Knowledge Discovery DRAFT

Knowledge Discovery based on the IPBES Assessments

Author

Affiliation

Rainer M Krug

University of Zürich

Published

July 23, 2024

Doi

xxxxxxxxxxxxxx4

Abstract

The assessments Linked Open Data is used to conduct analysis and searches to discover new knowledge related to the assessmwents.

Introduction

IPBES assessments were converted / enhanced into Linked Open Data (LOD) using the ttl format.

Three assessments available in ttl format are currently:

the First Global Assessment (GA1)
the Values Assessment (VA)
the Invasive Alien Species Assessment (IAS).

Methods

Manual fixes to ref list

The following DOIS are wrong in the original csv and were corrected manually: 10.1016/j.ecolmodel.2017,04.005 should be 10.1016/j.ecolmodel.2017.04.005

Import References and get OpenAlex Works

Show the code

fn <- file.path("output", "key_works.rds")
if (!file.exists(fn)) {
  refs_file <- file.path("input", "Query_Submessage_ref_GA.csv")

  refs <- refs_file |>
    read.csv(
      header = TRUE,
      sep = ",",
      quote = "\"",
      stringsAsFactors = FALSE
    ) |>
    tibble::as_tibble() |>
    dplyr::mutate(
      bm = gsub("http://ontology.ipbes.net/report/bgm/", "", Background.Message),
      sm = gsub("http://ontology.ipbes.net/report/subm/", "", Sub.Message),
      loc = Level.if.Confidence,
      zotero = zotero,
      doi = gsub("https://doi.org/", "", doi),
      citation = description,
      Level.if.Confidence = NULL,
      Background.Message = NULL,
      Sub.Message = NULL,
      X = NULL
    ) |>
    select(
      bm,
      sm,
      loc,
      zotero,
      doi,
      citation
    ) |>
    distinct()

  refs$loc[refs$loc == ""] <- as.character(NA)


  key_works <- openalexR::oa_fetch(
    entity = "works",
    doi = refs$doi[refs$doi != ""] |> unique(),
    options = list(
      # select = c(
      #     "id",
      #     "doi",
      #     "authorships",
      #     "abstract_inverted_index",
      #     "publication_year"
      # )
    ),
    verbose = TRUE
  )

  refs$doi <- ifelse(
    refs$doi == "",
    as.character(NA),
    paste0("https://doi.org/", refs$doi)
  )

  refs |>
    dplyr::left_join(
      y = key_works,
      by = "doi"
    ) |>
    saveRDS(
      file = fn
    )
}

key_works <- readRDS(fn)

Run Snowball Searches for each key-paper individually

Show the code

kws <- key_works |>
  dplyr::group_by(id) |>
  dplyr::summarise(
    bms = list(bm = bm),
    .groups = "keep"
  ) |>
  dplyr::ungroup() |>
  dplyr::mutate(
    id = gsub(
      pattern = "https://openalex.org/",
      replacement = "",
      x = id
    )
  )

dir.create(file.path("output", "snowballs"), showWarnings = FALSE)

tic()

pbapply::pblapply(
  seq_along(kws$id[!is.na(kws$id)]),
  function(i) {
    tic()
    fn <- file.path("output", "snowballs", paste0(kws$id[i], ".rds"))
    if (file.exists(fn)) {
      message("Skippig ", i, " of ", nrow(kws), " - file exists")
    } else {
      message("Snowballing ", kws$id[i], " --- ", i, " of ", nrow(kws), " ...")

      try(
        kws$id[[i]] |>
          openalexR::oa_snowball() |>
          saveRDS(file = fn)
      )
    }
    toc()
  }
) |>
  invisible()

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Skippig 476 of 2240 - file exists

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Skippig 488 of 2240 - file exists

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Skippig 523 of 2240 - file exists

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Skippig 528 of 2240 - file exists

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Snowballing W2033458484 --- 529 of 2240 ...

Error in stats::complete.cases(edges) : 
  no input has determined the number of cases
1.127 sec elapsed

Skippig 530 of 2240 - file exists

0.001 sec elapsed

Skippig 531 of 2240 - file exists

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Skippig 533 of 2240 - file exists

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Skippig 534 of 2240 - file exists

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Skippig 536 of 2240 - file exists

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Skippig 537 of 2240 - file exists

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Skippig 540 of 2240 - file exists

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Skippig 541 of 2240 - file exists

0.001 sec elapsed

Skippig 542 of 2240 - file exists

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Skippig 543 of 2240 - file exists

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Skippig 544 of 2240 - file exists

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Skippig 545 of 2240 - file exists

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Skippig 546 of 2240 - file exists

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Skippig 547 of 2240 - file exists

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Skippig 548 of 2240 - file exists

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Skippig 549 of 2240 - file exists

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Skippig 550 of 2240 - file exists

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Skippig 553 of 2240 - file exists

0.001 sec elapsed

Skippig 554 of 2240 - file exists

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Skippig 555 of 2240 - file exists

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Skippig 557 of 2240 - file exists

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Skippig 558 of 2240 - file exists

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Skippig 567 of 2240 - file exists

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Skippig 569 of 2240 - file exists

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Skippig 573 of 2240 - file exists

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Skippig 574 of 2240 - file exists

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Skippig 575 of 2240 - file exists

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Skippig 576 of 2240 - file exists

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Skippig 577 of 2240 - file exists

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Skippig 579 of 2240 - file exists

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Skippig 580 of 2240 - file exists

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Skippig 585 of 2240 - file exists

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Snowballing W2042138573 --- 586 of 2240 ...

