rOpenSci | Geospatial

Geospatial

Access, Manipulate, Convert Geospatial Data
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opentripplanner
CRAN Peer-reviewed

Setup and connect to OpenTripPlanner

Malcolm Morgan
Description

Setup and connect to OpenTripPlanner (OTP) http://www.opentripplanner.org/. OTP is an open source platform for multi-modal and multi-agency journey planning written in Java. The package allows you to manage a local version or connect to remote OTP server. This package has been peer-reviewed by rOpenSci (v. 0.2.0.0).

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Group Animal Relocation Data by Spatial and Temporal Relationship

Alec L. Robitaille
Description

Detects spatial and temporal groups in GPS relocations (Robitaille et al. (2020) doi:10.1111/2041-210X.13215). It can be used to convert GPS relocations to gambit-of-the-group format to build proximity-based social networks In addition, the randomizations function provides data-stream randomization methods suitable for GPS data.

Scientific use cases
  1. Robitaille, A. L., Webber, Q. M. R., & Vander Wal, E. (2018). Conducting social network analysis with animal telemetry data: applications and methods using spatsoc. https://doi.org/10.1101/447284
  2. Webber, Q. M. R., & Vander Wal, E. (2019). Trends and perspectives on the use of animal social network analysis in behavioural ecology: a bibliometric approach. Animal Behaviour, 149, 77–87. https://doi.org/10.1016/j.anbehav.2019.01.010
  3. Peignier, M., Webber, Q. M. R., Koen, E. L., Laforge, M. P., Robitaille, A. L., & Vander Wal, E. (2019). Space use and social association in a gregarious ungulate: Testing the conspecific attraction and resource dispersion hypotheses. Ecology and Evolution. https://doi.org/10.1002/ece3.5071
  4. Gilbertson, M. L. J., White, L. A., & Craft, M. E. (2020). Trade‐offs with telemetry‐derived contact networks for infectious disease studies in wildlife. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13355
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Convert Between WKT and GeoJSON

Scott Chamberlain
Description

Convert WKT to GeoJSON and GeoJSON to WKT. Functions included for converting between GeoJSON to WKT, creating both GeoJSON features, and non-features, creating WKT from R objects (e.g., lists, data.frames, vectors), and linting WKT.

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Parse Messy Geographic Coordinates

Scott Chamberlain
Description

Parse geographic coordinates from various formats to decimal degree numeric values. Parse coordinates into their parts (degree, minutes, seconds); calculate hemisphere from coordinates; pull out individually degrees, minutes, or seconds; add and subtract degrees, minutes, and seconds. C++ code herein originally inspired from code written by Jeffrey D. Bogan, but then completely re-written.

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Visualize Species Occurrence Data

Scott Chamberlain
Description

Utilities for visualizing species occurrence data. Includes functions to visualize occurrence data from spocc, rgbif, and other packages. Mapping options included for base R plots, ggplot2, leaflet and GitHub gists.

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Interface to the OpenCage API

Maëlle Salmon
Description

Tool for accessing the OpenCage API, which provides forward geocoding (from placename to longitude and latitude) and reverse geocoding (from longitude and latitude to placename).

Scientific use cases
  1. Cano, J., Rodríguez, A., Simpson, H., Tabah, E. N., Gómez, J. F., & Pullan, R. L. (2018). Modelling the spatial distribution of aquatic insects (Order Hemiptera) potentially involved in the transmission of Mycobacterium ulcerans in Africa. Parasites & Vectors, 11(1). http://doi.org/10.1186/s13071-018-3066-3
  2. Zizka, A., Silvestro, D., Andermann, T., Azevedo, J., Duarte Ritter, C., Edler, D., … Antonelli, A. (2019). CoordinateCleaner: standardized cleaning of occurrence records from biological collection databases. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13152
  3. Deribe, K., Simpson, H., Pullan, R. L., Bosco, M. J., Wanji, S., Weaver, N. D., … Cano, J. (2020). Predicting the Environmental Suitability and Population at Risk of Podoconiosis in Africa. https://doi.org/10.1101/2020.03.04.977827
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Import OpenStreetMap Data as Simple Features or Spatial Objects

Mark Padgham
Description

Download and import of OpenStreetMap (OSM) data as sf or sp objects. OSM data are extracted from the Overpass web server (http://overpass-api.de/) and processed with very fast C++ routines for return to R.

