Merge pull request #41 from massimoaria/for-ropensci

Getting ready for ropensci submission

.Rbuildignore

@@ -15,3 +15,5 @@
 ^vignettes/articles$
 ^data-raw$
 ^codecov\.yml$
+^dev$
+^codemeta\.json$

.github/CONTRIBUTING.md

@@ -0,0 +1,49 @@
+# Contributing to openalexR
+
+First, thank you for considering to contribute to openalexR!
+
+This outlines how to propose a change to this package. 
+For more detailed info about contributing to this, and other tidyverse packages, please see the
+[**development contributing guide**](https://rstd.io/tidy-contrib). 
+
+## Fixing typos
+
+You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the _source_ file. 
+This generally means you'll need to edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, not a `.Rd` file. 
+You can find the `.R` file that generates the `.Rd` by reading the comment in the first line.
+
+## Bigger changes
+
+If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed. 
+If you’ve found a bug, please file an issue that illustrates the bug with a minimal 
+[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed).
+
+### Pull request process
+
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("massimoaria/openalexR", fork = TRUE)`.
+
+*   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
+    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
+*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
+
+*   Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
+    The title of your PR should briefly describe the change.
+    The body of your PR should contain `Fixes #issue-number`.
+
+*  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>.
+
+### Code style
+
+*   New code should follow the tidyverse [style guide](https://style.tidyverse.org). 
+    You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.
+
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.
+
+*  We use [testthat](https://cran.r-project.org/package=testthat) for unit tests.
+   Contributions with test cases included are easier to accept.
+
+## Code of Conduct
+
+Please note that the openalexR project is released with a
+[Contributor Code of Conduct](https://ropensci.org/code-of-conduct/). 
+By contributing to this project you agree to abide by its terms.

.github/workflows/pkgcheck.yaml

@@ -0,0 +1,21 @@
+name: pkgcheck
+
+# This will cancel running jobs once a new run is triggered
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+on:
+  # Manually trigger the Action under Actions/pkgcheck
+  workflow_dispatch:
+  # Run on every push to main
+  push:
+    branches:
+      - main
+      - for-ropensci
+
+jobs:
+  pkgcheck:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: ropensci-review-tools/pkgcheck-action@main

.gitignore

@@ -10,3 +10,4 @@ docs
 vignettes/*.R
 vignettes/*.html
 concept-abbre.csv
+dev/

DESCRIPTION

@@ -2,7 +2,7 @@ Type: Package
 Package: openalexR
 Title: Getting Bibliographic Records from 'OpenAlex' Database Using 'DSL'
     API
-Version: 1.0.1
+Version: 1.0.2
 Authors@R: c(
     person(given = "Massimo",
            family = "Aria",

R/data.R

@@ -10,7 +10,8 @@
 
 #' Index of Countries and their alpha-2 and aplha-3 codes.
 #'
-#' Data frame contains the list of countries and their alpha-2 and aplha-3 codes.\cr
+#' Data frame contains the list of countries and their alpha-2 and
+#' aplha-3 codes.\cr
 #'
 #' @format A data frame with 250 rows and 3 variables:
 #'  \describe{

R/oa2df.R

@@ -10,6 +10,7 @@
 #' Ignored if entity is different from "works". Defaults to TRUE.
 #' @inheritParams oa_query
 #' @inheritParams oa_request
+#' @return A tibble/dataframe result of the original OpenAlex result list.
 #'
 #' @examples
 #' \dontrun{
@@ -38,16 +39,17 @@
 #' )
 #'
 #' oa2df(res, entity = "works")
-#'
 #' }
 #'
 #' @export
 oa2df <- function(data, entity, abstract = TRUE, count_only = FALSE, group_by = NULL, verbose = TRUE) {
-  if (!is.null(group_by)){
+  if (!is.null(group_by)) {
     return(do.call(rbind.data.frame, data))
   }
 
-  if (count_only && length(data) == 4) return(unlist(data))
+  if (count_only && length(data) == 4) {
+    return(unlist(data))
+  }
 
   switch(entity,
     works = works2df(data, abstract, verbose),
@@ -110,7 +112,7 @@ oa2df <- function(data, entity, abstract = TRUE, count_only = FALSE, group_by =
 #' }
 #'
 #' # @export
-
+#'
 works2df <- function(data, abstract = TRUE, verbose = TRUE) {
   if (!is.null(data$id)) {
     data <- list(data)
@@ -216,11 +218,11 @@ works2df <- function(data, abstract = TRUE, verbose = TRUE) {
 abstract_build <- function(ab) {
   w <- rep(names(ab), lengths(ab))
   ind <- unlist(ab)
-  if (is.null(ind)){
-    ab <- ""
-  } else {
-    ab <- paste(w[order(ind)], collapse = " ", sep = "")
+  if (is.null(ind)) {
+    return("")
   }
+
+  paste(w[order(ind)], collapse = " ", sep = "")
 }
 