Error in stats::complete.cases(edges) : 
  no input has determined the number of cases
0.859 sec elapsed

Skippig 587 of 2240 - file exists

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Skippig 588 of 2240 - file exists

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Skippig 592 of 2240 - file exists

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Skippig 594 of 2240 - file exists

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Skippig 595 of 2240 - file exists

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Skippig 597 of 2240 - file exists

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Skippig 599 of 2240 - file exists

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Skippig 600 of 2240 - file exists

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Skippig 601 of 2240 - file exists

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Skippig 602 of 2240 - file exists

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Skippig 603 of 2240 - file exists

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Skippig 604 of 2240 - file exists

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Skippig 605 of 2240 - file exists

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Skippig 606 of 2240 - file exists

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Skippig 607 of 2240 - file exists

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Skippig 608 of 2240 - file exists

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Skippig 609 of 2240 - file exists

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Skippig 610 of 2240 - file exists

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Skippig 611 of 2240 - file exists

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Skippig 612 of 2240 - file exists

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Skippig 613 of 2240 - file exists

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Skippig 614 of 2240 - file exists

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Skippig 615 of 2240 - file exists

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Skippig 616 of 2240 - file exists

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Skippig 617 of 2240 - file exists

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Skippig 618 of 2240 - file exists

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Skippig 633 of 2240 - file exists

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Skippig 638 of 2240 - file exists

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Skippig 639 of 2240 - file exists

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Skippig 650 of 2240 - file exists

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Skippig 651 of 2240 - file exists

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Skippig 660 of 2240 - file exists

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Skippig 661 of 2240 - file exists

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Skippig 662 of 2240 - file exists

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Skippig 665 of 2240 - file exists

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Skippig 666 of 2240 - file exists

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Skippig 667 of 2240 - file exists

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Skippig 668 of 2240 - file exists

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Skippig 669 of 2240 - file exists

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Skippig 676 of 2240 - file exists

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Skippig 711 of 2240 - file exists

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Skippig 718 of 2240 - file exists

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Skippig 725 of 2240 - file exists

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Skippig 727 of 2240 - file exists

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Skippig 730 of 2240 - file exists

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Skippig 737 of 2240 - file exists

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Skippig 739 of 2240 - file exists

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Skippig 740 of 2240 - file exists

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Skippig 741 of 2240 - file exists

0.001 sec elapsed

Skippig 742 of 2240 - file exists

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Skippig 744 of 2240 - file exists

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Skippig 750 of 2240 - file exists

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Skippig 767 of 2240 - file exists

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Skippig 768 of 2240 - file exists

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Skippig 774 of 2240 - file exists

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Skippig 777 of 2240 - file exists

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Skippig 782 of 2240 - file exists

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Skippig 787 of 2240 - file exists

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Skippig 788 of 2240 - file exists

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Skippig 789 of 2240 - file exists

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Skippig 791 of 2240 - file exists

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Skippig 792 of 2240 - file exists

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Skippig 793 of 2240 - file exists

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Skippig 794 of 2240 - file exists

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Skippig 797 of 2240 - file exists

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Skippig 798 of 2240 - file exists

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Skippig 799 of 2240 - file exists

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Skippig 800 of 2240 - file exists

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Skippig 801 of 2240 - file exists

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Skippig 802 of 2240 - file exists

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Skippig 803 of 2240 - file exists

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Skippig 804 of 2240 - file exists

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Skippig 806 of 2240 - file exists

0.001 sec elapsed

Skippig 807 of 2240 - file exists

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Skippig 808 of 2240 - file exists

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Skippig 809 of 2240 - file exists

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Skippig 812 of 2240 - file exists

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Skippig 814 of 2240 - file exists

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Skippig 815 of 2240 - file exists

0.001 sec elapsed

Skippig 816 of 2240 - file exists

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Skippig 817 of 2240 - file exists

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Skippig 818 of 2240 - file exists

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Skippig 819 of 2240 - file exists

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Skippig 820 of 2240 - file exists

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Skippig 824 of 2240 - file exists

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Skippig 825 of 2240 - file exists

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Skippig 826 of 2240 - file exists

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Skippig 827 of 2240 - file exists

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Skippig 834 of 2240 - file exists

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Skippig 850 of 2240 - file exists

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Skippig 1316 of 2240 - file exists

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Skippig 1317 of 2240 - file exists

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Skippig 1318 of 2240 - file exists

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Skippig 1319 of 2240 - file exists

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Skippig 1320 of 2240 - file exists

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Skippig 1321 of 2240 - file exists

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Skippig 1322 of 2240 - file exists

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Skippig 1323 of 2240 - file exists

0.001 sec elapsed

Skippig 1324 of 2240 - file exists

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Skippig 1325 of 2240 - file exists

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Skippig 1326 of 2240 - file exists

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Skippig 1327 of 2240 - file exists

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Skippig 1328 of 2240 - file exists

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Skippig 1329 of 2240 - file exists

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Skippig 1330 of 2240 - file exists

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Skippig 1331 of 2240 - file exists

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Skippig 1332 of 2240 - file exists

0.001 sec elapsed

Skippig 1333 of 2240 - file exists

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Skippig 1334 of 2240 - file exists

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Skippig 1335 of 2240 - file exists

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Skippig 1336 of 2240 - file exists

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Skippig 1337 of 2240 - file exists

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Skippig 1338 of 2240 - file exists

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Skippig 1339 of 2240 - file exists

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Skippig 1340 of 2240 - file exists

0 sec elapsed

Skippig 1341 of 2240 - file exists

0.001 sec elapsed

Skippig 1342 of 2240 - file exists

0 sec elapsed

Skippig 1343 of 2240 - file exists

0 sec elapsed

Skippig 1344 of 2240 - file exists

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Skippig 1345 of 2240 - file exists

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Skippig 1346 of 2240 - file exists

0 sec elapsed

Skippig 1347 of 2240 - file exists

0 sec elapsed

Skippig 1348 of 2240 - file exists

0 sec elapsed

Skippig 1349 of 2240 - file exists

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Skippig 1350 of 2240 - file exists

