R-universe search: vegetation

vegandevs

vegan:Community Ecology Package

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

Maintained by Jari Oksanen. Last updated 16 days ago.

ecological-modelling ecology ordination fortran openblas

11.6 match 472 stars 19.41 score 15k scripts 440 dependents

emf-creaf

vegclust:Fuzzy Clustering of Vegetation Data

A set of functions to: (1) perform fuzzy clustering of vegetation data (De Caceres et al, 2010) <doi:10.1111/j.1654-1103.2010.01211.x>; (2) to assess ecological community similarity on the basis of structure and composition (De Caceres et al, 2013) <doi:10.1111/2041-210X.12116>.

Maintained by Miquel De Cáceres. Last updated 8 months ago.

32.0 match 2 stars 6.28 score 52 scripts 6 dependents

adeverse

ade4:Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.

Maintained by Aurélie Siberchicot. Last updated 12 days ago.

openblas cpp

13.0 match 39 stars 14.96 score 2.2k scripts 256 dependents

ausgis

GD:Geographical Detectors for Assessing Spatial Factors

Geographical detectors for measuring spatial stratified heterogeneity, as described in Jinfeng Wang (2010) <doi:10.1080/13658810802443457> and Jinfeng Wang (2016) <doi:10.1016/j.ecolind.2016.02.052>. Includes the optimal discretization of continuous data, four primary functions of geographical detectors, comparison of size effects of spatial unit and the visualizations of results. To use the package and to refer the descriptions of the package, methods and case datasets, please cite Yongze Song (2020) <doi:10.1080/15481603.2020.1760434>. The model has been applied in factor exploration of road performance and multi-scale spatial segmentation for network data, as described in Yongze Song (2018) <doi:10.3390/rs10111696> and Yongze Song (2020) <doi:10.1109/TITS.2020.3001193>, respectively.

Maintained by Wenbo Lv. Last updated 4 months ago.

geographical-detector spatial-stratified-heterogeneity

12.6 match 13 stars 7.49 score 51 scripts

kamapu

vegtable:Handling Vegetation Data Sets

Import and handling data from vegetation-plot databases, especially data stored in 'Turboveg 2' (<https://www.synbiosys.alterra.nl/turboveg/>). Also import/export routines for exchange of data with 'Juice' (<https://www.sci.muni.cz/botany/juice/>) are implemented.

Maintained by Miguel Alvarez. Last updated 8 months ago.

21.2 match 7 stars 4.23 score 49 scripts

sarahgoslee-usda

VFS:Vegetated Filter Strip and Erosion Model

Empirical models for runoff, erosion, and phosphorus loss across a vegetated filter strip, given slope, soils, climate, and vegetation (Gall et al., 2018) <doi:10.1007/s00477-017-1505-x>. It also includes functions for deriving climate parameters from measured daily weather data, and for simulating rainfall. Models implemented include MUSLE (Williams, 1975) and APLE (Vadas et al., 2009 <doi:10.2134/jeq2008.0337>).

Maintained by Sarah Goslee. Last updated 3 years ago.

14.2 match 1 stars 5.56 score 36 scripts

ncss-tech

soilDB:Soil Database Interface

A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.

Maintained by Andrew Brown. Last updated 6 days ago.

kssl nasis nrcs soil soil-data-access soil-survey soilweb sql usda

7.0 match 87 stars 11.34 score 1.0k scripts 1 dependents

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 3 days ago.

ecological-modelling landscape-ecosystem-modelling spades

11.1 match 17 stars 6.07 score 12 scripts 4 dependents

geco-bern

rsofun:The P-Model and BiomeE Modelling Framework

Implements the Simulating Optimal FUNctioning framework for site-scale simulations of ecosystem processes, including model calibration. It contains 'Fortran 90' modules for the P-model (Stocker et al. (2020) <doi:10.5194/gmd-13-1545-2020>), SPLASH (Davis et al. (2017) <doi:10.5194/gmd-10-689-2017>) and BiomeE (Weng et al. (2015) <doi:10.5194/bg-12-2655-2015>).

Maintained by Benjamin Stocker. Last updated 13 days ago.

dgvm growth modeling p-model simulation vegetation-dynamics fortran

7.5 match 26 stars 8.77 score 119 scripts

florianjansen

vegdata:Access Vegetation Databases and Treat Taxonomy

Handling of vegetation data from different sources ( Turboveg 2.0 <https://www.synbiosys.alterra.nl/turboveg/>; the German national repository <https://www.vegetweb.de> and others. Taxonomic harmonization (given appropriate taxonomic lists, e.g. the German taxonomic standard list "GermanSL", <https://germansl.infinitenature.org>).

Maintained by Florian Jansen. Last updated 1 years ago.

17.1 match 2 stars 3.84 score 38 scripts 3 dependents

biorgeo

bioregion:Comparison of Bioregionalisation Methods

The main purpose of this package is to propose a transparent methodological framework to compare bioregionalisation methods based on hierarchical and non-hierarchical clustering algorithms (Kreft & Jetz (2010) <doi:10.1111/j.1365-2699.2010.02375.x>) and network algorithms (Lenormand et al. (2019) <doi:10.1002/ece3.4718> and Leroy et al. (2019) <doi:10.1111/jbi.13674>).

Maintained by Maxime Lenormand. Last updated 10 days ago.

biogeography bioregion bioregionalization cpp

10.4 match 7 stars 6.27 score 11 scripts

eco-hydro

phenofit:Extract Remote Sensing Vegetation Phenology

The merits of 'TIMESAT' and 'phenopix' are adopted. Besides, a simple and growing season dividing method and a practical snow elimination method based on Whittaker were proposed. 7 curve fitting methods and 4 phenology extraction methods were provided. Parameters boundary are considered for every curve fitting methods according to their ecological meaning. And 'optimx' is used to select best optimization method for different curve fitting methods. Reference: Kong, D., (2020). R package: A state-of-the-art Vegetation Phenology extraction package, phenofit version 0.3.1, <doi:10.5281/zenodo.5150204>; Kong, D., Zhang, Y., Wang, D., Chen, J., & Gu, X. (2020). Photoperiod Explains the Asynchronization Between Vegetation Carbon Phenology and Vegetation Greenness Phenology. Journal of Geophysical Research: Biogeosciences, 125(8), e2020JG005636. <doi:10.1029/2020JG005636>; Kong, D., Zhang, Y., Gu, X., & Wang, D. (2019). A robust method for reconstructing global MODIS EVI time series on the Google Earth Engine. ISPRS Journal of Photogrammetry and Remote Sensing, 155, 13–24; Zhang, Q., Kong, D., Shi, P., Singh, V.P., Sun, P., 2018. Vegetation phenology on the Qinghai-Tibetan Plateau and its response to climate change (1982–2013). Agric. For. Meteorol. 248, 408–417. <doi:10.1016/j.agrformet.2017.10.026>.

Maintained by Dongdong Kong. Last updated 1 months ago.

phenology remote-sensing openblas cpp openmp

7.0 match 78 stars 7.71 score 332 scripts

rnuske

vegperiod:Determine Thermal Vegetation Periods

Collection of common methods to determine growing season length in a simple manner. Start and end dates of the vegetation periods are calculated solely based on daily mean temperatures and the day of the year.

Maintained by Robert Nuske. Last updated 9 months ago.

dwd growing-season vegetation-period

13.1 match 7 stars 4.02 score 9 scripts 1 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

10.8 match 8 stars 4.90 score 5 scripts

inbo

forrescalc:Calculation of Aggregated Values on Dendrometry, Regeneration and Vegetation of Forests, Starting from Individual Tree Measures from Fieldmap

A collection of functions to load and aggregate measurements related to dendrometry, rejuvenation and vegetation, and to access plot level results from Flemish forest reserves in data package forresdat.

