#> 10 27540267 MED 27540267 <NA> <NA>
#> # ... with 121 more rows, and 22 more variables: title <chr>,
#> # authorString <chr>, journalTitle <chr>, issue <chr>,
#> # journalVolume <chr>, pubYear <chr>, journalIssn <chr>, pageInfo <chr>,
#> # pubType <chr>, isOpenAccess <chr>, inEPMC <chr>, inPMC <chr>,
#> # hasPDF <chr>, hasBook <chr>, hasSuppl <chr>, citedByCount <int>,
#> # A tibble: 132 × 27
#> id source pmid doi
#> <chr> <chr> <chr> <chr>
#> 1 28013277 MED 28013277 10.1093/pcp/pcw205
#> 2 27711162 MED 27711162 10.1371/journal.pone.0164321
#> 3 27230558 MED 27230558 10.1186/s12870-016-0805-5
#> 4 27214749 MED 27214749 10.1111/nph.14008
#> 5 26980001 MED 26980001 10.1186/s12864-016-2566-9
#> 6 27557761 MED 27557761 10.1007/978-1-4939-6396-6_5
#> 7 26676716 MED 26676716 10.1111/tpj.13103
#> 8 26343971 MED 26343971 10.1016/j.molp.2015.08.011
#> 9 26328666 MED 26328666 10.1186/s13059-015-0729-7
#> 10 27660776 MED 27660776 10.1128/genomea.00975-16
#> # ... with 122 more rows, and 23 more variables: title <chr>,
#> # authorString <chr>, journalTitle <chr>, pubYear <chr>,
#> # journalIssn <chr>, pubType <chr>, isOpenAccess <chr>, inEPMC <chr>,
#> # inPMC <chr>, hasPDF <chr>, hasBook <chr>, citedByCount <int>,
#> # hasReferences <chr>, hasTextMinedTerms <chr>,
#> # hasDbCrossReferences <chr>, hasLabsLinks <chr>, epmcAuthMan <chr>,
#> # hasTMAccessionNumbers <chr>
#> # hasTMAccessionNumbers <chr>, pmcid <chr>, issue <chr>,
#> # journalVolume <chr>, pageInfo <chr>, hasSuppl <chr>
```

### Include MeSH and UniProt synonyms
Expand All @@ -174,50 +174,50 @@ You may also want to include synonyms when searching Europe PMC. If
# with snyonyms
epmc_search('aspirin', synonym = TRUE)
#> # A tibble: 100 × 27
#> id source pmid doi
#> <chr> <chr> <chr> <chr>
#> 1 27888917 MED 27888917 10.1016/j.otc.2016.08.007
#> 2 28025961 MED 28025961 10.5414/cp202637
#> 3 28039526 MED 28039526 10.1007/s00246-016-1529-x
#> 4 28030443 MED 28030443 10.1097/eja.0000000000000581
#> 5 28039577 MED 28039577 10.1007/s12975-016-0516-0
#> 6 28056332 MED 28056332 <NA>
#> 7 28033561 MED 28033561 10.1016/j.ejogrb.2016.12.023
#> 8 28004997 MED 28004997 10.6002/ect.2016.0139
#> 9 28052291 MED 28052291 10.1159/000452361
#> 10 27987244 MED 27987244 10.1111/wrr.12502
#> # ... with 90 more rows, and 23 more variables: title <chr>,
#> id source pmid
#> <chr> <chr> <chr>
#> 1 28147891 MED 28147891
#> 2 28142297 MED 28142297
#> 3 28181214 MED 28181214
#> 4 28213047 MED 28213047
#> 5 28202405 MED 28202405
#> 6 28205318 MED 28205318
#> 7 28125730 MED 28125730
#> 8 28189429 MED 28189429
#> 9 28160159 MED 28160159
#> 10 28159866 MED 28159866
#> # ... with 90 more rows, and 24 more variables: title <chr>,
#> # authorString <chr>, journalTitle <chr>, issue <chr>,
#> # journalVolume <chr>, pubYear <chr>, journalIssn <chr>, pageInfo <chr>,
#> # pubType <chr>, isOpenAccess <chr>, inEPMC <chr>, inPMC <chr>,
#> # hasPDF <chr>, hasBook <chr>, citedByCount <int>, hasReferences <chr>,
#> # hasTextMinedTerms <chr>, hasDbCrossReferences <chr>,
#> # hasLabsLinks <chr>, epmcAuthMan <chr>, hasTMAccessionNumbers <chr>,
#> # pmcid <chr>, hasSuppl <chr>
#> # doi <chr>, pmcid <chr>, hasSuppl <chr>

# without synonyms
epmc_search('aspirin', synonym = FALSE)
#> # A tibble: 100 × 27
#> id source pmid doi
#> <chr> <chr> <chr> <chr>
#> 1 27888917 MED 27888917 10.1016/j.otc.2016.08.007
#> 2 28025961 MED 28025961 10.5414/cp202637
#> 3 28039526 MED 28039526 10.1007/s00246-016-1529-x
#> 4 27987244 MED 27987244 10.1111/wrr.12502
#> 5 27937054 MED 27937054 10.1080/14656566.2016.1269747
#> 6 28004997 MED 28004997 10.6002/ect.2016.0139
#> 7 28056332 MED 28056332 <NA>
#> 8 28030443 MED 28030443 10.1097/eja.0000000000000581
#> 9 28039577 MED 28039577 10.1007/s12975-016-0516-0
#> 10 27902693 MED 27902693 10.1371/journal.pone.0166103
#> # ... with 90 more rows, and 23 more variables: title <chr>,
#> id source pmid
#> <chr> <chr> <chr>
#> 1 28147891 MED 28147891
#> 2 28142297 MED 28142297
#> 3 28181214 MED 28181214
#> 4 28125730 MED 28125730
#> 5 27888917 MED 27888917
#> 6 28213047 MED 28213047
#> 7 28213669 MED 28213669
#> 8 28160159 MED 28160159
#> 9 28163951 MED 28163951
#> 10 28072691 MED 28072691
#> # ... with 90 more rows, and 24 more variables: title <chr>,
#> # authorString <chr>, journalTitle <chr>, issue <chr>,
#> # journalVolume <chr>, pubYear <chr>, journalIssn <chr>, pageInfo <chr>,
#> # pubType <chr>, isOpenAccess <chr>, inEPMC <chr>, inPMC <chr>,
#> # hasPDF <chr>, hasBook <chr>, citedByCount <int>, hasReferences <chr>,
#> # hasTextMinedTerms <chr>, hasDbCrossReferences <chr>,
#> # hasLabsLinks <chr>, epmcAuthMan <chr>, hasTMAccessionNumbers <chr>,
#> # pmcid <chr>, hasSuppl <chr>
#> # doi <chr>, pmcid <chr>, hasSuppl <chr>
```