 
@@ -290,8 +292,11 @@ authors2df <- function(data, verbose = TRUE) {
     item <- data[[i]]
 
     sub_identical <- item[
-      c("id", "works_count", "display_name", "orcid",
-        "works_api_url", "cited_by_count")]
+      c(
+        "id", "works_count", "display_name", "orcid",
+        "works_api_url", "cited_by_count"
+      )
+    ]
 
     sub_id <- list(
       ids = subs_na(item$ids, type = "col_df"),
@@ -300,11 +305,13 @@ authors2df <- function(data, verbose = TRUE) {
 
     sub_flat <- lapply(
       item[c("display_name_alternatives")],
-      subs_na, type = "flat"
+      subs_na,
+      type = "flat"
     )
     sub_rbind_dfs <- lapply(
       item[c("counts_by_year", "x_concepts")],
-      subs_na, type = "rbind_df"
+      subs_na,
+      type = "rbind_df"
     )
 
     sub_affiliation <- item$last_known_institution
@@ -314,7 +321,8 @@ authors2df <- function(data, verbose = TRUE) {
     sub_affiliation <- prepend(sub_affiliation, "affiliation")
 
     list_df[[i]] <- tibble::as_tibble(
-      c(sub_identical, sub_id, sub_flat, sub_rbind_dfs, sub_affiliation))
+      c(sub_identical, sub_id, sub_flat, sub_rbind_dfs, sub_affiliation)
+    )
   }
 
   col_order <- c(
@@ -385,10 +393,13 @@ institutions2df <- function(data, verbose = TRUE) {
 
     item <- data[[i]]
     sub_identical <- item[
-      c("id", "ror", "works_api_url", "type", "works_count",
+      c(
+        "id", "ror", "works_api_url", "type", "works_count",
         "display_name", "country_code", "homepage_url",
         "image_url", "image_thumbnail_url", "cited_by_count",
-        "updated_date", "created_date")]
+        "updated_date", "created_date"
+      )
+    ]
 
     sub_id <- list(
       ids = subs_na(item$ids, type = "col_df"),
@@ -397,21 +408,25 @@ institutions2df <- function(data, verbose = TRUE) {
 
     sub_flat <- lapply(
       item[c("display_name_alternatives", "display_name_acronyms")],
-      subs_na, type = "flat"
+      subs_na,
+      type = "flat"
     )
 
     sub_row <- lapply(
       item[c("international", "geo", "associated_institutions")],
-      subs_na, type = "row_df"
+      subs_na,
+      type = "row_df"
     )
 
     sub_rbind_dfs <- lapply(
       item[c("counts_by_year", "x_concepts")],
-      subs_na, type = "rbind_df"
+      subs_na,
+      type = "rbind_df"
     )
 
     list_df[[i]] <- tibble::as_tibble(
-      c(sub_flat, sub_row, sub_identical, sub_id, sub_rbind_dfs))
+      c(sub_flat, sub_row, sub_identical, sub_id, sub_rbind_dfs)
+    )
   }
 
 
@@ -487,12 +502,16 @@ venues2df <- function(data, verbose = TRUE) {
     item <- data[[i]]
 
     sub_identical <- item[
-      c("id", "display_name", "publisher", "works_count", "cited_by_count",
-        "is_oa", "is_in_doaj", "homepage_url", "works_api_url")]
+      c(
+        "id", "display_name", "publisher", "works_count", "cited_by_count",
+        "is_oa", "is_in_doaj", "homepage_url", "works_api_url"
+      )
+    ]
 
     sub_flat <- lapply(
       item[c("issn_l", "issn")],
-      subs_na, type = "flat"
+      subs_na,
+      type = "flat"
     )
 
     sub_id <- list(
@@ -502,11 +521,13 @@ venues2df <- function(data, verbose = TRUE) {
 
     sub_rbind_dfs <- lapply(
       item[c("counts_by_year", "x_concepts")],
-      subs_na, type = "rbind_df"
+      subs_na,
+      type = "rbind_df"
     )
 
     list_df[[i]] <- tibble::as_tibble(
-      c(sub_identical, sub_flat, sub_id, sub_rbind_dfs))
+      c(sub_identical, sub_flat, sub_id, sub_rbind_dfs)
+    )
   }
 
   col_order <- c(
@@ -578,9 +599,12 @@ concepts2df <- function(data, verbose = TRUE) {
     item <- data[[i]]
 
     sub_identical <- item[
-      c("id", "display_name", "wikidata", "level", "description",
-        "image_url", "image_thumbnail_url",  "works_count", "cited_by_count",
-        "works_api_url")]
+      c(
+        "id", "display_name", "wikidata", "level", "description",
+        "image_url", "image_thumbnail_url", "works_count", "cited_by_count",
+        "works_api_url"
+      )
+    ]
 
     sub_id <- list(
       ids = subs_na(item$ids, type = "col_df"),
@@ -589,12 +613,14 @@ concepts2df <- function(data, verbose = TRUE) {
 
     sub_rbind_dfs <- lapply(
       item[c("counts_by_year", "ancestors", "related_concepts")],
-      subs_na, type = "rbind_df"
+      subs_na,
+      type = "rbind_df"
     )
 
     sub_row <- lapply(
       item$international[c("display_name", "description")],
-      subs_na, type = "row_df"
+      subs_na,
+      type = "row_df"
     )
     names(sub_row) <- paste(names(sub_row), "international", sep = "_")
 
@@ -682,7 +708,8 @@ snowball2df <- function(data, verbose = FALSE) {
 
   nodes_augmented <- merge(
     merge(nodes, citing, all.x = TRUE),
-    cited_by, all.x = TRUE
+    cited_by,
+    all.x = TRUE
   )
 
   nodes_augmented$connection <- apply(