Maintained by Els Lommelen. Last updated 6 months ago.

13.9 match 3.79 score 123 scripts

usdaforestservice

FIESTA:Forest Inventory Estimation and Analysis

A research estimation tool for analysts that work with sample-based inventory data from the U.S. Department of Agriculture, Forest Service, Forest Inventory and Analysis (FIA) Program.

Maintained by Grayson White. Last updated 3 days ago.

6.7 match 30 stars 7.24 score 62 scripts

bioc

mina:Microbial community dIversity and Network Analysis

An increasing number of microbiome datasets have been generated and analyzed with the help of rapidly developing sequencing technologies. At present, analysis of taxonomic profiling data is mainly conducted using composition-based methods, which ignores interactions between community members. Besides this, a lack of efficient ways to compare microbial interaction networks limited the study of community dynamics. To better understand how community diversity is affected by complex interactions between its members, we developed a framework (Microbial community dIversity and Network Analysis, mina), a comprehensive framework for microbial community diversity analysis and network comparison. By defining and integrating network-derived community features, we greatly reduce noise-to-signal ratio for diversity analyses. A bootstrap and permutation-based method was implemented to assess community network dissimilarities and extract discriminative features in a statistically principled way.

Maintained by Rui Guan. Last updated 5 months ago.

software workflowstep cpp

9.9 match 5 stars 4.85 score 14 scripts

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.

7.8 match 10 stars 6.07 score 59 scripts

pecanproject

PEcAn.ED2:PEcAn Package for Integration of ED2 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 Ecosystem Demography Model, version 2, 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 jags cpp

5.4 match 216 stars 8.72 score 145 scripts

alexchristensen

SemNetDictionaries:Dictionaries for the 'SemNetCleaner' Package

Implements dictionaries that can be used in the 'SemNetCleaner' package. Also includes several functions aimed at facilitating the text cleaning analysis in the 'SemNetCleaner' package. This package is designed to integrate and update word lists and dictionaries based on each user's individual needs by allowing users to store and save their own dictionaries. Dictionaries can be added to the 'SemNetDictionaries' package by submitting user-defined dictionaries to <https://github.com/AlexChristensen/SemNetDictionaries>.

Maintained by Alexander P. Christensen. Last updated 3 years ago.

dictionaries semantic-network-analysis

9.0 match 4 stars 5.08 score 3 scripts 2 dependents

fvlampe

goeveg:Functions for Community Data and Ordinations

A collection of functions useful in (vegetation) community analyses and ordinations. Includes automatic species selection for ordination diagrams, NMDS stress/scree plots, species response curves, merging of taxa as well as calculation and sorting of synoptic tables.

Maintained by Friedemann von Lampe. Last updated 10 months ago.

8.1 match 4 stars 5.22 score 111 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

7.5 match 29 stars 5.60 score 13 scripts

szelepcsenyi

macroBiome:A Tool for Mapping the Distribution of the Biomes and Bioclimate

Procedures for simulating biomes by equilibrium vegetation models, with a special focus on paleoenvironmental applications. Three widely used equilibrium biome models are currently implemented in the package: the Holdridge Life Zone (HLZ) system (Holdridge 1947, <doi:10.1126/science.105.2727.367>), the Köppen-Geiger classification (KGC) system (Köppen 1936, <https://koeppen-geiger.vu-wien.ac.at/pdf/Koppen_1936.pdf>) and the BIOME model (Prentice et al. 1992, <doi:10.2307/2845499>). Three climatic forest-steppe models are also implemented. An approach for estimating monthly time series of relative sunshine duration from temperature and precipitation data (Yin 1999, <doi:10.1007/s007040050111>) is also adapted, allowing process-based biome models to be combined with high-resolution paleoclimate simulation datasets (e.g., CHELSA-TraCE21k v1.0 dataset: <https://chelsa-climate.org/chelsa-trace21k/>).

Maintained by Zoltán Szelepcsényi. Last updated 2 years ago.

14.7 match 2.70 score 2 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 18 days ago.

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

5.0 match 58 stars 7.69 score 8 scripts

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 27 days ago.

data

3.4 match 125 stars 11.02 score 1.7k scripts 2 dependents

neonscience

neonUtilities:Utilities for Working with NEON Data

NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org> or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.

Maintained by Claire Lunch. Last updated 1 months ago.

3.5 match 57 stars 10.66 score 944 scripts 15 dependents

dvrbts

labdsv:Ordination and Multivariate Analysis for Ecology

A variety of ordination and community analyses useful in analysis of data sets in community ecology. Includes many of the common ordination methods, with graphical routines to facilitate their interpretation, as well as several novel analyses.

Maintained by David W. Roberts. Last updated 2 years ago.

fortran

6.0 match 3 stars 6.08 score 452 scripts 13 dependents

emf-creaf

indicspecies:Relationship Between Species and Groups of Sites

Functions to assess the strength and statistical significance of the relationship between species occurrence/abundance and groups of sites [De Caceres & Legendre (2009) <doi:10.1890/08-1823.1>]. Also includes functions to measure species niche breadth using resource categories [De Caceres et al. (2011) <doi:10.1111/J.1600-0706.2011.19679.x>].

Maintained by Miquel De Cáceres. Last updated 24 days ago.

3.8 match 10 stars 9.49 score 386 scripts 4 dependents

phiala

ecodist:Dissimilarity-Based Functions for Ecological Analysis

Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community ecological data. The original package description is in Goslee and Urban (2007) <doi:10.18637/jss.v022.i07>, with further statistical detail in Goslee (2010) <doi:10.1007/s11258-009-9641-0>.

Maintained by Sarah Goslee. Last updated 1 years ago.

openblas

3.6 match 9 stars 9.84 score 566 scripts 9 dependents

garciadejalon

TreeDep:Air Pollution Removal by Dry Deposition on Trees

The model estimates air pollution removal by dry deposition on trees. It also estimates or uses hourly values for aerodynamic resistance, boundary layer resistance, canopy resistance, stomatal resistance, cuticular resistance, mesophyll resistance, soil resistance, friction velocity and deposition velocity. It also allows plotting graphical results for a specific time period. The pollutants are nitrogen dioxide, ozone, sulphur dioxide, carbon monoxide and particulate matter. Baldocchi D (1994) <doi:10.1093/treephys/14.7-8-9.1069>. Farquhar GD, von Caemmerer S, Berry JA (1980) Planta 149: 78-90. Hirabayashi S, Kroll CN, Nowak DJ (2015) i-Tree Eco Dry Deposition Model. Nowak DJ, Crane DE, Stevens JC (2006) <doi:10.1016/j.ufug.2006.01.007>. US EPA (1999) PCRAMMET User's Guide. EPA-454/B-96-001. Weiss A, Norman JM (1985) Agricultural and Forest Meteorology 34: 205—213.

Maintained by Silvestre Garcia de Jalon. Last updated 6 years ago.

17.3 match 1.69 score 49 scripts

gastonstat

plspm:Tools for Partial Least Squares Path Modeling (PLS-PM)

Partial Least Squares Path Modeling (PLS-PM) analysis for both metric and non-metric data, as well as REBUS analysis for latent class detection.