0 sec elapsed

Skippig 1351 of 2240 - file exists

0.001 sec elapsed

Skippig 1352 of 2240 - file exists

0 sec elapsed

Skippig 1353 of 2240 - file exists

0 sec elapsed

Skippig 1354 of 2240 - file exists

0 sec elapsed

Skippig 1355 of 2240 - file exists

0 sec elapsed

Skippig 1356 of 2240 - file exists

0 sec elapsed

Skippig 1357 of 2240 - file exists

0 sec elapsed

Skippig 1358 of 2240 - file exists

0 sec elapsed

Skippig 1359 of 2240 - file exists

0 sec elapsed

Skippig 1360 of 2240 - file exists

0 sec elapsed

Skippig 1361 of 2240 - file exists

0 sec elapsed

Skippig 1362 of 2240 - file exists

0 sec elapsed

Skippig 1363 of 2240 - file exists

0 sec elapsed

Skippig 1364 of 2240 - file exists

0 sec elapsed

Skippig 1365 of 2240 - file exists

0 sec elapsed

Skippig 1366 of 2240 - file exists

0 sec elapsed

Skippig 1367 of 2240 - file exists

0 sec elapsed

Skippig 1368 of 2240 - file exists

0 sec elapsed

Skippig 1369 of 2240 - file exists

0 sec elapsed

Skippig 1370 of 2240 - file exists

0.001 sec elapsed

Skippig 1371 of 2240 - file exists

0 sec elapsed

Skippig 1372 of 2240 - file exists

0 sec elapsed

Skippig 1373 of 2240 - file exists

0 sec elapsed

Skippig 1374 of 2240 - file exists

0 sec elapsed

Skippig 1375 of 2240 - file exists

0 sec elapsed

Skippig 1376 of 2240 - file exists

0.001 sec elapsed

Skippig 1377 of 2240 - file exists

0 sec elapsed

Skippig 1378 of 2240 - file exists

0 sec elapsed

Skippig 1379 of 2240 - file exists

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Skippig 1380 of 2240 - file exists

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Skippig 1381 of 2240 - file exists

0 sec elapsed

Skippig 1382 of 2240 - file exists

0.001 sec elapsed

Skippig 1383 of 2240 - file exists

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Skippig 1384 of 2240 - file exists

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Skippig 1385 of 2240 - file exists

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Skippig 1386 of 2240 - file exists

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Skippig 1387 of 2240 - file exists

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Skippig 1388 of 2240 - file exists

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Skippig 1389 of 2240 - file exists

0 sec elapsed

Skippig 1390 of 2240 - file exists

0.001 sec elapsed

Skippig 1391 of 2240 - file exists

0 sec elapsed

Skippig 1392 of 2240 - file exists

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Skippig 1393 of 2240 - file exists

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Skippig 1394 of 2240 - file exists

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Skippig 1395 of 2240 - file exists

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Skippig 1396 of 2240 - file exists

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Skippig 1397 of 2240 - file exists

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Skippig 1398 of 2240 - file exists

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Skippig 1399 of 2240 - file exists

0.001 sec elapsed

Skippig 1400 of 2240 - file exists

0 sec elapsed

Skippig 1401 of 2240 - file exists

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Skippig 1402 of 2240 - file exists

0 sec elapsed

Skippig 1403 of 2240 - file exists

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Skippig 1404 of 2240 - file exists

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Skippig 1405 of 2240 - file exists

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Skippig 1406 of 2240 - file exists

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Skippig 1407 of 2240 - file exists

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Skippig 1408 of 2240 - file exists

0 sec elapsed

Skippig 1409 of 2240 - file exists

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Skippig 1410 of 2240 - file exists

0.001 sec elapsed

Skippig 1411 of 2240 - file exists

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Skippig 1412 of 2240 - file exists

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Skippig 1413 of 2240 - file exists

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Skippig 1414 of 2240 - file exists

0 sec elapsed

Skippig 1415 of 2240 - file exists

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Skippig 1416 of 2240 - file exists

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Skippig 1417 of 2240 - file exists

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Skippig 1418 of 2240 - file exists

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Skippig 1419 of 2240 - file exists

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Skippig 1420 of 2240 - file exists

0.001 sec elapsed

Skippig 1421 of 2240 - file exists

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Skippig 1422 of 2240 - file exists

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Skippig 1423 of 2240 - file exists

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Skippig 1424 of 2240 - file exists

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Skippig 1425 of 2240 - file exists

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Skippig 1426 of 2240 - file exists

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Skippig 1427 of 2240 - file exists

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Skippig 1428 of 2240 - file exists

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Skippig 1429 of 2240 - file exists

0.001 sec elapsed

Skippig 1430 of 2240 - file exists

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Skippig 1431 of 2240 - file exists

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Skippig 1432 of 2240 - file exists

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Skippig 1433 of 2240 - file exists

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Skippig 1434 of 2240 - file exists

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Skippig 1436 of 2240 - file exists

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Skippig 1437 of 2240 - file exists

0.001 sec elapsed

Skippig 1438 of 2240 - file exists

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Skippig 1439 of 2240 - file exists

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Skippig 1440 of 2240 - file exists

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Skippig 1441 of 2240 - file exists

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Skippig 1442 of 2240 - file exists

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Skippig 1444 of 2240 - file exists

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Skippig 1445 of 2240 - file exists

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Skippig 1446 of 2240 - file exists

0.001 sec elapsed

Skippig 1447 of 2240 - file exists

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Skippig 1449 of 2240 - file exists

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Skippig 1450 of 2240 - file exists

0.001 sec elapsed

Skippig 1451 of 2240 - file exists

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Skippig 1453 of 2240 - file exists

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Skippig 1454 of 2240 - file exists

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Skippig 1455 of 2240 - file exists

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Skippig 1457 of 2240 - file exists

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Skippig 1459 of 2240 - file exists

0.001 sec elapsed

Skippig 1460 of 2240 - file exists

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Skippig 1461 of 2240 - file exists

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Skippig 1462 of 2240 - file exists

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Skippig 1463 of 2240 - file exists

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Skippig 1464 of 2240 - file exists

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Skippig 1465 of 2240 - file exists

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Skippig 1466 of 2240 - file exists

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Skippig 1467 of 2240 - file exists

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Skippig 1468 of 2240 - file exists

0.001 sec elapsed

Skippig 1469 of 2240 - file exists

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Skippig 1470 of 2240 - file exists

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Skippig 1471 of 2240 - file exists

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Skippig 1472 of 2240 - file exists

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Skippig 1473 of 2240 - file exists

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Skippig 1474 of 2240 - file exists

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Skippig 1475 of 2240 - file exists

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Skippig 1476 of 2240 - file exists

