Merge pull request #50 from ropensci/v0.4.2

V0.4.2

.github/workflows/R-CMD-check.yaml

@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -45,3 +45,5 @@ jobs:
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: europepmc
 Title: R Interface to the Europe PubMed Central RESTful Web Service
-Version: 0.4.1.09
+Version: 0.4.2
 Authors@R: c(
            person("Najko", "Jahn", email = "[email protected]",
            role = c("aut", "cre", "cph")),
@@ -36,7 +36,7 @@ Imports:
     tibble,
     tidyr,
     rlang
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 Suggests:
     testthat,
     knitr,

R/annotations_by_id.R

@@ -61,13 +61,13 @@ epmc_annotations_by_id_ <- function(ids = NULL, .pb = NULL) {
     out <- tibble::tibble(
       source = req[["source"]],
       ext_id = req[["extId"]],
-      pmcid = dplyr::if_else(
+      pmcid = ifelse(
         is.null(req[["pmcid"]]), NA_character_, req[["pmcid"]]
         ),
       annotations = req[["annotations"]]
     )
-    tidyr::unnest(tidyr::unnest(out, .data$annotations),
-                  .data$tags)
+    tidyr::unnest(tidyr::unnest(out, "annotations"),
+                  "tags")
   } else {
     NULL
   }

R/epmc_details.r

@@ -127,7 +127,7 @@ parse_aut <- function(res) {
     out <- tibble::tibble()
       }
   if("authorAffiliationDetailsList.authorAffiliation" %in% colnames(out))
-    out <- tidyr::unnest(out, cols = c(.data$authorAffiliationDetailsList.authorAffiliation))
+    out <- tidyr::unnest(out, cols = c("authorAffiliationDetailsList.authorAffiliation"))
   return(out)
 }
 

R/epmc_lablinks.r

@@ -5,7 +5,7 @@
 #' providers, which can be selected through Europe PMC's advanced search,
 #' include Wikipedia, Dryad Digital Repository or other open services.
 #' For more information, see
-#' \url{http://europepmc.org/labslink}.
+#' \url{https://europepmc.org/labslink}.
 #'
 #' @param ext_id publication identifier
 #' @param data_src data source, by default Pubmed/MedLine index will be searched.

R/epmc_lablinks_count.r

@@ -5,7 +5,7 @@
 #' providers, which can be selected through Europe PMC's advanced search,
 #' include Wikipedia, Dryad Digital Repository or the institutional repo of
 #' Bielefeld University. For more information, see
-#' \url{http://europepmc.org/labslink}.
+#' \url{https://europepmc.org/labslink}.
 #'
 #' @param ext_id publication identifier
 #' @param data_src data source, by default Pubmed/MedLine index will be searched.

R/epmc_profile.r

@@ -4,7 +4,7 @@
 #'   and breaks it down to the various publication types, data sources, and
 #'   subsets Europe PMC provides.
 #' @param query character, search query. For more information on how to
-#'   build a search query, see \url{http://europepmc.org/Help}
+#'   build a search query, see \url{https://europepmc.org/Help}
 #' @param synonym logical, synonym search. If TRUE, synonym terms from MeSH
 #'  terminology and the UniProt synonym list are queried, too. Enabled by
 #'  default.

R/epmc_search.r

@@ -1,15 +1,15 @@
 #' Search Europe PMC publication database
 #'
 #' @description This is the main function to search Europe PMC RESTful Web
-#'   Service (\url{http://europepmc.org/RestfulWebService}). It fully supports
+#'   Service (\url{https://europepmc.org/RestfulWebService}). It fully supports
 #'   the comprehensive Europe PMC query language. Simply copy & paste your query
 #'   terms to R. To get familiar with the Europe PMC query syntax, check the
 #'   Advanced Search Query Builder \url{https://europepmc.org/advancesearch}.
 #'
-#' @seealso \url{http://europepmc.org/Help}
+#' @seealso \url{https://europepmc.org/Help}
 #'
 #' @param query character, search query. For more information on how to build a
-#'   search query, see \url{http://europepmc.org/Help}
+#'   search query, see \url{https://europepmc.org/Help}
 #' @param output character, what kind of output should be returned. One of
 #'   'parsed', 'id_list' or 'raw' As default, parsed key metadata will be
 #'   returned as data.frame. 'id_list' returns a list of IDs and sources. Use
@@ -159,7 +159,7 @@ epmc_search <- function(query = NULL,
 #' pages within the defined limit.
 #'
 #' @param query character, search query. For more information on how to
-#'   build a search query, see \url{http://europepmc.org/Help}
+#'   build a search query, see \url{https://europepmc.org/Help}
 #' @param output character, what kind of output should be returned. One of 'parsed', 'id_list'
 #'   or 'raw' As default, parsed key metadata will be returned as data.frame.
 #'   'id_list returns a list of IDs and sources.