Maintained by Gaston Sanchez. Last updated 3 years ago.

path-modeling pls-sem plspm

4.0 match 67 stars 6.97 score 115 scripts

cldossantos

pacu:Precision Agriculture Computational Utilities

Support for a variety of commonly used precision agriculture operations. Includes functions to download and process raw satellite images from Sentinel-2 <https://documentation.dataspace.copernicus.eu/APIs/OData.html>. Includes functions that download vegetation index statistics for a given period of time, without the need to download the raw images <https://documentation.dataspace.copernicus.eu/APIs/SentinelHub/Statistical.html>. There are also functions to download and visualize weather data in a historical context. Lastly, the package also contains functions to process yield monitor data. These functions can build polygons around recorded data points, evaluate the overlap between polygons, clean yield data, and smooth yield maps.

Maintained by dos Santos Caio. Last updated 2 days ago.

3.9 match 14 stars 6.82 score 9 scripts

ladylavender

LandComp:Analysing Landscape Composition and Structure at Multiple Scales

Changes of landscape diversity and structure can be detected soon if relying on landscape class combinations and analysing patterns at multiple scales. 'LandComp' provides such an opportunity, based on Juhász-Nagy's functions (Juhász-Nagy P, Podani J 1983 <doi:10.1007/BF00129432>). Functions can handle multilayered data. Requirements of the input: binary data contained by a regular square or hexagonal grid, and the grid should have projected coordinates.

Maintained by Krisztina Dóra Konrád. Last updated 1 years ago.

7.2 match 3.70 score

atkinsjeff

forestr:Ecosystem and Canopy Structural Complexity Metrics from LiDAR

Provides a toolkit for calculating forest and canopy structural complexity metrics from terrestrial LiDAR (light detection and ranging). References: Atkins et al. 2018 <doi:10.1111/2041-210X.13061>; Hardiman et al. 2013 <doi:10.3390/f4030537>; Parker et al. 2004 <doi:10.1111/j.0021-8901.2004.00925.x>.

Maintained by Jeff Atkins. Last updated 1 years ago.

5.2 match 29 stars 4.95 score 31 scripts

cran

compositions:Compositional Data Analysis

Provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by J. Aitchison and V. Pawlowsky-Glahn.

Maintained by K. Gerald van den Boogaart. Last updated 1 years ago.

openblas

4.0 match 1 stars 6.35 score 36 dependents

thothorn

HSAUR3:A Handbook of Statistical Analyses Using R (3rd Edition)

Functions, data sets, analyses and examples from the third edition of the book ''A Handbook of Statistical Analyses Using R'' (Torsten Hothorn and Brian S. Everitt, Chapman & Hall/CRC, 2014). The first chapter of the book, which is entitled ''An Introduction to R'', is completely included in this package, for all other chapters, a vignette containing all data analyses is available. In addition, Sweave source code for slides of selected chapters is included in this package (see HSAUR3/inst/slides). The publishers web page is '<https://www.routledge.com/A-Handbook-of-Statistical-Analyses-using-R/Hothorn-Everitt/p/book/9781482204582>'.

Maintained by Torsten Hothorn. Last updated 7 months ago.

3.8 match 6 stars 6.72 score 120 scripts 2 dependents

aahani-r

FAO56:Evapotranspiration Based on FAO Penman-Monteith Equation

Calculation of Evapotranspiration by FAO Penman-Monteith equation based on Allen, R. G., Pereira, L. S., Raes, D., Smith, M. (1998, ISBN:92-5-104219-5) "Crop evapotranspiration - Guidelines for computing crop water requirements - FAO Irrigation and drainage paper 56".

Maintained by Ali Ahani. Last updated 1 years ago.

14.2 match 1.70 score 2 scripts

usepa

micromap:Linked Micromap Plots

This group of functions simplifies the creation of linked micromap plots. Please see <https://www.jstatsoft.org/v63/i02/> for additional details.

Maintained by Marcus W. Beck. Last updated 5 months ago.

ord

3.6 match 10 stars 6.20 score 53 scripts

revelle

psychTools:Tools to Accompany the 'psych' Package for Psychological Research

Support functions, data sets, and vignettes for the 'psych' package. Contains several of the biggest data sets for the 'psych' package as well as four vignettes. A few helper functions for file manipulation are included as well. For more information, see the <https://personality-project.org/r/> web page.

Maintained by William Revelle. Last updated 12 months ago.

3.6 match 5.89 score 178 scripts 5 dependents

gianlucafilippa

phenopix:Process Digital Images of a Vegetation Cover

A collection of functions to process digital images, depict greenness index trajectories and extract relevant phenological stages.

Maintained by Gianluca Filippa. Last updated 1 months ago.

8.3 match 5 stars 2.52 score 66 scripts

emf-creaf

ecotraj:Ecological Trajectory Analysis

Assists ecologists in the analysis of temporal changes of ecosystems, defined as trajectories on a chosen multivariate space, by providing a set of trajectory metrics and visual representations [De Caceres et al. (2019) <doi:10.1002/ecm.1350>; and Sturbois et al. (2021) <doi:10.1016/j.ecolmodel.2020.109400>]. Includes functions to estimate metrics for individual trajectories (length, directionality, angles, ...) as well as metrics to relate pairs of trajectories (dissimilarity and convergence). Functions are also provided to estimate the ecological quality of ecosystem with respect to reference conditions [Sturbois et al. (2023) <doi:10.1002/ecs2.4726>].

Maintained by Miquel De Cáceres. Last updated 18 days ago.

cpp

4.0 match 4 stars 5.21 score 21 scripts 1 dependents

opengeos

whitebox:'WhiteboxTools' R Frontend

An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. Suggested citation: Lindsay (2016) <doi:10.1016/j.cageo.2016.07.003>.

Maintained by Andrew Brown. Last updated 5 months ago.

geomorphometry geoprocessing geospatial gis hydrology remote-sensing rstudio

2.0 match 173 stars 9.65 score 203 scripts 2 dependents

spatial-ews

spatialwarnings:Spatial Early Warning Signals of Ecosystem Degradation

Tools to compute and assess significance of early-warnings signals (EWS) of ecosystem degradation on raster data sets. EWS are spatial metrics derived from raster data -- e.g. spatial autocorrelation -- that increase before an ecosystem undergoes a non-linear transition (Genin et al. (2018) <doi:10.1111/2041-210X.13058>).

Maintained by Alexandre Genin. Last updated 6 months ago.

catastrophic critical ecology indicators points shifts space transitions cpp

3.6 match 15 stars 5.32 score 46 scripts

kang-yu

visa:Vegetation Imaging Spectroscopy Analyzer

Provides easy-to-use tools for data analysis and visualization for hyperspectral remote sensing (also known as imaging spectroscopy), with a particular focus on vegetation hyperspectral data analysis. It consists of a set of functions, ranging from the organization of hyperspectral data in the proper data structure for spectral feature selection, calculation of vegetation index, multivariate analysis, as well as to the visualization of spectra and results of analysis in the 'ggplot2' style.

Maintained by Kang Yu. Last updated 20 hours ago.

3.9 match 2 stars 4.79 score 61 scripts

gustavobio

flora:Tools for Interacting with the Brazilian Flora 2020

Tools to quickly compile taxonomic and distribution data from the Brazilian Flora 2020.

Maintained by Gustavo Carvalho. Last updated 1 years ago.

3.5 match 29 stars 5.37 score 54 scripts 1 dependents

pecanproject

PEcAn.dvmdostem:PEcAn Package for Integration of the Dvmdostem Model

This module provides functions to link the dvmdostem model to PEcAn.

Maintained by Tobey Carman. Last updated 2 days ago.