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Skippig 1477 of 2240 - file exists

0.001 sec elapsed

Skippig 1478 of 2240 - file exists

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Skippig 1479 of 2240 - file exists

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Skippig 1480 of 2240 - file exists

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Skippig 1481 of 2240 - file exists

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Skippig 1482 of 2240 - file exists

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Skippig 1483 of 2240 - file exists

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Skippig 1484 of 2240 - file exists

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Skippig 1485 of 2240 - file exists

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Skippig 1486 of 2240 - file exists

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Skippig 1487 of 2240 - file exists

0.001 sec elapsed

Skippig 1488 of 2240 - file exists

0 sec elapsed

Skippig 1489 of 2240 - file exists

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Skippig 1490 of 2240 - file exists

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Skippig 1491 of 2240 - file exists

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Skippig 1492 of 2240 - file exists

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Skippig 1493 of 2240 - file exists

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Skippig 1494 of 2240 - file exists

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Skippig 1495 of 2240 - file exists

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Skippig 1496 of 2240 - file exists

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Skippig 1497 of 2240 - file exists

0.001 sec elapsed

Skippig 1498 of 2240 - file exists

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Skippig 1499 of 2240 - file exists

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Skippig 1500 of 2240 - file exists

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Skippig 1501 of 2240 - file exists

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Skippig 1502 of 2240 - file exists

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Skippig 1503 of 2240 - file exists

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Skippig 1504 of 2240 - file exists

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Skippig 1505 of 2240 - file exists

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Skippig 1507 of 2240 - file exists

0 sec elapsed

Skippig 1508 of 2240 - file exists

0 sec elapsed

Snowballing W2232195992 --- 1509 of 2240 ...

Error in stats::complete.cases(edges) : 
  no input has determined the number of cases
0.797 sec elapsed

Skippig 1510 of 2240 - file exists

0.001 sec elapsed

Skippig 1511 of 2240 - file exists

0 sec elapsed

Skippig 1512 of 2240 - file exists

0.001 sec elapsed

Skippig 1513 of 2240 - file exists

0 sec elapsed

Skippig 1514 of 2240 - file exists

0 sec elapsed

Skippig 1515 of 2240 - file exists

0 sec elapsed

Skippig 1516 of 2240 - file exists

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Skippig 1517 of 2240 - file exists

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Skippig 1518 of 2240 - file exists

0.001 sec elapsed

Skippig 1519 of 2240 - file exists

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Skippig 1520 of 2240 - file exists

0.001 sec elapsed

Skippig 1521 of 2240 - file exists

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Skippig 1522 of 2240 - file exists

0.001 sec elapsed

Skippig 1523 of 2240 - file exists

0 sec elapsed

Skippig 1524 of 2240 - file exists

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Skippig 1525 of 2240 - file exists

0.001 sec elapsed

Skippig 1526 of 2240 - file exists

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Skippig 1527 of 2240 - file exists

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Skippig 1528 of 2240 - file exists

0.001 sec elapsed

Skippig 1529 of 2240 - file exists

0 sec elapsed

Skippig 1530 of 2240 - file exists

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Skippig 1531 of 2240 - file exists

0 sec elapsed

Skippig 1532 of 2240 - file exists

0 sec elapsed

Skippig 1533 of 2240 - file exists

0 sec elapsed

Skippig 1534 of 2240 - file exists

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Skippig 1536 of 2240 - file exists

0.001 sec elapsed

Skippig 1537 of 2240 - file exists

0 sec elapsed

Skippig 1538 of 2240 - file exists

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Skippig 1539 of 2240 - file exists

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Skippig 1540 of 2240 - file exists

0.001 sec elapsed

Skippig 1541 of 2240 - file exists

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Skippig 1542 of 2240 - file exists

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Skippig 1543 of 2240 - file exists

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Skippig 1544 of 2240 - file exists

0.001 sec elapsed

Skippig 1545 of 2240 - file exists

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Skippig 1547 of 2240 - file exists

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0.001 sec elapsed

Skippig 1549 of 2240 - file exists

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Skippig 1550 of 2240 - file exists

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Skippig 1551 of 2240 - file exists

0.001 sec elapsed

Skippig 1552 of 2240 - file exists

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Skippig 1553 of 2240 - file exists

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Skippig 1554 of 2240 - file exists

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Skippig 1555 of 2240 - file exists

0.001 sec elapsed

Skippig 1556 of 2240 - file exists

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Skippig 1557 of 2240 - file exists

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Skippig 1558 of 2240 - file exists

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Skippig 1559 of 2240 - file exists

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Skippig 1560 of 2240 - file exists

0.001 sec elapsed

Skippig 1561 of 2240 - file exists

0 sec elapsed

Skippig 1562 of 2240 - file exists

0 sec elapsed

Skippig 1563 of 2240 - file exists

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Skippig 1564 of 2240 - file exists

0.001 sec elapsed

Skippig 1565 of 2240 - file exists

0 sec elapsed

Skippig 1566 of 2240 - file exists

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Skippig 1567 of 2240 - file exists

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Skippig 1568 of 2240 - file exists

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Skippig 1569 of 2240 - file exists