### Output types
Expand Down Expand Up @@ -334,18 +334,18 @@ str(my_list[[10]])
#> ..$ journal :List of 6
#> .. ..$ title : chr "Plant signaling & behavior"
#> .. ..$ medlineAbbreviation: chr "Plant Signal Behav"
#> .. ..$ isoabbreviation : chr "Plant Signal Behav"
#> .. ..$ essn : chr "1559-2324"
#> .. ..$ issn : chr "1559-2316"
#> .. ..$ isoabbreviation : chr "Plant Signal Behav"
#> .. ..$ nlmid : chr "101291431"
#> .. ..$ essn : chr "1559-2324"
#> $ pubYear : chr "2016"
#> $ pageInfo : chr "e1161876"
#> $ abstractText : chr "The essential micronutrient vitamin B6 is best known in its enzymatic cofactor form, pyridoxal 5'-phosphate (PLP). However, vit"| __truncated__
#> $ affiliation : chr "a Department of Botany and Plant Biology , University of Geneva , Geneva , Switzerland."
#> $ language : chr "eng"
#> $ pubModel : chr "Print"
#> $ pubTypeList :List of 1
#> ..$ pubType: chr [1:2] "Journal Article" "Research Support, Non-U.S. Gov't"
#> ..$ pubType: chr [1:3] "addendum" "Journal Article" "Research Support, Non-U.S. Gov't"
#> $ meshHeadingList :List of 1
#> ..$ meshHeading:List of 9
#> .. ..$ :List of 3
Expand Down Expand Up @@ -447,7 +447,7 @@ str(my_list[[10]])
#> $ hasPDF : chr "Y"
#> $ hasBook : chr "N"
#> $ hasSuppl : chr "N"
#> $ citedByCount : int 0
#> $ citedByCount : int 1
#> $ hasReferences : chr "Y"
#> $ hasTextMinedTerms : chr "Y"
#> $ hasDbCrossReferences : chr "N"
Expand All @@ -470,29 +470,29 @@ that represent articles referencing DataCite DOIs:
```r
query <- "ACCESSION_TYPE:doi"
epmc_hits(query)
#> [1] 6933
#> [1] 7323
# set limit to 10 records
my_data <- epmc_search(query = query, limit = 10)
head(my_data)
#> # A tibble: 6 × 27
#> id source pmid pmcid
#> <chr> <chr> <chr> <chr>
#> 1 27957387 MED 27957387 PMC5147021
#> 2 27927179 MED 27927179 PMC5142327
#> 3 27927161 MED 27927161 PMC5142403
#> 4 27924834 MED 27924834 PMC5141443
#> 5 27923923 MED 27923923 PMC5142621
#> 6 27922629 MED 27922629 PMC5139674
#> # ... with 23 more variables: title <chr>, authorString <chr>,
#> id source pmid pmcid doi
#> <chr> <chr> <chr> <chr> <chr>
#> 1 28079148 MED 28079148 PMC5228185 10.1038/srep40501
#> 2 28097071 MED 28097071 PMC5228508 10.7717/peerj.2874
#> 3 28097058 MED 28097058 PMC5228507 10.7717/peerj.2844
#> 4 28071681 MED 28071681 PMC5223163 10.1038/srep40034
#> 5 28071668 MED 28071668 PMC5223119 10.1038/srep40094
#> 6 28069623 MED 28069623 PMC5223632 10.1136/bmjopen-2016-013420
#> # ... with 22 more variables: title <chr>, authorString <chr>,
#> # journalTitle <chr>, journalVolume <chr>, pubYear <chr>,
#> # journalIssn <chr>, pageInfo <chr>, pubType <chr>, isOpenAccess <chr>,
#> # inEPMC <chr>, inPMC <chr>, hasPDF <chr>, hasBook <chr>,
#> # hasSuppl <chr>, citedByCount <int>, hasReferences <chr>,
#> # hasTextMinedTerms <chr>, hasDbCrossReferences <chr>,
#> # hasLabsLinks <chr>, epmcAuthMan <chr>, hasTMAccessionNumbers <chr>,
#> # issue <chr>, doi <chr>
#> # issue <chr>
attr(my_data, "hit_count")
#> [1] 6933
#> [1] 7323
```