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

2.4 match 216 stars 7.56 score 3 scripts

florianjansen

eHOF:Extended HOF (Huisman-Olff-Fresco) Models

Extended and enhanced hierarchical logistic regression models (called Huisman-Olff-Fresco in biology, see Huisman et al. 1993 Journal of Vegetation Science <doi:10.1111/jvs.12050>) models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.

Maintained by Florian Jansen. Last updated 3 months ago.

5.7 match 3.16 score 24 scripts

rimagination

ggmapcn:Customizable China Map Visualizations

ggmapcn is a ggplot2 extension package for visualizing China’s map with customizable projections and styling.

Maintained by Liang Ren. Last updated 4 months ago.

3.0 match 16 stars 5.81 score 4 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 12 days ago.

biodiversity conservation ecology r-spatial raster spatial vector

1.8 match 110 stars 9.55 score 736 scripts 2 dependents

ardenb

TSS.RESTREND:Time Series Segmentation of Residual Trends

Time Series Segmented Residual Trends is a method for the automated detection of land degradation from remotely sensed vegetation and climate datasets. TSS-RESTREND incorporates aspects of two existing degradation detection methods: RESTREND which is used to control for climate variability, and BFAST which is used to look for structural changes in the ecosystem. The full details of the testing and justification of the TSS-RESTREND method (version 0.1.02) are published in Burrell et al., (2017). <doi:10.1016/j.rse.2017.05.018>. The changes to the method introduced in version 0.2.03 focus on the inclusion of temperature as an additional climate variable. This allows for land degradation assessment in temperature limited drylands. A paper that details this work is currently under review. There are also a number of bug fixes and speed improvements. Version 0.3.0 introduces additional attribution for eCO2, climate change and climate variability the details of which are in press in Burrell et al., (2020). The version under active development and additional example scripts showing how the package can be applied can be found at <https://github.com/ArdenB/TSSRESTREND>.

Maintained by Arden Burrell. Last updated 5 years ago.

12.6 match 1 stars 1.36 score 23 scripts

jillbo1000

EZtune:Tunes AdaBoost, Elastic Net, Support Vector Machines, and Gradient Boosting Machines

Contains two functions that are intended to make tuning supervised learning methods easy. The eztune function uses a genetic algorithm or Hooke-Jeeves optimizer to find the best set of tuning parameters. The user can choose the optimizer, the learning method, and if optimization will be based on accuracy obtained through validation error, cross validation, or resubstitution. The function eztune_cv will compute a cross validated error rate. The purpose of eztune_cv is to provide a cross validated accuracy or MSE when resubstitution or validation data are used for optimization because error measures from both approaches can be misleading.

Maintained by Jill Lundell. Last updated 3 years ago.

3.6 match 4.76 score 38 scripts 1 dependents

jarioksa

twinspan:Two-Way Indicator Species Analysis

Classification of biological communities based on splitting first axis of Correspondence Analysis for the current subset of the data, and finding species that best indicate the splits. The method is particularly popular in vegetation science.

Maintained by Jari Oksanen. Last updated 4 months ago.

fortran

4.0 match 7 stars 4.10 score 18 scripts

kuadrat

growR:Implementation of the Vegetation Model ModVege

Run grass growth simulations using a grass growth model based on ModVege (Jouven, M., P. Carrère, and R. Baumont "Model Predicting Dynamics of Biomass, Structure and Digestibility of Herbage in Managed Permanent Pastures. 1. Model Description." (2006) <doi:10.1111/j.1365-2494.2006.00515.x>). The implementation in this package contains a few additions to the above cited version of ModVege, such as simulations of management decisions, and influences of snow cover. As such, the model is fit to simulate grass growth in mountainous regions, such as the Swiss Alps. The package also contains routines for calibrating the model and helpful tools for analysing model outputs and performance.

Maintained by Kevin Kramer. Last updated 7 months ago.

agronomy grass grassland modelling simulation-modeling

3.1 match 3 stars 5.28 score 14 scripts

jarioksa

natto:An Extreme 'vegan' Package of Experimental Code

Random code that is too experimental or too weird to be included in the vegan package.

Maintained by Jari Oksanen. Last updated 28 days ago.

3.5 match 8 stars 4.68 score 1 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

labgrs

npphen:Vegetation Phenological Cycle and Anomaly Detection using Remote Sensing Data

Calculates phenological cycle and anomalies using a non-parametric approach applied to time series of vegetation indices derived from remote sensing data or field measurements. The package implements basic and high-level functions for manipulating vector data (numerical series) and raster data (satellite derived products). Processing of very large raster files is supported. For more information, please check the following paper: Chávez et al. (2023) <doi:10.3390/rs15010073>.

Maintained by José A. Lastra. Last updated 3 months ago.

3.3 match 5 stars 4.32 score 14 scripts

predictiveecology

LandWebUtils:Helper functions for the LandWeb project

Additional utilities for LandWeb analyses.

Maintained by Alex M Chubaty. Last updated 1 months ago.

landscape-ecology simulation-modeling

5.3 match 2 stars 2.60 score 2 scripts

kelvynbladen

randomForestVIP:Tune Random Forests Based on Variable Importance and Plot Results

Functions for assessing variable relations and associations prior to modeling with a Random Forest algorithm (although these are relevant for any predictive model). Metrics such as partial correlations and variance inflation factors are tabulated as well as plotted for the user. A function is available for tuning the main Random Forest hyper-parameter based on model performance and variable importance metrics. This grid-search technique provides tables and plots showing the effect of the main hyper-parameter on each of the assessment metrics. It also returns each of the evaluated models to the user. The package also provides superior variable importance plots for individual models. All of the plots are developed so that the user has the ability to edit and improve further upon the plots. Derivations and methodology are described in Bladen (2022) <https://digitalcommons.usu.edu/etd/8587/>.

Maintained by Kelvyn Bladen. Last updated 1 years ago.

3.6 match 3.78 score 12 scripts

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.

3.7 match 3.70 score 9 scripts

pschmidtwalter

LWFBrook90R:Simulate Evapotranspiration and Soil Moisture with the SVAT Model LWF-Brook90

Provides a flexible and easy-to use interface for the soil vegetation atmosphere transport (SVAT) model LWF-BROOK90, written in Fortran. The model simulates daily transpiration, interception, soil and snow evaporation, streamflow and soil water fluxes through a soil profile covered with vegetation, as described in Hammel & Kennel (2001, ISBN:978-3-933506-16-0) and Federer et al. (2003) <doi:10.1175/1525-7541(2003)004%3C1276:SOAETS%3E2.0.CO;2>. A set of high-level functions for model set up, execution and parallelization provides easy access to plot-level SVAT simulations, as well as multi-run and large-scale applications.

Maintained by Paul Schmidt-Walter. Last updated 5 months ago.

evapotranspiration modeling waterbalance waterflux fortran

2.1 match 11 stars 6.38 score 27 scripts

richardli

surveyPrev:Mapping the Prevalence of Binary Indicators using Survey Data in Small Areas

Provides a pipeline to perform small area estimation and prevalence mapping of binary indicators using health and demographic survey data, described in Fuglstad et al. (2022) <doi:10.48550/arXiv.2110.09576> and Wakefield et al. (2020) <doi:10.1111/insr.12400>.

Maintained by Qianyu Dong. Last updated 4 days ago.

2.3 match 1 stars 5.76 score 11 scripts

aphalo

photobiologyWavebands:Waveband Definitions for UV, VIS, and IR Radiation

Constructors of waveband objects for commonly used biological spectral weighting functions (BSWFs) and for different wavebands describing named ranges of wavelengths in the ultraviolet (UV), visible (VIS) and infrared (IR) regions of the electromagnetic spectrum. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.

Maintained by Pedro J. Aphalo. Last updated 8 months ago.

