R-universe search: land

alstat

ALUES:Agricultural Land Use Evaluation System

Evaluates land suitability for different crops production. The package is based on the Food and Agriculture Organization (FAO) and the International Rice Research Institute (IRRI) methodology for land evaluation. Development of ALUES is inspired by similar tool for land evaluation, Land Use Suitability Evaluation Tool (LUSET). The package uses fuzzy logic approach to evaluate land suitability of a particular area based on inputs such as rainfall, temperature, topography, and soil properties. The membership functions used for fuzzy modeling are the following: Triangular, Trapezoidal and Gaussian. The methods for computing the overall suitability of a particular area are also included, and these are the Minimum, Maximum and Average. Finally, ALUES is a highly optimized library with core algorithms written in C++.

Maintained by Al-Ahmadgaid B. Asaad. Last updated 3 years ago.

agricultural-modelling agriculture cpp

823.5 match 11 stars 6.38 score 55 scripts

pecanproject

PEcAn.data.land:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by Mike Dietze. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

33.3 match 216 stars 9.32 score 19 scripts 10 dependents

kwstat

agridat:Agricultural Datasets

Datasets from books, papers, and websites related to agriculture. Example graphics and analyses are included. Data come from small-plot trials, multi-environment trials, uniformity trials, yield monitors, and more.

Maintained by Kevin Wright. Last updated 28 days ago.

data

17.3 match 125 stars 11.02 score 1.7k scripts 2 dependents

flr

FLCore:Core Package of FLR, Fisheries Modelling in R

Core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at <http://flr-project.org/>.

Maintained by Iago Mosqueira. Last updated 9 days ago.

fisheries flr fisheries-modelling

21.3 match 16 stars 8.78 score 956 scripts 23 dependents

xavi-rp

LPDynR:Land Productivity Dynamics Indicator

It uses 'phenological' and productivity-related variables derived from time series of vegetation indexes, such as the Normalized Difference Vegetation Index, to assess ecosystem dynamics and change, which eventually might drive to land degradation. The final result of the Land Productivity Dynamics indicator is a categorical map with 5 classes of land productivity dynamics, ranging from declining to increasing productivity. See www.sciencedirect.com/science/article/pii/S1470160X21010517/ for a description of the methods used in the package to calculate the indicator.

Maintained by Xavier Rotllan-Puig. Last updated 6 months ago.

copernicus-global-land-service earth-observation land-degradation land-productivity vegetation

31.0 match 8 stars 4.90 score 5 scripts

simonmoulds

lulcc:Land Use Change Modelling in R

Classes and methods for spatially explicit land use change modelling in R.

Maintained by Simon Moulds. Last updated 5 years ago.

19.4 match 41 stars 5.37 score 38 scripts

flr

FLBRP:Reference Points for Fisheries Management

Calculates a range of biological reference points based upon yield per recruit and stock recruit based equilibrium calculations. These include F based reference points like F0.1, FMSY and biomass based reference points like BMSY.

Maintained by Iago Mosqueira. Last updated 3 months ago.

reference points fisheries flr cpp

15.8 match 2 stars 6.58 score 350 scripts 4 dependents

ropensci

MODIStsp:Find, Download and Process MODIS Land Products Data

Allows automating the creation of time series of rasters derived from MODIS satellite land products data. It performs several typical preprocessing steps such as download, mosaicking, reprojecting and resizing data acquired on a specified time period. All processing parameters can be set using a user-friendly GUI. Users can select which layers of the original MODIS HDF files they want to process, which additional quality indicators should be extracted from aggregated MODIS quality assurance layers and, in the case of surface reflectance products, which spectral indexes should be computed from the original reflectance bands. For each output layer, outputs are saved as single-band raster files corresponding to each available acquisition date. Virtual files allowing access to the entire time series as a single file are also created. Command-line execution exploiting a previously saved processing options file is also possible, allowing users to automatically update time series related to a MODIS product whenever a new image is available. For additional documentation refer to the following article: Busetto and Ranghetti (2016) <doi:10.1016/j.cageo.2016.08.020>.

Maintained by Luigi Ranghetti. Last updated 8 months ago.

gdal modis modis-data modis-land-products peer-reviewed preprocessing remote-sensing satellite-imagery time-series

11.7 match 156 stars 8.04 score 86 scripts 1 dependents

reginalexavier

OpenLand:Quantitative Analysis and Visualization of LUCC

Tools for the analysis of land use and cover (LUC) time series. It includes support for loading spatiotemporal raster data and synthesized spatial plotting. Several LUC change (LUCC) metrics in regular or irregular time intervals can be extracted and visualized through one- and multistep sankey and chord diagrams. A complete intensity analysis according to Aldwaik and Pontius (2012) <doi:10.1016/j.landurbplan.2012.02.010> is implemented, including tools for the generation of standardized multilevel output graphics.

Maintained by Reginal Exavier. Last updated 11 months ago.

geography geospatial intensity-analysis land-use-and-land-cover-change luc-maps lulc plot rasters

15.9 match 22 stars 5.80 score 19 scripts

plotly

plotly:Create Interactive Web Graphics via 'plotly.js'

Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.

Maintained by Carson Sievert. Last updated 3 months ago.

d3js data-visualization ggplot2 javascript plotly shiny webgl

3.8 match 2.6k stars 19.43 score 93k scripts 797 dependents

e-sensing

sits:Satellite Image Time Series Analysis for Earth Observation Data Cubes

An end-to-end toolkit for land use and land cover classification using big Earth observation data, based on machine learning methods applied to satellite image data cubes, as described in Simoes et al (2021) <doi:10.3390/rs13132428>. Builds regular data cubes from collections in AWS, Microsoft Planetary Computer, Brazil Data Cube, Copernicus Data Space Environment (CDSE), Digital Earth Africa, Digital Earth Australia, NASA HLS using the Spatio-temporal Asset Catalog (STAC) protocol (<https://stacspec.org/>) and the 'gdalcubes' R package developed by Appel and Pebesma (2019) <doi:10.3390/data4030092>. Supports visualization methods for images and time series and smoothing filters for dealing with noisy time series. Includes functions for quality assessment of training samples using self-organized maps as presented by Santos et al (2021) <doi:10.1016/j.isprsjprs.2021.04.014>. Includes methods to reduce training samples imbalance proposed by Chawla et al (2002) <doi:10.1613/jair.953>. Provides machine learning methods including support vector machines, random forests, extreme gradient boosting, multi-layer perceptrons, temporal convolutional neural networks proposed by Pelletier et al (2019) <doi:10.3390/rs11050523>, and temporal attention encoders by Garnot and Landrieu (2020) <doi:10.48550/arXiv.2007.00586>. Supports GPU processing of deep learning models using torch <https://torch.mlverse.org/>. Performs efficient classification of big Earth observation data cubes and includes functions for post-classification smoothing based on Bayesian inference as described by Camara et al (2024) <doi:10.3390/rs16234572>, and methods for active learning and uncertainty assessment. Supports region-based time series analysis using package supercells <https://jakubnowosad.com/supercells/>. Enables best practices for estimating area and assessing accuracy of land change as recommended by Olofsson et al (2014) <doi:10.1016/j.rse.2014.02.015>. Minimum recommended requirements: 16 GB RAM and 4 CPU dual-core.

Maintained by Gilberto Camara. Last updated 1 months ago.

big-earth-data cbers earth-observation eo-datacubes geospatial image-time-series land-cover-classification landsat planetary-computer r-spatial remote-sensing rspatial satellite-image-time-series satellite-imagery sentinel-2 stac-api stac-catalog cpp

7.6 match 494 stars 9.50 score 384 scripts

bleutner

RStoolbox:Remote Sensing Data Analysis

Toolbox for remote sensing image processing and analysis such as calculating spectral indexes, principal component transformation, unsupervised and supervised classification or fractional cover analyses.

Maintained by Konstantin Mueller. Last updated 1 months ago.

ggplot2 land-cover-mapping remote-sensing spectral-unmixing supervised-classification unsupervised-classification openblas cpp

6.7 match 275 stars 10.10 score 1.1k scripts

pik-piam

magpie4:MAgPIE outputs R package for MAgPIE version 4.x

Common output routines for extracting results from the MAgPIE framework (versions 4.x).

Maintained by Benjamin Leon Bodirsky. Last updated 2 days ago.

8.4 match 2 stars 7.87 score 254 scripts 9 dependents

erichare

bulletr:Algorithms for Matching Bullet Lands

Analyze bullet lands using nonparametric methods. We provide a reading routine for x3p files (see <http://www.openfmc.org> for more information) and a host of analysis functions designed to assess the probability that two bullets were fired from the same gun barrel.

Maintained by Eric Hare. Last updated 7 years ago.

17.8 match 3.72 score 52 scripts

ptaconet

modisfast:Fast and Efficient Access to MODIS Earth Observation Data

Programmatic interface to several NASA Earth Observation 'OPeNDAP' servers (Open-source Project for a Network Data Access Protocol) (<https://www.opendap.org/>). Allows for easy downloads of MODIS subsets, as well as other Earth Observation datacubes, in a time-saving and efficient way : by sampling it at the very downloading phase (spatially, temporally and dimensionally).

Maintained by Paul Taconet. Last updated 5 days ago.

data-cube earth-science-data environmental-data gpm land modis nasa opendap precipitation-data temperature-data vegetation-data viirs

11.0 match 29 stars 5.60 score 13 scripts

land-info-lab

viewscape:Viewscape Analysis

A collection of functions to make R a more effective viewscape analysis tool for calculating viewscape metrics based on computing the viewable area for given a point/multiple viewpoints and a digital elevation model.The method of calculating viewscape metrics implemented in this package are based on the work of Tabrizian et al. (2020) <doi:10.1016/j.landurbplan.2019.103704>. The algorithm of computing viewshed is based on the work of Franklin & Ray. (1994) <https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=555780f6f5d7e537eb1edb28862c86d1519af2be>.

Maintained by Xiaohao Yang. Last updated 4 months ago.

cpp

14.5 match 1 stars 4.18 score 10 scripts

r-tmap

tmap:Thematic Maps

Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.

Maintained by Martijn Tennekes. Last updated 5 days ago.

choropleth-maps maps spatial thematic-maps visualisation

3.6 match 880 stars 16.73 score 13k scripts 24 dependents

dnychka

fields:Tools for Spatial Data

For curve, surface and function fitting with an emphasis on splines, spatial data, geostatistics, and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance function parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range parameter). A major feature is that any covariance function implemented in R and following a simple format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details as a companion to the manual pages. The commented source code can be viewed by expanding the source code version and looking in the R subdirectory. The reference for fields can be generated by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development of this package was supported in part by the National Science Foundation Grant 1417857, the National Center for Atmospheric Research, and Colorado School of Mines. See the Fields URL for a vignette on using this package and some background on spatial statistics.

Maintained by Douglas Nychka. Last updated 9 months ago.

fortran

4.5 match 15 stars 12.60 score 7.7k scripts 295 dependents

iiasa

mapspam2globiom:An R package to create crop distribution maps as input for GLOBIOM

The aim of the mapspam2globiom R package is to facilitate the creation of country level crop distribution maps, which can be used as input by the IIASA's Global Biosphere Management Model (GLOBIOM) for a selected country. mapspam2globiom includes several functions to aggregate crop distribution maps that were created with the mapspamc package (Van Dijk et al. 2022) to the GLOBIOM input format. mapspamc was specifically developed to create national crop distribution maps using the Spatial Production Allocation Model (SPAM) (You and Wood 2006; You, Wood, and Wood-Sichra 2009; You et al. 2014; Yu et al. 2020).

Maintained by Michiel van Dijk. Last updated 10 months ago.

15.5 match 2 stars 3.60 score 1 scripts

dsstoffer

astsa:Applied Statistical Time Series Analysis

Contains data sets and scripts for analyzing time series in both the frequency and time domains including state space modeling as well as supporting the texts Time Series Analysis and Its Applications: With R Examples (5th ed), by R.H. Shumway and D.S. Stoffer. Springer Texts in Statistics, 2025, <https://link.springer.com/book/9783031705830>, and Time Series: A Data Analysis Approach Using R. Chapman-Hall, 2019, <DOI:10.1201/9780429273285>.

Maintained by David Stoffer. Last updated 2 months ago.

6.8 match 7 stars 7.88 score 2.2k scripts 8 dependents

iembry

ie2miscdata:Irucka Embry's Miscellaneous USGS Data Collection

A collection of Irucka Embry's miscellaneous USGS data sets (USGS Parameter codes with fixed values, USGS global time zone codes, and US Air Force Global Engineering Weather Data). Irucka created these data sets while a Cherokee Nation Technology Solutions (CNTS) United States Geological Survey (USGS) Contractor and/or USGS employee.

Maintained by Irucka Embry. Last updated 2 years ago.

13.1 match 4.00 score

jmlondon

pathroutr:An R Package for (Re-)Routing Paths Around Barriers

The `pathroutr` package aims to provide a set of tools for routing marine animal tracks around land barriers based on the shortest path through a visibility graph network. The foundation of the package is a graph network created from a Delaunay Triangle mesh created from the vertices of land polygons within the study area. Any network edges that cross or fall completely within the land (barrier) polygons are removed.

Maintained by Josh London. Last updated 1 years ago.

10.6 match 16 stars 4.91 score 17 scripts 1 dependents

kadyb

rgugik:Search and Retrieve Spatial Data from 'GUGiK'

Automatic open data acquisition from resources of Polish Head Office of Geodesy and Cartography ('Główny Urząd Geodezji i Kartografii') (<https://www.gov.pl/web/gugik>). Available datasets include various types of numeric, raster and vector data, such as orthophotomaps, digital elevation models (digital terrain models, digital surface model, point clouds), state register of borders, spatial databases, geometries of cadastral parcels, 3D models of buildings, and more. It is also possible to geocode addresses or objects using the geocodePL_get() function.

Maintained by Krzysztof Dyba. Last updated 7 days ago.

cartography geodesy gis open-data poland

6.7 match 34 stars 7.69 score 30 scripts

jasdumas

shinyLP:Bootstrap Landing Home Pages for Shiny Applications

Provides functions that wrap HTML Bootstrap components code to enable the design and layout of informative landing home pages for Shiny applications. This can lead to a better user experience for the users and writing less HTML for the developer.

Maintained by Jasmine Daly. Last updated 13 days ago.

bootstrap r-shiny shiny ui-design

6.7 match 115 stars 7.29 score 85 scripts 2 dependents

insightsengineering

teal:Exploratory Web Apps for Analyzing Clinical Trials Data

A 'shiny' based interactive exploration framework for analyzing clinical trials data. 'teal' currently provides a dynamic filtering facility and different data viewers. 'teal' 'shiny' applications are built using standard 'shiny' modules.