Scientific use cases
  1. Hawker, L., Rougier, J., Neal, J., Bates, P., Archer, L., & Yamazaki, D. (2018). Implications of Simulating Global Digital Elevation Models for Flood Inundation Studies. Water Resources Research. https://doi.org/10.1029/2018wr023279
  2. Briz-Redón, Á. (2019). SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks. Research Ideas and Outcomes, 5. https://doi.org/10.3897/rio.5.e33521
  3. Morelle, K., Jezek, M., Licoppe, A., & Podgorski, T. (2019). Deathbed choice by ASF‐infected wild boar can help find carcasses. Transboundary and Emerging Diseases. https://doi.org/10.1111/tbed.13267
  4. Lara-Lizardi, F., Hoyos-Padilla, M., Hearn, A., Klimley, A. P., Galván-Magaña, F., Arauz, R., … Ketchum, J. T. (2020). Shark movements in the Revillagigedo Archipelago and connectivity with the Eastern Tropical Pacific. https://doi.org/10.1101/2020.03.02.972844
  5. Borgoni, R., Gilardi, A., & Zappa, D. (2020). Assessing the Risk of Car Crashes in Road Networks. Social Indicators Research. https://doi.org/10.1007/s11205-020-02295-x
  6. Dunnett, S., Sorichetta, A., Taylor, G., & Eigenbrod, F. (2020). Harmonised global datasets of wind and solar farm locations and power. Scientific Data, 7(1). https://doi.org/10.1038/s41597-020-0469-8
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Print Maps, Draw on Them, Scan Them Back in

Mark Padgham
Description

Print maps, draw on them, scan them back in, and convert to spatial objects.

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addressable
Staff maintained

Email Address Validation

Scott Chamberlain
Description

Email Address Validation.

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Marine Regions Data from Marineregions.org

Lennert Schepers
Description

Tools to get marine regions data from http://www.marineregions.org/. Includes tools to get region metadata, as well as data in GeoJSON format, as well as Shape files. Use cases include using data downstream to visualize geospatial data by marine region, mapping variation among different regions, and more.

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Convert Data from and to GeoJSON or TopoJSON

Scott Chamberlain
Description

Convert data to GeoJSON or TopoJSON from various R classes, including vectors, lists, data frames, shape files, and spatial classes. geojsonio does not aim to replace packages like sp, rgdal, rgeos, but rather aims to be a high level client to simplify conversions of data from and to GeoJSON and TopoJSON.

Scientific use cases
  1. von Schmidt, A., Cyganski, R., & Heinrichs, M. 2019. Web-based Visualization of Daily Mobility Patterns in R. International Journal on Advances in Internet Technology, vol 12 (3 & 4). https://elib.dlr.de/133599/1/inttech_v12_n34_2019_2.pdf
  2. Ranghetti, L., Boschetti, M., Nutini, F., & Busetto, L. (2020). “sen2r”: An R toolbox for automatically downloading and preprocessing Sentinel-2 satellite data. Computers & Geosciences, 139, 104473. https://doi.org/10.1016/j.cageo.2020.104473
  3. Shrestha, R. K., & Shrestha, R. (2020). Group segmentation and heterogeneity in the choice of cooking fuels in post-earthquake Nepal. arXiv preprint arXiv:2005.09616. https://arxiv.org/pdf/2005.09616.pdf
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landscapetools
CRAN Peer-reviewed

Landscape Utility Toolbox

Marco Sciaini
Description

Provides utility functions for some of the less-glamorous tasks involved in landscape analysis. It includes functions to coerce raster data to the common tibble format and vice versa, it helps with flexible reclassification tasks of raster data and it provides a function to merge multiple raster. Furthermore, landscapetools helps landscape scientists to visualize their data by providing optional themes and utility functions to plot single landscapes, rasterstacks, -bricks and lists of raster.

