diff --git a/.Rbuildignore b/.Rbuildignore index 0eb295b..b1dab27 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -13,3 +13,4 @@ ^index\.md$ ^README\.md$ ^R/\.setup\.R +^\.github$ diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..909fbdf --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,81 @@ +on: + push: + branches: + - master + - main + - dev + pull_request: + branches: + - master + - main + - dev + +name: R-CMD-check + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macOS-latest, r: 'release'} + - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: windows-latest, r: 'devel'} + - {os: windows-latest, r: 'oldrel'} + - {os: windows-latest, r: 'release'} + + env: + R_REMOTES_NO_ERRORS_FROM_WARNINGS: true + RSPM: ${{ matrix.config.rspm }} + + steps: + - uses: actions/checkout@v2 + + - uses: r-lib/actions/setup-r@master + with: + r-version: ${{ matrix.config.r }} + + - uses: r-lib/actions/setup-pandoc@master + + - name: Query dependencies + run: | + install.packages('remotes') + saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2) + shell: Rscript {0} + + - name: Cache R packages + if: runner.os != 'Windows' + uses: actions/cache@v1 + with: + path: ${{ env.R_LIBS_USER }} + key: ${{ runner.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('depends.Rds') }} + restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-3- + + - name: Install system dependencies + if: runner.os == 'Linux' + env: + RHUB_PLATFORM: linux-x86_64-ubuntu-gcc + run: | + Rscript -e "remotes::install_github('r-hub/sysreqs')" + sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") + sudo -s eval "$sysreqs" + - name: Install dependencies + run: | + remotes::install_deps(dependencies = TRUE) + remotes::install_cran("rcmdcheck") + shell: Rscript {0} + + - name: Check + run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check") + shell: Rscript {0} + + - name: Upload check results + if: failure() + uses: actions/upload-artifact@master + with: + name: ${{ runner.os }}-r${{ matrix.config.r }}-results + path: check diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml new file mode 100644 index 0000000..58a9d79 --- /dev/null +++ b/.github/workflows/pkgdown.yaml @@ -0,0 +1,49 @@ +on: + push: + branches: + - main + - master + - dev + +name: pkgdown + +jobs: + pkgdown: + runs-on: macOS-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - uses: actions/checkout@v2 + + - uses: r-lib/actions/setup-r@master + + - uses: r-lib/actions/setup-pandoc@master + + - name: Query dependencies + run: | + install.packages('remotes') + saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) + writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") + shell: Rscript {0} + + - name: Cache R packages + uses: actions/cache@v2 + with: + path: ${{ env.R_LIBS_USER }} + key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- + + - name: Install dependencies + run: | + remotes::install_deps(dependencies = TRUE) + install.packages("pkgdown", type = "binary") + shell: Rscript {0} + + - name: Install package + run: R CMD INSTALL . + + - name: Deploy package + run: | + git config --local user.email "actions@github.com" + git config --local user.name "GitHub Actions" + Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)' diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml new file mode 100644 index 0000000..0d3cb71 --- /dev/null +++ b/.github/workflows/pr-commands.yaml @@ -0,0 +1,51 @@ +on: + issue_comment: + types: [created] +name: Commands +jobs: + document: + if: startsWith(github.event.comment.body, '/document') + name: document + runs-on: macOS-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - uses: actions/checkout@v2 + - uses: r-lib/actions/pr-fetch@master + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} + - uses: r-lib/actions/setup-r@master + - name: Install dependencies + run: Rscript -e 'install.packages(c("remotes", "roxygen2"))' -e 'remotes::install_deps(dependencies = TRUE)' + - name: Document + run: Rscript -e 'roxygen2::roxygenise()' + - name: commit + run: | + git add man/\* NAMESPACE + git commit -m 'Document' + - uses: r-lib/actions/pr-push@master + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} + style: + if: startsWith(github.event.comment.body, '/style') + name: style + runs-on: macOS-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - uses: actions/checkout@v2 + - uses: r-lib/actions/pr-fetch@master + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} + - uses: r-lib/actions/setup-r@master + - name: Install dependencies + run: Rscript -e 'install.packages("styler")' + - name: Style + run: Rscript -e 'styler::style_pkg()' + - name: commit + run: | + git add \*.R + git commit -m 'Style' + - uses: r-lib/actions/pr-push@master + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml new file mode 100644 index 0000000..4efc7ab --- /dev/null +++ b/.github/workflows/test-coverage.yaml @@ -0,0 +1,48 @@ +on: + push: + branches: + - master + - main + pull_request: + branches: + - master + - main + +name: test-coverage + +jobs: + test-coverage: + runs-on: macOS-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - uses: actions/checkout@v2 + + - uses: r-lib/actions/setup-r@master + + - uses: r-lib/actions/setup-pandoc@master + + - name: Query dependencies + run: | + install.packages('remotes') + saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) + writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") + shell: Rscript {0} + + - name: Cache R packages + uses: actions/cache@v1 + with: + path: ${{ env.R_LIBS_USER }} + key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- + + - name: Install dependencies + run: | + install.packages(c("remotes")) + remotes::install_deps(dependencies = TRUE) + remotes::install_cran("covr") + shell: Rscript {0} + + - name: Test coverage + run: covr::codecov() + shell: Rscript {0} diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 9f30333..0000000 --- a/.travis.yml +++ /dev/null @@ -1,31 +0,0 @@ -############################################################################## -### Autogenerated with R package kwb.pkgbuild v0.1.1 -### (installed from 'Github (kwb-r/kwb.pkgbuild@0ac3694)' source code on 2019-09-06) -### by calling the function kwb.pkgbuild::use_travis() -### (file created at: 2019-09-09 10:34:55) -############################################################################## - - -language: r -sudo: required -cache: packages -r_packages: -- remotes -- covr -matrix: - include: - - r: devel - - r: release - after_success: - - Rscript -e 'covr::codecov()' - before_deploy: - - Rscript -e 'remotes::install_cran("pkgdown")' - deploy: - provider: script - script: Rscript -e 'pkgdown::deploy_site_github(verbose = TRUE)' - skip_cleanup: 'true' - on: - branch: - - master - - dev - - r: oldrel diff --git a/DESCRIPTION b/DESCRIPTION index 74c7e38..1667770 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: kwb.endnote Title: Helper Functions for Analysing KWB Endnote Library (Exported as .xml) -Version: 0.1.0 +Version: 0.2.0 Authors@R: c(person(given = "Michael", family = "Rustler", @@ -13,6 +13,8 @@ Authors@R: role = "ctb", email = "hauke.sonnenberg@kompetenz-wasser.de", comment = c(ORCID = "0000-0001-9134-2871")), + person(given = "FAKIN", + role = "fnd"), person(given = "Kompetenzzentrum Wasser Berlin gGmbH (KWB)", role = "cph")) Description: Helper Functions For Analysing KWB Endnote Library @@ -35,7 +37,8 @@ Imports: tibble, tidyr, wordcloud2, - xml2 + xml2, + plotly Suggests: covr, knitr, @@ -46,5 +49,5 @@ Remotes: github::kwb-r/kwb.utils Encoding: