Merge pull request #53 from ropensci/v0.4.3

V0.4.3
ropensci · Sep 20, 2023 · 7aa1cc6 · 7aa1cc6
2 parents b30f317 + 70670fa
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,12 +1,12 @@
 Package: europepmc
 Title: R Interface to the Europe PubMed Central RESTful Web Service
-Version: 0.4.2.009
+Version: 0.4.3
 Authors@R: c(
            person("Najko", "Jahn", email = "najko.jahn@gmail.com",
            role = c("aut", "cre", "cph")),
            person("Maëlle", "Salmon", role = c("ctb")))
 License: GPL-3
-Date: 2023-08-20
+Date: 2023-09-20
 URL: https://docs.ropensci.org/europepmc/, https://github.com/ropensci/europepmc/
 BugReports: https://github.com/ropensci/europepmc/issues
 Description: An R Client for the Europe PubMed Central RESTful Web Service

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# europepmc 0.4.3
+
+- Skip test on CRAN
+
 # europepmc 0.4.2
 
 - Minor fixes documentation

diff --git a/README.Rmd b/README.Rmd
@@ -13,7 +13,6 @@ 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://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)
@@ -100,7 +99,7 @@ See vignette [Introducing europepmc, an R interface to Europe PMC RESTful API](h
 There is also a nice function allowing you to easily create review graphs like described in Maëlle
 Salmon's [blog post](https://masalmon.eu/2017/05/14/evergreenreviewgraph/):
 
-```{r, fig.path="man/figures/"}
+```{r, fig.path="man/figures/", fig.retina = 1}
 tt_oa <- europepmc::epmc_hits_trend("Malaria", period = 1995:2019, synonym = FALSE)
 tt_oa
 # we use ggplot2 for plotting the graph

diff --git a/README.md b/README.md
@@ -6,7 +6,6 @@ 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://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)
@@ -82,25 +81,24 @@ PMC search syntax to `epmc_search()`.
 ```r
 europepmc::epmc_search(query = '"2019-nCoV" OR "2019nCoV"')
 #> # A tibble: 100 × 29
-#>    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    
+#>    id        source pmid     pmcid doi   title authorString journalTitle issue journalVolume
+#>    <chr>     <chr>  <chr>    <chr> <chr> <chr> <chr>        <chr>        <chr> <chr>        
+#>  1 36754560  MED    36754560 PMC9… 10.1… Inno… Yerlikaya S… BMJ Open     2     13           
+#>  2 37400836  MED    37400836 PMC1… 10.1… Effe… Ebrahimi T,… BMC Oral He… 1     23           
+#>  3 37223279  MED    37223279 PMC1… 10.1… Bill… Lamsal R, R… Data Brief   <NA>  48           
+#>  4 36727245  MED    36727245 PMC1… 10.1… Vasc… Morrissey E… JBI Evid Sy… 5     21           
+#>  5 37648680  MED    37648680 <NA>  10.3… [Cli… Liu ZT, Che… Zhonghua Ya… 10    59           
+#>  6 37211453  MED    37211453 PMC1… 10.1… Safe… Smith K, He… Vaccine      26    41           
+#>  7 37479685  MED    37479685 PMC1… 10.1… SuPA… Wei C, Datt… Nat Commun   1     14           
+#>  8 37652823  MED    37652823 <NA>  10.1… Immu… Raiser F, D… Vaccine      <NA>  <NA>         
+#>  9 37714559  MED    37714559 <NA>  10.1… New-… Kobayashi N… BMJ Case Rep 9     16           
+#> 10 PPR525786 PPR    <NA>     <NA>  10.1… The … Alihsan B, … <NA>         <NA>  <NA>         
 #> # 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>, …
+#> # ℹ 19 more variables: 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>, versionNumber <int>
 ```
 