Scientific use cases
  1. Langhammer, M., Thober, J., Lange, M., Frank, K., & Grimm, V. (2019). Agricultural landscape generators for simulation models: A review of existing solutions and an outline of future directions. Ecological Modelling, 393, 135–151. https://doi.org/10.1016/j.ecolmodel.2018.12.010
  2. Etherington, T., & Omondiagbe, O. (2019). virtualNicheR: generating virtual fundamental and realised niches for use in virtual ecology experiments. Journal of Open Source Software, 4(41), 1661. https://doi.org/10.21105/joss.01661
  3. Betts, M. G., Wolf, C., Pfeifer, M., Banks-Leite, C., Arroyo-Rodríguez, V., Ribeiro, D. B., … Ewers, R. M. (2019). Extinction filters mediate the global effects of habitat fragmentation on animals. Science, 366(6470), 1236–1239. https://doi.org/10.1126/science.aax9387
  4. Scherer, C., Radchuk, V., Franz, M., Thulke, H., Lange, M., Grimm, V., & Kramer‐Schadt, S. (2020). Moving infections: individual movement decisions drive disease persistence in spatially structured landscapes. Oikos. https://doi.org/10.1111/oik.07002
  5. Silva, I., Crane, M., Marshall, B. M., & Strine, C. T. (2020). Revisiting reptile home ranges: moving beyond traditional estimators with dynamic Brownian Bridge Movement Models. https://doi.org/10.1101/2020.02.10.941278
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A Tidy Approach to NetCDF Data Exploration and Extraction

Michael Sumner
Description

Tidy tools for NetCDF data sources. Explore the contents of a NetCDF source (file or URL) presented as variables organized by grid with a database-like interface. The hyper_filter() interactive function translates the filter value or index expressions to array-slicing form. No data is read until explicitly requested, as a data frame or list of arrays via hyper_tibble() or hyper_array().

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Classes for GeoJSON

Scott Chamberlain
Description

Classes for GeoJSON to make working with GeoJSON easier. Includes S3 classes for GeoJSON classes with brief summary output, and a few methods such as extracting and adding bounding boxes, properties, and coordinate reference systems; working with newline delimited GeoJSON; linting through the geojsonlint package; and serializing to/from Geobuf binary GeoJSON format.

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grainchanger

Moving-Window and Direct Data Aggregation

Laura Graham
Description

Data aggregation via moving window or direct methods. Aggregate a fine-resolution raster to a grid. The moving window method smooths the surface using a specified function within a moving window of a specified size and shape prior to aggregation. The direct method simply aggregates to the grid using the specified function.

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GeoJSON Topology Calculations and Operations

Scott Chamberlain
Description

Tools for doing calculations and manipulations on GeoJSON, a geospatial data interchange format (https://tools.ietf.org/html/rfc7946). GeoJSON is also valid JSON.

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Client for Turfjs for Geospatial Analysis

Scott Chamberlain
Description

Client for Turfjs (http://turfjs.org) for geospatial analysis. The package revolves around using GeoJSON data. Functions are included for creating GeoJSON data objects, measuring aspects of GeoJSON, and combining, transforming, and creating random GeoJSON data objects.

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PostcodesioR
CRAN Peer-reviewed

API Wrapper Around Postcodes.io

Eryk Walczak
Description

Free UK geocoding using data from Office for National Statistics. It is using several functions to get information about post codes, outward codes, reverse geocoding, nearest post codes/outward codes, validation, or randomly generate a post code. API wrapper around https://postcodes.io.

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Bespoke Images of OpenStreetMap Data

Mark Padgham
Description

Bespoke images of OpenStreetMap (OSM) data and data visualisation using OSM objects.

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Tools for Validating GeoJSON

Scott Chamberlain
Description

Tools for linting GeoJSON. Includes tools for interacting with the online tool http://geojsonlint.com, the Javascript library geojsonhint (https://www.npmjs.com/package/geojsonhint), and validating against a GeoJSON schema via the Javascript library (https://www.npmjs.com/package/is-my-json-valid). Some tools work locally while others require an internet connection.