R/europepmc.r

@@ -15,9 +15,11 @@
 #' to other databases hosted by the European Bioinformatics Institute (EBI).
 #'
 #' For more information about Europe PMC, see their current paper:
-#' Levchenko, M., Gou, Y., Graef, F., Hamelers, A., Huang, Z., Ide-Smith, M.,
-#'  … McEntyre, J. (2017). Europe PMC in 2017. Nucleic Acids Research, 46(D1),
-#'  D1254–D1260. \doi{10.1093/nar/gkx1005}.
+#' Ferguson, C., Araújo, D., Faulk, L., Gou, Y., Hamelers, A., Huang, Z., 
+#' Ide-Smith, M., Levchenko, M., Marinos, N., Nambiar, R., Nassar, M., Parkin, M.,
+#' Pi, X., Rahman, F., Rogers, F., Roochun, Y., Saha, S., Selim, M., Shafique, Z.,
+#' … McEntyre, J. (2020). Europe PMC in 2020. Nucleic Acids Research, 49(D1), 
+#' D1507–D1514. \doi{10.1093/nar/gkaa994}.
 
 #'
 #' @name europepmc
@@ -38,4 +40,4 @@
 #' @importFrom tibble as_tibble tibble
 #' @importFrom tidyr unnest
 #' @importFrom rlang .data
-NULL
+"_PACKAGE"

README.Rmd

@@ -14,7 +14,7 @@ knitr::opts_chunk$set(
 
 [![R build status](https://github.com/ropensci/europepmc/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/europepmc/actions)
 [![Build status](https://ci.appveyor.com/api/projects/status/f8xtpvhhr074lk44?svg=true)](https://ci.appveyor.com/project/sckott/europepmc)
-[![codecov.io](https://codecov.io/github/ropensci/europepmc/coverage.svg?branch=master)](https://codecov.io/github/ropensci/europepmc?branch=master)
+[![codecov.io](https://codecov.io/github/ropensci/europepmc/coverage.svg?branch=master)](https://app.codecov.io/github/ropensci/europepmc?branch=master)
 [![cran version](https://www.r-pkg.org/badges/version/europepmc)](https://cran.r-project.org/package=europepmc)
 [![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/europepmc)](https://github.com/r-hub/cranlogs.app)
 [![](https://badges.ropensci.org/29_status.svg)](https://github.com/ropensci/software-review/issues/29)
@@ -30,7 +30,8 @@ For more infos on Europe PMC, see:
 
 <https://europepmc.org/About>
 
-Levchenko, M., Gou, Y., Graef, F., Hamelers, A., Huang, Z., Ide-Smith, M., … McEntyre, J. (2017). Europe PMC in 2017. Nucleic Acids Research, 46(D1), D1254–D1260. <https://doi.org/10.1093/nar/gkx1005>
+Ferguson, C., Araújo, D., Faulk, L., Gou, Y., Hamelers, A., Huang, Z., 
+Ide-Smith, M., Levchenko, M., Marinos, N., Nambiar, R., Nassar, M., Parkin, M., Pi, X., Rahman, F., Rogers, F., Roochun, Y., Saha, S., Selim, M., Shafique, Z., … McEntyre, J. (2020). Europe PMC in 2020. Nucleic Acids Research, 49(D1), D1507–D1514. <https://doi.org/10.1093/nar/gkaa994>.
 