2.0 match 1 stars 6.53 score 378 scripts 3 dependents

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

3.6 match 8 stars 3.60 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.

2.2 match 9 stars 5.73 score 6 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.

5.5 match 2.28 score 38 scripts

tesselle

folio:Datasets for Teaching Archaeology and Paleontology

Datasets for teaching quantitative approaches and modeling in archaeology and paleontology. This package provides several types of data related to broad topics (cultural evolution, radiocarbon dating, paleoenvironments, etc.), which can be used to illustrate statistical methods in the classroom (multivariate data analysis, compositional data analysis, diversity measurement, etc.).

Maintained by Nicolas Frerebeau. Last updated 1 months ago.

archaeology archaeological-science paleontology datasets

4.0 match 3.02 score 2 scripts 1 dependents

bluegreen-labs

phenocamr:Facilitates 'PhenoCam' Data Access and Time Series Post-Processing

Programmatic interface to the 'PhenoCam' web services (<https://phenocam.nau.edu/webcam>). Allows for easy downloading of 'PhenoCam' data directly to your R workspace or your computer and provides post-processing routines for consistent and easy timeseries outlier detection, smoothing and estimation of phenological transition dates. Methods for this package are described in detail in Hufkens et. al (2018) <doi:10.1111/2041-210X.12970>.

Maintained by Koen Hufkens. Last updated 1 years ago.

phenocam phenocam-data phenology-modelling remote-sensing

1.8 match 22 stars 6.69 score 75 scripts 1 dependents

babaknaimi

rts:Raster Time Series Analysis

This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).

Maintained by Babak Naimi. Last updated 9 months ago.

1.7 match 6 stars 6.59 score 107 scripts 1 dependents

ericbarba

ExpDes:Experimental Designs Package

Package for analysis of simple experimental designs (CRD, RBD and LSD), experiments in double factorial schemes (in CRD and RBD), experiments in a split plot in time schemes (in CRD and RBD), experiments in double factorial schemes with an additional treatment (in CRD and RBD), experiments in triple factorial scheme (in CRD and RBD) and experiments in triple factorial schemes with an additional treatment (in CRD and RBD), performing the analysis of variance and means comparison by fitting regression models until the third power (quantitative treatments) or by a multiple comparison test, Tukey test, test of Student-Newman-Keuls (SNK), Scott-Knott, Duncan test, t test (LSD) and Bonferroni t test (protected LSD) - for qualitative treatments; residual analysis (Ferreira, Cavalcanti and Nogueira, 2014) <doi:10.4236/am.2014.519280>.

Maintained by Eric Batista Ferreira. Last updated 3 years ago.

3.8 match 1 stars 2.86 score 73 scripts

nowosad

spDataLarge:Large datasets for spatial analysis

Large datasets for spatial analysis. The data from this package could be retrived using the spData package.

Maintained by Jakub Nowosad. Last updated 5 months ago.

raster sf spatial spatial-data

1.7 match 27 stars 6.15 score 1.2k scripts 1 dependents

michaelgreenacre

easyCODA:Compositional Data Analysis in Practice

Univariate and multivariate methods for compositional data analysis, based on logratios. The package implements the approach in the book Compositional Data Analysis in Practice by Michael Greenacre (2018), where accent is given to simple pairwise logratios. Selection can be made of logratios that account for a maximum percentage of logratio variance. Various multivariate analyses of logratios are included in the package.

Maintained by Michael Greenacre. Last updated 7 months ago.

4.5 match 1 stars 2.26 score 46 scripts

cran

GPoM:Generalized Polynomial Modelling

Platform dedicated to the Global Modelling technique. Its aim is to obtain ordinary differential equations of polynomial form directly from time series. It can be applied to single or multiple time series under various conditions of noise, time series lengths, sampling, etc. This platform is developped at the Centre d'Etudes Spatiales de la Biosphere (CESBIO), UMR 5126 UPS/CNRS/CNES/IRD, 18 av. Edouard Belin, 31401 TOULOUSE, FRANCE. The developments were funded by the French program Les Enveloppes Fluides et l'Environnement (LEFE, MANU, projets GloMo, SpatioGloMo and MoMu). The French program Defi InFiNiTi (CNRS) and PNTS are also acknowledged (projects Crops'IChaos and Musc & SlowFast). The method is described in the article : Mangiarotti S. and Huc M. (2019) <doi:10.1063/1.5081448>.

Maintained by Mireille Huc. Last updated 2 years ago.

3.5 match 2.90 score

brownag

rapr:Interface to Rangeland Analysis Platform (RAP) Vegetation Biomass and Cover Products

Provides access to Rangeland Analysis Platform (RAP) products <https://rangelands.app/products> for arbitrary extents via GDAL virtual file system.

Maintained by Andrew Brown. Last updated 6 months ago.

2.8 match 4 stars 3.60 score

trotsiuk

r3PG:Simulating Forest Growth using the 3-PG Model

Provides a flexible and easy-to-use interface for the Physiological Processes Predicting Growth (3-PG) model written in Fortran. The r3PG serves as a flexible and easy-to-use interface for the 3-PGpjs (monospecific, evenaged and evergreen forests) described in Landsberg & Waring (1997) <doi:10.1016/S0378-1127(97)00026-1> and the 3-PGmix (deciduous, uneven-aged or mixed-species forests) described in Forrester & Tang (2016) <doi:10.1016/j.ecolmodel.2015.07.010>.

Maintained by Volodymyr Trotsiuk. Last updated 10 months ago.

fortran glibc

1.7 match 27 stars 5.83 score 25 scripts

pakillo

vegetools:Tools for vegetation analysis

By now, just tools to calculate vegetation cover from field transects data.

Maintained by Francisco Rodriguez-Sanchez. Last updated 5 years ago.

5.6 match 1.70 score

ropensci

taxlist:Handling Taxonomic Lists

Handling taxonomic lists through objects of class 'taxlist'. This package provides functions to import species lists from 'Turboveg' (<https://www.synbiosys.alterra.nl/turboveg/>) and the possibility to create backups from resulting R-objects. Also quick displays are implemented as summary-methods.

Maintained by Miguel Alvarez. Last updated 6 months ago.

1.2 match 12 stars 7.07 score 81 scripts 2 dependents

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.

8.1 match 1.00 score 10 scripts

cran

diffval:Vegetation Patterns

Find, visualize and explore patterns of differential taxa in vegetation data (namely in a phytosociological table), using the Differential Value (DiffVal). Patterns are searched through mathematical optimization algorithms. Ultimately, Total Differential Value (TDV) optimization aims at obtaining classifications of vegetation data based on differential taxa, as in the traditional geobotanical approach. The Gurobi optimizer, as well as the R package 'gurobi', can be installed from <https://www.gurobi.com/products/gurobi-optimizer/>. The useful vignette Gurobi Installation Guide, from package 'prioritizr', can be found here: <https://prioritizr.net/articles/gurobi_installation_guide.html>.

Maintained by Tiago Monteiro-Henriques. Last updated 2 years ago.

4.5 match 1.70 score

sandrinepavoine

adiv:Analysis of Diversity

Functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. The package also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.

Maintained by Sandrine Pavoine. Last updated 1 years ago.

3.3 match 1 stars 2.28 score 63 scripts

jarioksa

gravy:Gradient Analysis of Vegetation

Experimental tools for gradient analysis of community data. Most of the functionality is now included in package 'eHOF', but there are still some divergent features.

Maintained by Jari Oksanen. Last updated 10 months ago.