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wicket
CRAN

Utilities to Handle WKT Spatial Data

Oliver Keyes
Description

Utilities to generate bounding boxes from WKT (Well-Known Text) objects and R data types, validate WKT objects and convert object types from the sp package into WKT representations.

Scientific use cases
  1. Bachman, S., Walker, B., Barrios, S., Copeland, A., & Moat, J. (2020). Rapid Least Concern: towards automating Red List assessments. Biodiversity Data Journal, 8. https://doi.org/10.3897/bdj.8.e47018
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Create Geographic and Non-Geographic Map Tiles

Matthew Leonawicz
Description

Creates geographic map tiles from geospatial map files or non-geographic map tiles from simple image files. This package provides a tile generator function for creating map tile sets for use with packages such as leaflet. In addition to generating map tiles based on a common raster layer source, it also handles the non-geographic edge case, producing map tiles from arbitrary images. These map tiles, which have a non-geographic, simple coordinate reference system (CRS), can also be used with leaflet when applying the simple CRS option. Map tiles can be created from an input file with any of the following extensions: tif, grd and nc for spatial maps and png, jpg and bmp for basic images. This package requires Python and the gdal library for Python. Windows users are recommended to install OSGeo4W (https://trac.osgeo.org/osgeo4w/) as an easy way to obtain the required gdal support for Python.

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rnaturalearthdata
CRAN

World Vector Map Data from Natural Earth Used in rnaturalearth

Andy South
Description

Vector map data from http://www.naturalearthdata.com/. Access functions are provided in the accompanying package rnaturalearth.

Scientific use cases
  1. Rice, A., Šmarda, P., Novosolov, M., Drori, M., Glick, L., Sabath, N., … Mayrose, I. (2019). The global biogeography of polyploid plants. Nature Ecology & Evolution, 3(2), 265–273. https://doi.org/10.1038/s41559-018-0787-9
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Generate Random WKT or GeoJSON

Scott Chamberlain
Description

Generate random positions (latitude/longitude), Well-known text (WKT) points or polygons, or GeoJSON points or polygons.

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Split Geospatial Objects into Pieces

Scott Chamberlain
Description

Split geospatial objects into pieces. Includes support for some spatial object inputs, Well-Known Text, and GeoJSON.

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rnaturalearth
CRAN Peer-reviewed

World Map Data from Natural Earth

Andy South
Description

Facilitates mapping by making natural earth map data from http://www.naturalearthdata.com/ more easily available to R users.