 Be aware that Europe PMC expands queries with MeSH synonyms by default. You can turn this behavior off using the `synonym = FALSE` parameter.
@@ -124,14 +122,14 @@ tt_oa
 #>    <int>    <dbl>      <dbl>
 #>  1  1995   449216       1471
 #>  2  1996   458644       1529
-#>  3  1997   456805       1834
-#>  4  1998   474695       1756
+#>  3  1997   456804       1834
+#>  4  1998   474693       1756
 #>  5  1999   493837       1951
 #>  6  2000   532142       2078
-#>  7  2001   545709       2179
-#>  8  2002   561496       2350
+#>  7  2001   545702       2180
+#>  8  2002   561497       2351
 #>  9  2003   588612       2596
-#> 10  2004   628192       2830
+#> 10  2004   628176       2831
 #> # ℹ 15 more rows
 # we use ggplot2 for plotting the graph
 library(ggplot2)

diff --git a/cran-comments.md b/cran-comments.md
@@ -23,7 +23,8 @@ Status: OK
 
 ---
 
-This submission fixes the package manual entry as requested by the CRAN team.
+This submission fixes the problems shown on
+<https://cran.r-project.org/web/checks/check_results_europepmc.html>
 
 Thanks!
 

diff --git a/man/figures/unnamed-chunk-4-1.png b/man/figures/unnamed-chunk-4-1.png
diff --git a/tests/testthat/test_epmc_hits_trend.R b/tests/testthat/test_epmc_hits_trend.R
@@ -36,6 +36,8 @@ test_that("epmc_hits_trend fails correctly", {
 })
 
 test_that("epmc_hits_trend synonym search works correctly", {
+  skip_on_cran()
+
   a <- epmc_hits_trend('malaria', period = 2012:2016, synonym = FALSE)
   b <- epmc_hits_trend('malaria', period = 2012:2016, synonym = TRUE)
 

diff --git a/vignettes/evergreenreviewgraphs.Rmd b/vignettes/evergreenreviewgraphs.Rmd
@@ -1,7 +1,7 @@
 ---
 title: "Making trend graphs"
 author: "Najko Jahn"
-date: "2023-08-21"
+date: "2023-09-20"
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteEngine{knitr::rmarkdown}
@@ -27,19 +27,19 @@ europepmc::epmc_hits_trend(query = "aspirin", period = 2010:2022)
 #> # A tibble: 13 × 3
 #>     year all_hits query_hits
 #>    <int>    <dbl>      <dbl>
-#>  1  2010   851063       5507
-#>  2  2011   904794       6003
-#>  3  2012   946175       6833
-#>  4  2013  1004386       7652
-#>  5  2014  1055159       8210
-#>  6  2015  1096370       8779
-#>  7  2016  1117117       8950
-#>  8  2017  1138383       9394
-#>  9  2018  1180056      10103
-#> 10  2019  1243536      10666
-#> 11  2020  1450476      14294
-#> 12  2021  1549953      16643
-#> 13  2022  1542398      15975
+#>  1  2010   851106       5513
+#>  2  2011   904847       6009
+#>  3  2012   946206       6840
+#>  4  2013  1004432       7658
+#>  5  2014  1055201       8226
+#>  6  2015  1096429       8789
+#>  7  2016  1117164       8965
+#>  8  2017  1138419       9411
+#>  9  2018  1180115      10116
+#> 10  2019  1243574      10675
+#> 11  2020  1450562      14358
+#> 12  2021  1550459      16755
+#> 13  2022  1542959      16214
 ```
 
 By default, synonym search is disabled and only Medline/PubMed index is searched.
@@ -52,7 +52,7 @@ By default, synonym search is disabled and only Medline/PubMed index is searched
 
 ### Use Case: Growth of Open Access Literature
 
-There is a growing interest in knowing the proportion of open access to scholarly literature. Europe PMC allows searching for open access content with the [`OPEN_ACCESS:Y` parameter](https://europepmc.org/search?query=OPEN_ACCESS:Y&page=1&sortby=Relevance). At the moment, Europe PMC contains 5,509,277 open access full-texts. Let's see how they are relatively distributed over the period 2010 - 2022.
+There is a growing interest in knowing the proportion of open access to scholarly literature. Europe PMC allows searching for open access content with the [`OPEN_ACCESS:Y` parameter](https://europepmc.org/search?query=OPEN_ACCESS:Y&page=1&sortby=Relevance). At the moment, Europe PMC contains 5,641,836 open access full-texts. Let's see how they are relatively distributed over the period 2010 - 2022.
 
 
 ```r
@@ -61,19 +61,19 @@ tt_oa
 #> # A tibble: 13 × 3
 #>     year all_hits query_hits
 #>    <int>    <dbl>      <dbl>
-#>  1  2010   851063      78677
-#>  2  2011   904794     105675
-#>  3  2012   946175     140016
-#>  4  2013  1004386     176541
-#>  5  2014  1055159     212039
-#>  6  2015  1096370     244234
-#>  7  2016  1117117     273364
-#>  8  2017  1138383     312717
-#>  9  2018  1180056     352067
-#> 10  2019  1243536     405927
-#> 11  2020  1450476     585116
-#> 12  2021  1549953     714017
-#> 13  2022  1542398     790600
+#>  1  2010   851106      78743
+#>  2  2011   904847     105737
+#>  3  2012   946206     140082
+#>  4  2013  1004432     176617
+#>  5  2014  1055201     212221
+#>  6  2015  1096429     244342
+#>  7  2016  1117164     273575
+#>  8  2017  1138419     312877
+#>  9  2018  1180115     352369
+#> 10  2019  1243574     406182
+#> 11  2020  1450562     585074
+#> 12  2021  1550459     714651
+#> 13  2022  1542959     794387
 # we use ggplot2 for plotting the graph
 library(ggplot2)
 ggplot(tt_oa, aes(factor(year), query_hits / all_hits, group = 1)) +
@@ -141,16 +141,16 @@ my_df
 #> # A tibble: 70 × 5
 #>     year all_hits refs_hits query_hits query_id                 
 #>    <int>    <dbl>     <dbl>      <dbl> <chr>                    
-#>  1  2009   793211    555994         13 "REF:\"code.google.com\""
-#>  2  2010   851063    541440         40 "REF:\"code.google.com\""
-#>  3  2011   904794    604311         65 "REF:\"code.google.com\""
-#>  4  2012   946175    636818         92 "REF:\"code.google.com\""
-#>  5  2013  1004386    763699        135 "REF:\"code.google.com\""
-#>  6  2014  1055159    797691        140 "REF:\"code.google.com\""
-#>  7  2015  1096370    780509        117 "REF:\"code.google.com\""
-#>  8  2016  1117117    783865         65 "REF:\"code.google.com\""
-#>  9  2017  1138383    819481         52 "REF:\"code.google.com\""
-#> 10  2018  1180056    757547         29 "REF:\"code.google.com\""
+#>  1  2009   793210    556002         13 "REF:\"code.google.com\""
+#>  2  2010   851106    541447         40 "REF:\"code.google.com\""
+#>  3  2011   904847    604315         65 "REF:\"code.google.com\""
+#>  4  2012   946206    636843         92 "REF:\"code.google.com\""
+#>  5  2013  1004432    763720        135 "REF:\"code.google.com\""
+#>  6  2014  1055201    797730        140 "REF:\"code.google.com\""
+#>  7  2015  1096429    780777        117 "REF:\"code.google.com\""
+#>  8  2016  1117164    784272         65 "REF:\"code.google.com\""
+#>  9  2017  1138419    819735         52 "REF:\"code.google.com\""
+#> 10  2018  1180115    757852         29 "REF:\"code.google.com\""
 #> # ℹ 60 more rows
 