 ## Implemented API methods
 
@@ -140,7 +141,7 @@ The package maintainer, Chris Stubben (@cstubben), has also created an Shiny App
 
 - use rOpenSci's `oai` to get metadata and full text via Europe PMC's OAI interface: <https://github.com/ropensci/oai>
 - use rOpenSci's `rentrez` to interact with [NCBI databases](https://www.ncbi.nlm.nih.gov/) such as PubMed: <https://github.com/ropensci/rentrez>
-- rOpenSci's `fulltext` package gives access to supplementary material of open access life-science publications in Europe PMC: <https://github.com/ropensci/fulltext>
+- rOpenSci's `fulltext` package gives access to supplementary material of open access life-science publications in Europe PMC: <https://github.com/ropensci-archive/fulltext>
 
 ## Meta
 

README.md

@@ -7,7 +7,7 @@ europepmc - R Interface to Europe PMC RESTful Web Service
 
 [![R build status](https://github.com/ropensci/europepmc/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/europepmc/actions)
 [![Build status](https://ci.appveyor.com/api/projects/status/f8xtpvhhr074lk44?svg=true)](https://ci.appveyor.com/project/sckott/europepmc)
-[![codecov.io](https://codecov.io/github/ropensci/europepmc/coverage.svg?branch=master)](https://codecov.io/github/ropensci/europepmc?branch=master)
+[![codecov.io](https://codecov.io/github/ropensci/europepmc/coverage.svg?branch=master)](https://app.codecov.io/github/ropensci/europepmc?branch=master)
 [![cran version](https://www.r-pkg.org/badges/version/europepmc)](https://cran.r-project.org/package=europepmc)
 [![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/europepmc)](https://github.com/r-hub/cranlogs.app)
 [![](https://badges.ropensci.org/29_status.svg)](https://github.com/ropensci/software-review/issues/29)
@@ -23,7 +23,8 @@ For more infos on Europe PMC, see:
 
 <https://europepmc.org/About>
 
-Levchenko, M., Gou, Y., Graef, F., Hamelers, A., Huang, Z., Ide-Smith, M., … McEntyre, J. (2017). Europe PMC in 2017. Nucleic Acids Research, 46(D1), D1254–D1260. <https://doi.org/10.1093/nar/gkx1005>
+Ferguson, C., Araújo, D., Faulk, L., Gou, Y., Hamelers, A., Huang, Z., 
+Ide-Smith, M., Levchenko, M., Marinos, N., Nambiar, R., Nassar, M., Parkin, M., Pi, X., Rahman, F., Rogers, F., Roochun, Y., Saha, S., Selim, M., Shafique, Z., … McEntyre, J. (2020). Europe PMC in 2020. Nucleic Acids Research, 49(D1), D1507–D1514. <https://doi.org/10.1093/nar/gkaa994>.
 