Maintained by Dawid Kaledkowski. Last updated 21 days ago.

clinical-trials nest shiny webapp

3.8 match 197 stars 12.68 score 176 scripts 5 dependents

bluegreen-labs

MODISTools:Interface to the 'MODIS Land Products Subsets' Web Services

Programmatic interface to the Oak Ridge National Laboratories 'MODIS Land Products Subsets' web services (<https://modis.ornl.gov/data/modis_webservice.html>). Allows for easy downloads of 'MODIS' time series directly to your R workspace or your computer.

Maintained by Koen Hufkens. Last updated 1 years ago.

api remote-sensing satellite-data

6.9 match 1 stars 6.90 score 155 scripts 4 dependents

bappa10085

LST:Land Surface Temperature Retrieval for Landsat 8

Calculates Land Surface Temperature from Landsat band 10 and 11. Revision of the Single-Channel Algorithm for Land Surface Temperature Retrieval From Landsat Thermal-Infrared Data. Jimenez-Munoz JC, Cristobal J, Sobrino JA, et al (2009). <doi: 10.1109/TGRS.2008.2007125>. Land surface temperature retrieval from LANDSAT TM 5. Sobrino JA, Jiménez-Muñoz JC, Paolini L (2004). <doi:10.1016/j.rse.2004.02.003>. Surface temperature estimation in Singhbhum Shear Zone of India using Landsat-7 ETM+ thermal infrared data. Srivastava PK, Majumdar TJ, Bhattacharya AK (2009). <doi: 10.1016/j.asr.2009.01.023>. Mapping land surface emissivity from NDVI: Application to European, African, and South American areas. Valor E (1996). <doi:10.1016/0034-4257(96)00039-9>. On the relationship between thermal emissivity and the normalized difference vegetation index for natural surfaces. Van de Griend AA, Owe M (1993). <doi:10.1080/01431169308904400>. Land Surface Temperature Retrieval from Landsat 8 TIRS—Comparison between Radiative Transfer Equation-Based Method, Split Window Algorithm and Single Channel Method. Yu X, Guo X, Wu Z (2014). <doi:10.3390/rs6109829>. Calibration and Validation of land surface temperature for Landsat8-TIRS sensor. Land product validation and evolution. Skoković D, Sobrino JA, Jimenez-Munoz JC, Soria G, Julien Y, Mattar C, Cristóbal J. (2014).

Maintained by Bappa Das. Last updated 4 months ago.

12.4 match 3.70 score 9 scripts

r-forge

robustbase:Basic Robust Statistics

"Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.

Maintained by Martin Maechler. Last updated 4 months ago.

fortran openblas

3.4 match 13.33 score 1.7k scripts 480 dependents

evolecolgroup

pastclim:Manipulate Time Series of Climate Reconstructions

Methods to easily extract and manipulate climate reconstructions for ecological and anthropological analyses, as described in Leonardi et al. (2023) <doi:10.1111/ecog.06481>. The package includes datasets of palaeoclimate reconstructions, present observations, and future projections from multiple climate models.

Maintained by Andrea Manica. Last updated 3 days ago.

climate-data paleoclimate species-distribution-modelling

5.6 match 38 stars 8.12 score 49 scripts

gadget-framework

gadget3:Globally-Applicable Area Disaggregated General Ecosystem Toolbox V3

A framework to assist creation of marine ecosystem models, generating either 'R' or 'C++' code which can then be optimised using the 'TMB' package and standard 'R' tools. Principally designed to reproduce gadget2 models in 'TMB', but can be extended beyond gadget2's capabilities. Kasper Kristensen, Anders Nielsen, Casper W. Berg, Hans Skaug, Bradley M. Bell (2016) <doi:10.18637/jss.v070.i05> "TMB: Automatic Differentiation and Laplace Approximation.". Begley, J., & Howell, D. (2004) <https://core.ac.uk/download/pdf/225936648.pdf> "An overview of Gadget, the globally applicable area-disaggregated general ecosystem toolbox. ICES.".

Maintained by Jamie Lentin. Last updated 30 days ago.

5.1 match 8 stars 8.66 score 170 scripts

rcapell

HYPEtools:Tools for Processing and Analyzing Files from the Hydrological Catchment Model HYPE

Work with model files (setup, input, output) from the hydrological catchment model HYPE: Streamlined file import and export, standard evaluation plot routines, diverse post-processing and aggregation routines for hydrological model analysis. The HYPEtools package is also archived at <doi:10.5281/zenodo.7627955> and can be cited in publications with Brendel et al. (2024) <doi:10.1016/j.envsoft.2024.106094>.

Maintained by Rene Capell. Last updated 26 days ago.

5.8 match 17 stars 7.54 score 26 scripts

flr

FLFishery:Classes and Methods for Simpler Fleet/Fishery Modelling

A set of classes and methods for modelling of fleet dynamics. Fisheries are groups of vessels sharing an effort time series, with static or changing spatio-temporal patterns in selectivity.

Maintained by Iago Mosqueira. Last updated 3 months ago.

fisheries flr

14.3 match 3.02 score 8 scripts 7 dependents

mikkovihtakari

ggOceanMaps:Plot Data on Oceanographic Maps using 'ggplot2'

Allows plotting data on bathymetric maps using 'ggplot2'. Plotting oceanographic spatial data is made as simple as feasible, but also flexible for custom modifications. Data that contain geographic information from anywhere around the globe can be plotted on maps generated by the basemap() or qmap() functions using 'ggplot2' layers separated by the '+' operator. The package uses spatial shape- ('sf') and raster ('stars') files, geospatial packages for R to manipulate, and the 'ggplot2' package to plot these files. The package ships with low-resolution spatial data files and higher resolution files for detailed maps are stored in the 'ggOceanMapsLargeData' repository on GitHub and downloaded automatically when needed.

Maintained by Mikko Vihtakari. Last updated 5 months ago.

7.2 match 46 stars 5.95 score 193 scripts

rafapereirabr

aopdata:Data from the 'Access to Opportunities Project (AOP)'

Download data from the 'Access to Opportunities Project (AOP)'. The 'aopdata' package brings annual estimates of access to employment, health, education and social assistance services by transport mode, as well as data on the spatial distribution of population, jobs, health care, schools and social assistance facilities at a fine spatial resolution for all cities included in the project. More info on the 'AOP' website <https://www.ipea.gov.br/acessooportunidades/en/>.

Maintained by Rafael H. M. Pereira. Last updated 2 months ago.

9.1 match 4.70 score 72 scripts

flr

mse:Tools for Running Management Strategy Evaluations using FLR

A set of functions and methods to enable the development and running of Management Strategy Evaluation (MSE) analyses, using the FLR packages and classes and the a4a methods and algorithms.

Maintained by Iago Mosqueira. Last updated 21 days ago.

simulation mse fisheries flr a4a

6.0 match 4 stars 7.04 score 137 scripts 3 dependents

atsa-es

atsalibrary:Packages, data and scripts for ATSA course and lab book

This package will load the needed packages and data files for the ATSA course material when students install from GitHub.

Maintained by Elizabeth E. Holmes. Last updated 2 years ago.

17.1 match 4 stars 2.41 score 13 scripts

svmiller

stevedata:Steve's Toy Data for Teaching About a Variety of Methodological, Social, and Political Topics

This is a collection of various kinds of data with broad uses for teaching. My students, and academics like me who teach the same topics I teach, should find this useful if their teaching workflow is also built around the R programming language. The applications are multiple but mostly cluster on topics of statistical methodology, international relations, and political economy.

Maintained by Steve Miller. Last updated 4 days ago.

6.9 match 8 stars 5.97 score 178 scripts

predictiveecology

LandR:Landscape Ecosystem Modelling in R

Utilities for 'LandR' suite of landscape simulation models. These models simulate forest vegetation dynamics based on LANDIS-II, and incorporate fire and insect disturbance, as well as other important ecological processes. Models are implemented as 'SpaDES' modules.

Maintained by Eliot J B McIntire. Last updated 4 days ago.

ecological-modelling landscape-ecosystem-modelling spades

6.7 match 17 stars 6.07 score 12 scripts 4 dependents

kvasilopoulos

uklr:Client to United Kingdom Land Registry

Access data from Land Registry Open Data <http://landregistry.data.gov.uk/> through 'SPARQL' queries. 'uklr' supports the house price index, transaction and price paid data.

Maintained by Kostas Vasilopoulos. Last updated 7 months ago.

8.9 match 7 stars 4.54 score 6 scripts

niehs

amadeus:Accessing and Analyzing Large-Scale Environmental Data

Functions are designed to facilitate access to and utility with large scale, publicly available environmental data in R. The package contains functions for downloading raw data files from web URLs (download_data()), processing the raw data files into clean spatial objects (process_covariates()), and extracting values from the spatial data objects at point and polygon locations (calculate_covariates()). These functions call a series of source-specific functions which are tailored to each data sources/datasets particular URL structure, data format, and spatial/temporal resolution. The functions are tested, versioned, and open source and open access. For sum_edc() method details, see Messier, Akita, and Serre (2012) <doi:10.1021/es203152a>.

Maintained by Kyle Messier. Last updated 19 days ago.

5.6 match 8 stars 7.16 score 13 scripts

adriancorrendo

metrica:Prediction Performance Metrics

A compilation of more than 80 functions designed to quantitatively and visually evaluate prediction performance of regression (continuous variables) and classification (categorical variables) of point-forecast models (e.g. APSIM, DSSAT, DNDC, supervised Machine Learning). For regression, it includes functions to generate plots (scatter, tiles, density, & Bland-Altman plot), and to estimate error metrics (e.g. MBE, MAE, RMSE), error decomposition (e.g. lack of accuracy-precision), model efficiency (e.g. NSE, E1, KGE), indices of agreement (e.g. d, RAC), goodness of fit (e.g. r, R2), adjusted correlation coefficients (e.g. CCC, dcorr), symmetric regression coefficients (intercept, slope), and mean absolute scaled error (MASE) for time series predictions. For classification (binomial and multinomial), it offers functions to generate and plot confusion matrices, and to estimate performance metrics such as accuracy, precision, recall, specificity, F-score, Cohen's Kappa, G-mean, and many more. For more details visit the vignettes <https://adriancorrendo.github.io/metrica/>.

Maintained by Adrian A. Correndo. Last updated 9 months ago.

4.9 match 77 stars 8.18 score 49 scripts

adamlilith

fasterRaster:Faster Raster and Spatial Vector Processing Using 'GRASS GIS'

Processing of large-in-memory/large-on disk rasters and spatial vectors using 'GRASS GIS' <https://grass.osgeo.org/>. Most functions in the 'terra' package are recreated. Processing of medium-sized and smaller spatial objects will nearly always be faster using 'terra' or 'sf', but for large-in-memory/large-on-disk objects, 'fasterRaster' may be faster. To use most of the functions, you must have the stand-alone version (not the 'OSGeoW4' installer version) of 'GRASS GIS' 8.0 or higher.

Maintained by Adam B. Smith. Last updated 19 days ago.

aspect distance fragmentation fragmentation-indices gis grass grass-gis raster raster-projection rasterize slope topography vectorization

5.2 match 58 stars 7.69 score 8 scripts

globalecologylab

poems:Pattern-Oriented Ensemble Modeling System

A framework of interoperable R6 classes (Chang, 2020, <https://CRAN.R-project.org/package=R6>) for building ensembles of viable models via the pattern-oriented modeling (POM) approach (Grimm et al.,2005, <doi:10.1126/science.1116681>). The package includes classes for encapsulating and generating model parameters, and managing the POM workflow. The workflow includes: model setup; generating model parameters via Latin hyper-cube sampling (Iman & Conover, 1980, <doi:10.1080/03610928008827996>); running multiple sampled model simulations; collating summary results; and validating and selecting an ensemble of models that best match known patterns. By default, model validation and selection utilizes an approximate Bayesian computation (ABC) approach (Beaumont et al., 2002, <doi:10.1093/genetics/162.4.2025>), although alternative user-defined functionality could be employed. The package includes a spatially explicit demographic population model simulation engine, which incorporates default functionality for density dependence, correlated environmental stochasticity, stage-based transitions, and distance-based dispersal. The user may customize the simulator by defining functionality for translocations, harvesting, mortality, and other processes, as well as defining the sequence order for the simulator processes. The framework could also be adapted for use with other model simulators by utilizing its extendable (inheritable) base classes.

Maintained by July Pilowsky. Last updated 20 days ago.

biogeography population-model process-based

4.9 match 10 stars 8.05 score 59 scripts 2 dependents

lightbluetitan

timeSeriesDataSets:Time Series Data Sets

Provides a diverse collection of time series datasets spanning various fields such as economics, finance, energy, healthcare, and more. Designed to support time series analysis in R by offering datasets from multiple disciplines, making it a valuable resource for researchers and analysts.

Maintained by Renzo Caceres Rossi. Last updated 6 months ago.

6.8 match 10 stars 5.71 score 103 scripts

spatlyu

HSAR:Hierarchical Spatial Autoregressive Model

A Hierarchical Spatial Autoregressive Model (HSAR), based on a Bayesian Markov Chain Monte Carlo (MCMC) algorithm (Dong and Harris (2014) <doi:10.1111/gean.12049>). The creation of this package was supported by the Economic and Social Research Council (ESRC) through the Applied Quantitative Methods Network: Phase II, grant number ES/K006460/1.

Maintained by Wenbo Lv. Last updated 3 months ago.

spatial-econometrics spatial-regression spatial-statistics openblas cpp openmp

6.9 match 6 stars 5.43 score 30 scripts

matthias-da

robCompositions:Compositional Data Analysis

Methods for analysis of compositional data including robust methods (<doi:10.1007/978-3-319-96422-5>), imputation of missing values (<doi:10.1016/j.csda.2009.11.023>), methods to replace rounded zeros (<doi:10.1080/02664763.2017.1410524>, <doi:10.1016/j.chemolab.2016.04.011>, <doi:10.1016/j.csda.2012.02.012>), count zeros (<doi:10.1177/1471082X14535524>), methods to deal with essential zeros (<doi:10.1080/02664763.2016.1182135>), (robust) outlier detection for compositional data, (robust) principal component analysis for compositional data, (robust) factor analysis for compositional data, (robust) discriminant analysis for compositional data (Fisher rule), robust regression with compositional predictors, functional data analysis (<doi:10.1016/j.csda.2015.07.007>) and p-splines (<doi:10.1016/j.csda.2015.07.007>), contingency (<doi:10.1080/03610926.2013.824980>) and compositional tables (<doi:10.1111/sjos.12326>, <doi:10.1111/sjos.12223>, <doi:10.1080/02664763.2013.856871>) and (robust) Anderson-Darling normality tests for compositional data as well as popular log-ratio transformations (addLR, cenLR, isomLR, and their inverse transformations). In addition, visualisation and diagnostic tools are implemented as well as high and low-level plot functions for the ternary diagram.