Scientific use cases
  1. Chapman, C. A., Omeja, P. A., Kalbitzer, U., Fan, P., & Lawes, M. J. (2018). Restoration Provides Hope for Faunal Recovery: Changes in Primate Abundance Over 45 Years in Kibale National Park, Uganda. Tropical Conservation Science, 11, 194008291878737. https://doi.org/10.1177/1940082918787376
  2. Farache, F. H. A., Pereira, C. B., Koschnitzke, C., Barros, L. O., Souza, E. M. de C., Felício, D. T., … Pereira, R. A. S. (2018). The unknown followers: Discovery of a new species of Sycobia Walker (Hymenoptera: Epichrysomallinae) associated with Ficus benjamina L (Moraceae) in the Neotropical region. Journal of Hymenoptera Research. 67, 85–102. https://doi.org/10.3897/jhr.67.29733
  3. Zizka, A., Silvestro, D., Andermann, T., Azevedo, J., Duarte Ritter, C., Edler, D., … Antonelli, A. (2019). CoordinateCleaner: standardized cleaning of occurrence records from biological collection databases. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13152
  4. Atickem, A., Stenseth, N. C., Fashing, P. J., Nguyen, N., Chapman, C. A., Bekele, A., … Kalbitzer, U. (2019). Build science in Africa. Nature, 570(7761), 297–300. https://doi.org/10.1038/d41586-019-01885-1
  5. Umlauf, N., Klein, N., Simon, T., & Zeileis, A. (2019). bamlss: A Lego Toolbox for Flexible Bayesian Regression (and Beyond). arXiv preprint arXiv:1909.11784. https://arxiv.org/abs/1909.11784
  6. Rodewald, A. D., Strimas-Mackey, M., Schuster, R., & Arcese, P. (2019). Tradeoffs in the value of biodiversity feature and cost data in conservation prioritization. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-52241-2
  7. Næss, M. W. (2019). From hunter-gatherers to nomadic pastoralists: forager bands do not tell the whole story of the evolution of human cooperation. https://doi.org/10.31235/osf.io/9c8bm
  8. Marshall, B. M., & Strine, C. T. (2019). Exploring snake occurrence records: Spatial biases and marginal gains from accessible social media. PeerJ, 7, e8059. https://doi.org/10.7717/peerj.8059
  9. Czernecki, B., Głogowski, A., & Nowosad, J. (2020). Climate: An R Package to Access Free In-Situ Meteorological and Hydrological Datasets For Environmental Assessment. Sustainability, 12(1), 394. https://doi.org/10.3390/su12010394
  10. Rego, A., Sousa, A. G. G., Santos, J. P., Pascoal, F., Canário, J., Leão, P. N., & Magalhães, C. (2020). Diversity of Bacterial Biosynthetic Genes in Maritime Antarctica. Microorganisms, 8(2), 279. https://doi.org/10.3390/microorganisms8020279
  11. Eastman, R. T., Roth, J. S., Brimacombe, K. R., Simeonov, A., Shen, M., Patnaik, S., & Hall, M. D. (2020). Remdesivir: A Review of Its Discovery and Development Leading to Emergency Use Authorization for Treatment of COVID-19. ACS Central Science, 6(5), 672–683. https://doi.org/10.1021/acscentsci.0c00489
  12. Ozturk, R. C., & Altinok, I. (2020). Interaction of Plastics with Marine Species. Turkish Journal of Fisheries and Aquatic Sciences, 20(8). https://doi.org/10.4194/1303-2712-v20_8_07
  13. Deconinck, D., Volckaert, F. A. M., Hostens, K., Panicz, R., Eljasik, P., Faria, M., … Derycke, S. (2020). A high-quality genetic reference database for European commercial fishes reveals substitution fraud of processed Atlantic cod (Gadus morhua) and common sole (Solea solea) at different steps in the Belgian supply chain. Food and Chemical Toxicology, 141, 111417. https://doi.org/10.1016/j.fct.2020.111417
  14. Connors, B., Malick, M. J., Ruggerone, G. T., Rand, P., Adkison, M., Irvine, J. R., … Gorman, K. (2020). Climate and competition influence sockeye salmon population dynamics across the Northeast Pacific Ocean. Canadian Journal of Fisheries and Aquatic Sciences, 77(6), 943–949. https://doi.org/10.1139/cjfas-2019-0422
  15. Runge, C. A., Hausner, V. H., Daigle, R. M., & Monz, C. A. (2020). Pan-Arctic analysis of cultural ecosystem services using social media and automated content analysis. Environmental Research Communications, 2(7), 075001. https://doi.org/10.1088/2515-7620/ab9c33
  16. Swetnam, D. M., Stuart, J. B., Young, K., Maharaj, P. D., Fang, Y., Garcia, S., … Coffey, L. L. (2020). Movement of St. Louis encephalitis virus in the Western United States, 2014- 2018. PLOS Neglected Tropical Diseases, 14(6), e0008343. https://doi.org/10.1371/journal.pntd.0008343
  17. Kurose, D., Pollard, K. M., & Ellison, C. A. (2020). Chloroplast DNA analysis of the invasive weed, Himalayan balsam (Impatiens glandulifera), in the British Isles. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-67871-0
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Simulating Neutral Landscape Models

Marco Sciaini
Description

Provides neutral landscape models (doi:10.1007/BF02275262, http://sci-hub.tw/10.1007/bf02275262).
Neutral landscape models range from “hard” neutral models (completely random distributed), to “soft” neutral models (definable spatial characteristics) and generate landscape patterns that are independent of ecological processes. Thus, these patterns can be used as null models in landscape ecology. nlmr combines a large number of algorithms from other published software for simulating neutral landscapes. The simulation results are obtained in a geospatial data format (raster* objects from the raster package) and can, therefore, be used in any sort of raster data operation that is performed with standard observation data.

