From df910d0d4112566ed3c415fddc03429eb87ed427 Mon Sep 17 00:00:00 2001
From: Raffaele Mancuso <raffaele.mancuso4@unibo.it>
Date: Tue, 4 Feb 2025 12:48:33 +0100
Subject: [PATCH] Fix checks

Fixes #314
---
 DESCRIPTION                    |   2 +-
 R/oa_fetch.R                   |  10 +++++-----
 data-raw/coverage-works.csv    |   3 ++-
 data-raw/gen-data.R            |   5 ++++-
 data/concept_abbrev.rda        | Bin 672 -> 677 bytes
 data/oa2df_coverage.rda        | Bin 2421 -> 2441 bytes
 man/oa_fetch.Rd                |  10 +++++-----
 man/oa_random.Rd               |  10 +++++-----
 man/snowball2df.Rd             |   5 +----
 tests/testthat/test-oa_fetch.R |   9 ++++-----
 10 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ff53ac9..92237d7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -54,4 +54,4 @@ LazyData: true
 RoxygenNote: 7.3.2
 Config/testthat/edition: 3
 Depends: 
-    R (>= 2.10)
+    R (>= 3.5)
diff --git a/R/oa_fetch.R b/R/oa_fetch.R
index 98dd75d..050fbe2 100644
--- a/R/oa_fetch.R
+++ b/R/oa_fetch.R
@@ -22,11 +22,11 @@ oa_entities <- function() {
 #' The argument is ignored if entity is different from "works".
 #' @param output Character.
 #' Type of output, one of `"tibble"`, `"dataframe"`, `"list"`, or `"raw"`.
-##' \itemize{
-##'  \item{"tibble"}: {a tibble tidy data}
-##'  \item{"dataframe"}: {a base data.frame tidy data}
-##'  \item{"list"}: {a list of parsed JSON contents}
-##'  \item{"raw"}: {a list of raw JSON strings (length depends on query)}
+##' \describe{
+##'  \item{tibble}{a tibble tidy data}
+##'  \item{dataframe}{a base data.frame tidy data}
+##'  \item{list}{a list of parsed JSON contents}
+##'  \item{raw}{a list of raw JSON strings (length depends on query)}
 ##' }
 #'
 #' @return A data.frame or a list. Result of the query.
diff --git a/data-raw/coverage-works.csv b/data-raw/coverage-works.csv
index 0182d81..ab9d6ac 100644
--- a/data-raw/coverage-works.csv
+++ b/data-raw/coverage-works.csv
@@ -1,5 +1,6 @@
 original,oa2df,comment
 abstract_inverted_index,abstract,reconstructed from inverted index
+abstract_inverted_index_v3,NA,
 apc_list.currency,apc.currency,
 apc_list.provenance,apc.provenance,
 apc_list.value,apc.value,
@@ -83,4 +84,4 @@ topics,topics,
 type,type,
 type_crossref,NA,
 updated_date,NA,
-versions,NA,
\ No newline at end of file
+versions,NA,
diff --git a/data-raw/gen-data.R b/data-raw/gen-data.R
index fde1f63..a92d67e 100644
--- a/data-raw/gen-data.R
+++ b/data-raw/gen-data.R
@@ -1,3 +1,5 @@
+source("./R/oa_fetch.R")
+
 # concept_abbrev <- tibble::tribble(
 #                                 ~id,           ~display_name, ~abbreviation,
 #    "https://openalex.org/C41008148",      "Computer science",  "Comput Sci",
@@ -47,7 +49,8 @@ concept_abbrev <- tibble::tribble(
 oa2df_coverage <- list()
 for (entity in setdiff(oa_entities(), "concepts")) {
   oa2df_coverage[[entity]] <- readr::read_csv(
-    sprintf("data-raw/coverage-%s.csv", entity)
+    sprintf("data-raw/coverage-%s.csv", entity),
+    show_col_types = FALSE
   )
 }
 
diff --git a/data/concept_abbrev.rda b/data/concept_abbrev.rda
index bdfa93a602f2608a6bbc8fbbcb2c2265806e382c..8d3c7f40a1467dc3656cd542974632a450a7afd6 100644
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diff --git a/data/oa2df_coverage.rda b/data/oa2df_coverage.rda
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diff --git a/man/oa_fetch.Rd b/man/oa_fetch.Rd
index 3d21c7d..c261ff3 100644
--- a/man/oa_fetch.Rd
+++ b/man/oa_fetch.Rd
@@ -68,11 +68,11 @@ See more at <https://docs.openalex.org/how-to-use-the-api/get-groups-of-entities
 