Maintained by Matthias Templ. Last updated 26 days ago.

cpp

4.0 match 11 stars 9.19 score 226 scripts 2 dependents

mapme-initiative

mapme.biodiversity:Efficient Monitoring of Global Biodiversity Portfolios

Biodiversity areas, especially primary forest, serve a multitude of functions for local economy, regional functionality of the ecosystems as well as the global health of our planet. Recently, adverse changes in human land use practices and climatic responses to increased greenhouse gas emissions, put these biodiversity areas under a variety of different threats. The present package helps to analyse a number of biodiversity indicators based on freely available geographical datasets. It supports computational efficient routines that allow the analysis of potentially global biodiversity portfolios. The primary use case of the package is to support evidence based reporting of an organization's effort to protect biodiversity areas under threat and to identify regions were intervention is most duly needed.

Maintained by Darius A. Görgen. Last updated 3 months ago.

environment eo gis mapme spatial sustainability

3.9 match 35 stars 9.24 score 287 scripts

cran

MASS:Support Functions and Datasets for Venables and Ripley's MASS

Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).

Maintained by Brian Ripley. Last updated 16 days ago.

3.4 match 19 stars 10.53 score 11k dependents

katlande

PCBS:Principal Component BiSulfite

A system for fast, accurate, and flexible whole genome bisulfite sequencing (WGBS) data analysis of two-condition comparisons. Principal Component BiSulfite, 'PCBS', assigns methylated loci eigenvector values from the treatment-delineating principal component in lieu of running millions of pairwise statistical tests, which dramatically increases analysis flexibility and reduces computational requirements. Methods: <https://katlande.github.io/PCBS/articles/Differential_Methylation.html>.

Maintained by Kathryn Lande. Last updated 6 months ago.

9.3 match 1 stars 3.85 score

ctmm-initiative

ctmm:Continuous-Time Movement Modeling

Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic-process movement models to animal tracking data. The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559>, with models and methods based on those introduced and detailed in Fleming & Calabrese et al (2014) <doi:10.1086/675504>, Fleming et al (2014) <doi:10.1111/2041-210X.12176>, Fleming et al (2015) <doi:10.1103/PhysRevE.91.032107>, Fleming et al (2015) <doi:10.1890/14-2010.1>, Fleming et al (2016) <doi:10.1890/15-1607>, Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>, Fleming & Calabrese (2017) <doi:10.1111/2041-210X.12673>, Péron et al (2017) <doi:10.1002/ecm.1260>, Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>, Fleming et al (2018) <doi:10.1002/eap.1704>, Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>, Fleming et al (2019) <doi:10.1111/2041-210X.13270>, Noonan & Fleming et al (2019) <doi:10.1186/s40462-019-0177-1>, Fleming et al (2020) <doi:10.1101/2020.06.12.130195>, Noonan et al (2021) <doi:10.1111/2041-210X.13597>, Fleming et al (2022) <doi:10.1111/2041-210X.13815>, Silva et al (2022) <doi:10.1111/2041-210X.13786>, Alston & Fleming et al (2023) <doi:10.1111/2041-210X.14025>.

Maintained by Christen H. Fleming. Last updated 2 months ago.

3.4 match 49 stars 10.57 score 534 scripts 4 dependents

hgerritsen

mapplots:Data Visualisation on Maps

Create simple maps; add sub-plots like pie plots to a map or any other plot; format, plot and export gridded data. The package was developed for displaying fisheries data but most functions can be used for more generic data visualisation.

Maintained by Hans Gerritsen. Last updated 2 years ago.

7.3 match 2 stars 4.90 score 442 scripts 3 dependents

josesamos

clc:CORINE Land Cover Data and Styles

Streamline the management, analysis, and visualization of CORINE Land Cover data. Addresses challenges associated with its classification system and related styles, such as color mappings and descriptive labels.

Maintained by Jose Samos. Last updated 3 months ago.

7.9 match 4.52 score 11 scripts 1 dependents

bioc

iSEEindex:iSEE extension for a landing page to a custom collection of data sets

This package provides an interface to any collection of data sets within a single iSEE web-application. The main functionality of this package is to define a custom landing page allowing app maintainers to list a custom collection of data sets that users can selected from and directly load objects into an iSEE web-application.

Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.

software infrastructure bioconductor hacktoberfest

6.2 match 2 stars 5.65 score 8 scripts

ropensci

FedData:Download Geospatial Data Available from Several Federated Data Sources

Download geospatial data available from several federated data sources (mainly sources maintained by the US Federal government). Currently, the package enables extraction from nine datasets: The National Elevation Dataset digital elevation models (<https://www.usgs.gov/3d-elevation-program> 1 and 1/3 arc-second; USGS); The National Hydrography Dataset (<https://www.usgs.gov/national-hydrography/national-hydrography-dataset>; USGS); The Soil Survey Geographic (SSURGO) database from the National Cooperative Soil Survey (<https://websoilsurvey.sc.egov.usda.gov/>; NCSS), which is led by the Natural Resources Conservation Service (NRCS) under the USDA; the Global Historical Climatology Network (<https://www.ncei.noaa.gov/products/land-based-station/global-historical-climatology-network-daily>; GHCN), coordinated by National Climatic Data Center at NOAA; the Daymet gridded estimates of daily weather parameters for North America, version 4, available from the Oak Ridge National Laboratory's Distributed Active Archive Center (<https://daymet.ornl.gov/>; DAAC); the International Tree Ring Data Bank; the National Land Cover Database (<https://www.mrlc.gov/>; NLCD); the Cropland Data Layer from the National Agricultural Statistics Service (<https://www.nass.usda.gov/Research_and_Science/Cropland/SARS1a.php>; NASS); and the PAD-US dataset of protected area boundaries (<https://www.usgs.gov/programs/gap-analysis-project/science/pad-us-data-overview>; USGS).

Maintained by R. Kyle Bocinsky. Last updated 3 months ago.

peer-reviewed

4.2 match 100 stars 8.20 score 364 scripts

karlines

plot3D:Plotting Multi-Dimensional Data

Functions for viewing 2-D and 3-D data, including perspective plots, slice plots, surface plots, scatter plots, etc. Includes data sets from oceanography.

Maintained by Karline Soetaert. Last updated 1 years ago.

3.5 match 3 stars 9.59 score 2.1k scripts 78 dependents

framverse

framrsquared:FRAM Database Interface

A convenient tool for interfacing with FRAM access databases in R environments.

Maintained by Ty Garber. Last updated 2 months ago.

6.6 match 6 stars 5.06 score 9 scripts

mikejohnson51

climateR:climateR

Find, subset, and retrive geospatial data by AOI.

Maintained by Mike Johnson. Last updated 3 months ago.

aoi climate dataset geospatial gridded-climate-data weather

3.6 match 187 stars 8.74 score 156 scripts 1 dependents

tagteam

Publish:Format Output of Various Routines in a Suitable Way for Reports and Publication

A bunch of convenience functions that transform the results of some basic statistical analyses into table format nearly ready for publication. This includes descriptive tables, tables of logistic regression and Cox regression results as well as forest plots.

Maintained by Thomas A. Gerds. Last updated 11 days ago.

3.1 match 15 stars 10.11 score 274 scripts 36 dependents

pik-piam

mrland:MadRaT land data package

The package provides land related data via the madrat framework.

Maintained by Jan Philipp Dietrich. Last updated 9 days ago.

5.6 match 5.61 score 3 scripts 4 dependents

pilaboratory

sads:Maximum Likelihood Models for Species Abundance Distributions

Maximum likelihood tools to fit and compare models of species abundance distributions and of species rank-abundance distributions.

Maintained by Paulo I. Prado. Last updated 1 years ago.

3.6 match 23 stars 8.66 score 244 scripts 3 dependents

cran

BoundaryStats:Boundary Overlap Statistics

Analysis workflow for finding geographic boundaries of ecological or landscape traits and comparing the placement of geographic boundaries of two traits. If data are trait values, trait data are transformed to boundary intensities based on approximate first derivatives across latitude and longitude. The package includes functions to create custom null models based on the input data. The boundary statistics are described in: Fortin, Drapeau, and Jacquez (1996) <doi:10.2307/3545584>.

Maintained by Amy Luo. Last updated 5 months ago.

11.5 match 2.70 score 3 scripts

hmorlon

RPANDA:Phylogenetic ANalyses of DiversificAtion

Implements macroevolutionary analyses on phylogenetic trees. See Morlon et al. (2010) <DOI:10.1371/journal.pbio.1000493>, Morlon et al. (2011) <DOI:10.1073/pnas.1102543108>, Condamine et al. (2013) <DOI:10.1111/ele.12062>, Morlon et al. (2014) <DOI:10.1111/ele.12251>, Manceau et al. (2015) <DOI:10.1111/ele.12415>, Lewitus & Morlon (2016) <DOI:10.1093/sysbio/syv116>, Drury et al. (2016) <DOI:10.1093/sysbio/syw020>, Manceau et al. (2016) <DOI:10.1093/sysbio/syw115>, Morlon et al. (2016) <DOI:10.1111/2041-210X.12526>, Clavel & Morlon (2017) <DOI:10.1073/pnas.1606868114>, Drury et al. (2017) <DOI:10.1093/sysbio/syx079>, Lewitus & Morlon (2017) <DOI:10.1093/sysbio/syx095>, Drury et al. (2018) <DOI:10.1371/journal.pbio.2003563>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, Maliet et al. (2019) <DOI:10.1038/s41559-019-0908-0>, Billaud et al. (2019) <DOI:10.1093/sysbio/syz057>, Lewitus et al. (2019) <DOI:10.1093/sysbio/syz061>, Aristide & Morlon (2019) <DOI:10.1111/ele.13385>, Maliet et al. (2020) <DOI:10.1111/ele.13592>, Drury et al. (2021) <DOI:10.1371/journal.pbio.3001270>, Perez-Lamarque & Morlon (2022) <DOI:10.1111/mec.16478>, Perez-Lamarque et al. (2022) <DOI:10.1101/2021.08.30.458192>, Mazet et al. (2023) <DOI:10.1111/2041-210X.14195>, Drury et al. (2024) <DOI:10.1016/j.cub.2023.12.055>.

Maintained by Hélène Morlon. Last updated 2 months ago.

3.6 match 24 stars 8.50 score 255 scripts

isciences

exactextractr:Fast Extraction from Raster Datasets using Polygons

Quickly and accurately summarizes raster values over polygonal areas ("zonal statistics").

Maintained by Daniel Baston. Last updated 7 months ago.

gis raster rcpp geos cpp

2.5 match 286 stars 12.13 score 1.4k scripts 14 dependents

alanarnholt

BSDA:Basic Statistics and Data Analysis

Data sets for book "Basic Statistics and Data Analysis" by Larry J. Kitchens.

Maintained by Alan T. Arnholt. Last updated 2 years ago.

3.3 match 7 stars 9.11 score 1.3k scripts 6 dependents

f-rousset

spaMM:Mixed-Effect Models, with or without Spatial Random Effects

Inference based on models with or without spatially-correlated random effects, multivariate responses, or non-Gaussian random effects (e.g., Beta). Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model. Both classical geostatistical models (Rousset and Ferdy 2014 <doi:10.1111/ecog.00566>), and Markov random field models on irregular grids (as considered in the 'INLA' package, <https://www.r-inla.org>), can be fitted, with distinct computational procedures exploiting the sparse matrix representations for the latter case and other autoregressive models. Laplace approximations are used for likelihood or restricted likelihood. Penalized quasi-likelihood and other variants discussed in the h-likelihood literature (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) are also implemented.

Maintained by François Rousset. Last updated 9 months ago.

gsl cpp openmp

6.0 match 4.94 score 208 scripts 5 dependents

ropensci

mbquartR:Finding Manitoba Quarter Sections

This package has four main functions: 1) download the Manitoba Original Survey Legal Descriptions data set; 2) find the coordinates of a quarter sections given the legal land description (e.g., "NE-11-33-29W"); 3) find the legal land description using coordinates (lat and long); and 4) plot these points on a map.

Maintained by Alex Koiter. Last updated 5 days ago.

6.7 match 4.15 score

landscitech

roads:Road Network Projection

Iterative least cost path and minimum spanning tree methods for projecting forest road networks. The methods connect a set of target points to an existing road network using 'igraph' <https://igraph.org> to identify least cost routes. The cost of constructing a road segment between adjacent pixels is determined by a user supplied weight raster and a weight function; options include the average of adjacent weight raster values, and a function of the elevation differences between adjacent cells that penalizes steep grades. These road network projection methods are intended for integration into R workflows and modelling frameworks used for forecasting forest change, and can be applied over multiple time-steps without rebuilding a graph at each time-step.

Maintained by Sarah Endicott. Last updated 7 months ago.

4.2 match 4 stars 6.58 score 29 scripts

tbep-tech

tbeptools:Data and Indicators for the Tampa Bay Estuary Program

Several functions are provided for working with Tampa Bay Estuary Program data and indicators, including the water quality report card, tidal creek assessments, Tampa Bay Nekton Index, Tampa Bay Benthic Index, seagrass transect data, habitat report card, and fecal indicator bacteria. Additional functions are provided for miscellaneous tasks, such as reference library curation.

Maintained by Marcus Beck. Last updated 9 days ago.

data-analysis tampa-bay tbep water-quality

3.4 match 10 stars 7.86 score 133 scripts

heike

x3ptools:Tools for Working with 3D Surface Measurements

The x3p file format is specified in ISO standard 5436:2000 to describe 3d surface measurements. 'x3ptools' allows reading, writing and basic modifications to the 3D surface measurements.

Maintained by Heike Hofmann. Last updated 6 months ago.

3.6 match 8 stars 7.48 score 281 scripts 2 dependents

iiasa

insights:An R implementation of the InSiGHTS framework

The package provides an implementation of the InSiGHTS modelling framework for creating climate and land-use indicators. This package acts a simple wrapper to do an area-of-habitat refinements on top of climatic envelope models or species distribution models (SDMs). By default it is assumed that such models are obtained through the ibis.iSDM package and this package contains a simple wrapper to link the two approaches.

Maintained by Martin Jung. Last updated 4 months ago.

area-of-habitat biodiversity biodiversity-indicators iucn land-use range

11.5 match 2.30 score 5 scripts

flr

AAP:Aarts and Poos Stock Assessment Model that Estimates Bycatch

FLR version of Aarts and Poos stock assessment model.

Maintained by Iago Mosqueira. Last updated 1 years ago.

9.8 match 2.70 score 5 scripts

cidree

forestdata:Download Forestry Data

Functions for downloading forestry and land use data for use in spatial analysis. This packages offers a user-friendly solution to quickly obtain datasets such as forest height, forest types, tree species under various climate change scenarios, or land use data among others.