You may also use `epmc_profile` to retrieve a summary of hit counts.
Expand All @@ -501,28 +501,29 @@ You may also use `epmc_profile` to retrieve a summary of hit counts.
```r
epmc_profile(query = 'malaria')
#> $source
#> # A tibble: 9 × 2
#> name count
#> * <chr> <int>
#> 1 AGR 121
#> 2 CBA 118
#> 3 CTX 8
#> 4 ETH 239
#> 5 HIR 4
#> 6 MED 127023
#> 7 PAT 2295
#> 8 CIT 0
#> 9 PMC 10728
#> # A tibble: 10 × 2
#> name count
#> * <chr> <int>
#> 1 AGR 121
#> 2 CBA 113
#> 3 CTX 7
#> 4 ETH 179
#> 5 HIR 4
#> 6 MED 114975
#> 7 PAT 2252
#> 8 CIT 0
#> 9 PMC 10384
#> 10 PPR 2
#>
#> $pubType
#> # A tibble: 5 × 2
#> name count
#> * <chr> <int>
#> 1 ALL 140536
#> 2 FULL TEXT 79247
#> 3 OPEN ACCESS 33853
#> 4 REVIEW 16562
#> 5 BOOKS AND DOCUMENTS 94
#> 1 ALL 128037
#> 2 FULL TEXT 78505
#> 3 OPEN ACCESS 34244
#> 4 REVIEW 15548
#> 5 BOOKS AND DOCUMENTS 97
#>
#> $subset
#> # A tibble: 1 × 2
Expand Down Expand Up @@ -557,11 +558,12 @@ epmc_details(ext_id = '24270414')
#> # electronicPublicationDate <chr>, firstPublicationDate <chr>
#>
#> $author_details
#> # A tibble: 2 × 4
#> fullName firstName lastName initials
#> * <chr> <chr> <chr> <chr>
#> 1 Malaga-Dieguez L Laura Malaga-Dieguez L
#> 2 Susztak K Katalin Susztak K
#> # A tibble: 2 × 6
#> fullName firstName lastName initials authorId.type
#> * <chr> <chr> <chr> <chr> <chr>
#> 1 Malaga-Dieguez L Laura Malaga-Dieguez L ORCID
#> 2 Susztak K Katalin Susztak K <NA>
#> # ... with 1 more variables: authorId.value <chr>
#>
#> $journal_info
#> # A tibble: 1 × 13
Expand All @@ -570,8 +572,8 @@ epmc_details(ext_id = '24270414')
#> 1 12 123 2099360 2013 Dec 12
#> # ... with 8 more variables: yearOfPublication <int>,
#> # printPublicationDate <chr>, journal.title <chr>,
#> # journal.medlineAbbreviation <chr>, journal.isoabbreviation <chr>,
#> # journal.issn <chr>, journal.nlmid <chr>, journal.essn <chr>
#> # journal.medlineAbbreviation <chr>, journal.essn <chr>,
#> # journal.issn <chr>, journal.isoabbreviation <chr>, journal.nlmid <chr>
#>
#> $ftx
#> # A tibble: 5 × 5
Expand Down Expand Up @@ -671,7 +673,7 @@ my_cites
#> # citedByCount <int>, text <chr>
# hits:
attr(my_cites, 'hit_count')
#> [1] 197
#> [1] 199
```