3.3 match 2 stars 2.00 score

fchianucci

LAIr:Converting NDVI to LAI of Field, Proximal and Satellite Data

Convert Leaf Area Index (LAI) from the Normalized Difference Vegetation Index (NDVI) using available equations from literature. Detailed description of conversion equations in Bajocco et al. 2022 <doi:10.3390/rs14153554>.

Maintained by Francesco Chianucci. Last updated 1 years ago.

3.8 match 1 stars 1.70 score 2 scripts

prabhanjan-tattar

gpk:100 Data Sets for Statistics Education

Collection of datasets as prepared by Profs. A.P. Gore, S.A. Paranjape, and M.B. Kulkarni of Department of Statistics, Poona University, India. With their permission, first letter of their names forms the name of this package, the package has been built by me and made available for the benefit of R users. This collection requires a rich class of models and can be a very useful building block for a beginner.

Maintained by Prabhanjan Tattar. Last updated 12 years ago.

3.8 match 1.69 score 49 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

0.9 match 12 stars 6.64 score 3 scripts

predictiveecology

usefulFuns:Useful functions for my modules and packages

A few functions and wrappers around useful code.

Maintained by Tati Micheletti. Last updated 4 months ago.

3.4 match 1.70 score 1 scripts

bijoy231997

vegIndexCalc:Vegetation Indices (VIs) Calculation for Remote Sensing Analysis

It provides a comprehensive toolkit for calculating a suite of common vegetation indices (VIs) derived from remote sensing imagery. VIs are essential tools used to quantify vegetation characteristics, such as biomass, leaf area index (LAI) and photosynthetic activity, which are essential parameters in various ecological, agricultural, and environmental studies. Applications of this package include biomass estimation, crop monitoring, forest management, land use and land cover change analysis and climate change studies. For method details see, Deb,D.,Deb,S.,Chakraborty,D.,Singh,J.P.,Singh,A.K.,Dutta,P.and Choudhury,A.(2020)<doi:10.1080/10106049.2020.1756461>. Utilizing this R package, users can effectively extract and analyze critical information from remote sensing imagery, enhancing their comprehension of vegetation dynamics and their importance in global ecosystems. The package includes the function vegetation_indices().

Maintained by Bijoy Chanda. Last updated 2 months ago.

5.6 match 1.00 score

matutosi

ecan:Ecological Analysis and Visualization

Support ecological analyses such as ordination and clustering. Contains consistent and easy wrapper functions of 'stat', 'vegan', and 'labdsv' packages, and visualisation functions of ordination and clustering.

Maintained by Toshikazu Matsumura. Last updated 6 months ago.

2.0 match 2.70 score 5 scripts

cran

ExpImage:Analysis of Images in Experiments

Tools created for image analysis in researches. There are functions associated with image editing, segmentation, and obtaining biometric measurements (Este pacote foi idealizado para para a analise de imagens em pesquisas. Ha funcoes associadas a edicao de imagens, segmentacao, e obtencao de medidas biometricas) <https://www.expstat.com/pacotes-do-r/expimage>.

Maintained by Alcinei Mistico Azevedo. Last updated 10 months ago.

1.7 match 3.08 score

cran

ecoCopula:Graphical Modelling and Ordination using Copulas

Creates 'graphs' of species associations (interactions) and ordination biplots from co-occurrence data by fitting discrete gaussian copula graphical models. Methods described in Popovic, GC., Hui, FKC., Warton, DI., (2018) <doi:10.1016/j.jmva.2017.12.002>.

Maintained by Gordana Popovic. Last updated 3 years ago.

1.2 match 4.17 score 49 scripts 2 dependents

nschuwirth

ecoval:Procedures for Ecological Assessment of Surface Waters

Functions for evaluating and visualizing ecological assessment procedures for surface waters containing physical, chemical and biological assessments in the form of value functions.

Maintained by Nele Schuwirth. Last updated 3 years ago.

3.5 match 1.34 score 22 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.

3.6 match 1.30 score 1 scripts

nutriverse

riycf:Utilities for Calculating Infant and Young Child Feeding Indicators

This package aims to generate updated indicators to assess infant and young child feeding (IYCF) practices at the individual under 2 years old children level. The indicators were developed using the technical guideline from the Indicators for assessing infant and young child feeding practices: definitions and measurement methods <https://www.who.int/publications/i/item/9789240018389>.

Maintained by Nicholus Tint Zaw. Last updated 1 months ago.

iycf nutrition survey

1.1 match 2 stars 3.60 score

cran

SPEDInstabR:Estimation of the Relative Importance of Factors Affecting Species Distribution Based on Stability Concept

From output files obtained from the software 'ModestR', the relative contribution of factors to explain species distribution is depicted using several plots. A global geographic raster file for each environmental variable may be also obtained with the mean relative contribution, considering all species present in each raster cell, of the factor to explain species distribution. Finally, for each variable it is also possible to compare the frequencies of any variable obtained in the cells where the species is present with the frequencies of the same variable in the cells of the extent.

Maintained by Castor Guisande Gonzalez. Last updated 1 years ago.

4.0 match 1.00 score

jmmonnet

lidaRtRee:Forest Analysis with Airborne Laser Scanning (LiDAR) Data

Provides functions for forest objects detection, structure metrics computation, model calibration and mapping with airborne laser scanning: co-registration of field plots (Monnet and Mermin (2014) <doi:10.3390/f5092307>); tree detection (method 1 in Eysn et al. (2015) <doi:10.3390/f6051721>) and segmentation; forest parameters estimation with the area-based approach: model calibration with ground reference, and maps export (Aussenac et al. (2023) <doi:10.12688/openreseurope.15373.2>); extraction of both physical (gaps, edges, trees) and statistical features useful for e.g. habitat suitability modeling (Glad et al. (2020) <doi:10.1002/rse2.117>) and forest maturity mapping (Fuhr et al. (2022) <doi:10.1002/rse2.274>).

Maintained by Jean-Matthieu Monnet. Last updated 2 months ago.

1.8 match 3 stars 2.18 score

emf-creaf

medfate:Mediterranean Forest Simulation

Simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].

Maintained by Miquel De Cáceres. Last updated 9 days ago.

cpp

0.5 match 11 stars 7.49 score 183 scripts 1 dependents

dvrbts

coenoflex:Gradient-Based Coenospace Vegetation Simulator

Simulates the composition of samples of vegetation according to gradient-based vegetation theory. Features a flexible algorithm incorporating competition and complex multi-gradient interaction.

Maintained by David W. Roberts. Last updated 8 years ago.

fortran

3.8 match 1.00 score 2 scripts

ecodynizw

imageseg:Deep Learning Models for Image Segmentation

A general-purpose workflow for image segmentation using TensorFlow models based on the U-Net architecture by Ronneberger et al. (2015) <arXiv:1505.04597> and the U-Net++ architecture by Zhou et al. (2018) <arXiv:1807.10165>. We provide pre-trained models for assessing canopy density and understory vegetation density from vegetation photos. In addition, the package provides a workflow for easily creating model input and model architectures for general-purpose image segmentation based on grayscale or color images, both for binary and multi-class image segmentation.

Maintained by Juergen Niedballa. Last updated 1 years ago.

image-segmentation keras tensorflow

0.8 match 18 stars 4.95 score 9 scripts

cran

EnviroPRA2:Environmental Probabilistic Risk Assessment Tools

It contains functions for dose calculation for different routes, fitting data to probability distributions, random number generation (Monte Carlo simulation) and calculation of systemic and carcinogenic risks. For more information see the publication: Barrio-Parra et al. (2019) "Human-health probabilistic risk assessment: the role of exposure factors in an urban garden scenario" <doi:10.1016/j.landurbplan.2019.02.005>.

