Snowball Search and global quantification of the references

Setup

Code

#|

# library(bibtex)
library(openalexR)

Thank you for using openalexR!
To acknowledge our work, please cite the package by calling
`citation("openalexR")`.

Code

library(writexl)
library(tibble)
library(dplyr)


Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Code

library(ggplot2)
library(ggraph)
library(tidygraph)


Attaching package: 'tidygraph'

The following object is masked from 'package:stats':

    filter

Code

library(knitr)

list.files(
    "R",
    full.names = TRUE,
    recursive = TRUE
) |>
    sapply(
        FUN <- source
    )

        R/plot_snowball.R R/to_xlsx.R
value   ?                 ?          
visible FALSE             FALSE

Code

kp <- read.csv("./key_papers.csv")
kp <- split(kp, kp$ro)

Searches

OpenAlex

Setup OpelAnex usage and do snowball serarch

Code

#|

key_works <- lapply(
    kp,
    function(x) {
        oa_fetch(
            entity = "works",
            doi = x$doi,
            verbose = FALSE
        )
    }
)

saveRDS(key_works, "key_works.rds")

ids <- lapply(
    key_works,
    function(x){
        openalexR:::shorten_oaid(x$id)
    }
)

fn <- file.path(".", "data", "snowball.rds")
if (file.exists(fn)) {
    snowball <- readRDS(fn)
} else {
    snowball <- lapply(
        ids,
        function(x) {
            oa_snowball(
                identifier = x,
                verbose = FALSE
            )
        }
    )
    saveRDS(snowball, fn)
}

flat_snow <- lapply(
    snowball,
    function(x){
        snowball2df(x) |>
        as_tibble()
    }
)

Save snowball as Excel file (`snowball_excel.xlsx`)

Code

#|

###

lapply(
    names(snowball),
    function(x) {
        fn <- file.path(".", "data", paste0(x, ".xlsx"))
        to_xlsx(
            snowball = snowball[[x]], 
            flat_snow = flat_snow[[x]], 
            xls_filename = fn
        )    
    }
)

[[1]]
[1] "/Users/rainerkrug/Documents_Local/git/IPBES_data_tsu/Assessments/Transformative Change/IPBES_TFC_Ch5/data/ agriculture.xlsx"

[[2]]
[1] "/Users/rainerkrug/Documents_Local/git/IPBES_data_tsu/Assessments/Transformative Change/IPBES_TFC_Ch5/data/ dams.xlsx"

[[3]]
[1] "/Users/rainerkrug/Documents_Local/git/IPBES_data_tsu/Assessments/Transformative Change/IPBES_TFC_Ch5/data/ fertilizer.xlsx"

The column are: (the Concept columns are not that relevant at the moment)

id: internal id fromOpenAlex
author: authors of the paper
publication_year: publication year
title: title of the paper
doi: doi of the paper
no_referenced_works: number of references in the paper which are also in OpenAlex
cited_global: Number of times the paper has been cited
cited_global_per_year: standardised number of times cirted (cited_global / number of years published)
no_connections: number of connections in the rgaph, i.e. either cited or citing a paper in the snowball corpus
concepts_l0: Concept 0. level assigned by OpenAlex
concepts_l1: Concept 1. level assigned by OpenAlex
concepts_l2: Concept 2. level assigned by OpenAlex
concepts_l3: Concept 3. level assigned by OpenAlex
concepts_l4: Concept 4. level assigned by OpenAlex
concepts_l5: Concept 5. level assigned by OpenAlex
author_institute: Institute of the authors
institute_country: Country of the institute
abstract: the abstract of the paper

Graph of links between references

Code

#|

lapply(
    names(snowball),
    function(x){
        plot_snowball(
            snowball[[x]],
            name = x
        )
    }
)

Warning: Using the `size` aesthetic in this geom was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` in the `default_aes` field and elsewhere instead.