Maintained by Adrián Cidre González. Last updated 3 months ago.

6.3 match 13 stars 4.14 score 7 scripts

stscl

geocn:Loads Spatial Data Sets of China

Providing various commonly used spatial data related to Chinese regions in the R programming environment.

Maintained by Wenbo Lv. Last updated 3 months ago.

china china-region geospatial-visualization maps

5.3 match 17 stars 4.93 score 10 scripts

krahim

multitaper:Spectral Analysis Tools using the Multitaper Method

Implements multitaper spectral analysis using discrete prolate spheroidal sequences (Slepians) and sine tapers. It includes an adaptive weighted multitaper spectral estimate, a coherence estimate, Thomson's Harmonic F-test, and complex demodulation. The Slepians sequences are generated efficiently using a tridiagonal matrix solution, and jackknifed confidence intervals are available for most estimates. This package is an implementation of the method described in D.J. Thomson (1982) "Spectrum estimation and harmonic analysis" <doi:10.1109/PROC.1982.12433>.

Maintained by Karim Rahim. Last updated 8 months ago.

fortran openblas

3.4 match 10 stars 7.62 score 67 scripts 26 dependents

mlr-org

mlr3spatial:Support for Spatial Objects Within the 'mlr3' Ecosystem

Extends the 'mlr3' ML framework with methods for spatial objects. Data storage and prediction are supported for packages 'terra', 'raster' and 'stars'.

Maintained by Marc Becker. Last updated 1 years ago.

mlr3 raster-prediction spatial spatial-modelling

3.8 match 43 stars 6.94 score 66 scripts

bioc

iSEE:Interactive SummarizedExperiment Explorer

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

Maintained by Kevin Rue-Albrecht. Last updated 10 days ago.

cellbasedassays clustering dimensionreduction featureextraction geneexpression gui immunooncology shinyapps singlecell transcription transcriptomics visualization dimension-reduction feature-extraction gene-expression hacktoberfest human-cell-atlas shiny single-cell

2.0 match 225 stars 12.86 score 380 scripts 9 dependents

ropensci

rfisheries:Programmatic Interface to the 'openfisheries.org' API

A programmatic interface to 'openfisheries.org'. This package is part of the 'rOpenSci' suite (https://ropensci.org).

Maintained by Karthik Ram. Last updated 5 years ago.

fisheries open-data openfisheries

4.8 match 26 stars 5.31 score 39 scripts

ices-tools-prod

icesFO:Functions to support the creation of ICES Fisheries Overviews

Functions to support the creation of ICES Fisheries Overviews.

Maintained by Adriana Villamor. Last updated 9 months ago.

7.2 match 2 stars 3.41 score 260 scripts

morrowcj

remotePARTS:Spatiotemporal Autoregression Analyses for Large Data Sets

These tools were created to test map-scale hypotheses about trends in large remotely sensed data sets but any data with spatial and temporal variation can be analyzed. Tests are conducted using the PARTS method for analyzing spatially autocorrelated time series (Ives et al., 2021: <doi:10.1016/j.rse.2021.112678>). The method's unique approach can handle extremely large data sets that other spatiotemporal models cannot, while still appropriately accounting for spatial and temporal autocorrelation. This is done by partitioning the data into smaller chunks, analyzing chunks separately and then combining the separate analyses into a single, correlated test of the map-scale hypotheses.

Maintained by Clay Morrow. Last updated 2 years ago.

autocorrelation big-data remote-sensing-in-r statistical-analysis cpp openmp

4.6 match 22 stars 5.25 score 16 scripts

robinsones

funneljoin:Time-Based Joins to Analyze Sequences of Events

Time-based joins to analyze sequence of events, both in memory and out of memory. after_join() joins two tables of events, while funnel_start() and funnel_step() join events in the same table. With the type argument, you can switch between different funnel types, like first-first and last-firstafter.

Maintained by Emily Robinson. Last updated 2 years ago.

3.8 match 69 stars 6.38 score 23 scripts

ices-tools-prod

fisheryO:Fisheries Overviews for ICES Advice

Functions that work with International Council for the Exploration of the Sea (ICES) web services and databases to collate, aggregate, and plot Fisheries Overview products.

Maintained by Scott Large. Last updated 7 years ago.

9.4 match 3 stars 2.45 score 19 scripts

cran

GE:General Equilibrium Modeling

Some tools for developing general equilibrium models and some general equilibrium models. These models can be used for teaching economic theory and are built by the methods of new structural economics (see LI Wu, 2019, ISBN: 9787521804225, General Equilibrium and Structural Dynamics: Perspectives of New Structural Economics. Beijing: Economic Science Press). The model form and mathematical methods can be traced back to J. von Neumann (1945, A Model of General Economic Equilibrium. The Review of Economic Studies, 13. pp. 1-9), J. G. Kemeny, O. Morgenstern and G. L. Thompson (1956, A Generalization of the von Neumann Model of an Expanding Economy, Econometrica, 24, pp. 115-135) et al. By the way, J. G. Kemeny is a co-inventor of the computer language BASIC.

Maintained by Wu LI. Last updated 2 months ago.

8.6 match 1 stars 2.64 score

schochastics

networkdata:Repository of Network Datasets

The package contains a large collection of network dataset with different context. This includes social networks, animal networks and movie networks. All datasets are in 'igraph' format.

Maintained by David Schoch. Last updated 12 months ago.

dataset network-analysis

4.5 match 143 stars 5.01 score 143 scripts

ocean-tracking-network

glatos:A package for the Great Lakes Acoustic Telemetry Observation System

Functions useful to members of the Great Lakes Acoustic Telemetry Observation System https://glatos.glos.us; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.

Maintained by Christopher Holbrook. Last updated 6 months ago.

3.5 match 10 stars 6.38 score 112 scripts

r-spatial

stars:Spatiotemporal Arrays, Raster and Vector Data Cubes

Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.

Maintained by Edzer Pebesma. Last updated 30 days ago.

raster satellite-images spatial

1.2 match 571 stars 18.27 score 7.2k scripts 137 dependents

blakedickson

Morphoscape:Computation and Visualization of Adaptive Landscapes

Implements adaptive landscape methods first described by Polly et al. (2016) <doi:10.1080/02724634.2016.1111225> for the integration, analysis and visualization of biological trait data on a phenotypic morphospace - typically defined by shape metrics.

Maintained by Blake Dickson. Last updated 9 months ago.

3.9 match 4 stars 5.56 score 8 scripts

core-bioinformatics

ClustAssess:Tools for Assessing Clustering

A set of tools for evaluating clustering robustness using proportion of ambiguously clustered pairs (Senbabaoglu et al. (2014) <doi:10.1038/srep06207>), as well as similarity across methods and method stability using element-centric clustering comparison (Gates et al. (2019) <doi:10.1038/s41598-019-44892-y>). Additionally, this package enables stability-based parameter assessment for graph-based clustering pipelines typical in single-cell data analysis.

Maintained by Andi Munteanu. Last updated 1 months ago.

software singlecell rnaseq atacseq normalization preprocessing dimensionreduction visualization qualitycontrol clustering classification annotation geneexpression differentialexpression bioinformatics genomics machine-learning parameter-optimization robustness single-cell unsupervised-learning cpp

3.8 match 23 stars 5.70 score 18 scripts

doserjef

rFIA:Estimation of Forest Variables using the FIA Database

The goal of 'rFIA' is to increase the accessibility and use of the United States Forest Services (USFS) Forest Inventory and Analysis (FIA) Database by providing a user-friendly, open source toolkit to easily query and analyze FIA Data. Designed to accommodate a wide range of potential user objectives, 'rFIA' simplifies the estimation of forest variables from the FIA Database and allows all R users (experts and newcomers alike) to unlock the flexibility inherent to the Enhanced FIA design. Specifically, 'rFIA' improves accessibility to the spatial-temporal estimation capacity of the FIA Database by producing space-time indexed summaries of forest variables within user-defined population boundaries. Direct integration with other popular R packages (e.g., 'dplyr', 'tidyr', and 'sf') facilitates efficient space-time query and data summary, and supports common data representations and API design. The package implements design-based estimation procedures outlined by Bechtold & Patterson (2005) <doi:10.2737/SRS-GTR-80>, and has been validated against estimates and sampling errors produced by FIA 'EVALIDator'. Current development is focused on the implementation of spatially-enabled model-assisted and model-based estimators to improve population, change, and ratio estimates.

Maintained by Jeffrey Doser. Last updated 9 days ago.

compute-estimates fia fia-database fia-datamart forest-inventory forest-variables inventories space-time spatial

3.6 match 49 stars 5.93 score

pik-piam

mrremind:MadRat REMIND Input Data Package

The mrremind packages contains data preprocessing for the REMIND model.

Maintained by Lavinia Baumstark. Last updated 3 days ago.

3.4 match 4 stars 6.25 score 15 scripts 1 dependents

covidr

sfo:San Francisco International Airport Monthly Air Passengers

Provides monthly statistics on the number of monthly air passengers at SFO airport such as operating airline, terminal, geo, etc. Data source: San Francisco data portal (DataSF) <https://data.sfgov.org/Transportation/Air-Traffic-Passenger-Statistics/rkru-6vcg>.

Maintained by Rami Krispin. Last updated 2 years ago.

6.9 match 3.04 score 11 scripts

flr

FLBEIA:Bio-Economic Impact Assessment of Management Strategies using FLR

A simulation toolbox that describes a fishery system under a Management Strategy Estrategy approach. The objective of the model is to facilitate the Bio-Economic evaluation of Management strategies. It is multistock, multifleet and seasonal. The simulation is divided in 2 main blocks, the Operating Model (OM) and the Management Procedure (MP). In turn, each of these two blocks is divided in 3 components: the biological, the fleets and the covariables on the one hand, and the observation, the assessment and the advice on the other.

Maintained by FLBEIA Team. Last updated 6 days ago.

cpp

3.5 match 11 stars 5.97 score 156 scripts

biodiverse

spAbundance:Univariate and Multivariate Spatial Modeling of Species Abundance

Fits single-species (univariate) and multi-species (multivariate) non-spatial and spatial abundance models in a Bayesian framework using Markov Chain Monte Carlo (MCMC). Spatial models are fit using Nearest Neighbor Gaussian Processes (NNGPs). Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2022) <doi:10.18637/jss.v103.i05>. Fits single-species and multi-species spatial and non-spatial versions of generalized linear mixed models (Gaussian, Poisson, Negative Binomial), N-mixture models (Royle 2004 <doi:10.1111/j.0006-341X.2004.00142.x>) and hierarchical distance sampling models (Royle, Dawson, Bates (2004) <doi:10.1890/03-3127>). Multi-species spatial models are fit using a spatial factor modeling approach with NNGPs for computational efficiency.

Maintained by Jeffrey Doser. Last updated 17 days ago.

openblas cpp openmp

3.3 match 17 stars 6.15 score 43 scripts 1 dependents

forest-economics-goettingen

optimLanduse:Robust Land-Use Optimization

Robust multi-criteria land-allocation optimization that explicitly accounts for the uncertainty of the indicators in the objective function. Solves the problem of allocating scarce land to various land-use options with regard to multiple, coequal indicators. The method aims to find the land allocation that represents the indicator composition with the best possible trade-off under uncertainty. optimLanduse includes the actual optimization procedure as described by Knoke et al. (2016) <doi:10.1038/ncomms11877> and the post-hoc calculation of the portfolio performance as presented by Gosling et al. (2020) <doi:10.1016/j.jenvman.2020.110248>.

Maintained by Kai Husmann. Last updated 1 years ago.

5.6 match 2 stars 3.60 score 2 scripts

fishr-core-team

FSAdata:Data to Support Fish Stock Assessment ('FSA') Package

The datasets to support the Fish Stock Assessment ('FSA') package.

Maintained by Derek Ogle. Last updated 2 years ago.

fish fisheries fisheries-stock-assessment fishr-website stock-assessment

3.5 match 13 stars 5.75 score 285 scripts

ianjonsen

aniMotum:Fit Continuous-Time State-Space and Latent Variable Models for Quality Control of Argos Satellite (and Other) Telemetry Data and for Estimating Changes in Animal Movement

Fits continuous-time random walk, correlated random walk and move persistence state-space models for location estimation and behavioural inference from animal tracking data ('Argos', processed light-level 'geolocation', 'GPS'). Template Model Builder ('TMB') is used for fast random-effects estimation. The 'Argos' data can be: (older) least squares-based locations; (newer) Kalman filter-based locations with error ellipse information; or a mixture of both. The models estimate two sets of location states corresponding to: 1) each observation, which are (usually) irregularly timed; and 2) user-specified time intervals (regular or irregular). A track re-routing function is provided to adjust location estimates for known movement barriers. Track simulation functions are provided. Latent variable models are also provided to estimate move persistence from track data not requiring state-space model filtering.

Maintained by Ian Jonsen. Last updated 10 days ago.

animal-movement animal-tracking random-effects-model state-space-models tmb cpp

2.8 match 39 stars 7.16 score 59 scripts

cont-limno

LAGOSNE:Interface to the Lake Multi-Scaled Geospatial and Temporal Database

Client for programmatic access to the Lake Multi-scaled Geospatial and Temporal database <https://lagoslakes.org>, with functions for accessing lake water quality and ecological context data for the US.

Maintained by Jemma Stachelek. Last updated 2 years ago.

ecology geoscience limnology water-quality

2.9 match 15 stars 6.77 score 98 scripts

spedygiorgio

markovchain:Easy Handling Discrete Time Markov Chains

Functions and S4 methods to create and manage discrete time Markov chains more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of their structural proprieties) analysis are provided. See Spedicato (2017) <doi:10.32614/RJ-2017-036>. Some functions for continuous times Markov chains depend on the suggested ctmcd package.

Maintained by Giorgio Alfredo Spedicato. Last updated 4 months ago.

ctmc dtmc markov-chain markov-model r-programming rcpp openblas cpp

1.5 match 104 stars 12.78 score 712 scripts 4 dependents

aphalo

photobiologyFilters:Spectral Transmittance and Spectral Reflectance Data

Spectral 'transmittance' data for frequently used filters and similar materials. Plastic sheets and films; photography filters; theatrical gels; machine-vision filters; various types of window glass; optical glass and some laboratory plastics and glassware. Spectral reflectance data for frequently encountered materials. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.

Maintained by Pedro J. Aphalo. Last updated 6 days ago.

3.8 match 5.08 score 40 scripts

statmanrobin

Stat2Data:Datasets for Stat2

Datasets for the textbook Stat2: Modeling with Regression and ANOVA (second edition). The package also includes data for the first edition, Stat2: Building Models for a World of Data and a few functions for plotting diagnostics.

Maintained by Robin Lock. Last updated 6 years ago.

