anim_behavior/name_standardizer.R at main · BrunaLab/anim_behavior · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
names_standardizer <- function(combined_data) {
  names(combined_data)[names(combined_data) == "prism:url"] <- "URL"
  names(combined_data)[names(combined_data) == "dc:identifier"] <- "scopus_article_id"
  names(combined_data)[names(combined_data) == "eid"] <- "eid"
  names(combined_data)[names(combined_data) == "dc:title"] <- "TI"
  names(combined_data)[names(combined_data) == "prism:publicationName"] <- "SO"
  names(combined_data)[names(combined_data) == "prism:issn"] <- "SN"
  names(combined_data)[names(combined_data) == "prism:volume"] <- "VL"
  names(combined_data)[names(combined_data) == "prism:issueIdentifier"] <- "IS"
  names(combined_data)[names(combined_data) == "prism:pageRange"] <- "page_range"
  names(combined_data)[names(combined_data) == "prism:coverDisplayDate"] <- "PY"
  names(combined_data)[names(combined_data) == "prism:doi"] <- "DI"
  names(combined_data)[names(combined_data) == "dc:description"] <- "AB"
  names(combined_data)[names(combined_data) == "citedby-count"] <- "TC"
  names(combined_data)[names(combined_data) == "pubmed-id"] <- "PI"
  names(combined_data)[names(combined_data) == "prism:aggregationType"] <- "PT"
  names(combined_data)[names(combined_data) == "subtypeDescription"] <- "DT"
  names(combined_data)[names(combined_data) == "authkeywords"] <- "DE"
  names(combined_data)[names(combined_data) == "source-id"] <- "scopus_source_id"
  names(combined_data)[names(combined_data) == "fund-no"] <- "funder_id"
  names(combined_data)[names(combined_data) == "openaccess"] <- "OA"
  names(combined_data)[names(combined_data) == "entry_number"] <- "entry_no"
  names(combined_data)[names(combined_data) == "article-number"] <- "article_number"
  names(combined_data)[names(combined_data) == "prism:eIssn"] <- "EI"
  names(combined_data)[names(combined_data) == "fund-sponsor"] <- "FU"
  names(combined_data)[names(combined_data) == "pii"] <- "UT" #elsevier_pub_identifier

  # from data_authors
  names(combined_data)[names(combined_data) == "@seq"] <- "author_order"
  names(combined_data)[names(combined_data) == "authid"] <- "SID"
  names(combined_data)[names(combined_data) == "authname"] <- "AF"
  names(combined_data)[names(combined_data) == "surname"] <- "surname"
  names(combined_data)[names(combined_data) == "given-name"] <- "given_name"
  names(combined_data)[names(combined_data) == "initials"] <- "first_middle_initials"
  names(combined_data)[names(combined_data) == "afid.$"] <- "affil_id"
  names(combined_data)[names(combined_data) == "orcid"] <- "OI"

  # from affiliations
  names(combined_data)[names(combined_data) == "afid"] <- "affil_id"
  names(combined_data)[names(combined_data) == "affilname"] <- "affiliation"
  names(combined_data)[names(combined_data) == "affiliation-city"] <- "city"
  names(combined_data)[names(combined_data) == "affiliation-country"] <- "country"


  # to be deleted
  names(combined_data)[names(combined_data) == "dc:creator"] <- "creator"
  names(combined_data)[names(combined_data) == "prism:coverDate"] <- "cover_date"
  names(combined_data)[names(combined_data) == "subtype"] <- "document_type_abbrev"
  names(combined_data)[names(combined_data) == "author-count.@limit"] <- "author_count_limit"
  names(combined_data)[names(combined_data) == "author-count.@total"] <- "author_count_total"
  names(combined_data)[names(combined_data) == "author-count.$"] <- "author_count"
  names(combined_data)[names(combined_data) == "openaccessFlag"] <- "open_access_tf"

  names(combined_data)[names(combined_data) == "freetoread.value.$"] <- "free_to_read"
  names(combined_data)[names(combined_data) == "freetoreadLabel.value.$"] <- "free_to_read_label"


  names(combined_data)[names(combined_data) == "fund-acr"] <- "funder_acronym"
  names(combined_data)[names(combined_data) == "author-url"] <- "author_url"
  names(combined_data)[names(combined_data) == "affiliation-url"] <- "affil_url"

  combined_data<-replace(combined_data, combined_data =="", NA)
  #
  combined_data<-combined_data %>%
    mutate(source=str_replace(source, "./data_raw/scopus_api/papers/scopus_", "")) %>%
    mutate(source=str_replace(source, "_papers", "")) %>%
    mutate(source=str_replace(source, "./data_raw/scopus_api/authors/scopus_", "")) %>%
    mutate(source=str_replace(source, "_authors", "")) %>%
    mutate(source=str_replace(source, "./data_raw/scopus_api/affils/scopus_", "")) %>%
    mutate(source=str_replace(source, "_affils", "")) %>%

    relocate(entry_no,.before = 1)

  return(combined_data)
}