 \item{output}{Character.
 Type of output, one of `"tibble"`, `"dataframe"`, `"list"`, or `"raw"`.
-\itemize{
- \item{"tibble"}: {a tibble tidy data}
- \item{"dataframe"}: {a base data.frame tidy data}
- \item{"list"}: {a list of parsed JSON contents}
- \item{"raw"}: {a list of raw JSON strings (length depends on query)}
+\describe{
+ \item{tibble}{a tibble tidy data}
+ \item{dataframe}{a base data.frame tidy data}
+ \item{list}{a list of parsed JSON contents}
+ \item{raw}{a list of raw JSON strings (length depends on query)}
 }}
 
 \item{abstract}{Logical. If TRUE, the function returns also the abstract of each item.
diff --git a/man/oa_random.Rd b/man/oa_random.Rd
index 42ad3da..61d5f95 100644
--- a/man/oa_random.Rd
+++ b/man/oa_random.Rd
@@ -18,11 +18,11 @@ If not provided, `entity` is guessed from `identifier`.}
 
 \item{output}{Character.
 Type of output, one of `"tibble"`, `"dataframe"`, `"list"`, or `"raw"`.
-\itemize{
- \item{"tibble"}: {a tibble tidy data}
- \item{"dataframe"}: {a base data.frame tidy data}
- \item{"list"}: {a list of parsed JSON contents}
- \item{"raw"}: {a list of raw JSON strings (length depends on query)}
+\describe{
+ \item{tibble}{a tibble tidy data}
+ \item{dataframe}{a base data.frame tidy data}
+ \item{list}{a list of parsed JSON contents}
+ \item{raw}{a list of raw JSON strings (length depends on query)}
 }}
 
 \item{endpoint}{Character. URL of the OpenAlex Endpoint API server.
diff --git a/man/snowball2df.Rd b/man/snowball2df.Rd
index 919d10c..cb7cb63 100644
--- a/man/snowball2df.Rd
+++ b/man/snowball2df.Rd
@@ -27,10 +27,7 @@ for each work/row i:
 - connection_count: number of works in the universe linked to i (degree of i)
 }
 \description{
-|  id|title |...|cited_by_count| referenced_works   |cited_by |...|
-| 100|foo   |...|             1| 98, 99             |101      |...|
-| 200|bar   |...|             2| 198, 199           |201, 202 |...|
-| 300|wug   |...|             2| 296, 297, 298, 299 |301, 302 |...|
+Flatten snowball result
 }
 \examples{
 \dontrun{
diff --git a/tests/testthat/test-oa_fetch.R b/tests/testthat/test-oa_fetch.R
index ace97ae..996cf9e 100644
--- a/tests/testthat/test-oa_fetch.R
+++ b/tests/testthat/test-oa_fetch.R
@@ -416,20 +416,19 @@ test_that("different paging methods yield the same result", {
     entity = "works",
     title.search = c("bibliometric analysis", "science mapping"),
     cited_by_count = ">50",
+    options = list(select = "id"),
     from_publication_date = "2021-01-01",
     to_publication_date = "2021-12-31",
-    options = list(select = "id"),
+    verbose = TRUE,
     pages = c(2, 4:5),
-    per_page = 10,
-    verbose = TRUE
+    per_page = 10
   )
+  
   expect_equal(
     w0[c(11:20, 31:min(50, nrow(w0))), ],
     w24
   )
 
-
-
 })
 
 test_that("pages works", {