3.8 match 5 stars 4.94 score 544 scripts

ices-tools-prod

icesVMS:Link to the ICES Vessel Monitoring System and Logbook Database Web Services

Links to the ICES Vessel Monitoring System (VMS) and logbook database web services <https://data.ices.dk/vms/webservices> to allow users to download summaries and data products.

Maintained by Colin Millar. Last updated 6 months ago.

6.9 match 2 stars 2.66 score 46 scripts

noaa-nwfsc

zoid:Bayesian Zero-and-One Inflated Dirichlet Regression Modelling

Fits Dirichlet regression and zero-and-one inflated Dirichlet regression with Bayesian methods implemented in Stan. These models are sometimes referred to as trinomial mixture models; covariates and overdispersion can optionally be included.

Maintained by Eric J. Ward. Last updated 11 months ago.

mixture-models nwfsc-cb stan cpp

3.0 match 8 stars 5.89 score 12 scripts

europeanifcbgroup

iRfcb:Tools for Managing Imaging FlowCytobot (IFCB) Data

A comprehensive suite of tools for managing, processing, and analyzing data from the IFCB. I R FlowCytobot ('iRfcb') supports quality control, geospatial analysis, and preparation of IFCB data for publication in databases like <https://www.gbif.org>, <https://www.obis.org>, <https://emodnet.ec.europa.eu/en>, <https://shark.smhi.se/>, and <https://www.ecotaxa.org>. The package integrates with the MATLAB 'ifcb-analysis' tool, which is described in Sosik and Olson (2007) <doi:10.4319/lom.2007.5.204>, and provides features for working with raw, manually classified, and machine learning–classified image datasets. Key functionalities include image extraction, particle size distribution analysis, taxonomic data handling, and biomass concentration calculations, essential for plankton research.

Maintained by Anders Torstensson. Last updated 11 hours ago.

3.1 match 1 stars 5.72 score

hankstevens

primer:Functions and Data for the Book, a Primer of Ecology with R

Functions are primarily functions for systems of ordinary differential equations, difference equations, and eigenanalysis and projection of demographic matrices; data are for examples.

Maintained by Hank Stevens. Last updated 4 years ago.

3.0 match 14 stars 5.92 score 118 scripts

dankelley

ocedata:Oceanographic Data Sets for 'oce' Package

Several Oceanographic data sets are provided for use by the 'oce' package, and for other purposes.

Maintained by Dan Kelley. Last updated 2 years ago.

3.4 match 8 stars 5.07 score 146 scripts

fchamroukhi

meteorits:Mixture-of-Experts Modeling for Complex Non-Normal Distributions

Provides a unified mixture-of-experts (ME) modeling and estimation framework with several original and flexible ME models to model, cluster and classify heterogeneous data in many complex situations where the data are distributed according to non-normal, possibly skewed distributions, and when they might be corrupted by atypical observations. Mixtures-of-Experts models for complex and non-normal distributions ('meteorits') are originally introduced and written in 'Matlab' by Faicel Chamroukhi. The references are mainly the following ones. The references are mainly the following ones. Chamroukhi F., Same A., Govaert, G. and Aknin P. (2009) <doi:10.1016/j.neunet.2009.06.040>. Chamroukhi F. (2010) <https://chamroukhi.com/FChamroukhi-PhD.pdf>. Chamroukhi F. (2015) <arXiv:1506.06707>. Chamroukhi F. (2015) <https://chamroukhi.com/FChamroukhi-HDR.pdf>. Chamroukhi F. (2016) <doi:10.1109/IJCNN.2016.7727580>. Chamroukhi F. (2016) <doi:10.1016/j.neunet.2016.03.002>. Chamroukhi F. (2017) <doi:10.1016/j.neucom.2017.05.044>.

Maintained by Florian Lecocq. Last updated 5 years ago.

artificial-intelligence clustering em-algorithm mixture-of-experts neural-networks non-linear-regression prediction robust-learning skew-normal skew-t skewed-data statistical-inference statistical-learning t-distribution unsupervised-learning openblas cpp

3.3 match 3 stars 5.12 score 11 scripts

jeffreyevans

spatialEco:Spatial Analysis and Modelling Utilities

Utilities to support spatial data manipulation, query, sampling and modelling in ecological applications. Functions include models for species population density, spatial smoothing, multivariate separability, point process model for creating pseudo- absences and sub-sampling, Quadrant-based sampling and analysis, auto-logistic modeling, sampling models, cluster optimization, statistical exploratory tools and raster-based metrics.

Maintained by Jeffrey S. Evans. Last updated 13 days ago.

biodiversity conservation ecology r-spatial raster spatial vector

1.7 match 110 stars 9.55 score 736 scripts 2 dependents

fgashakamba

hypsoLoop:A Tool Used to Conduct Hypsometric Analysis of a Watershed

Functions for generating tables required for drawing and calculating hypsometric curves and hypsometric integrals. These functions accept as input the DEM of the region of interest (your watershed) and a spatial data frame file specifying delineation of sub-catchments within the watershed. They then generate output in the form of PNG images and HTML files contained in a folder named "HYPSO_OUTPUT" created in the current directory. S. K. Sharma, S. Gajbhiye, et al. (2018) <doi:10.1007/978-981-10-5801-1_19>. Omvir Singh, A. Sarangi, and Milap C. Sharma (2006) <doi:10.1007/s11269-008-9242-z>. James A. Vanderwaal and Herbert Ssegane (2013) <doi:10.1111/jawr.12089>.

Maintained by Faustin GASHAKAMBA. Last updated 3 years ago.

6.0 match 1 stars 2.70 score 2 scripts

carlos-alberto-silva

ICESat2VegR:NASA's Ice, Cloud, and Elevation Satellite (ICESat-2) Data Analysis for Land and Vegetation Applications

Set of tools for downloading, reading, visualizing, processing and exporting NASA's ICESat-2 ATL03 (Global Geolocated Photon Data) and ATL08 (Land and Vegetation Height) products for Land and Vegetation Applications.

Maintained by Caio Hamamura. Last updated 6 months ago.

gdal proj cpp

3.5 match 11 stars 4.57 score 21 scripts

achubaty

grainscape:Landscape Connectivity, Habitat, and Protected Area Networks

Given a landscape resistance surface, creates minimum planar graph (Fall et al. (2007) <doi:10.1007/s10021-007-9038-7>) and grains of connectivity (Galpern et al. (2012) <doi:10.1111/j.1365-294X.2012.05677.x>) models that can be used to calculate effective distances for landscape connectivity at multiple scales. Documentation is provided by several vignettes, and a paper (Chubaty, Galpern & Doctolero (2020) <doi:10.1111/2041-210X.13350>).

Maintained by Alex M Chubaty. Last updated 2 months ago.

habitat-connectivity landscape-connectivity spatial-graphs cpp

2.4 match 20 stars 6.78 score 20 scripts

pieterprovoost

landr:Add land polygons to ggplot2 maps

Add land polygons to ggplot2 maps.

Maintained by Pieter Provoost. Last updated 2 years ago.

9.0 match 1 stars 1.78 score 12 scripts

sanfordweisberg

alr4:Data to Accompany Applied Linear Regression 4th Edition

Datasets to Accompany S. Weisberg (2014, ISBN: 978-1-118-38608-8), "Applied Linear Regression," 4th edition. Many data files in this package are included in the `alr3` package as well, so only one of them should be used.

Maintained by Sanford Weisberg. Last updated 7 years ago.

4.5 match 1 stars 3.45 score 306 scripts

hong-kong-districts-info

hkdatasets:Datasets Related to Hong Kong

Datasets related to Hong Kong, including information on the 2019 elected District Councillors (<https://www.districtcouncils.gov.hk> and <https://dce2019.hk01.com/>) and traffic collision data from the Hong Kong Department of Transport (<https://www.td.gov.hk/>). All of the data in this package is available in the public domain.

Maintained by Martin Chan. Last updated 4 years ago.

dataset hong-kong

3.3 match 18 stars 4.69 score 27 scripts

sevvandi

stxplore:Exploration of Spatio-Temporal Data

A set of statistical tools for spatio-temporal data exploration. Includes simple plotting functions, covariance calculations and computations similar to principal component analysis for spatio-temporal data. Can use both dataframes and stars objects for all plots and computations. For more details refer 'Spatio-Temporal Statistics with R' (Christopher K. Wikle, Andrew Zammit-Mangion, Noel Cressie, 2019, ISBN:9781138711136).

Maintained by Sevvandi Kandanaarachchi. Last updated 2 years ago.

3.3 match 5 stars 4.70 score 7 scripts

pecanproject

PEcAn.data.remote:PEcAn Functions Used for Extracting Remote Sensing Data

PEcAn module for processing remote data. Python module requirements: requests, json, re, ast, panads, sys. If any of these modules are missing, install using pip install <module name>.

Maintained by Bailey Morrison. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

1.7 match 216 stars 8.74 score 6 scripts 5 dependents

alinamateikondylis

sampling:Survey Sampling

Functions to draw random samples using different sampling schemes are available. Functions are also provided to obtain (generalized) calibration weights, different estimators, as well some variance estimators.

Maintained by Alina Matei. Last updated 1 years ago.

1.9 match 2 stars 7.98 score 772 scripts 29 dependents

icra

ediblecity:Modeling Urban Agriculture at City Scale

The purpose of this package is to estimate the potential of urban agriculture to contribute to addressing several urban challenges at the city-scale. Within this aim, we selected 8 indicators directly related to one or several urban challenges. Also, a function is provided to compute new scenarios of urban agriculture. Methods are described by Pueyo-Ros, Comas & Corominas (2023) <doi:10.12688/openreseurope.16054.1>.

Maintained by Josep Pueyo-Ros. Last updated 1 years ago.

4.0 match 3.70 score 10 scripts

apear9

rdwplus:Inverse Distance Weighted Percent Land Use for Streams

Compute spatially explicit land-use metrics for stream survey sites in GRASS GIS and R as an open-source implementation of IDW-PLUS (Inverse Distance Weighted Percent Land Use for Streams). The package includes functions for preprocessing digital elevation and streams data, and one function to compute all the spatially explicit land use metrics described in Peterson et al. (2011) <doi:10.1111/j.1365-2427.2010.02507.x> and previously implemented by Peterson and Pearse (2017) <doi:10.1111/1752-1688.12558> in ArcGIS-Python as IDW-PLUS.

Maintained by Alan Pearse. Last updated 1 months ago.

3.8 match 4 stars 3.90 score 6 scripts

psolymos

opticut:Likelihood Based Optimal Partitioning and Indicator Species Analysis

Likelihood based optimal partitioning and indicator species analysis. Finding the best binary partition for each species based on model selection, with the possibility to take into account modifying/confounding variables as described in Kemencei et al. (2014) <doi:10.1556/ComEc.15.2014.2.6>. The package implements binary and multi-level response models, various measures of uncertainty, Lorenz-curve based thresholding, with native support for parallel computations.

Maintained by Peter Solymos. Last updated 10 months ago.

ecology indicator-species-analysis likelihood optimal-partitioning species

3.8 match 2 stars 3.91 score 82 scripts

mountainmath

VancouvR:Access the 'City of Vancouver' Open Data API

Wrapper around the 'City of Vancouver' Open Data API <https://opendata.vancouver.ca/api/v2/console> to simplify and standardize access to 'City of Vancouver' open data. Functionality to list the data catalogue and access data and geographic records.

Maintained by Jens von Bergmann. Last updated 9 months ago.

2.3 match 19 stars 5.98 score 25 scripts

rwoldford

qqtest:Self Calibrating Quantile-Quantile Plots for Visual Testing

Provides the function qqtest which incorporates uncertainty in its qqplot display(s) so that the user might have a better sense of the evidence against the specified distributional hypothesis. qqtest draws a quantile quantile plot for visually assessing whether the data come from a test distribution that has been defined in one of many ways. The vertical axis plots the data quantiles, the horizontal those of a test distribution. The default behaviour generates 1000 samples from the test distribution and overlays the plot with shaded pointwise interval estimates for the ordered quantiles from the test distribution. A small number of independently generated exemplar quantile plots can also be overlaid. Both the interval estimates and the exemplars provide different comparative information to assess the evidence provided by the qqplot for or against the hypothesis that the data come from the test distribution (default is normal or gaussian). Finally, a visual test of significance (a lineup plot) can also be displayed to test the null hypothesis that the data come from the test distribution.

Maintained by Wayne Oldford. Last updated 5 years ago.

3.1 match 1 stars 4.18 score 30 scripts

laylaparast

landest:Landmark Estimation of Survival and Treatment Effect

Provides functions to estimate survival and a treatment effect using a landmark estimation approach.

Maintained by Layla Parast. Last updated 2 years ago.

11.8 match 1.08 score 12 scripts

idem-lab

sdmtools:Utility tools for Species Distribution Modelling

What the package does (one paragraph).

Maintained by Gerry Ryan. Last updated 3 months ago.

2.0 match 9 stars 6.13 score 674 scripts

jgregoriods

spDates:Analysis of Spatial Gradients in Radiocarbon Dates

Inspired by space-time regressions often performed to assess the expansion of the Neolithic from the Near East to Europe (Pinhasi et al. 2005 <doi:10.1371/journal.pbio.0030410>). Test for significant correlations between the (earliest) radiocarbon dates of archaeological sites and their respective distances from a hypothetical center of origin. Both ordinary least squares (OLS) and reduced major axis (RMA) methods are supported (Russell et al. 2014 <doi:10.1371/journal.pone.0087854>). It is also possible to iterate over many sites to identify the most likely origin.

Maintained by Jonas Gregorio de Souza. Last updated 2 years ago.

radiocarbon-dates

4.5 match 1 stars 2.70 score 2 scripts

marcohlmann

metanetwork:Handling and Representing Trophic Networks in Space and Time

A toolbox to handle and represent trophic networks in space or time across aggregation levels. This package contains a layout algorithm specifically designed for trophic networks, using dimension reduction on a diffusion graph kernel and trophic levels. Importantly, this package provides a layout method applicable for large trophic networks. The package also implements network diversity indices at different aggregation levels and connectance computation.

Maintained by Marc Ohlmann. Last updated 2 years ago.

3.1 match 2 stars 3.89 score 77 scripts

isabella84

SECFISH:Disaggregate Variable Costs

These functions were developed within SECFISH project (Strengthening regional cooperation in the area of fisheries data collection-Socio-economic data collection for fisheries, aquaculture and the processing industry at EU level). They are aimed at identifying correlations between costs and transversal variables by metier using individual vessel data and for disaggregating variable costs from fleet segment to metier level.

Maintained by Isabella Bitetto. Last updated 6 years ago.