Maintained by Fernando Barrio-Parra. Last updated 1 years ago.

3.7 match 1.00 score

cran

geotoolsR:Tools to Improve the Use of Geostatistic

The basic idea of this package is provides some tools to help the researcher to work with geostatistics. Initially, we present a collection of functions that allow the researchers to deal with spatial data using bootstrap procedure. There are five methods available and two ways to display them: bootstrap confidence interval - provides a two-sided bootstrap confidence interval; bootstrap plot - a graphic with the original variogram and each of the B bootstrap variograms.

Maintained by Diogo Francisco Rossoni. Last updated 8 months ago.

3.6 match 1.00 score 5 scripts

cran

HYDROCAL:Hydraulic Roughness Calculator

Estimates frictional constants for hydraulic analysis of rivers. This HYDRaulic ROughness CALculator (HYDROCAL) was previously developed as a spreadsheet tool and accompanying documentation by McKay and Fischenich (2011, <https://erdc-library.erdc.dren.mil/jspui/bitstream/11681/2034/1/CHETN-VII-11.pdf>).

Maintained by Colton Shaw. Last updated 2 years ago.

3.3 match 1.00 score

cran

soilassessment:Soil Health Assessment Models for Assessing Soil Conditions and Suitability

Soil health assessment builds information to improve decision in soil management. It facilitates assessment of soil conditions for crop suitability [such as those given by FAO <https://www.fao.org/land-water/databases-and-software/crop-information/en/>], groundwater recharge, fertility, erosion, salinization [<doi:10.1002/ldr.4211>], carbon sequestration, irrigation potential, and status of soil resources.

Maintained by Christian Thine Omuto. Last updated 2 months ago.

3.3 match 1 stars 1.00 score

marcodvisser

ccrtm:Coupled Chain Radiative Transfer Models

A set of radiative transfer models to quantitatively describe the absorption, reflectance and transmission of solar energy in vegetation, and model remotely sensed spectral signatures of vegetation at distinct spatial scales (leaf,canopy and stand). The main principle behind ccrtm is that many radiative transfer models can form a coupled chain, basically models that feed into each other in a linked chain (from leaf, to canopy, to stand, to atmosphere). It allows the simulation of spectral datasets in the solar spectrum (400-2500nm) using leaf models as PROSPECT5, 5b, and D which can be coupled with canopy models as 'FLIM', 'SAIL','SAIL2' and 'INFORM' for top of canopy reflectance, and with atmospheric models such as 'SKYL'and 'SMAC' for calculation of top of the atmosphere reflectance. All models can run in forward mode, and a selection are invertable (backward simulations) if provided with spectral data. Jacquemoud et al 2008 provides a comprehensive overview of these and other models <doi:10.1016/j.rse.2008.01.026>.

Maintained by Marco D. Visser. Last updated 4 days ago.

cpp

0.8 match 15 stars 4.18 score 1 scripts

cost-fp1304-profound

ProfoundData:Downloading and Exploring Data from the PROFOUND Database

Provides an R interface for the PROFOUND database <doi:10.5880/PIK.2019.008>. The PROFOUND database contains a wide range of data to evaluate vegetation models and simulate climate impacts at the forest stand scale. It includes 9 forest sites across Europe, and provides for them a site description as well as soil, climate, CO2, Nitrogen deposition, tree-level, forest stand-level and remote sensing data. Moreover, for a subset of 5 sites, also time series of carbon fluxes, energy balances and soil water are available.

Maintained by Florian Hartig. Last updated 5 years ago.

0.5 match 9 stars 5.58 score 14 scripts

ogarciav

siplab:Spatial Individual-Plant Modelling

A platform for computing competition indices and experimenting with spatially explicit individual-based vegetation models.

Maintained by Oscar Garcia. Last updated 3 years ago.

plant-ecology plant-growth simulation

0.5 match 3 stars 4.97 score 31 scripts

mlampros

CopernicusDEM:Copernicus Digital Elevation Models

Copernicus Digital Elevation Model datasets (DEM) of 90 and 30 meters resolution using the 'awscli' command line tool. The Copernicus (DEM) is included in the Registry of Open Data on 'AWS (Amazon Web Services)' and represents the surface of the Earth including buildings, infrastructure and vegetation.

Maintained by Lampros Mouselimis. Last updated 3 months ago.

awscli awscliv2 copernicus digital-elevation-model

0.5 match 17 stars 5.23 score 1 scripts

cran

agrifeature:Agriculture Image Feature

Functions to calculate Gray Level Co-occurrence Matrix(GLCM), RGB-based Vegetative Index(RGB VI) and Normalized Difference Vegetation Index(NDVI) family image features. GLCM calculations are based on Haralick (1973) <doi:10.1109/TSMC.1973.4309314>.

Maintained by Chun-Han Lee. Last updated 3 years ago.

2.6 match 1.00 score

aphalo

photobiologySun:Data for Sunlight Spectra

Data for the extraterrestrial solar spectral irradiance and ground level solar spectral irradiance and irradiance. In addition data for shade light under vegetation and irradiance time series from different broadband sensors. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.

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

0.5 match 5.03 score 27 scripts

lcgodoy

sapo:Spatial Association of Different Types of Polygon

In ecology, spatial data is often represented using polygons. These polygons can represent a variety of spatial entities, such as ecological patches, animal home ranges, or gaps in the forest canopy. Researchers often need to determine if two spatial processes, represented by these polygons, are independent of each other. For instance, they might want to test if the home range of a particular animal species is influenced by the presence of a certain type of vegetation. To address this, Godoy et al. (2022) (<doi:10.1016/j.spasta.2022.100695>) developed conditional Monte Carlo tests. These tests are designed to assess spatial independence while taking into account the shape and size of the polygons.

Maintained by Lucas da Cunha Godoy. Last updated 5 months ago.

0.5 match 1 stars 4.48 score 3 scripts

syoung9836

knfi:Analysis of Korean National Forest Inventory Database

Understanding the current status of forest resources is essential for monitoring changes in forest ecosystems and generating related statistics. In South Korea, the National Forest Inventory (NFI) surveys over 4,500 sample plots nationwide every five years and records 70 items, including forest stand, forest resource, and forest vegetation surveys. Many researchers use NFI as the primary data for research, such as biomass estimation or analyzing the importance value of each species over time and space, depending on the research purpose. However, the large volume of accumulated forest survey data from across the country can make it challenging to manage and utilize such a vast dataset. To address this issue, we developed an R package that efficiently handles large-scale NFI data across time and space. The package offers a comprehensive workflow for NFI data analysis. It starts with data processing, where read_nfi() function reconstructs NFI data according to the researcher's needs while performing basic integrity checks for data quality.Following this, the package provides analytical tools that operate on the verified data. These include functions like summary_nfi() for summary statistics, diversity_nfi() for biodiversity analysis, iv_nfi() for calculating species importance value, and biomass_nfi() and cwd_biomass_nfi() for biomass estimation. Finally, for visualization, the tsvis_nfi() function generates graphs and maps, allowing users to visualize forest ecosystem changes across various spatial and temporal scales. This integrated approach and its specialized functions can enhance the efficiency of processing and analyzing NFI data, providing researchers with insights into forest ecosystems. The NFI Excel files (.xlsx) are not included in the R package and must be downloaded separately. Users can access these NFI Excel files by visiting the Korea Forest Service Forestry Statistics Platform <https://kfss.forest.go.kr/stat/ptl/article/articleList.do?curMenu=11694&bbsId=microdataboard> to download the annual NFI Excel files, which are bundled in .zip archives. Please note that this website is only available in Korean, and direct download links can be found in the notes section of the read_nfi() function.