0.001 sec elapsed

Skippig 1570 of 2240 - file exists

0 sec elapsed

Skippig 1571 of 2240 - file exists

0 sec elapsed

Skippig 1572 of 2240 - file exists

0 sec elapsed

Skippig 1573 of 2240 - file exists

0.001 sec elapsed

Skippig 1574 of 2240 - file exists

0 sec elapsed

Skippig 1575 of 2240 - file exists

0 sec elapsed

Skippig 1576 of 2240 - file exists

0 sec elapsed

Skippig 1577 of 2240 - file exists

0 sec elapsed

Skippig 1578 of 2240 - file exists

0.001 sec elapsed

Skippig 1579 of 2240 - file exists

0 sec elapsed

Skippig 1580 of 2240 - file exists

0 sec elapsed

Skippig 1581 of 2240 - file exists

0 sec elapsed

Skippig 1582 of 2240 - file exists

0 sec elapsed

Skippig 1583 of 2240 - file exists

0.001 sec elapsed

Skippig 1584 of 2240 - file exists

0 sec elapsed

Skippig 1585 of 2240 - file exists

0 sec elapsed

Skippig 1586 of 2240 - file exists

0 sec elapsed

Skippig 1587 of 2240 - file exists

0.001 sec elapsed

Skippig 1588 of 2240 - file exists

0 sec elapsed

Skippig 1589 of 2240 - file exists

0 sec elapsed

Skippig 1590 of 2240 - file exists

0 sec elapsed

Skippig 1591 of 2240 - file exists

0.001 sec elapsed

Skippig 1592 of 2240 - file exists

0 sec elapsed

Skippig 1593 of 2240 - file exists

0 sec elapsed

Skippig 1594 of 2240 - file exists

0 sec elapsed

Skippig 1595 of 2240 - file exists

0 sec elapsed

Skippig 1596 of 2240 - file exists

0 sec elapsed

Skippig 1597 of 2240 - file exists

0.001 sec elapsed

Skippig 1598 of 2240 - file exists

0 sec elapsed

Skippig 1599 of 2240 - file exists

0 sec elapsed

Skippig 1600 of 2240 - file exists

0 sec elapsed

Skippig 1601 of 2240 - file exists

0 sec elapsed

Skippig 1602 of 2240 - file exists

0.001 sec elapsed

Skippig 1603 of 2240 - file exists

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Skippig 1604 of 2240 - file exists

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Skippig 1605 of 2240 - file exists

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Skippig 1606 of 2240 - file exists

0 sec elapsed

Skippig 1607 of 2240 - file exists

0 sec elapsed

Skippig 1608 of 2240 - file exists

0 sec elapsed

Skippig 1609 of 2240 - file exists

0 sec elapsed

Skippig 1610 of 2240 - file exists

0 sec elapsed

Skippig 1611 of 2240 - file exists

0 sec elapsed

Skippig 1612 of 2240 - file exists

0.001 sec elapsed

Skippig 1613 of 2240 - file exists

0 sec elapsed

Skippig 1614 of 2240 - file exists

0 sec elapsed

Skippig 1615 of 2240 - file exists

0 sec elapsed

Skippig 1616 of 2240 - file exists

0 sec elapsed

Skippig 1617 of 2240 - file exists

0 sec elapsed

Skippig 1618 of 2240 - file exists

0.001 sec elapsed

Skippig 1619 of 2240 - file exists

0 sec elapsed

Skippig 1620 of 2240 - file exists

0 sec elapsed

Skippig 1621 of 2240 - file exists

0 sec elapsed

Skippig 1622 of 2240 - file exists

0 sec elapsed

Skippig 1623 of 2240 - file exists

0 sec elapsed

Skippig 1624 of 2240 - file exists

0.001 sec elapsed

Skippig 1625 of 2240 - file exists

0 sec elapsed

Skippig 1626 of 2240 - file exists

0 sec elapsed

Skippig 1627 of 2240 - file exists

0 sec elapsed

Skippig 1628 of 2240 - file exists

0 sec elapsed

Skippig 1629 of 2240 - file exists

0.001 sec elapsed

Skippig 1630 of 2240 - file exists

0 sec elapsed

Skippig 1631 of 2240 - file exists

0 sec elapsed

Skippig 1632 of 2240 - file exists

0 sec elapsed

Skippig 1633 of 2240 - file exists

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Skippig 1634 of 2240 - file exists

0 sec elapsed

Skippig 1635 of 2240 - file exists

0.001 sec elapsed

Skippig 1636 of 2240 - file exists

0 sec elapsed

Skippig 1637 of 2240 - file exists

0 sec elapsed

Skippig 1638 of 2240 - file exists

0 sec elapsed

Skippig 1639 of 2240 - file exists

0 sec elapsed

Skippig 1640 of 2240 - file exists

0 sec elapsed

Skippig 1641 of 2240 - file exists

0.001 sec elapsed

Skippig 1642 of 2240 - file exists

0 sec elapsed

Skippig 1643 of 2240 - file exists

0 sec elapsed

Skippig 1644 of 2240 - file exists

0 sec elapsed

Skippig 1645 of 2240 - file exists

0 sec elapsed

Skippig 1646 of 2240 - file exists

0 sec elapsed

Skippig 1647 of 2240 - file exists

0.001 sec elapsed

Skippig 1648 of 2240 - file exists

0 sec elapsed

Skippig 1649 of 2240 - file exists

0 sec elapsed

Skippig 1650 of 2240 - file exists

0 sec elapsed

Skippig 1651 of 2240 - file exists

0 sec elapsed

Skippig 1652 of 2240 - file exists

0 sec elapsed

Skippig 1653 of 2240 - file exists

0.001 sec elapsed

Skippig 1654 of 2240 - file exists

0 sec elapsed

Skippig 1655 of 2240 - file exists

0 sec elapsed

Skippig 1656 of 2240 - file exists

0 sec elapsed

Skippig 1657 of 2240 - file exists

0 sec elapsed

Skippig 1658 of 2240 - file exists

0 sec elapsed

Skippig 1659 of 2240 - file exists

0.001 sec elapsed

Skippig 1660 of 2240 - file exists

0 sec elapsed

Skippig 1661 of 2240 - file exists

0 sec elapsed

Skippig 1662 of 2240 - file exists

0 sec elapsed

Skippig 1663 of 2240 - file exists

0 sec elapsed

Skippig 1664 of 2240 - file exists

0 sec elapsed

Skippig 1665 of 2240 - file exists

0 sec elapsed

Skippig 1666 of 2240 - file exists

0 sec elapsed

Skippig 1667 of 2240 - file exists

0 sec elapsed

Skippig 1668 of 2240 - file exists

0 sec elapsed

Skippig 1669 of 2240 - file exists

0 sec elapsed

Skippig 1670 of 2240 - file exists

0 sec elapsed

Skippig 1671 of 2240 - file exists

0 sec elapsed

Skippig 1672 of 2240 - file exists

0.001 sec elapsed

Skippig 1673 of 2240 - file exists

0 sec elapsed

Skippig 1674 of 2240 - file exists

0 sec elapsed

Skippig 1675 of 2240 - file exists

0 sec elapsed

Skippig 1676 of 2240 - file exists

0 sec elapsed

Skippig 1677 of 2240 - file exists

0.001 sec elapsed

Skippig 1678 of 2240 - file exists

0 sec elapsed

Skippig 1679 of 2240 - file exists

0 sec elapsed

Skippig 1680 of 2240 - file exists

0 sec elapsed

Skippig 1681 of 2240 - file exists

0 sec elapsed

Skippig 1682 of 2240 - file exists

0 sec elapsed

Skippig 1683 of 2240 - file exists

0.001 sec elapsed

Skippig 1684 of 2240 - file exists

0 sec elapsed

Skippig 1685 of 2240 - file exists

0 sec elapsed

Snowballing W2498935279 --- 1686 of 2240 ...