6.0 match 1 stars 2.00 score

lilyclements

carbonr:Calculate Carbon-Equivalent Emissions

Provides a flexible tool for calculating carbon-equivalent emissions. Mostly using data from the UK Government's Greenhouse Gas Conversion Factors report <https://www.gov.uk/government/publications/greenhouse-gas-reporting-conversion-factors-2023>, it facilitates transparent emissions calculations for various sectors, including travel, accommodation, and clinical activities. The package is designed for easy integration into R workflows, with additional support for 'shiny' applications and community-driven extensions.

Maintained by Lily Clements. Last updated 5 months ago.

3.5 match 3.16 score 29 scripts

cran

erer:Empirical Research in Economics with R

Several functions, datasets, and sample codes related to empirical research in economics are included. They cover the marginal effects for binary or ordered choice models, static and dynamic Almost Ideal Demand System (AIDS) models, and a typical event analysis in finance.

Maintained by Changyou Sun. Last updated 6 months ago.

3.3 match 3 stars 3.34 score 211 scripts 1 dependents

confoobio

GMSE:Generalised Management Strategy Evaluation Simulator

Integrates game theory and ecological theory to construct social-ecological models that simulate the management of populations and stakeholder actions. These models build off of a previously developed management strategy evaluation (MSE) framework to simulate all aspects of management: population dynamics, manager observation of populations, manager decision making, and stakeholder responses to management decisions. The newly developed generalised management strategy evaluation (GMSE) framework uses genetic algorithms to mimic the decision-making process of managers and stakeholders under conditions of change, uncertainty, and conflict. Simulations can be run using gmse(), gmse_apply(), and gmse_gui() functions.

Maintained by A. Bradley Duthie. Last updated 3 years ago.

adaptive-management agricultural-modelling conflict conflict-resolution conservation ecological-modelling ecological-models ecology food-security game-theory genetic-algorithm genetic-algorithms management-decisions management-strategy-evaluation population-model simulation wildlife-management

2.0 match 10 stars 5.43 score 178 scripts

pedrocoutinhosilva

shiny.pwa:Progressive Web App Support for Shiny

Adds Progressive Web App support for Shiny apps, including desktop and mobile installations.

Maintained by Pedro Silva. Last updated 4 years ago.

pwa shiny

1.9 match 57 stars 5.76 score 20 scripts

arni-magnusson

scape:Statistical Catch-at-Age Plotting Environment

Import, plot, and diagnose results from statistical catch-at-age models, used in fisheries stock assessment.

Maintained by Arni Magnusson. Last updated 5 months ago.

1.9 match 5.72 score 35 scripts

rafapereirabr

geobr:Download Official Spatial Data Sets of Brazil

Easy access to official spatial data sets of Brazil as 'sf' objects in R. The package includes a wide range of geospatial data available at various geographic scales and for various years with harmonized attributes, projection and fixed topology.

Maintained by Rafael H. M. Pereira. Last updated 6 months ago.

1.8 match 5.89 score 1.4k scripts 1 dependents

haydarde

dLagM:Time Series Regression Models with Distributed Lag Models

Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Demirhan (2020)(<doi:10.1371/journal.pone.0228812>) and Baltagi (2011)(<doi:10.1007/978-3-642-20059-5>) for more information.

Maintained by Haydar Demirhan. Last updated 1 years ago.

3.2 match 2 stars 3.18 score 127 scripts

emf-creaf

medfateland:Mediterranean Landscape Simulation

Simulate forest hydrology, forest function and dynamics over landscapes [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>]. Parallelization is allowed in several simulation functions and simulations may be conducted including spatial processes such as lateral water transfer and seed dispersal.

Maintained by Miquel De Cáceres. Last updated 25 days ago.

cpp

1.9 match 5 stars 5.41 score 41 scripts

mobreza

genesysr:Genesys PGR Client

Access data on plant genetic resources from genebanks around the world published on Genesys (<https://www.genesys-pgr.org>). Your use of data is subject to terms and conditions available at <https://www.genesys-pgr.org/content/legal/terms>.

Maintained by Matija Obreza. Last updated 1 years ago.

3.2 match 3.00 score 6 scripts

nmfs-ost

satf:Stock Assessment Tables and Figures

Creates exploratory and finished tables and figures for stock assessment documents from U.S. stock assessment model outputs. This packages addresses parts of the stock assessment workflow that interprets outputs of stock assessment models as well as allows the analyst to create report ready tables and figures, reducing the need to create their own and format then when adding into a report. This package is intended to be used in conjuction with `asar`, a partially automated template for writing various stock assessment reports. Throughout development, we will be creating a set of standardized figures and tables for a stock assessment report, developing functions to produce a variety of diagonostic plots, and other helpful materials. The advantage of using this package over others is that it applies to a range of stock assessment model outputs and standardizes them.

Maintained by Samantha Schiano. Last updated 30 days ago.

1.9 match 2 stars 4.88 score 5 scripts

tuncerkerem

experimentr:Datasets Used in Social Science Experiments: A Hands-on Introduction

Contains all the datasets that were used in Social Science Experiments: A Hands-On Introduction and in its R Companion. Relevant materials can be found at <https://osf.io/b78je>.

Maintained by Kerem Tuncer. Last updated 3 years ago.

3.3 match 2.70 score 8 scripts

mattwarkentin

fidelius:Browser-Side Password-Protected HTML Documents

Create secure, encrypted, and password-protected static HTML documents that include the machinery for secure in-browser authentication and decryption.

Maintained by Matthew T. Warkentin. Last updated 3 years ago.

1.9 match 32 stars 4.68 score 4 scripts 1 dependents

ptitle

rangeBuilder:Occurrence Filtering, Geographic Standardization and Generation of Species Range Polygons

Provides tools for filtering occurrence records, generating alpha-hull-derived range polygons and mapping species distributions.

Maintained by Pascal Title. Last updated 5 months ago.

cpp

1.8 match 9 stars 4.99 score 72 scripts 1 dependents

drj001

hett:Heteroscedastic t-Regression

Functions for the fitting and summarizing of heteroscedastic t-regression.

Maintained by Julian Taylor. Last updated 4 years ago.

3.8 match 2.19 score 26 scripts 2 dependents

uribo

jpndistrict:Create Japanese Administration Area and Office Maps

Utilizing the data that Japanese administration area provided by the National Land Numerical Information download service (<https://nlftp.mlit.go.jp/ksj/index.html>). This package provide map data is based on the Digital Map 25000 (Map Image) published by Geospatial Information Authority of Japan (Approval No.603FY2017 information usage <https://www.gsi.go.jp>).

Maintained by Shinya Uryu. Last updated 4 years ago.

japan map visualization

2.1 match 22 stars 3.94 score 40 scripts

pik-piam

mrwater:madrat based MAgPIE water Input Data Library

Provides functions for MAgPIE cellular input data generation and stand-alone water calculations.

Maintained by Felicitas Beier. Last updated 5 months ago.

1.3 match 6.45 score 4 scripts 3 dependents

cbw1243

CropScapeR:Access Cropland Data Layer Data via the 'CropScape' Web Service

Interface to easily access Cropland Data Layer (CDL) data for any area of interest via the 'CropScape' <https://nassgeodata.gmu.edu/CropScape/> web service.

Maintained by Bowen Chen. Last updated 2 years ago.

3.5 match 2.22 score 33 scripts

core-bioinformatics

bulkAnalyseR:Interactive Shiny App for Bulk Sequencing Data

Given an expression matrix from a bulk sequencing experiment, pre-processes it and creates a shiny app for interactive data analysis and visualisation. The app contains quality checks, differential expression analysis, volcano and cross plots, enrichment analysis and gene regulatory network inference, and can be customised to contain more panels by the user.

Maintained by Ilias Moutsopoulos. Last updated 1 years ago.

1.8 match 27 stars 4.47 score 11 scripts

langema

sperich:Auxiliary Functions to Estimate Centers of Biodiversity

Provides some easy-to-use functions to interpolate species range based on species occurrences and to estimate centers of biodiversity.

Maintained by Maximilian Lange. Last updated 2 years ago.

5.6 match 1.36 score 23 scripts

forestscientist

StemAnalysis:Reconstructing Tree Growth and Carbon Accumulation with Stem Analysis Data

Use stem analysis data to reconstructing tree growth and carbon accumulation. Users can independently or in combination perform a number of standard tasks for any tree species. (i) Age class determination. (ii) The cumulative growth, mean annual increment, and current annual increment of diameter at breast height (DBH) with bark, tree height, and stem volume with bark are estimated. (iii) Tree biomass and carbon storage estimation from volume and allometric models are calculated. (iv) Height-diameter relationship is fitted with nonlinear models, if diameter at breast height (DBH) or tree height are available, which can be used to retrieve tree height and diameter at breast height (DBH). <https://github.com/forestscientist/StemAnalysis>.

Maintained by Huili Wu. Last updated 2 years ago.

1.7 match 4 stars 4.38 score 12 scripts

rjauslin

StratifiedSampling:Different Methods for Stratified Sampling

Integrating a stratified structure in the population in a sampling design can considerably reduce the variance of the Horvitz-Thompson estimator. We propose in this package different methods to handle the selection of a balanced sample in stratified population. For more details see Raphaël Jauslin, Esther Eustache and Yves Tillé (2021) <doi:10.1007/s42081-021-00134-y>. The package propose also a method based on optimal transport and balanced sampling, see Raphaël Jauslin and Yves Tillé <doi:10.1016/j.jspi.2022.12.003>.

Maintained by Raphael Jauslin. Last updated 1 months ago.

openblas cpp

2.0 match 3.70 score

predictiveecology

fireSenseUtils:Utilities for Working With the 'fireSense' Group of 'SpaDES' Modules

Utilities for working with the 'fireSense' group of 'SpaDES' modules.

Maintained by Eliot J B McIntire. Last updated 30 days ago.

1.6 match 1 stars 4.51 score 2 scripts

igorrigolon

datazoom.amazonia:Simplify Access to Data from the Amazon Region

Functions to download and treat data regarding the Brazilian Amazon region from a variety of official sources.

Maintained by Igor Rigolon Veiga. Last updated 1 years ago.

1.7 match 4.29 score 15 scripts

sylvainschmitt

rcontroll:Individual-Based Forest Growth Simulator 'TROLL'

'TROLL' is coded in C++ and it typically simulates hundreds of thousands of individuals over hundreds of years. The 'rcontroll' R package is a wrapper of 'TROLL'. 'rcontroll' includes functions that generate inputs for simulations and run simulations. Finally, it is possible to analyse the 'TROLL' outputs through tables, figures, and maps taking advantage of other R visualisation packages. 'rcontroll' also offers the possibility to generate a virtual LiDAR point cloud that corresponds to a snapshot of the simulated forest.

Maintained by Sylvain Schmitt. Last updated 6 months ago.

gsl cpp

1.3 match 5 stars 5.76 score 19 scripts

ropensci

fireexposuR:Compute and Visualize Wildfire Exposure

This package computes and visualizes wildfire exposure using the methods documented in a series of scientific publications.

Maintained by Air Forbes. Last updated 20 days ago.

1.3 match 5 stars 5.23 score 4 scripts

jonathanlees

GEOmap:Topographic and Geologic Mapping

Set of routines for making map projections (forward and inverse), topographic maps, perspective plots, geological maps, geological map symbols, geological databases, interactive plotting and selection of focus regions.

Maintained by Jonathan M. Lees. Last updated 8 months ago.

2.0 match 3.38 score 162 scripts 3 dependents

bioc

ReUseData:Reusable and reproducible Data Management

ReUseData is an _R/Bioconductor_ software tool to provide a systematic and versatile approach for standardized and reproducible data management. ReUseData facilitates transformation of shell or other ad hoc scripts for data preprocessing into workflow-based data recipes. Evaluation of data recipes generate curated data files in their generic formats (e.g., VCF, bed). Both recipes and data are cached using database infrastructure for easy data management and reuse. Prebuilt data recipes are available through ReUseData portal ("https://rcwl.org/dataRecipes/") with full annotation and user instructions. Pregenerated data are available through ReUseData cloud bucket that is directly downloadable through "getCloudData()".

Maintained by Qian Liu. Last updated 5 months ago.

software infrastructure dataimport preprocessing immunooncology

1.3 match 4 stars 5.38 score 7 scripts

uribo

kuniumi:Load and Handles Geo-Spatial Data on Japan's National Land

Reads datasets provided by National Land Numerical Information download service <https://nlftp.mlit.go.jp/ksj/index.html> and treats them as 'sf' of a R spatial objects.

Maintained by Shinya Uryu. Last updated 1 years ago.

3.3 match 2 stars 2.00 score 6 scripts

evolecolgroup

geoGraph:Walking through the geographic space using graphs

Classes and methods for spatial graphs interfaced with support for GIS shapefiles.

Maintained by Andrea Manica. Last updated 9 days ago.

2.0 match 4 stars 3.30 score 2 scripts

sprfmo

FLjjm:Running the JJM Stock Assessment Model Inside the MSE FLR System

Runs the JJM stock assessment model for Chilean Jack Mackerel inside the MSE system of FLR's mse package.

Maintained by Iago Mosqueira. Last updated 9 days ago.

1.8 match 3.74 score 3 scripts

calfarog

GREENeR:Geospatial Regression Equation for European Nutrient Losses (GREEN)

Tools and methods to apply the model Geospatial Regression Equation for European Nutrient losses (GREEN); Grizzetti et al. (2005) <doi:10.1016/j.jhydrol.2004.07.036>; Grizzetti et al. (2008); Grizzetti et al. (2012) <doi:10.1111/j.1365-2486.2011.02576.x>; Grizzetti et al. (2021) <doi:10.1016/j.gloenvcha.2021.102281>.

Maintained by C. Alfaro. Last updated 7 months ago.

calibration geospatial nutrient plots

1.6 match 1 stars 4.00 score 9 scripts

rspatial

geodata:Download Geographic Data

Functions for downloading of geographic data for use in spatial analysis and mapping. The package facilitates access to climate, crops, elevation, land use, soil, species occurrence, accessibility, administrative boundaries and other data.

Maintained by Robert J. Hijmans. Last updated 1 months ago.

0.5 match 162 stars 10.75 score 1.5k scripts 7 dependents

cran

siland:Spatial Influence of Landscape

Method to estimate the spatial influence scales of landscape variables on a response variable. The method is based on Chandler and Hepinstall-Cymerman (2016) Estimating the spatial scales of landscape effects on abundance, Landscape ecology, 31: 1383-1394, <doi:10.1007/s10980-016-0380-z>.

Maintained by Martin Olivier. Last updated 2 years ago.

2.3 match 2.34 score 22 scripts

ycroissant

pder:Panel Data Econometrics with R

Data sets for the Panel Data Econometrics with R <doi:10.1002/9781119504641> book.

Maintained by Yves Croissant. Last updated 3 years ago.