UTF-8 LazyData: true -RoxygenNote: 6.1.1 +RoxygenNote: 7.1.1 VignetteBuilder: knitr diff --git a/NEWS.md b/NEWS.md index 308aaac..d876a88 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # kwb.endnote 0.0.0.9000 +* Move to GitHub Actions as CI (from Travis/Appveyor) * Added a `NEWS.md` file to track changes to the package. * see https://style.tidyverse.org/news.html for writing a good `NEWS.md` diff --git a/R/check_for_differences.R b/R/check_for_differences.R index 6fb860c..ffc2561 100644 --- a/R/check_for_differences.R +++ b/R/check_for_differences.R @@ -17,8 +17,8 @@ #' ### Check differences between two different versions of "KWB_documents.xml" #' ############################################################################ #' -#' old_xml <- extdata_file("2019-01-14_KWB_documents.xml") -#' new_xml <- extdata_file("2019-07-09_KWB_documents.xml") +#' old_xml <- extdata_file("2020-05-25_KWB-documents.xml") +#' new_xml <- extdata_file("2020-06-17_KWB-documents.xml") #' old_list <- kwb.endnote::create_endnote_list(old_xml) #' new_list <- kwb.endnote::create_endnote_list(new_xml) #' old_df <- kwb.endnote::create_references_df(old_list) diff --git a/R/create_references_df_from_list.R b/R/create_references_df_from_list.R index b78fa35..604c7a0 100644 --- a/R/create_references_df_from_list.R +++ b/R/create_references_df_from_list.R @@ -1,3 +1,17 @@ +# colbind: Wrapper around dplyr::bind_cols(). Makes sure that no rows get lost +# if the data frame to add has no rows. +colbind <- function(df, df_2) { + if (nrow(df_2) == 0L) { + # Return the original data frame if the data frame to add has no columns + if (ncol(df_2) == 0L) { + return(df) + } + # Give the data frame to add one empty row (full of NA) + df_2 <- df_2[1L, ] + } + dplyr::bind_cols(df, df_2) +} + #' @noRd #' @keywords internal null_to_na <- function(x, na_fill = NA_character_) { @@ -154,6 +168,11 @@ record_list_to_df <- function(record_list, collapse = FALSE) { collapse_val = "", element = 1) } + + replace_newline_with_semicolon <- function(text) { + gsub("\r", ", ", text) + } + get_titles_style <- function(path) get_style(c("titles", path)) get_period_style <- function(path) get_style(c("periodical", path)) get_dates_style <- function(path) get_style(c("dates", path)) @@ -164,11 +183,11 @@ record_list_to_df <- function(record_list, collapse = FALSE) { ref_type_name = attr(get_record_entry("ref-type"), which = "name"), abstract = get_abstract(record_list, collapse) ) %>% - dplyr::bind_cols(get_keywords(record_list, collapse = collapse)) %>% - dplyr::bind_cols(get_authors(record_list, collapse = collapse)) %>% - dplyr::bind_cols(get_secondary_authors(record_list, collapse = collapse)) %>% - dplyr::bind_cols(get_tertiary_authors(record_list, collapse = collapse)) %>% - dplyr::bind_cols( + colbind(get_keywords(record_list, collapse = collapse)) %>% + colbind(get_authors(record_list, collapse = collapse)) %>% + colbind(get_secondary_authors(record_list, collapse = collapse)) %>% + colbind(get_tertiary_authors(record_list, collapse = collapse)) %>% + colbind( tibble::tibble( database_name = get_record_entry("database")[[1]], database_path = attr(get_record_entry("database"), which = "path"), @@ -191,13 +210,13 @@ record_list_to_df <- function(record_list, collapse = FALSE) { authaddress = get_style("auth-address"), edition = get_style("edition"), worktype = get_style("work-type"), - label = get_style("label"), + label = replace_newline_with_semicolon(get_style("label")), isbn = get_style("isbn"), - language = get_style("language") + language = replace_newline_with_semicolon(get_style("language")) ) ) %>% - dplyr::bind_cols(get_pdfurls(record_list, collapse = collapse)) %>% - dplyr::bind_cols(tibble::tibble( + colbind(get_pdfurls(record_list, collapse = collapse)) %>% + colbind(tibble::tibble( urls_related = get_style(c("urls", "related-urls", "url")), electronic_resource_num = get_style("electronic-resource-num"), custom1 = get_style("custom1"), diff --git a/R/helper.R b/R/helper.R index f464845..5275e72 100644 --- a/R/helper.R +++ b/R/helper.R @@ -20,7 +20,7 @@ colname_i <- function(name, i) { #' @export #' default_xml <- function() { - extdata_file("2019-07-09_KWB_documents.xml") + extdata_file("2020-06-17_KWB-documents.xml") } # first_of_element ------------------------------------------------------------- diff --git a/R/utils-pipe.R b/R/utils-pipe.R index fb8c818..e79f3d8 100644 --- a/R/utils-pipe.R +++ b/R/utils-pipe.R @@ -1,6 +1,6 @@ #' Pipe operator #' -#' See \code{magrittr::\link[magrittr]{\%>\%}} for details. +#' See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details. #' #' @name %>% #' @rdname pipe diff --git a/README.md b/README.md index fac1793..f4465b6 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ -[![Appveyor build Status](https://ci.appveyor.com/api/projects/status/jp6vfegit5c6hhwl?svg=true)](https://ci.appveyor.com/project/KWB-R/kwb-endnote) -[![Travis build Status](https://travis-ci.org/KWB-R/kwb.endnote.svg?branch=master)](https://travis-ci.org/KWB-R/kwb.endnote) +[![R-CMD-check](https://github.com/KWB-R/kwb.endnote/workflows/R-CMD-check/badge.svg)](https://github.com/KWB-R/kwb.endnote/actions?query=workflow%3AR-CMD-check) +[![pkgdown](https://github.com/KWB-R/kwb.endnote/workflows/pkgdown/badge.svg)](https://github.com/KWB-R/kwb.endnote/actions?query=workflow%3Apkgdown) [![codecov](https://codecov.io/github/KWB-R/kwb.endnote/branch/master/graphs/badge.svg)](https://codecov.io/github/KWB-R/kwb.endnote) [![Project Status](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental) [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/kwb.endnote)]() diff --git a/_pkgdown.yml b/_pkgdown.yml index 8f99bae..d9e3e9c 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -3,6 +3,10 @@ authors: href: https://mrustl.de Hauke Sonnenberg: href: https://github.com/hsonne + FAKIN: + href: https://www.kompetenz-wasser.de/en/project/fakin/ + html: Kompetenzzentrum Wasser Berlin gGmbH (KWB): href: https://www.kompetenz-wasser.de html: KWB-documents_20191205.enlEndNote1134113447<style face="normal" font="default" size="100%">Unterstützung der Kanalsanierungsplanung durch statistische und datengetriebene Alterungsmodelle</style>KWB-documents_20191205.enlEndNote1128112847<style face="normal" font="default" size="100%">Organische Spurenstoffe im Regenwasserabfluss Berlins – Jahresfrachten und Vergleich mit Abwassereinträgen</style>internal-pdf://2521957492/WIM 249 - 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internal-pdf://2707206542/Habibi-2020-1247.pdfKWB-documents_20191205.enlEndNote1248124817<style face="normal" font="default" size="100%">Das Mikrosieb als Vorklärung zur Verringerung des Energiebedarfs kleiner Kläranlagen</style>
internal-pdf://4013204759/Schubert-2020-1248.pdf \ No newline at end of file diff --git a/inst/extdata/read_sqlite_file.R b/inst/extdata/read_sqlite_file.R index 21b7471..ff58aff 100644 --- a/inst/extdata/read_sqlite_file.R +++ b/inst/extdata/read_sqlite_file.R @@ -7,22 +7,29 @@ # #install.packages("RSQLite") -library(DBI) +#library(DBI) + +grammar <- list( + dms = "~/Projekte2/dms", + dms_hs = "~/../Downloads/endnote-db/KWB-documents_20191205.Data/sdb", + sdb = "/sdb.eni", + pdb = "/pdb.eni" +) + +#paths <- kwb.utils::resolve(grammar, root = "dms") +paths <- kwb.utils::resolve(grammar, root = "dms_hs") # Create an ephemeral in-memory RSQLite database -#con <- dbConnect(RSQLite::SQLite(), "~/Projekte2/dms/pdb.eni") -con <- dbConnect(RSQLite::SQLite(), "~/Projekte2/dms/sdb.eni") +con <- DBI::dbConnect(RSQLite::SQLite(), paths$pdb) -table_names <- dbListTables(con) +table_names <- DBI::dbListTables(con) -contents <- lapply(setNames(nm = table_names), dbReadTable, con = con) +contents <- lapply(setNames(nm = table_names), DBI::dbReadTable, con = con) -str(contents, 2) +write.csv2(contents$pdf_index[, c(1, 3, 5)], "~/tmp/pdf_index.csv") x <- contents$refs[, c("id", "keywords")] -View(x) - #write.csv(x, "keywords.csv", row.names = FALSE) -dbDisconnect(con) +DBI::dbDisconnect(con) diff --git a/man/check_for_differences.Rd b/man/check_for_differences.Rd index aa80abb..40c179d 100644 --- a/man/check_for_differences.Rd +++ b/man/check_for_differences.Rd @@ -28,8 +28,8 @@ Check two Dataframes for Differences ### Check differences between two different versions of "KWB_documents.xml" ############################################################################ -old_xml <- extdata_file("2019-01-14_KWB_documents.xml") -new_xml <- extdata_file("2019-07-09_KWB_documents.xml") +old_xml <- extdata_file("2020-05-25_KWB-documents.xml") +new_xml <- extdata_file("2020-06-17_KWB-documents.xml") old_list <- kwb.endnote::create_endnote_list(old_xml) new_list <- kwb.endnote::create_endnote_list(new_xml) old_df <- kwb.endnote::create_references_df(old_list) diff --git a/man/get_authors.Rd b/man/get_authors.Rd index 9e9e11d..c72fc1f 100644 --- a/man/get_authors.Rd +++ b/man/get_authors.Rd @@ -4,8 +4,12 @@ \alias{get_authors} \title{Helper function: get authors from list for a reference} \usage{ -get_authors(record_list, col_name = "author", - extract_value = "authors", collapse = FALSE) +get_authors( + record_list, + col_name = "author", + extract_value = "authors", + collapse = FALSE +) } \arguments{ \item{record_list}{list with one record of create_endnote_list()} diff --git a/man/get_keywords.Rd b/man/get_keywords.Rd index 20ee78d..acc14be 100644 --- a/man/get_keywords.Rd +++ b/man/get_keywords.Rd @@ -4,8 +4,12 @@ \alias{get_keywords} \title{Helper function: get keywords from list for a reference} \usage{ -get_keywords(record_list, col_name = "keyword", - extract_value = "keywords", collapse = FALSE) +get_keywords( + record_list, + col_name = "keyword", + extract_value = "keywords", + collapse = FALSE +) } \arguments{ \item{record_list}{list with one record of create_endnote_list()} diff --git a/man/pipe.Rd b/man/pipe.Rd index b7daf6a..0eec752 100644 --- a/man/pipe.Rd +++ b/man/pipe.Rd @@ -7,6 +7,6 @@ lhs \%>\% rhs } \description{ -See \code{magrittr::\link[magrittr]{\%>\%}} for details. +See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details. } \keyword{internal} diff --git a/man/write_clean_references_df_to_xlsx.Rd b/man/write_clean_references_df_to_xlsx.Rd index 18e6399..307ea46 100644 --- a/man/write_clean_references_df_to_xlsx.Rd +++ b/man/write_clean_references_df_to_xlsx.Rd @@ -4,9 +4,14 @@ \alias{write_clean_references_df_to_xlsx} \title{Write Clean References Dataframe to XLSX} \usage{ -write_clean_references_df_to_xlsx(endnote_list, - file = default_clean_xlsx(endnote_list), export_dir = ".", - give_hints = FALSE, dbg = TRUE, ...) +write_clean_references_df_to_xlsx( + endnote_list, + file = default_clean_xlsx(endnote_list), + export_dir = ".", + give_hints = FALSE, + dbg = TRUE, + ... +) } \arguments{ \item{endnote_list}{list created with create_endnote_list()} diff --git a/man/write_references_df_to_xlsx.Rd b/man/write_references_df_to_xlsx.Rd index f59d29e..0f37fc1 100644 --- a/man/write_references_df_to_xlsx.Rd +++ b/man/write_references_df_to_xlsx.Rd @@ -4,9 +4,13 @@ \alias{write_references_df_to_xlsx} \title{Write References Dataframe to XLSX} \usage{ -write_references_df_to_xlsx(endnote_list, - file = default_xlsx(endnote_list), export_dir = ".", dbg = TRUE, - ...) +write_references_df_to_xlsx( + endnote_list, + file = default_xlsx(endnote_list), + export_dir = ".", + dbg = TRUE, + ... +) } \arguments{ \item{endnote_list}{list created with create_endnote_list()} diff --git a/vignettes/analyse-endnote.Rmd b/vignettes/analyse-endnote.Rmd index 122a156..a0ae2ce 100644 --- a/vignettes/analyse-endnote.Rmd +++ b/vignettes/analyse-endnote.Rmd @@ -24,7 +24,8 @@ library(kwb.endnote) endnote_xml <- kwb.endnote::default_xml() -references_df <- kwb.endnote::create_df_from_endnote_xml(endnote_xml) +references_df <- kwb.endnote::create_df_from_endnote_xml(endnote_xml) %>% + dplyr::filter(.data$ref_type_name != "Generic") n_publications <- length(unique(references_df$record_id)) ``` @@ -47,65 +48,70 @@ knitr::kable(refs_by_type) ## By Year -```{r echo=TRUE} -endnote_list <- kwb.endnote::create_endnote_list(endnote_xml) -refs_df <- kwb.endnote::create_references_df(endnote_list) -refs_by_year <- refs_df %>% -dplyr::count(ref_type_name, year) - -knitr::kable(refs_by_year) -``` - ```{r echo=TRUE, fig.width=8, fig.height=9} +endnote_list <- kwb.endnote::create_endnote_list(endnote_xml) +refs_df <- kwb.endnote::create_references_df(endnote_list) -kwb.endnote::plot_pubs_by_year(refs_df) +p1 <- kwb.endnote::plot_pubs_by_year(refs_df) +plotly::ggplotly(p1) ``` -## By Keywords +## By Language ```{r echo=TRUE} +refs_by_language <- refs_df %>% +dplyr::count(language) %>% +dplyr::mutate(percent = round(100*n/nrow(refs_df), 1)) - keywords_df <- kwb.endnote::create_keywords_df(references_df) - - keywords_df %>% - dplyr::filter(.data$n > 1) %>% - knitr::kable() + +knitr::kable(refs_by_language) ``` -Create a word cloud for the keywords + -```{r echo=TRUE, fig.width=7, fig.height=7} + + + -kwb.endnote::plot_wordcloud_keywords(keywords_df) -``` + + + + -## Which fields are filled? + -## Ordered Alphabetically -```{r echo=TRUE} -references_df %>% -dplyr::count(key1, key2, key3, key4) %>% -knitr::kable() -``` + + + + -## Ordered By Frequency -```{r echo=TRUE} -references_df %>% -dplyr::count(key1, key2, key3, key4) %>% -dplyr::arrange(dplyr::desc(n)) %>% -knitr::kable() -``` + -## Ordered By Ref Type Name and Frequency + + + + + + -```{r echo=TRUE} -references_df %>% -dplyr::count(ref_type_name, key1, key2, key3, key4) %>% -dplyr::arrange(ref_type_name, dplyr::desc(n)) %>% -knitr::kable() -``` + + + + + + + + + + + + + + + + ## Has an Abstract? @@ -113,7 +119,7 @@ knitr::kable() ```{r echo=TRUE} refs_with_abstract <- references_df %>% dplyr::filter(.data$key1 == "abstract") %>% - dplyr::count(.data$record_id, .data$rec_number, .data$ref_type_name) + dplyr::count(.data$record_id, .data$rec_number, .data$ref_type_name) n_pubs_with_abstract <- nrow(refs_with_abstract) ### Percent of Publications with Abstracts @@ -144,38 +150,38 @@ These need to be corrected manually! ## By Accessibility Level -Is the accessibility level for the referenc defined in the fiel"custom3" +Is the accessibility level for the referenc defined in the fiel"caption" (confidential or not?) ```{r echo=TRUE} -refs_with_accessability_level <- references_df %>% - dplyr::filter(.data$key1 == "custom3") %>% - dplyr::count(.data$value) +refs_with_accessability_level <- refs_df %>% + dplyr::count(.data$caption) %>% + dplyr::mutate(percent = round(100*n/nrow(refs_df), 1)) + -n_pubs_with_accessability_level <- sum(refs_with_accessability_level$n) +n_pubs_with_accessability_level <- sum(refs_with_accessability_level$n[1:2]) percent_with_accessibility_level <- round(100*n_pubs_with_accessability_level/n_publications, 1) + +is_confidential <- refs_with_accessability_level$caption=="confidential" & !is.na(refs_with_accessability_level$caption) + + knitr::kable(refs_with_accessability_level) -is_confidential <- grepl(paste(c("conf", "PU", "intern", "private"), collapse="|"), - refs_with_accessability_level$value) -n_pubs_confidential <-sum(refs_with_accessability_level$n[is_confidential]) -### in percent -percent_confidential <- 100*sum(refs_with_accessability_level$n[is_confidential])/n_pubs_with_accessability_level ``` Only for `r n_pubs_with_accessability_level` (i.e. `r percent_with_accessibility_level` percent) meta information on the accessibility level is explicitly defined, out of which -`r n_pubs_confidential` are defined as confidential (i.e. -`r round(percent_confidential,1)` of the publications with metadata on the +`r refs_with_accessability_level$n[is_confidential]` are defined as confidential (i.e. +`r refs_with_accessability_level$percent[is_confidential]` of the publications with metadata on the accessibility level). **Recommendation:** -Fill the field **custom3** for all publications with either: +Fill the field **caption** for all publications with either: - **public** or @@ -186,11 +192,10 @@ Fill the field **custom3** for all publications with either: ## By Project -Group references by "custom2" (i.e. "project names") +Group references by "label" (i.e. "project names") ```{r echo=TRUE} -refs_with_project <- references_df %>% - dplyr::filter(.data$key1 == "custom2") +refs_with_project <- refs_df[!is.na(refs_df$label),] n_pubs_with_project_meta <- nrow(refs_with_project) @@ -200,7 +205,7 @@ percent_pubs_with_project_meta <- round(100*n_pubs_with_project_meta/n_publicati unique_project_names <- refs_with_project %>% - dplyr::count(.data$value) + dplyr::count(.data$label) knitr::kable(unique_project_names) @@ -228,7 +233,8 @@ refs_by_author_lastfirst <- references_df %>% dplyr::count(.data$value) %>% dplyr::arrange(dplyr::desc(.data$n)) -kwb.endnote::plot_pubs_by_author(refs_by_author_lastfirst[1:50, ]) +p2 <- kwb.endnote::plot_pubs_by_author(refs_by_author_lastfirst[1:50, ]) +plotly::ggplotly(p2) ``` @@ -272,8 +278,8 @@ refs_by_author_last <- references_df %>% dplyr::count(.data$value) %>% dplyr::arrange(dplyr::desc(.data$n)) -kwb.endnote::plot_pubs_by_author(refs_by_author_last[1:50, ]) - +p3 <- kwb.endnote::plot_pubs_by_author(refs_by_author_last[1:50, ]) +plotly::ggplotly(p3) ``` @@ -330,21 +336,22 @@ for how many we have this metadata: ```{r echo=TRUE} -has_doi <- stringr::str_detect(pubs_in_journals$value, "doi") -pubs_in_journals_with_doi <- pubs_in_journals[has_doi, ] +has_doi <- pubs_in_journals %>% + dplyr::filter(.data$key1 == "electronic-resource-num", + .data$value != "") + -n_pubs_in_journals_with_doi <- nrow(pubs_in_journals_with_doi) +n_pubs_in_journals_with_doi <- nrow(has_doi) -knitr::kable(pubs_in_journals_with_doi) +knitr::kable(has_doi) ``` -Only `r n_pubs_in_journals_with_doi` journal publications have a DOI which is -either encoded in the field **electronic-resource-num** and **urls**. +Only `r n_pubs_in_journals_with_doi` (`r round(100*n_pubs_in_journals_with_doi/n_pubs_in_journals,1)` %) journal publications have a DOI which is encoded in the field **electronic-resource-num**. All DOIs should be entered in the field **electronic-resource-num** in the following format, i.e.: -**https://doi.org/10.6084/m9.figshare.828487** +**10.6084/m9.figshare.828487** # Export References To XLSX diff --git a/vignettes/workflow.Rmd b/vignettes/workflow.Rmd index 48e1621..c975bb3 100644 --- a/vignettes/workflow.Rmd +++ b/vignettes/workflow.Rmd @@ -55,8 +55,8 @@ diffs_df %>% ```{r echo=TRUE} -en_old_xml <- kwb.endnote::extdata_file("2019-01-14_KWB_documents.xml") -en_new_xml <- kwb.endnote::extdata_file("2019-07-09_KWB_documents.xml") +en_old_xml <- kwb.endnote::extdata_file("2020-05-25_KWB-documents.xml") +en_new_xml <- kwb.endnote::extdata_file("2020-06-17_KWB-documents.xml") en_old_list <- kwb.endnote::create_endnote_list(en_old_xml) en_new_list <- kwb.endnote::create_endnote_list(en_new_xml)