Please note, that citation counts are often smaller than those held by toll-
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23 changes: 7 additions & 16 deletions cran-comments.md
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Expand Up @@ -3,19 +3,16 @@
## Test environments

* local OS X install, R 3.3.2
* ubuntu 12.04 (on travis-ci), R 3.3.1
* ubuntu 12.04 (on travis-ci), R 3.3.2
* win-builder (devel and release) and appveyor CI

## R CMD check results

I have run R CMD check locally using option "--as-cran" and one note:
On local machine (OS):

* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Najko Jahn <[email protected]>’
Status: OK

Days since last update: 2

The win-builder furthermore send one Note about possibly mis-spelled words in DESCRIPTION,
The win-builder send one NOTE about possibly mis-spelled words in DESCRIPTION,
which are, in fact, correctly spelled.

## Reverse dependencies
Expand All @@ -25,14 +22,8 @@ and found no problems related to this new version.

---

Dear CRAN team,

Apologies for this submission of a new version after two days.

This version should fix issues reported by CRAN checks and Uwe Ligges. These errors occured while building the vignette, more specifically some functions stopped because the web service sometimes returned HTTP 500 errors. There is now a new function caching 500 errors. It also re-tries a call up to five times when a 500 occur. I will also report the HTTP 500 errors to the maintainer of the web service.

This submission should also fix a note on importing the xml2 package.
This submission supports the most recent API version and should fix warning messages.

This submission adds a new function, epmc_profile(), returning a profile of hit counts.
Thanks!

Thanks! Najko Jahn
Najko Jahn

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