[[1]]


[[2]]


[[3]]

Identification of references with more than one edge

This is the number of connections (connection_count)of the paper (id)

Code

#|

mult_edge <- lapply(
    flat_snow,
    function(flat_snow) {
        mult_edge <- flat_snow |>
            select(id, connection_count) |>
            filter(connection_count > 1) |>
            arrange(desc(connection_count))
    }
)

links <- lapply(
    names(flat_snow),
    function(x) {
        flat_snow[[x]] |>
            filter(id %in% mult_edge[[x]]$id)
    }
)

lapply(
    links,
    function(links) {
        links |>
            select(id, display_name, publication_year, doi, connection_count) |>
            arrange(desc(connection_count)) |>
            knitr::kable()
    }
)

[[1]]


|id          |display_name                                                                                                        | publication_year|doi                                      | connection_count|
|:-----------|:-------------------------------------------------------------------------------------------------------------------|----------------:|:----------------------------------------|----------------:|
|W2551698534 |Drought Tolerance and Water Use of Cereal Crops: A Focus on Sorghum as a Food Security Crop in Sub-Saharan Africa   |             2016|https://doi.org/10.1111/jac.12191        |              207|
|W3193742663 |Adaptive Crop Management under Climate Uncertainty: Changing the Game for Sustainable Water Use                     |             2021|https://doi.org/10.3390/atmos12081080    |               44|
|W1910020066 |ADVANCES AND CHALLENGES WITH MICRO-IRRIGATION                                                                       |             2013|https://doi.org/10.1002/ird.1704         |               38|
|W3136104434 |Sustainable alternative futures for agriculture in India—the energy, emissions, and resource implications           |             2021|https://doi.org/10.1088/1748-9326/abf0cd |               33|
|W4200458514 |The State of the World’s Land and Water Resources for Food and Agriculture – Systems at breaking point (SOLAW 2021) |             2021|https://doi.org/10.4060/cb7654en         |               29|

[[2]]


|id          |display_name                                                                                                                                                                                                        | publication_year|doi                                              | connection_count|
|:-----------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------:|:------------------------------------------------|----------------:|
|W4386422911 |A metasystem approach to designing environmental flows                                                                                                                                                              |             2023|https://doi.org/10.1093/biosci/biad067           |              157|
|W4214623905 |Do dams improve water security in India? A review of post facto assessments                                                                                                                                         |             2022|https://doi.org/10.1016/j.wasec.2022.100112      |               66|
|W2753435791 |Assessing the feasibility of integrating ecosystem-based with engineered water resource governance and management for water security in semi-arid landscapes: A case study in the Banas catchment, Rajasthan, India |             2018|https://doi.org/10.1016/j.scitotenv.2017.08.308  |               63|
|W4379966281 |Optimizing environmental flow based on a new optimization model in balancing objectives among river ecology, water supply and power generation in a high-latitude river                                             |             2023|https://doi.org/10.1016/j.jenvman.2023.118261    |               42|
|W2096113236 |The Natural Flow Regime                                                                                                                                                                                             |             1997|https://doi.org/10.2307/1313099                  |                2|
|W2151941169 |How much water does a river need?                                                                                                                                                                                   |             1997|https://doi.org/10.1046/j.1365-2427.1997.00153.x |                2|
|W2156113027 |Environmental flows for natural, hybrid, and novel riverine ecosystems in a changing world                                                                                                                          |             2014|https://doi.org/10.1890/130134                   |                2|
|W2156353061 |The ecological limits of hydrologic alteration (ELOHA): a new framework for developing regional environmental flow standards                                                                                        |             2010|https://doi.org/10.1111/j.1365-2427.2009.02204.x |                2|