 ## Implemented API methods
 
@@ -81,25 +82,25 @@ PMC search syntax to `epmc_search()`.
 ```r
 europepmc::epmc_search(query = '"2019-nCoV" OR "2019nCoV"')
 #> # A tibble: 100 × 29
-#>    id       source pmid     doi   title authorString journalTitle issue journalVolume
-#>    <chr>    <chr>  <chr>    <chr> <chr> <chr>        <chr>        <chr> <chr>        
-#>  1 33406042 MED    33406042 10.1… 2019… Xiao M, Liu… IEEE/ACM Tr… 4     18           
-#>  2 34059225 MED    34059225 10.1… Livi… Santillan-G… Med Intensi… 5     45           
-#>  3 34181072 MED    34181072 10.1… Self… Varghese JJ… Support Car… <NA>  <NA>         
-#>  4 34108756 MED    34108756 10.2… COVI… Gabarron E,… Bull World … 6     99           
-#>  5 33197230 MED    33197230 10.2… Sear… Lazarus JV,… J Med Inter… 11    22           
-#>  6 33181701 MED    33181701 10.1… The … Kim YJ, Qia… Medicine (B… 46    99           
-#>  7 34291001 MED    34291001 10.4… How … Moradi G, G… Med J Islam… <NA>  35           
-#>  8 33521188 MED    33521188 10.1… Tota… Chen AZ, Sh… Arthroplast… <NA>  8            
-#>  9 33009914 MED    33009914 10.1… A da… Zhu Z, Meng… Database (O… <NA>  2020         
-#> 10 32341597 MED    32341597 10.1… Obes… Carretero G… Rev Clin Es… 6     220          
-#> # … with 90 more rows, and 20 more variables: pubYear <chr>, journalIssn <chr>,
+#>    id        source pmid     pmcid   doi   title authorString journalTitle issue
+#>    <chr>     <chr>  <chr>    <chr>   <chr> <chr> <chr>        <chr>        <chr>
+#>  1 36754560  MED    36754560 PMC992… 10.1… Inno… Yerlikaya S… BMJ Open     2    
+#>  2 37400836  MED    37400836 PMC103… 10.1… Effe… Ebrahimi T,… BMC Oral He… 1    
+#>  3 37223279  MED    37223279 PMC101… 10.1… Bill… Lamsal R, R… Data Brief   <NA> 
+#>  4 36727245  MED    36727245 PMC101… 10.1… Vasc… Morrissey E… JBI Evid Sy… 5    
+#>  5 37211453  MED    37211453 PMC101… 10.1… Safe… Smith K, He… Vaccine      26   
+#>  6 PPR525786 PPR    <NA>     <NA>    10.1… The … Alihsan B, … <NA>         <NA> 
+#>  7 PPR621660 PPR    <NA>     <NA>    10.1… Safe… Smith K, He… <NA>         <NA> 
+#>  8 36679914  MED    36679914 PMC986… 10.3… The … Cherif YYS,… Vaccines (B… 1    
+#>  9 PPR689808 PPR    <NA>     <NA>    10.2… Perf… MOUNA L, BO… <NA>         <NA> 
+#> 10 37258070  MED    37258070 PMC102… 10.1… Comp… Hui L, Garn… BMJ Open     5    
+#> # ℹ 90 more rows
+#> # ℹ 20 more variables: 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>,
-#> #   hasTMAccessionNumbers <chr>, firstIndexDate <chr>,
-#> #   firstPublicationDate <chr>, pmcid <chr>, versionNumber <int>
+#> #   hasTMAccessionNumbers <chr>, firstIndexDate <chr>, …
 ```
 
 Be aware that Europe PMC expands queries with MeSH synonyms by default. You can turn this behavior off using the `synonym = FALSE` parameter.
@@ -121,17 +122,17 @@ tt_oa
 #> # A tibble: 25 × 3
 #>     year all_hits query_hits
 #>    <int>    <dbl>      <dbl>
-#>  1  1995   449064       1495
-#>  2  1996   458526       1572
-#>  3  1997   456744       1873
-#>  4  1998   474613       1762
-#>  5  1999   493745       1947
-#>  6  2000   532019       2092
-#>  7  2001   545674       2187
-#>  8  2002   561425       2378
-#>  9  2003   588572       2612
-#> 10  2004   628141       2845
-#> # … with 15 more rows
+#>  1  1995   449216       1471
+#>  2  1996   458644       1529
+#>  3  1997   456805       1834
+#>  4  1998   474695       1756
+#>  5  1999   493837       1951
+#>  6  2000   532142       2078
+#>  7  2001   545709       2179
+#>  8  2002   561496       2350
+#>  9  2003   588612       2596
+#> 10  2004   628192       2830
+#> # ℹ 15 more rows
 # we use ggplot2 for plotting the graph
 library(ggplot2)
 ggplot(tt_oa, aes(year, query_hits / all_hits)) + 
@@ -172,7 +173,7 @@ The package maintainer, Chris Stubben (@cstubben), has also created an Shiny App
 
 - use rOpenSci's `oai` to get metadata and full text via Europe PMC's OAI interface: <https://github.com/ropensci/oai>
 - use rOpenSci's `rentrez` to interact with [NCBI databases](https://www.ncbi.nlm.nih.gov/) such as PubMed: <https://github.com/ropensci/rentrez>
-- rOpenSci's `fulltext` package gives access to supplementary material of open access life-science publications in Europe PMC: <https://github.com/ropensci/fulltext>
+- rOpenSci's `fulltext` package gives access to supplementary material of open access life-science publications in Europe PMC: <https://github.com/ropensci-archive/fulltext>
 
 ## Meta