Citations

If you use PhyloNext pipeline for your analysis, please cite it as:

Mikryukov V, Abarenkov K, Laffan S, Robertson T, McTavish EJ, Jeppesen TS, Waller J, Blissett M, Kõljalg U, Miller JT (2024). PhyloNext: A pipeline for phylogenetic diversity analysis of GBIF-mediated data. BMC Ecology and Evolution, 24(1), 76. DOI:10.1186/s12862-024-02256-9

Biodiverse:
Laffan SW, Lubarsky E, Rosauer DF (2010) Biodiverse, a tool for the spatial analysis of biological and related diversity. Ecography, 33: 643-647. DOI: 10.1111/j.1600-0587.2010.06237.x

CANAPE analysis:
Mishler BD, Knerr N, González-Orozco CE, Thornhill AH, Laffan SW, Miller JT (2014) Phylogenetic measures of biodiversity and neo- and paleo-endemism in Australian Acacia. Nature Communications, 5(1), 4473. DOI:10.1038/ncomms5473

Open Tree of Life synthetic phylogeny:
Hinchliff CE, Smith SA, Allman JF, Burleigh JG, Chaudhary R, Coghill LM, Crandall KA, Deng J, Drew BT, Gazis R, Gude K, Hibbett DS, Katz LA, Laughinghouse HD, McTavish EJ, Midford PE, Owen CL, Ree RH, Rees JA, Cranston KA (2015) Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Sciences, 112(41), 12764–12769. DOI:10.1073/pnas.1423041112

Pipeline dependencies

Nextflow:
Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C (2017) Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316–319. DOI:10.1038/nbt.3820

Apache arrow:
Richardson N, Cook I, Crane N, Dunnington D, François R, Keane J, Moldovan-Grünfeld D, Ooms J (2022) arrow: Integration to Apache Arrow. https://arrow.apache.org/docs/r/

data.table:
Dowle M, Srinivasan A (2022) data.table: Extension of data.frame. https://r-datatable.com

sf:
Pebesma E (2018) Simple Features for R: Standardized Support for Spatial Vector Data. The R Journal, 10(1), 439. DOI:10.32614/RJ-2018-009

H3 bindings:
Kuethe S (2021) h3: R Bindings for H3. https://github.com/crazycapivara/h3-r

rgbif:
Chamberlain SA, Boettiger C (2017) R, Python, and Ruby clients for GBIF species occurrence data. PeerJ Preprints, 5, e3304v1. DOI:10.7287/peerj.preprints.3304v1

rotl:
Michonneau F, Brown JW, Winter DJ (2016) rotl: An R package to interact with the Open Tree of Life data. Methods in Ecology and Evolution, 7(12), 1476–1481. DOI:10.1111/2041-210X.12593

leaflet:
Cheng J, Karambelkar B, Xie Y (2022) leaflet: Create interactive web maps with the JavaScript “Leaflet” library. https://rstudio.github.io/leaflet/

Datasets

World base map and polygons of land and urban areas:
Natural Earth

WGSRPD (World Geographic Scheme for Recording Plant Distributions):
Brummitt RK, Pando F, Hollis S, Brummitt NA (2001) World Geographic Scheme for Recording Plant Distributions. http://rs.tdwg.org/wgsrpd/doc/data/

Bio-geographical regions for terrestrial animals:
Shen Q, Lu J, Zhang S, You Z, Ren Y, Shen X (2022) The Bio-Geographical Regions Division of Global Terrestrial Animal by Multivariate Similarity Clustering Analysis Method. Open Journal of Ecology, 12(3), Article 3. DOI:10.4236/oje.2022.123014

CoordinateCleaner-based datasets for removal of common geospatial errors:
Zizka A, Silvestro D, Andermann T, Azevedo J, Duarte Ritter C, Edler D, Farooq H, Herdean A, Ariza M, Scharn R, Svantesson S, Wengström N, Zizka V, Antonelli A (2019) CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases. Methods in Ecology and Evolution, 10(5), 744–751. DOI:10.1111/2041-210X.13152