Error in stats::complete.cases(edges) : 
  no input has determined the number of cases
0.763 sec elapsed

Skippig 1687 of 2240 - file exists

0 sec elapsed

Skippig 1688 of 2240 - file exists

0 sec elapsed

Skippig 1689 of 2240 - file exists

0.001 sec elapsed

Skippig 1690 of 2240 - file exists

0 sec elapsed

Skippig 1691 of 2240 - file exists

0 sec elapsed

Skippig 1692 of 2240 - file exists

0.001 sec elapsed

Skippig 1693 of 2240 - file exists

0 sec elapsed

Skippig 1694 of 2240 - file exists

0 sec elapsed

Skippig 1695 of 2240 - file exists

0 sec elapsed

Skippig 1696 of 2240 - file exists

0 sec elapsed

Skippig 1697 of 2240 - file exists

0 sec elapsed

Skippig 1698 of 2240 - file exists

0 sec elapsed

Skippig 1699 of 2240 - file exists

0 sec elapsed

Skippig 1700 of 2240 - file exists

0 sec elapsed

Skippig 1701 of 2240 - file exists

0 sec elapsed

Skippig 1702 of 2240 - file exists

0.001 sec elapsed

Skippig 1703 of 2240 - file exists

0 sec elapsed

Skippig 1704 of 2240 - file exists

0 sec elapsed

Skippig 1705 of 2240 - file exists

0 sec elapsed

Skippig 1706 of 2240 - file exists

0 sec elapsed

Skippig 1707 of 2240 - file exists

0 sec elapsed

Skippig 1708 of 2240 - file exists

0.001 sec elapsed

Skippig 1709 of 2240 - file exists

0 sec elapsed

Skippig 1710 of 2240 - file exists

0 sec elapsed

Skippig 1711 of 2240 - file exists

0 sec elapsed

Skippig 1712 of 2240 - file exists

0 sec elapsed

Skippig 1713 of 2240 - file exists

0 sec elapsed

Skippig 1714 of 2240 - file exists

0.001 sec elapsed

Skippig 1715 of 2240 - file exists

0 sec elapsed

Skippig 1716 of 2240 - file exists

0 sec elapsed

Skippig 1717 of 2240 - file exists

0 sec elapsed

Skippig 1718 of 2240 - file exists

0 sec elapsed

Skippig 1719 of 2240 - file exists

0.001 sec elapsed

Skippig 1720 of 2240 - file exists

0 sec elapsed

Skippig 1721 of 2240 - file exists

0 sec elapsed

Skippig 1722 of 2240 - file exists

0 sec elapsed

Skippig 1723 of 2240 - file exists

0 sec elapsed

Skippig 1724 of 2240 - file exists

0 sec elapsed

Skippig 1725 of 2240 - file exists

0.001 sec elapsed

Skippig 1726 of 2240 - file exists

0 sec elapsed

Skippig 1727 of 2240 - file exists

0 sec elapsed

Skippig 1728 of 2240 - file exists

0 sec elapsed

Skippig 1729 of 2240 - file exists

0 sec elapsed

Skippig 1730 of 2240 - file exists

0 sec elapsed

Skippig 1731 of 2240 - file exists

0.001 sec elapsed

Skippig 1732 of 2240 - file exists

0 sec elapsed

Skippig 1733 of 2240 - file exists

0 sec elapsed

Skippig 1734 of 2240 - file exists

0 sec elapsed

Skippig 1735 of 2240 - file exists

0.001 sec elapsed

Skippig 1736 of 2240 - file exists

0 sec elapsed

Skippig 1737 of 2240 - file exists

0 sec elapsed

Skippig 1738 of 2240 - file exists

0 sec elapsed

Skippig 1739 of 2240 - file exists

0.001 sec elapsed

Skippig 1740 of 2240 - file exists

0 sec elapsed

Skippig 1741 of 2240 - file exists

0 sec elapsed

Skippig 1742 of 2240 - file exists

0 sec elapsed

Skippig 1743 of 2240 - file exists

0 sec elapsed

Skippig 1744 of 2240 - file exists

0 sec elapsed

Skippig 1745 of 2240 - file exists

0.001 sec elapsed

Skippig 1746 of 2240 - file exists

0 sec elapsed

Skippig 1747 of 2240 - file exists

0 sec elapsed

Skippig 1748 of 2240 - file exists

0 sec elapsed

Skippig 1749 of 2240 - file exists

0 sec elapsed

Skippig 1750 of 2240 - file exists

0 sec elapsed

Skippig 1751 of 2240 - file exists

0.001 sec elapsed

Skippig 1752 of 2240 - file exists

0 sec elapsed

Skippig 1753 of 2240 - file exists

0 sec elapsed

Skippig 1754 of 2240 - file exists

0 sec elapsed

Skippig 1755 of 2240 - file exists

0 sec elapsed

Skippig 1756 of 2240 - file exists

0 sec elapsed

Skippig 1757 of 2240 - file exists

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Show the code

toc()