Scientific use cases
  1. Langhammer, M., Thober, J., Lange, M., Frank, K., & Grimm, V. (2019). Agricultural landscape generators for simulation models: A review of existing solutions and an outline of future directions. Ecological Modelling, 393, 135–151. https://doi.org/10.1016/j.ecolmodel.2018.12.010
  2. Fletcher, R., & Fortin, M.-J. (2018). Land-Cover Pattern and Change. Spatial Ecology and Conservation Modeling, 55–100. https://doi.org/10.1007/978-3-030-01989-1_3
  3. Harris, M. (2019). KLRfome - Kernel Logistic Regression on Focal Mean Embeddings. Journal of Open Source Software, 4(35), 722. https://doi.org/10.21105/joss.00722
  4. Etherington, T., & Omondiagbe, O. (2019). virtualNicheR: generating virtual fundamental and realised niches for use in virtual ecology experiments. Journal of Open Source Software, 4(41), 1661. https://doi.org/10.21105/joss.01661
  5. Betts, M. G., Wolf, C., Pfeifer, M., Banks-Leite, C., Arroyo-Rodríguez, V., Ribeiro, D. B., … Ewers, R. M. (2019). Extinction filters mediate the global effects of habitat fragmentation on animals. Science, 366(6470), 1236–1239. https://doi.org/10.1126/science.aax9387
  6. Scherer, C., Radchuk, V., Franz, M., Thulke, H., Lange, M., Grimm, V., & Kramer‐Schadt, S. (2020). Moving infections: individual movement decisions drive disease persistence in spatially structured landscapes. Oikos. https://doi.org/10.1111/oik.07002
  7. Silva, I., Crane, M., Marshall, B. M., & Strine, C. T. (2020). Revisiting reptile home ranges: moving beyond traditional estimators with dynamic Brownian Bridge Movement Models. https://doi.org/10.1101/2020.02.10.941278
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geonames
CRAN

Interface to the "Geonames" Spatial Query Web Service

Barry Rowlingson
Description

The web service at https://www.geonames.org/ provides a number of spatial data queries, including administrative area hierarchies, city locations and some country postal code queries. A (free) username is required and rate limits exist.

Scientific use cases
  1. Harsch, M. A., & HilleRisLambers, J. (2016). Climate Warming and Seasonal Precipitation Change Interact to Limit Species Distribution Shifts across Western North America. PLOS ONE, 11(7), e0159184. https://doi.org/10.1371/journal.pone.0159184
  2. Ummel, K. (2012). CARMA revisited: an updated database of carbon dioxide emissions from power plants worldwide. Center for Global Development Working Paper, (304). http://www.cgdev.org/publication/carma-revisited-updated-database-carbon-dioxide-emissions-power-plants-worldwide-working
  3. Kolb, J.-P. (2016). Visualizing GeoData with R. Austrian Journal of Statistics, 45(1), 45. https://doi.org/10.17713/ajs.v45i1.88
  4. Kevin Ummel. 2012. “CARMA Revisited: An Updated Database of Carbon Dioxide Emissions from Power Plants Worldwide.” CGD Working Paper 304. Washington, D.C.: Center for Global Development. http://www.cgdev.org/content/publications/detail/1426429
  5. Holzmeyer, L., Hartig, A.-K., Franke, K., Brandt, W., Muellner-Riehl, A. N., Wessjohann, L. A., & Schnitzler, J. (2020). Evaluation of plant sources for antiinfective lead compound discovery by correlating phylogenetic, spatial, and bioactivity data. Proceedings of the National Academy of Sciences, 117(22), 12444–12451. https://doi.org/10.1073/pnas.1915277117
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