Maintained by Sinyoung Park. Last updated 3 months ago.

data-analysis-r forestry

0.5 match 1 stars 4.48 score 2 scripts

bbcrown

solrad:Calculating Solar Radiation and Related Variables Based on Location, Time and Topographical Conditions

For surface energy models and estimation of solar positions and components with varying topography, time and locations. The functions calculate solar top-of-atmosphere, open, diffuse and direct components, atmospheric transmittance and diffuse factors, day length, sunrise and sunset, solar azimuth, zenith, altitude, incidence, and hour angles, earth declination angle, equation of time, and solar constant. Details about the methods and equations are explained in Seyednasrollah, Bijan, Mukesh Kumar, and Timothy E. Link. 'On the role of vegetation density on net snow cover radiation at the forest floor.' Journal of Geophysical Research: Atmospheres 118.15 (2013): 8359-8374, <doi:10.1002/jgrd.50575>.

Maintained by Bijan Seyednasrollah. Last updated 6 years ago.

0.5 match 10 stars 4.32 score 42 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

biagolini

bwimage:Describe Image Patterns in Natural Structures

A computational tool to describe patterns in black and white images from natural structures. 'bwimage' implemented functions for exceptionally broad subject. For instance, 'bwimage' provide examples that range from calculation of canopy openness, description of patterns in vertical vegetation structure, to patterns in bird nest structure.

Maintained by Carlos Biagolini-Jr.. Last updated 5 years ago.

0.5 match 3.70 score

jeroenpullens

NUCOMBog:NUtrient Cycling and COMpetition Model Undisturbed Open Bog Ecosystems in a Temperate to Sub-Boreal Climate

Modelling the vegetation, carbon, nitrogen and water dynamics of undisturbed open bog ecosystems in a temperate to sub-boreal climate. The executable of the model can downloaded from <https://github.com/jeroenpullens/NUCOMBog>.

Maintained by J.W.M. Pullens. Last updated 7 years ago.

0.5 match 1 stars 3.36 score 46 scripts

hrlai

novelforestSG:Dataset from the Novel Forests of Singapore

The raw dataset and model used in Lai et al. (2021) Decoupled responses of native and exotic tree diversities to distance from old-growth forest and soil phosphorous in novel secondary forests. Applied Vegetation Science, 24, e12548.

Maintained by Hao Ran Lai. Last updated 1 years ago.

data diversity ecology forest singapore

0.5 match 2 stars 3.30 score 4 scripts

cran

Rveg:Digitization of Phytosociological Relevés

Simple and fast tool for transforming phytosociological vegetation data into digital form for the following analysis. Danihelka, Chrtek, and Kaplan (2012, ISSN:00327786). Hennekens, and Schaminée (2001) <doi:10.2307/3237010>. Tichý (2002) <doi:10.1111/j.1654-1103.2002.tb02069.x>. Wickham, François, Henry, Müller (2022) <https://CRAN.R-project.org/package=dplyr>.

Maintained by Přemysl Král. Last updated 4 months ago.

0.5 match 3.18 score 3 scripts

villegar

splash:Simple Process-Led Algorithms for Simulating Habitats

This program calculates bioclimatic indices and fluxes (radiation, evapotranspiration, soil moisture) for use in studies of ecosystem function, species distribution, and vegetation dynamics under changing climate scenarios. Predictions are based on a minimum of required inputs: latitude, precipitation, air temperature, and cloudiness. Davis et al. (2017) <doi:10.5194/gmd-10-689-2017>.

Maintained by Roberto Villegas-Diaz. Last updated 2 years ago.

0.5 match 1 stars 2.70 score 10 scripts

daniel-dok

phenex:Auxiliary Functions for Phenological Data Analysis

Provides some easy-to-use functions for spatial analyses of (plant-) phenological data sets and satellite observations of vegetation.

Maintained by Daniel Doktor. Last updated 8 years ago.

0.5 match 2 stars 2.28 score 32 scripts 1 dependents

hristotomov

DBEST:Detecting Breakpoints and Estimating Segments in Trend

A program for analyzing vegetation time series, with two algorithms: 1) change detection algorithm that detects trend changes, determines their type (abrupt or non-abrupt), and estimates their timing, magnitude, number, and direction; 2) generalization algorithm that simplifies the temporal trend into main features. The user can set the number of major breakpoints or magnitude of greatest changes of interest for detection, and can control the generalization process by setting an additional parameter of generalization-percentage.

Maintained by Hristo Tomov. Last updated 7 years ago.

0.5 match 5 stars 2.18 score 10 scripts

cran

wdiEF:Calculation of the Water Deficit Index (WDI) and the Evaporative Fraction (EF) on Rasters

Calculates the Water Deficit Index (WDI) and the Evaporative Fraction (EF) using geospatial data, such as fractional vegetation cover (FVC) and surface-air temperature difference (TS-TA). Terms like "raster", "CRS" are part of standard geospatial terminology.

Maintained by Gaelle Hamelin. Last updated 25 days ago.

0.5 match 2.00 score 4 scripts

cran

gaussratiovegind:Distribution of Gaussian Ratios

It is well known that the distribution of a Gaussian ratio does not follow a Gaussian distribution. The lack of awareness among users of vegetation indices about this non-Gaussian nature could lead to incorrect statistical modeling and interpretation. This package provides tools to accurately handle and analyse such ratios: density function, parameter estimation, simulation. An example on the study of chlorophyll fluorescence can be found in A. El Ghaziri et al. (2023) <doi:10.3390/rs15020528>.

Maintained by Pierre Santagostini. Last updated 1 months ago.

0.5 match 1.70 score

rodolfomssouza

Ecohydmod:Ecohydrological Modelling

Simulates the soil water balance (soil moisture, evapotranspiration, leakage and runoff), rainfall series by using the marked Poisson process and the vegetation growth through the normalized difference vegetation index (NDVI). Please see Souza et al. (2016) <doi:10.1002/hyp.10953>.

Maintained by Rodolfo Souza. Last updated 8 years ago.

0.8 match 1 stars 1.00 score 6 scripts

cran

rPAex:Automatic Detection of Experimental Unit in Precision Agriculture

A part of precision agriculture is linked to the spectral image obtained from the cameras. With the image information of the agricultural experiment, the included functions facilitate the collection of spectral data associated with the experimental units. Some designs generated in R are linked to the images, which allows the use of the information of each pixel of the image in the experimental unit and the treatment. Tables and images are generated for the analysis of the precision agriculture experiment during the entire vegetative period of the crop.

Maintained by Felipe de Mendiburu. Last updated 1 years ago.

0.5 match 1.04 score 11 scripts

himadriiasri

PMEvapotranspiration:Calculation of the Penman-Monteith Evapotranspiration using Weather Variables

The Food and Agriculture Organization-56 Penman-Monteith is one of the important method for estimating evapotranspiration from vegetated land areas. This package helps to calculate reference evapotranspiration using the weather variables collected from weather station. Evapotranspiration is the process of water transfer from the land surface to the atmosphere through evaporation from soil and other surfaces and transpiration from plants. The package aims to support agricultural, hydrological, and environmental research by offering accurate and accessible reference evapotranspiration calculation. This package has been developed using concept of Córdova et al. (2015)<doi:10.1016/j.apm.2022.09.004> and Debnath et al. (2015) <doi:10.1007/s40710-015-0107-1>.

Maintained by Dr. Himadri Shekhar Roy. Last updated 1 years ago.

0.5 match 1.00 score