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Convert to Parquet Database

Show the code

#|

path_nodes <- file.path("output", "nodes")
path_edges <- file.path("output", "edges")

if (!(dir.exists(path_nodes) & dir.exists(path_edges))) {
  dir.create(path_nodes, showWarnings = FALSE)
  dir.create(path_edges, showWarnings = FALSE)

  for (sm1 in unique(key_works$sm)) {
    bm1 <- strsplit(
      sm1,
      split = "-"
    )
    bm1 <- paste0(bm1[[1]][[1]], "-", bm1[[1]][[2]])
    message("\nProcessing ", sm1, " - ", which(unique(key_works$bm) == sm1), " of ", length(unique(key_works$sm)))

    tic()
    ids <- key_works |>
      dplyr::filter(
        sm == sm1,
        id != is.na(id)
      ) |>
      dplyr::select(
        id
      ) |>
      dplyr::mutate(
        id = gsub(
          pattern = "https://openalex.org/",
          replacement = "",
          x = id
        )
      ) |>
      unlist() |>
      unique()

    ### Loading
    message("  |- Loading files")
    snowballs <- pbapply::pblapply(
      ids,
      function(id) {
        result <- NULL
        try(
          result <- readRDS(file.path("output", "snowballs", paste0(id, ".rds"))),
          silent = TRUE
        )
        return(result)
      }
    )

    ### Converting and saving nodes
    message("  |- Combining and writing nodes")
    pbapply::pblapply(
      snowballs,
      function(x) {
        if (is.null(x)) {
          node <- NULL
        } else {
          node <- x[["nodes"]]
          node$author <- IPBES.R::abbreviate_authors(node)
          if (!"ab" %in% colnames(node)) {
            node <- node |>
              dplyr::mutate(
                ab = as.character(NA)
              )
          }
          if (!"doi" %in% colnames(node)) {
            node <- node |>
              dplyr::mutate(
                doi = as.character(NA)
              )
          }
          node <- node |>
            dplyr::mutate(
              grants = NULL,
              counts_by_year = NULL,
              referenced_works = NULL,
              related_works = NULL,
              concepts = NULL,
              topics = NULL
            )
          #     dplyr::select(
          #       id,
          #       doi,
          #       author,
          #       publication_year,
          #       title,
          #       ab,
          #       oa_input
          #     )
        }
        return(node)
      }
    ) |>
      dplyr::bind_rows() |>
      dplyr::distinct() |>
      dplyr::mutate(
        bm = bm1,
        sm = sm1
      ) |>
      arrow::write_dataset(
        path = path_nodes,
        format = "parquet",
        partitioning = c("bm", "sm"),
        existing_data_behavior = "delete_matching"
      )

    ### Converting and saving edges
    message("  |- Combining and writing edges")
    pbapply::pblapply(
      snowballs,
      function(x) {
        x[["edges"]]
      }
    ) |>
      dplyr::bind_rows() |>
      dplyr::distinct() |>
      dplyr::mutate(
        bm = bm1,
        sm = sm1
      ) |>
      arrow::write_dataset(
        path = path_edges,
        format = "parquet",
        partitioning = c("bm", "sm"),
        existing_data_behavior = "delete_matching"
      )
    toc()
  }
}

nodes <- arrow::open_dataset(
  sources = path_nodes
)

edges <- arrow::open_dataset(
  sources = path_edges
)

Extract number of references per background message per year

Show the code

refs_per_year_sm <- nodes |>
  dplyr::group_by(
    sm,
    publication_year
  ) |>
  dplyr::summarise(
    n = dplyr::n()
  ) |>
  dplyr::arrange(
    sm,
    publication_year
  ) |>
  dplyr::collect() |>
  saveRDS(file = file.path("output", "refs_per_year_sm.rds"))

Warning: Invalid metadata$r
Warning: Invalid metadata$r

Figures

Publications per year

Show the code

#|

figname <- file.path("figures", "fig_pub_per_year")
if (length(list.files("figures", "fig_pub_per_year")) < 2) {
  fig <- file.path("output", "refs_per_year_sm.rds") |>
    readRDS() |>
    dplyr::collect() |>
    ggplot(
      aes(
        x = publication_year,
        y = n,
        group = sm,
        color = sm
      )
    ) +
    geom_line() +
    geom_point() +
    geom_vline(
      xintercept = 2019,
      linetype = "dashed"
    ) +
    theme_minimal() +
    labs(
      title = "Number of New Publications per Year by Background Message",
      x = "Publication Year",
      y = "Number of Publications",
      color = "Background Message"
    ) +
    theme(
      legend.position = "bottom",
      legend.title = element_blank()
    ) +
    xlim(2000, 2025) +
    scale_y_log10()

  ggplot2::ggsave(
    filename = paste0(figname, ".png"),
    plot = fig,
    width = 10,
    height = 20
  )
  ggplot2::ggsave(
    filename = paste0(figname, ".pdf"),
    plot = fig,
    width = 10,
    height = 20
  )
  ggplot2::ggsave(
    filename = paste0(figname, ".svg"),
    plot = fig,
    width = 10,
    height = 20
  )
}

Overlap

Show the code

#|

fn <- file.path("output", "overlap_key_paper_sub_messages.rds")

if (!file.exists(fn)) {
  overlap_keypapers <- nodes |>
    dplyr::filter(
      oa_input,
      !is.na(id)
    ) |>
    dplyr::collect() |>
    dplyr::summarise(
      n = n(),
      author,
      title,
      doi = gsub("https://doi.org/", "", doi),
      sms = list(sm),
      .by = id
    ) |>
    dplyr::distinct() |>
    dplyr::arrange(
      desc(n)
    ) |>
    dplyr::filter(
      n > 1,
      !is.na(id)
    ) |>
    dplyr::mutate(
      id = paste0('<a href="https://openalex.org/', id, '" target="_blank">', id, "</a>"),
      doi = paste0('<a href="https://doi.org/', doi, '" target="_blank">', doi, "</a>")
    ) |>
    dplyr::select(
      n,
      id,
      author,
      title,
      doi,
      sms
    )

  saveRDS(
    overlap_keypapers,
    file = fn
  )

  overlap_keypapers |>
    IPBES.R::table_dt(
      fixedColumns = list(leftColumns = 2)
    ) |>
    htmlwidgets::saveWidget(
      file = file.path("output", "overlap_key_paper_sub_messages.html"),
      selfcontained = TRUE
    )