 ### total
@@ -162,14 +162,14 @@ hits_summary
 #> # A tibble: 5 × 2
 #>   query_id                       all
 #>   <chr>                        <dbl>
-#> 1 "REF:\"cran.r-project.org\"" 44677
-#> 2 "REF:\"github.com\""         28886
-#> 3 "REF:\"sourceforge.net\""     1777
-#> 4 "REF:\"code.google.com\""      896
-#> 5 "REF:\"bitbucket.org\""        440
+#> 1 "REF:\"cran.r-project.org\"" 44864
+#> 2 "REF:\"github.com\""         29009
+#> 3 "REF:\"sourceforge.net\""     1779
+#> 4 "REF:\"code.google.com\""      897
+#> 5 "REF:\"bitbucket.org\""        442
 ```
 
-The proportion of papers where Europe PMC was able to make the cited literature available was 63 for the period 2009-2022. There also seems to be a time-lag between indexing reference lists because the absolute number of publication was decreasing over the years. This is presumably because Europe PMC also includes delayed open access content, i.e. content which is not added immediately with the original publication.[^4]
+The proportion of papers where Europe PMC was able to make the cited literature available was 64 for the period 2009-2022. There also seems to be a time-lag between indexing reference lists because the absolute number of publication was decreasing over the years. This is presumably because Europe PMC also includes delayed open access content, i.e. content which is not added immediately with the original publication.[^4]
 
 [^4]: Ebd.