3.8 match 1.36 score 15 scripts

mlampros

IceSat2R:ICESat-2 Altimeter Data using R

Programmatic connection to the 'OpenAltimetry API' <https://openaltimetry.earthdatacloud.nasa.gov/data/openapi/swagger-ui/index.html/> to download and process 'ATL03' (Global Geolocated Photon Data), 'ATL06' (Land Ice Height), 'ATL07' (Sea Ice Height), 'ATL08' (Land and Vegetation Height), 'ATL10' (Sea Ice Freeboard), 'ATL12' (Ocean Surface Height) and 'ATL13' (Inland Water Surface Height) 'ICESat-2' Altimeter Data. The user has the option to download the data by selecting a bounding box from a 1- or 5-degree grid globally utilizing a shiny application. The 'ICESat-2' mission collects altimetry data of the Earth's surface. The sole instrument on 'ICESat-2' is the Advanced Topographic Laser Altimeter System (ATLAS) instrument that measures ice sheet elevation change and sea ice thickness, while also generating an estimate of global vegetation biomass. 'ICESat-2' continues the important observations of ice-sheet elevation change, sea-ice freeboard, and vegetation canopy height begun by 'ICESat' in 2003.

Maintained by Lampros Mouselimis. Last updated 1 months ago.

icesat-2 openaltimetry

0.8 match 12 stars 6.64 score 3 scripts

forest-economics-goettingen

woodValuationDE:Wood Valuation Germany

Monetary valuation of wood in German forests (stumpage values), including estimations of harvest quantities, wood revenues, and harvest costs. The functions are sensitive to tree species, mean diameter of the harvested trees, stand quality, and logging method. The functions include estimations for the consequences of disturbances on revenues and costs. The underlying assortment tables are taken from Offer and Staupendahl (2018) with corresponding functions for salable and skidded volume derived in Fuchs et al. (2023). Wood revenue and harvest cost functions were taken from v. Bodelschwingh (2018). The consequences of disturbances refer to Dieter (2001), Moellmann and Moehring (2017), and Fuchs et al. (2022a, 2022b). For the full references see documentation of the functions, package README, and Fuchs et al. (2023). Apart from Dieter (2001) and Moellmann and Moehring (2017), all functions and factors are based on data from HessenForst, the forest administration of the Federal State of Hesse in Germany.

Maintained by Jasper M. Fuchs. Last updated 8 months ago.

1.5 match 2 stars 3.30 score 2 scripts

environmentalinformatics-marburg

satellite:Handling and Manipulating Remote Sensing Data

Herein, we provide a broad variety of functions which are useful for handling, manipulating, and visualizing satellite-based remote sensing data. These operations range from mere data import and layer handling (eg subsetting), over Raster* typical data wrangling (eg crop, extend), to more sophisticated (pre-)processing tasks typically applied to satellite imagery (eg atmospheric and topographic correction). This functionality is complemented by a full access to the satellite layers' metadata at any stage and the documentation of performed actions in a separate log file. Currently available sensors include Landsat 4-5 (TM), 7 (ETM+), and 8 (OLI/TIRS Combined), and additional compatibility is ensured for the Landsat Global Land Survey data set.

Maintained by Florian Detsch. Last updated 1 years ago.

cpp

0.5 match 22 stars 9.88 score 61 scripts 27 dependents

ddalthorp

dwp:Density-Weighted Proportion

Fit a Poisson regression to carcass distance data and integrate over the searched area at a wind farm to estimate the fraction of carcasses falling in the searched area and format the output for use as the dwp parameter in the 'GenEst' or 'eoa' package for estimating bird and bat mortality, following Dalthorp, et al. (2022) <arXiv:2201.10064>.

Maintained by Daniel Dalthorp. Last updated 2 years ago.

1.8 match 1 stars 2.70 score

mikkoku

efdm:Simulate Forest Resources with the European Forestry Dynamics Model

An implementation of European Forestry Dynamics Model (EFDM) and an estimation algorithm for the transition probabilities. The EFDM is a large-scale forest model that simulates the development of the forest and estimates volume of wood harvested for any given forested area. This estimate can be broken down by, for example, species, site quality, management regime and ownership category. See Packalen et al. (2015) <doi:10.2788/153990>.

Maintained by Mikko Kuronen. Last updated 2 months ago.

1.2 match 3.78 score 12 scripts

bioc

iSEEhub:iSEE for the Bioconductor ExperimentHub

This package defines a custom landing page for an iSEE app interfacing with the Bioconductor ExperimentHub. The landing page allows users to browse the ExperimentHub, select a data set, download and cache it, and import it directly into a Bioconductor iSEE app.

Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.

dataimport immunooncology infrastructure shinyapps singlecell software bioconductor bioconductor-package hacktoberfest isee

0.8 match 3 stars 5.56 score 4 scripts

ropensci

weatherOz:An API Client for Australian Weather and Climate Data Resources

Provides automated downloading, parsing and formatting of weather data for Australia through API endpoints provided by the Department of Primary Industries and Regional Development ('DPIRD') of Western Australia and by the Science and Technology Division of the Queensland Government's Department of Environment and Science ('DES'). As well as the Bureau of Meteorology ('BOM') of the Australian government precis and coastal forecasts, and downloading and importing radar and satellite imagery files. 'DPIRD' weather data are accessed through public 'APIs' provided by 'DPIRD', <https://www.agric.wa.gov.au/weather-api-20>, providing access to weather station data from the 'DPIRD' weather station network. Australia-wide weather data are based on data from the Australian Bureau of Meteorology ('BOM') data and accessed through 'SILO' (Scientific Information for Land Owners) Jeffrey et al. (2001) <doi:10.1016/S1364-8152(01)00008-1>. 'DPIRD' data are made available under a Creative Commons Attribution 3.0 Licence (CC BY 3.0 AU) license <https://creativecommons.org/licenses/by/3.0/au/deed.en>. SILO data are released under a Creative Commons Attribution 4.0 International licence (CC BY 4.0) <https://creativecommons.org/licenses/by/4.0/>. 'BOM' data are (c) Australian Government Bureau of Meteorology and released under a Creative Commons (CC) Attribution 3.0 licence or Public Access Licence ('PAL') as appropriate, see <http://www.bom.gov.au/other/copyright.shtml> for further details.

Maintained by Rodrigo Pires. Last updated 20 days ago.

dpird bom meteorological-data weather-forecast australia weather weather-data meteorology western-australia australia-bureau-of-meteorology western-australia-agriculture australia-agriculture australia-climate australia-weather api-client climate data rainfall weather-api

0.5 match 32 stars 8.54 score 40 scripts

kjhealy

gssrdoc:Document General Social Survey Variable

The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.

Maintained by Kieran Healy. Last updated 11 months ago.

1.9 match 2.28 score 38 scripts

cseljatib

datana:Datasets and Functions to Accompany Analisis De Datos Con R

Datasets and functions to accompany the book 'Analisis de datos con el programa estadistico R: una introduccion aplicada' by Salas-Eljatib (2021, ISBN: 9789566086109). The package helps carry out data management, exploratory analyses, and model fitting.

Maintained by Christian Salas-Eljatib. Last updated 6 months ago.

3.2 match 1.30 score 1 scripts

mehdisarparast

LSRS:Land Surface Remote Sensing

Rapid satellite data streams in operational applications have clear benefits for monitoring land cover, especially when information can be delivered as fast as changing surface conditions. Over the past decade, remote sensing has become a key tool for monitoring and predicting environmental variables by using satellite data. This package presents the main applications in remote sensing for land surface monitoring and land cover mapping (soil, vegetation, water...). Tomlinson, C.J., Chapman, L., Thornes, E., Baker, C (2011) <doi:10.1002/met.287>.

Maintained by Mehdi Sarparast. Last updated 7 years ago.

4.0 match 1.00 score 10 scripts

cran

axisandallies:Axis and Allies Spring

Simulates battles in the board game Axis and Allies Spring 1942, and calculates your probability of winning a battle. This speeds the game up significantly.

Maintained by TJ Weaver. Last updated 2 months ago.

4.0 match 1.00 score

robitalec

camtrapmonitoring:Camera Trap Monitoring For Estimating Wildlife Density

Evaluating potential camera trap locations. Potential locations are evaluated using relevant spatial layers producing a dataset of selected locations with covariates that can be used to quantify sampling bias. Soon - density estimation methods.

Maintained by Alec L. Robitaille. Last updated 9 months ago.

camera-trap camera-traps spatial wildlife

2.0 match 2 stars 2.00 score 2 scripts

ipeagit

accessibility:Transport Accessibility Measures

A set of fast and convenient functions to help conducting accessibility analyses. Given a pre-computed travel cost matrix and a land use dataset (containing the location of jobs, healthcare and population, for example), the package allows one to calculate accessibility levels and accessibility poverty and inequality. The package covers the majority of the most commonly used accessibility measures (such as cumulative opportunities, gravity-based and floating catchment areas methods), as well as the most frequently used inequality and poverty metrics (such as the Palma ratio, the concentration and Theil indices and the FGT family of measures).

Maintained by Daniel Herszenhut. Last updated 2 months ago.

accessibility transport transport-accessibility

0.5 match 55 stars 7.82 score 88 scripts

ivanlizaga

fingerPro:Sediment Source Fingerprinting

Quantifies the provenance of the sediments in a catchment or study area. Based on a comprehensive characterization of the sediment sources and the end sediment mixtures a mixing model algorithm is applied to the sediment mixtures in order to estimate the relative contribution of each potential source. The package includes several statistical methods such as Kruskal-Wallis test, discriminant function analysis ('DFA'), principal component plot ('PCA') to select the optimal subset of tracer properties. The variability within each sediment source is also considered to estimate the statistical distribution of the sources contribution.

Maintained by Ivan Lizaga. Last updated 7 years ago.

gsl cpp

3.5 match 1.11 score 13 scripts

pecanproject

PEcAn.CLM45:PEcAn Package for Integration of CLM4.5 Model

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. This package provides functions to link the Community Land Model, version 4.5, to PEcAn.

Maintained by Mike Dietze. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

0.5 match 216 stars 7.56 score 1 scripts

zhaokg

Rbeast:Bayesian Change-Point Detection and Time Series Decomposition

Interpretation of time series data is affected by model choices. Different models can give different or even contradicting estimates of patterns, trends, and mechanisms for the same data--a limitation alleviated by the Bayesian estimator of abrupt change,seasonality, and trend (BEAST) of this package. BEAST seeks to improve time series decomposition by forgoing the "single-best-model" concept and embracing all competing models into the inference via a Bayesian model averaging scheme. It is a flexible tool to uncover abrupt changes (i.e., change-points), cyclic variations (e.g., seasonality), and nonlinear trends in time-series observations. BEAST not just tells when changes occur but also quantifies how likely the detected changes are true. It detects not just piecewise linear trends but also arbitrary nonlinear trends. BEAST is applicable to real-valued time series data of all kinds, be it for remote sensing, economics, climate sciences, ecology, and hydrology. Example applications include its use to identify regime shifts in ecological data, map forest disturbance and land degradation from satellite imagery, detect market trends in economic data, pinpoint anomaly and extreme events in climate data, and unravel system dynamics in biological data. Details on BEAST are reported in Zhao et al. (2019) <doi:10.1016/j.rse.2019.04.034>.

Maintained by Kaiguang Zhao. Last updated 6 months ago.

anomoly-detection bayesian-time-series breakpoint-detection changepoint-detection interrupted-time-series seasonality-analysis structural-breakpoint technical-analysis time-series time-series-decomposition trend trend-analysis

0.5 match 302 stars 7.63 score 89 scripts

willemijnvroege

RCGLS:Download and Open Data Provided by the Copernicus Global Land Service

Download and open manifest files provided by the Copernicus Global Land Service data <https://land.copernicus.eu/global/>. The manifest files are available at: <https://land.copernicus.vgt.vito.be/manifest/>. Also see: <https://land.copernicus.eu/global/access/>. Before you can download the data, you will first need to register to create a username and password.

Maintained by Willemijn Vroege. Last updated 5 years ago.

3.8 match 1.00 score 2 scripts

wherewindstay

halfcircle:Plot Halfcircle Diagram

There are growing concerns on flow data in diverse fields including trade, migration, knowledge diffusion, disease spread, and transportation. The package is an effective visual support to learn the pattern of flow which is called halfcircle diagram. The flow between two nodes placed on the center line of a circle is represented using a half circle drawn from the origin to the destination in a clockwise direction. Through changing the order of nodes, the halfcircle diagram enables users to examine the complex relationship between bidirectional flow and each potential determinants. Furthermore, the halfmeancenter function, which calculates (un) weighted mean center of half circles, makes the comparison easier.

Maintained by Sohyun Park. Last updated 6 years ago.

3.8 match 1.00 score 2 scripts

kwb-r

urbanAnnualRunoff:R Package for Deriving Urban Surfaces for Storm Runoff Analysis

Used in Project KEYS for generating inputs to runoff model ABIMO for application in cities with data scarcity.

Maintained by Michael Rustler. Last updated 3 years ago.

abimo project-keys

1.3 match 3.00 score 2 scripts

juergenknauer

bigleaf:Physical and Physiological Ecosystem Properties from Eddy Covariance Data

Calculation of physical (e.g. aerodynamic conductance, surface temperature), and physiological (e.g. canopy conductance, water-use efficiency) ecosystem properties from eddy covariance data and accompanying meteorological measurements. Calculations assume the land surface to behave like a 'big-leaf' and return bulk ecosystem/canopy variables.

Maintained by Juergen Knauer. Last updated 8 months ago.

0.5 match 7.23 score 124 scripts 17 dependents

openair-project

worldmet:Import Surface Meteorological Data from NOAA Integrated Surface Database (ISD)

Functions to import data from more than 30,000 surface meteorological sites around the world managed by the National Oceanic and Atmospheric Administration (NOAA) Integrated Surface Database (ISD, see <https://www.ncei.noaa.gov/products/land-based-station/integrated-surface-database>).

Maintained by David Carslaw. Last updated 2 months ago.

meteorology openair

0.5 match 55 stars 7.06 score 77 scripts

ifpri

COLUMNIST:Calculator fOr Land Use harMoNIzation dataSeT

Calculator fOr Land Use harMoNIzation dataSeT.

Maintained by Abhijeet Mishra. Last updated 2 years ago.

3.6 match 1.00 score

ropensci

getCRUCLdata:'CRU' 'CL' v. 2.0 Climatology Client

Provides functions that automate downloading and importing University of East Anglia Climate Research Unit ('CRU') 'CL' v. 2.0 climatology data, facilitates the calculation of minimum temperature and maximum temperature and formats the data into a data.table object or a list of 'terra' 'rast' objects for use. 'CRU' 'CL' v. 2.0 data are a gridded climatology of 1961-1990 monthly means released in 2002 and cover all land areas (excluding Antarctica) at 10 arc minutes (0.1666667 degree) resolution. For more information see the description of the data provided by the University of East Anglia Climate Research Unit, <https://crudata.uea.ac.uk/cru/data/hrg/tmc/readme.txt>.