[[3]]


|id          |display_name                                                                                                                                             | publication_year|doi                                                             | connection_count|
|:-----------|:--------------------------------------------------------------------------------------------------------------------------------------------------------|----------------:|:---------------------------------------------------------------|----------------:|
|W2094218359 |Consequence of altered nitrogen cycles in the coupled human and ecological system under changing climate: The need for long-term and site-based research |             2014|https://doi.org/10.1007/s13280-014-0545-4                       |              177|
|W4223483518 |Nitrogenous fertilizers: impact on environment sustainability, mitigation strategies, and challenges                                                     |             2022|https://doi.org/10.1007/s13762-022-04027-9                      |              135|
|W3159296798 |Spatially explicit boundaries for agricultural nitrogen inputs in the European Union to meet air and water quality targets                               |             2021|https://doi.org/10.1016/j.scitotenv.2021.147283                 |              100|
|W4360615396 |A better use of fertilizers is needed for global food security and environmental sustainability                                                          |             2023|https://doi.org/10.1186/s40066-023-00409-5                      |               89|
|W2020023668 |How a century of ammonia synthesis changed the world                                                                                                     |             2008|https://doi.org/10.1038/ngeo325                                 |                3|
|W2097004990 |The Nitrogen Cascade                                                                                                                                     |             2003|https://doi.org/10.1641/0006-3568(2003)053[0341:tnc]2.0.co;2    |                3|
|W1999167944 |Planetary boundaries: Guiding human development on a changing planet                                                                                     |             2015|https://doi.org/10.1126/science.1259855                         |                2|
|W2019990444 |Nutrient Imbalances in Agricultural Development                                                                                                          |             2009|https://doi.org/10.1126/science.1170261                         |                2|
|W2030467995 |Global agriculture and nitrous oxide emissions                                                                                                           |             2012|https://doi.org/10.1038/nclimate1458                            |                2|
|W2089894319 |Ecological and toxicological effects of inorganic nitrogen pollution in aquatic ecosystems: A global assessment                                          |             2006|https://doi.org/10.1016/j.envint.2006.05.002                    |                2|
|W2102235270 |The contribution of manure and fertilizer nitrogen to atmospheric nitrous oxide since 1860                                                               |             2009|https://doi.org/10.1038/ngeo608                                 |                2|
|W2128888862 |Assessing planetary and regional nitrogen boundaries related to food security and adverse environmental impacts                                          |             2013|https://doi.org/10.1016/j.cosust.2013.07.004                    |                2|
|W2132041826 |Nitrogen Pollution in the Northeastern United States: Sources, Effects, and Management Options                                                           |             2003|https://doi.org/10.1641/0006-3568(2003)053[0357:npitnu]2.0.co;2 |                2|
|W2146323422 |Transformation of the Nitrogen Cycle: Recent Trends, Questions, and Potential Solutions                                                                  |             2008|https://doi.org/10.1126/science.1136674                         |                2|
|W2149352713 |Nitrogen Cycles: Past, Present, and Future                                                                                                               |             2004|https://doi.org/10.1007/s10533-004-0370-0                       |                2|
|W2175999181 |Nitrogen and Food Production: Proteins for Human Diets                                                                                                   |             2002|https://doi.org/10.1579/0044-7447-31.2.126                      |                2|
|W2884859931 |Drinking Water Nitrate and Human Health: An Updated Review                                                                                               |             2018|https://doi.org/10.3390/ijerph15071557                          |                2|
|W3158945551 |Reconciling food production and environmental boundaries for nitrogen in the European Union                                                              |             2021|https://doi.org/10.1016/j.scitotenv.2021.147427                 |                2|
|W3189362205 |Reconciling regional nitrogen boundaries with global food security                                                                                       |             2021|https://doi.org/10.1038/s43016-021-00366-x                      |                2|

Finalize

To convert to pdf run e.g.

Code

    wkhtmltopdf snowball.html snowball.pdf

Setup

Searches

OpenAlex

Setup OpelAnex usage and do snowball serarch

Save snowball as Excel file (snowball_excel.xlsx)

Graph of links between references

Identification of references with more than one edge

Finalize

Save snowball as Excel file (`snowball_excel.xlsx`)