openalexR::oa2bibliometrix

[OAIWetz]

Hello everyone,

it seems that there may be an issue with openalexR::oa2bibliometrix: See Manual p. 7 https://cran.r-project.org/web/packages/openalexR/openalexR.pdf

It keeps telling: "Error in openalexR::oa2bibliometrix(df = x) : object 'countrycode' not found In addition: Warning message: In utils::data("countrycode", envir = environment()) : data set ‘countrycode’ not found

When I do variable2 <- openalexR::oa2df(entity = "works", data = (variable1)), it works fine. Then I define a column and values with mutate() in dplyr according to country_code specs and still openalexR::oa2bibliometrix issues a warning and doesn't convert. I could not coerce either.

Working with tidyjson() in a previous step didn't help me as country_code Elements are available from the downloaded data sets.

Could anyone help, please?

Thank you in advance

[trangdata]

Thank you for reporting @OAIWetz. Could you give me a reproducible example (a small snippet of code) that is giving you issues? Or a work id that you're having problems with? I'm not sure if the error is in oa2bibliometrix or oa2df...

[OAIWetz]

My code is the following Coming from openalex API call

https://api.openalex.org/works?filter=authorships.institutions.id:I32021983,locations.source.publisher_lineage:P4310310987|P4310320527|P4310320503|P4310319945|P4310320017|P4310320083|P4310317820|P4310313990|P4310319871&filter=locations.is_oa

(1)

cau_deep_oa <- openalexR::oa_query(entity = "works", authorships.institutions.id = "I32021983", locations.source.publisher_lineage = "(P4310310987 OR P4310320527 OR P4310320503 OR P4310319945 OR P4310320017 OR P4310320083 OR P4310317820 OR P4310313990 OR P4310319871", endpoint = "https://api.openalex.org", identifier = NULL)

(2)

cau_deep_oa_data <- openalexR::oa_request(query_url = cau_deep_oa, count_only = FALSE,verbose = TRUE)

(3)

cau_deep_oa_data_df <- openalexR::oa2df(data = cau_deep_oa_data, entity = "works", verbose = TRUE) converting [===============================] 100% eta: 0s

(4)

cau_deep_oa_bibmet <- openalexR::oa2bibliometrix(cau_deep_oa_data_df)

Error in openalexR::oa2bibliometrix(cau_deep_oa_data_df) : object 'countrycode' not found In addition: Warning message: In utils::data("countrycode", envir = environment()) : data set ‘countrycode’ not found

Best regards

[trangdata]

Oh I see. countrycode is a dataset exported by openalexR, so you would need to call library(openalexR) in your code. I will find a way to fix this so you don't need to do this, but in the mean time, this is a good workaround.

Another note I want to add: in OpenAlex queries, the OR operator is denoted as |, which is already implemented in the package for you. So all you need to supply to the argument is the vector.

So, to simplify your code above:

library(openalexR)
lineages <- c("P4310310987", "P4310320527", "P4310320503", "P4310319945", "P4310320017", "P4310320083", "P4310317820", "P4310313990", "P4310319871")
cau_deep_oa_data_df <- oa_fetch(
  entity = "works",
  authorships.institutions.id = "I32021983", 
  locations.source.publisher_lineage = lineages,
  verbose = TRUE
)
#> Requesting url: https://api.openalex.org/works?filter=authorships.institutions.id%3AI32021983%2Clocations.source.publisher_lineage%3AP4310310987%7CP4310320527%7CP4310320503%7CP4310319945%7CP4310320017%7CP4310320083%7CP4310317820%7CP4310313990%7CP4310319871
#> Getting 39 pages of results with a total of 7646 records...
cau_deep_oa_bibmet <- oa2bibliometrix(cau_deep_oa_data_df)

^{Created on 2023-07-04 with reprex v2.0.2}

[trangdata]

Resolved in #121. Now you can do:

lineages <- c("P4310320017", "P4310320083", "P4310317820")
cau_deep_oa_data_df <- openalexR::oa_fetch(
  entity = "works",
  authorships.institutions.id = "I32021983", 
  locations.source.publisher_lineage = lineages,
  verbose = TRUE
)
#> Requesting url: https://api.openalex.org/works?filter=authorships.institutions.id%3AI3...
#> Getting 7 pages of results with a total of 1233 records...
cau_deep_oa_bibmet <- openalexR::oa2bibliometrix(cau_deep_oa_data_df)

^{Created on 2023-07-20 with reprex v2.0.2}