Maintained by Adam H. Sparks. Last updated 11 days ago.

anglia-cru climate-data cru-cl2 temperature rainfall elevation data-access wind relative-humidity solar-radiation diurnal-temperature frost cru peer-reviewed

0.5 match 18 stars 6.83 score 18 scripts

manuelabrunner

PRSim:Stochastic Simulation of Streamflow Time Series using Phase Randomization

Provides a simulation framework to simulate streamflow time series with similar main characteristics as observed data. These characteristics include the distribution of daily streamflow values and their temporal correlation as expressed by short- and long-range dependence. The approach is based on the randomization of the phases of the Fourier transform or the phases of the wavelet transform. The function prsim() is applicable to single site simulation and uses the Fourier transform. The function prsim.wave() extends the approach to multiple sites and is based on the complex wavelet transform. The function prsim.weather() extends the approach to multiple variables for weather generation. We further use the flexible four-parameter Kappa distribution, which allows for the extrapolation to yet unobserved low and high flows. Alternatively, the empirical or any other distribution can be used. A detailed description of the simulation approach for single sites and an application example can be found in Brunner et al. (2019) <doi:10.5194/hess-23-3175-2019>. A detailed description and evaluation of the wavelet-based multi-site approach can be found in Brunner and Gilleland (2020) <doi:10.5194/hess-24-3967-2020>. A detailed description and evaluation of the multi-variable and multi-site weather generator can be found in Brunner et al. (2021) <doi:10.5194/esd-12-621-2021>. A detailed description and evaluation of the non-stationary streamflow generator can be found in Brunner and Gilleland (2024) <doi:10.1029/2023EF004238>.

Maintained by Manuela Brunner. Last updated 11 months ago.

3.3 match 1.00 score 8 scripts

eldho1983

SSplots:Stock Status Plots (SSPs)

Pauly et al. (2008) <http://legacy.seaaroundus.s3.amazonaws.com/doc/Researcher+Publications/dpauly/PDF/2008/Books%26Chapters/FisheriesInLargeMarineEcosystems.pdf> created (and coined the name) 'Stock Status Plots' for a UNEP compendium on Large Marine Ecosystems(LMEs, Sherman and Hempel (2009)<https://marineinfo.org/imis?module=ref&refid=142061&printversion=1&dropIMIStitle=1>). Stock status plots are bivariate graphs summarizing the status (e.g., developing, fully exploited, overexploited, etc.), through time, of the multispecies fisheries of a fished area or ecosystem. This package contains three functions to generate stock status plots viz., SSplots_pauly() (as per the criteria proposed by Pauly et al.,2008), SSplots_kleisner() (as per the criteria proposed by Kleisner and Pauly (2011) <http://www.ecomarres.com/downloads/regional.pdf> and Kleisner et al. (2013) <doi:10.1111/j.1467-2979.2012.00469.x>)and SSplots_EPI() (as per the criteria proposed by Jayasankar et al.,2021 <https://eprints.cmfri.org.in/11364/>).

Maintained by Eldho Varghese. Last updated 6 months ago.

3.3 match 1.00 score

eldho1983

FESta:Fishing Effort Standardisation

Original idea was presented in the reference paper. Varghese et al. (2020, 74(1):35-42) "Bayesian State-space Implementation of Schaefer Production Model for Assessment of Stock Status for Multi-gear Fishery". Marine fisheries governance and management practices are very essential to ensure the sustainability of the marine resources. A widely accepted resource management strategy towards this is to derive sustainable fish harvest levels based on the status of marine fish stock. Various fish stock assessment models that describe the biomass dynamics using time series data on fish catch and fishing effort are generally used for this purpose. In the scenario of complex multi-species marine fishery in which different species are caught by a number of fishing gears and each gear harvests a number of species make it difficult to obtain the fishing effort corresponding to each fish species. Since the capacity of the gears varies, the effort made to catch a resource cannot be considered as the sum of efforts expended by different fishing gears. This necessitates standardisation of fishing effort in unit base.

Maintained by Eldho Varghese. Last updated 5 years ago.

3.2 match 1.00 score

cran

geoTS:Methods for Handling and Analyzing Time Series of Satellite Images

Provides functions and methods for: splitting large raster objects into smaller chunks, transferring images from a binary format into raster layers, transferring raster layers into an 'RData' file, calculating the maximum gap (amount of consecutive missing values) of a numeric vector, and fitting harmonic regression models to periodic time series. The homoscedastic harmonic regression model is based on G. Roerink, M. Menenti and W. Verhoef (2000) <doi:10.1080/014311600209814>.

Maintained by Inder Tecuapetla-Gómez. Last updated 2 years ago.

1.8 match 1.78 score 9 scripts 2 dependents

ternaustralia

ausplotsR:TERN AusPlots Australian Ecosystem Monitoring Data

Extraction, preparation, visualisation and analysis of TERN AusPlots ecosystem monitoring data. Direct access to plot-based data on vegetation and soils across Australia, including physical sample barcode numbers. Simple function calls extract the data and merge them into species occurrence matrices for downstream analysis, or calculate things like basal area and fractional cover. TERN AusPlots is a national field plot-based ecosystem surveillance monitoring method and dataset for Australia. The data have been collected across a national network of plots and transects by the Terrestrial Ecosystem Research Network (TERN - <https://www.tern.org.au>), an Australian Government NCRIS-enabled project, and its Ecosystem Surveillance platform (<https://www.tern.org.au/tern-land-observatory/ecosystem-surveillance-and-environmental-monitoring/>).

Maintained by Greg Guerin. Last updated 1 years ago.

0.5 match 10 stars 6.07 score 59 scripts

ropensci

nuts:Convert European Regional Data

Motivated by changing administrative boundaries over time, the 'nuts' package can convert European regional data with NUTS codes between versions (2006, 2010, 2013, 2016 and 2021) and levels (NUTS 1, NUTS 2 and NUTS 3). The package uses spatial interpolation as in Lam (1983) <doi:10.1559/152304083783914958> based on granular (100m x 100m) area, population and land use data provided by the European Commission's Joint Research Center.

Maintained by Moritz Hennicke. Last updated 5 months ago.

europe european-union eurostat nomenclature nuts nuts-codes nuts-regions regional-data

0.5 match 8 stars 5.86 score 3 scripts

ropensci

rOPTRAM:Derive Soil Moisture Using the OPTRAM Algorithm

The OPtical TRapezoid Model (OPTRAM) derives soil moisture based on the linear relation between a vegetation index and Land Surface Temperature (LST). The Short Wave Infra-red (SWIR) band is used as a proxy for LST. See: Sadeghi, M. et al., 2017. <https://doi.org/10.1016/j.rse.2017.05.041> .

Maintained by Micha Silver. Last updated 1 months ago.

0.5 match 9 stars 5.73 score 6 scripts

m-path-io

mpathr:Easily Handling Data from the ‘m-Path’ Platform

Provides tools for importing and cleaning Experience Sampling Method (ESM) data collected via the 'm-Path' platform. The goal is to provide with a few utility functions to be able to read and perform some common operations in ESM data collected through the 'm-Path' platform (<https://m-path.io/landing/>). Functions include raw data handling, format standardization, and basic data checks, as well as to calculate the response rate in data from ESM studies.

Maintained by Merijn Mestdagh. Last updated 4 months ago.

0.5 match 3 stars 5.32 score 7 scripts

ysosirius

windfarmGA:Genetic Algorithm for Wind Farm Layout Optimization

The genetic algorithm is designed to optimize wind farms of any shape. It requires a predefined amount of turbines, a unified rotor radius and an average wind speed value for each incoming wind direction. A terrain effect model can be included that downloads an 'SRTM' elevation model and loads a Corine Land Cover raster to approximate surface roughness.

Maintained by Sebastian Gatscha. Last updated 2 months ago.

windfarm-layout optimization genetic-algorithm renewable-energy cpp

0.5 match 27 stars 5.06 score 17 scripts

dariomasante

landscapeR:Categorical Landscape Simulation Facility

Simulates categorical maps on actual geographical realms, starting from either empty landscapes or landscapes provided by the user (e.g. land use maps). Allows to tweak or create landscapes while retaining a high degree of control on its features, without the hassle of specifying each location attribute. In this it differs from other tools which generate null or neutral landscapes in a theoretical space. The basic algorithm currently implemented uses a simple agent style/cellular automata growth model, with no rules (apart from areas of exclusion) and von Neumann neighbourhood (four cells, aka Rook case). Outputs are raster dataset exportable to any common GIS format.

Maintained by Dario Masante. Last updated 3 months ago.

cpp

0.5 match 5.02 score 35 scripts

emilio-berti

GHCNr:Download Weather Station Data from GHCNd

The goal of 'GHCNr' is to provide a fast and friendly interface with the Global Historical Climatology Network daily (GHCNd) database, which contains daily summaries of weather station data worldwide (<https://www.ncei.noaa.gov/products/land-based-station/global-historical-climatology-network-daily>). GHCNd is accessed through the web API <https://www.ncei.noaa.gov/access/services/data/v1>. 'GHCNr' main functionalities consist of downloading data from GHCNd, filter it, and to aggregate it at monthly and annual scales.

Maintained by Emilio Berti. Last updated 2 months ago.

0.5 match 2 stars 4.95 score 3 scripts

simonpcouch

forested:Forest Attributes in Washington State

A small subset of plots in Washington State are sampled and assessed "on-the-ground" as forested or non-forested by the U.S. Department of Agriculture, Forest Service, Forest Inventory and Analysis (FIA) Program, but the FIA also has access to remotely sensed data for all land in the state. The 'forested' package contains a data frame by the same name intended for use in predictive modeling applications where the more easily-accessible remotely sensed data can be used to predict whether a plot is forested or non-forested.

Maintained by Simon Couch. Last updated 7 months ago.

0.5 match 7 stars 4.66 score 33 scripts

rachel-carroll

eiExpand:Utilities for Expanding Functionality of 'eiCompare'

Augments the 'eiCompare' package's Racially Polarized Voting (RPV) functionality to streamline analyses and visualizations used to support voting rights and redistricting litigation. The package implements methods described in Barreto, M., Collingwood, L., Garcia-Rios, S., & Oskooii, K. A. (2022). "Estimating Candidate Support in Voting Rights Act Cases: Comparing Iterative EI and EI-R×C Methods" <doi:10.1177/0049124119852394>.

Maintained by Rachel Carroll. Last updated 2 years ago.

1.8 match 1.23 score 17 scripts

olehprylutskyi

spectralR:Obtain and Visualize Spectral Reflectance Data for Earth Surface Polygons

Tools for obtaining, processing, and visualizing spectral reflectance data for the user-defined land or water surface classes for visual exploring in which wavelength the classes differ. Input should be a shapefile with polygons of surface classes (it might be different habitat types, crops, vegetation, etc.). The Sentinel-2 L2A satellite mission optical bands pixel data are obtained through the Google Earth Engine service (<https://earthengine.google.com/>) and used as a source of spectral data.

Maintained by Oleh Prylutskyi. Last updated 2 years ago.

0.5 match 10 stars 4.18 score 1 scripts

mhpob

simfish:simulate fish tracks & acoustic detections

facilitates simulation of fish tracks in featureless and semi-realistic environments (coastal oceans, fjords, and lakes). A user-defined raster defining the water body - land boundaries is used to constrain simulated tracks. Fish movements are simulated (currently) as either a correlated random walk or a biased & correlated random walk, with the bias toward a defined Centre-of-Attraction. A potential function is used to ensure the tracks avoid land. The package can also be used to simulate detections of acoustically-tagged fish by acoustic receivers at user-defined locations.

Maintained by Ian Jonsen. Last updated 1 years ago.

0.8 match 2.70 score 3 scripts

david6marsh

himach:Find Routes for Supersonic Aircraft

For supersonic aircraft, flying subsonic over land, find the best route between airports. Allow for coastal buffer and potentially closed regions. Use a minimal model of aircraft performance: the focus is on time saved versus subsonic flight, rather than on vertical flight profile. For modelling and forecasting, not for planning your flight!

Maintained by David Marsh. Last updated 1 years ago.

aircraft routes supersonic

0.5 match 1 stars 4.00 score 7 scripts

kasselhingee

lacunaritycovariance:Gliding Box Lacunarity and Other Metrics for 2D Random Closed Sets

Functions for estimating the gliding box lacunarity (GBL), covariance, and pair-correlation of a random closed set (RACS) in 2D from a binary coverage map (e.g. presence-absence land cover maps). Contains a number of newly-developed covariance-based estimators of GBL (Hingee et al., 2019) <doi:10.1007/s13253-019-00351-9> and balanced estimators, proposed by Picka (2000) <http://www.jstor.org/stable/1428408>, for covariance, centred covariance, and pair-correlation. Also contains methods for estimating contagion-like properties of RACS and simulating 2D Boolean models. Binary coverage maps are usually represented as raster images with pixel values of TRUE, FALSE or NA, with NA representing unobserved pixels. A demo for extracting such a binary map from a geospatial data format is provided. Binary maps may also be represented using polygonal sets as the foreground, however for most computations such maps are converted into raster images. The package is based on research conducted during the author's PhD studies.

Maintained by Kassel Liam Hingee. Last updated 1 years ago.

0.5 match 2 stars 4.00 score 3 scripts

cug-hydro

VIC5:The Variable Infiltration Capacity (VIC) Hydrological Model

The Variable Infiltration Capacity (VIC) model is a macroscale hydrologic model that solves full water and energy balances, originally developed by Xu Liang at the University of Washington (UW). The version of VIC source code used is of 5.0.1 on <https://github.com/UW-Hydro/VIC/>, see Hamman et al. (2018). Development and maintenance of the current official version of the VIC model at present is led by the UW Hydro (Computational Hydrology group) in the Department of Civil and Environmental Engineering at UW. VIC is a research model and in its various forms it has been applied to most of the major river basins around the world, as well as globally <http://vic.readthedocs.io/en/master/Documentation/References/>. References: "Liang, X., D. P. Lettenmaier, E. F. Wood, and S. J. Burges (1994), A simple hydrologically based model of land surface water and energy fluxes for general circulation models, J. Geophys. Res., 99(D7), 14415-14428, <doi:10.1029/94JD00483>"; "Hamman, J. J., Nijssen, B., Bohn, T. J., Gergel, D. R., and Mao, Y. (2018), The Variable Infiltration Capacity model version 5 (VIC-5): infrastructure improvements for new applications and reproducibility, Geosci. Model Dev., 11, 3481-3496, <doi:10.5194/gmd-11-3481-2018>".

Maintained by Dongdong Kong. Last updated 1 years ago.

cpp openmp

0.5 match 8 stars 3.60 score 3 scripts