  rm(overlap_keypapers)
}

Show the code

#|

fn <- file.path("output", "overlap_after_2018_sub_messages.rds")

if (!file.exists(fn)) {
  after_2018_overlap <- nodes |>
    dplyr::filter(
      !oa_input,
      !is.na(id),
      publication_year > 2018
    ) |>
    collect() |>
    summarise(
      n = n(),
      author,
      title,
      doi = gsub("https://doi.org/", "", doi),
      sms = list(sm),
      .by = id
    ) |>
    dplyr::distinct() |>
    dplyr::arrange(
      desc(n)
    ) |>
    dplyr::filter(
      n > 5,
      !is.na(id)
    ) |>
    dplyr::mutate(
      id = paste0('<a href="https://openalex.org/', id, '" target="_blank">', id, "</a>"),
      doi = paste0('<a href="https://doi.org/', doi, '" target="_blank">', doi, "</a>")
    ) |>
    dplyr::select(
      n,
      id,
      author,
      title,
      doi,
      sms
    )

  saveRDS(
    after_2018_overlap,
    file = fn
  )

  after_2018_overlap |>
    IPBES.R::table_dt(
      fixedColumns = list(leftColumns = 2)
    ) |>
    htmlwidgets::saveWidget(
      file = file.path("output", "overlap_after_2018_sub_messages.html"),
      selfcontained = TRUE
    )

  rm(after_2018_overlap)
}

Show the code

#|

fn <- file.path("output", "overlap_after_2018_background_messages.rds")

if (!file.exists(fn)) {
  after_2018_overlap <- nodes |>
    dplyr::filter(
      !oa_input,
      !is.na(id),
      publication_year > 2018
    ) |>
    dplyr::select(
      author,
      title,
      doi,
      bm,
      id,
      abstract = ab
    ) |>
    dplyr::mutate(
      sm = NULL
    ) |>
    dplyr::distinct() |>
    collect() |>
    summarise(
      n = n(),
      author,
      title,
      abstract,
      doi = gsub("https://doi.org/", "", doi),
      bms = list(bm),
      .by = id
    ) |>
    dplyr::distinct() |>
    dplyr::arrange(
      desc(n)
    ) |>
    dplyr::filter(
      n > 5,
      !is.na(id)
    ) |>
    dplyr::mutate(
      id = paste0('<a href="https://openalex.org/', id, '" target="_blank">', id, "</a>"),
      doi = paste0('<a href="https://doi.org/', doi, '" target="_blank">', doi, "</a>")
    ) |>
    dplyr::select(
      n,
      id,
      author,
      title,
      doi,
      abstract,
      bms
    )

  saveRDS(
    after_2018_overlap,
    file = fn
  )

  after_2018_overlap |>
    IPBES.R::table_dt(
      fixedColumns = list(leftColumns = 2)
    ) |>
    htmlwidgets::saveWidget(
      file = file.path("output", "overlap_after_2018_background_messages.html"),
      selfcontained = TRUE
    )

  rm(after_2018_overlap)
}

Results

The dataset contains 2681 paper referenced in the background messages. Out of these, 2234 were usable for the snowball search and also yielded results.

Show the code

#|

nodes |>
  dplyr::summarise(
    n = dplyr::n(),
    n_key_paper = sum(oa_input == TRUE, na.rm = TRUE),
    n_non_key_paper = sum(oa_input == FALSE, na.rm = TRUE),
    n_nkp_pre_2018 = sum(((oa_input == FALSE) & (publication_year <= 2018)), na.rm = TRUE), # Count of papers with publication_year <= 2018
    n_nkp_post_2018 = sum(((oa_input == FALSE) & (publication_year > 2018)), na.rm = TRUE), # Count of papers with publication_year > 2018,
    .by = sm
  ) |>
  dplyr::arrange(
    sm
  ) |>
  dplyr::collect() |>
  IPBES.R::table_dt()

Warning: Invalid metadata$r
Warning: Invalid metadata$r

Publication types after 2018

Here we show the different types of publication after 2018 as identified by the snowbal search. All Sub-background messages are grouped.

Warning: Invalid metadata$r
Warning: Invalid metadata$r

type	n
article	1325722
book-chapter	143030
preprint	85911
review	28496
dissertation	22201
peer-review	9120
other	8603
book	7062
paratext	2555
report	1702
editorial	1316
dataset	892
reference-entry	67
letter	33
erratum	14
supplementary-materials	1

This table shows the number of work types per sub-background message. It allows filtering as well as sorting and downloading.

Warning: Invalid metadata$r
Warning: Invalid metadata$r

Publications per year

Overlap

In this section we will look at the number of background messages in which a given paper, as identified by their OpenAlex id. We willlook at that separatr for key-papers and non key-papers.

In the following tables only the papers which occur in more than one background message are included and only papers which were published after 2018.

This overlap can have different causes. Either there is an overlap of the key-papers, ehich results in an overlap of the new publications, or there is a topical overlap betweent the new paper themselves.

Overlap of Key Papers in Sub Messages

The first table shows the overlap of the key-papers only regarding sub messages.

Only papers with in more then 1 Sub Messages are shown.

Overlap of Papers after 2018 in Sub Messages

The second table shows the overlap of all papers after 2018 regarding sub messages.

Only papers with in more then 5 Sub Messages are shown.

Overlap of Papers after 2018 in Background Messages

The third table shows the overlap of all papers after 2018 regarding background messages.

Only papers with in more then 5 Background Messages are shown.

Reuse

CC BY 4.0

Citation

BibTeX citation:

@report{m_krug2024,
  author = {M Krug, Rainer},
  title = {Knowledge {Discovery} {DRAFT}},
  date = {2024-07-23},
  doi = {xxxxxxxxxxxxxx},
  langid = {en},
  abstract = {The assessments Linked Open Data is used to conduct
    analysis and searches to discover new knowledge related to the
    assessmwents.}
}

For attribution, please cite this work as:

M Krug, Rainer. 2024. “Knowledge Discovery DRAFT.” https://doi.org/xxxxxxxxxxxxxx.