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.

Last updated 5 months ago

10.60 score 154 stars 7 dependents 1.3k scripts 9.7k downloads

SpaDES.core - Core Utilities for Developing and Running Spatially Explicit Discrete Event Models

Provides the core framework for a discrete event system to implement a complete data-to-decisions, reproducible workflow. The core components facilitate the development of modular pieces, and enable the user to include additional functionality by running user-built modules. Includes conditional scheduling, restart after interruption, packaging of reusable modules, tools for developing arbitrary automated workflows, automated interweaving of modules of different temporal resolution, and tools for visualizing and understanding the within-project dependencies. The suggested package 'NLMR' can be installed from the repository (<https://PredictiveEcology.r-universe.dev>).

Last updated 30 days ago

discrete-events-simulationssimulation-frameworksimulation-modeling

10.48 score 9 stars 5 dependents 266 scripts 932 downloads

reproducible - Enhance Reproducibility of R Code

A collection of high-level, machine- and OS-independent tools for making reproducible and reusable content in R. The two workhorse functions are Cache() and prepInputs(). Cache() allows for nested caching, is robust to environments and objects with environments (like functions), and deals with some classes of file-backed R objects e.g., from terra and raster packages. Both functions have been developed to be foundational components of data retrieval and processing in continuous workflow situations. In both functions, efforts are made to make the first and subsequent calls of functions have the same result, but faster at subsequent times by way of checksums and digesting. Several features are still under development, including cloud storage of cached objects allowing for sharing between users. Several advanced options are available, see ?reproducibleOptions().

Last updated 14 days ago

reproducibilityreproducible-research

10.24 score 41 stars 15 dependents 122 scripts 1.3k downloads

Require - Installing and Loading R Packages for Reproducible Workflows

A single key function, 'Require' that makes rerun-tolerant versions of 'install.packages' and `require` for CRAN packages, packages no longer on CRAN (i.e., archived), specific versions of packages, and GitHub packages. This approach is developed to create reproducible workflows that are flexible and fast enough to use while in development stages, while able to build snapshots once a stable package collection is found. As with other functions in a reproducible workflow, this package emphasizes functions that return the same result whether it is the first or subsequent times running the function, with subsequent times being sufficiently fast that they can be run every time without undue waiting burden on the user or developer.

Last updated 9 days ago

9.33 score 21 stars 13 dependents 146 scripts 859 downloads

SpaDES - Develop and Run Spatially Explicit Discrete Event Simulation Models

Metapackage for implementing a variety of event-based models, with a focus on spatially explicit models. These include raster-based, event-based, and agent-based models. The core simulation components (provided by 'SpaDES.core') are built upon a discrete event simulation (DES; see Matloff (2011) ch 7.8.3 <https://nostarch.com/artofr.htm>) framework that facilitates modularity, and easily enables the user to include additional functionality by running user-built simulation modules (see also 'SpaDES.tools'). Included are numerous tools to visualize rasters and other maps (via 'quickPlot'), and caching methods for reproducible simulations (via 'reproducible'). Tools for running simulation experiments are provided by 'SpaDES.experiment'. Additional functionality is provided by the 'SpaDES.addins' and 'SpaDES.shiny' packages.

Last updated 30 days ago

simulation-frameworksimulation-toolkitspatially-explicit-models

9.09 score 55 stars 309 scripts 302 downloads

rgdal - Bindings for the 'Geospatial' Data Abstraction Library

Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ' library. Please note that 'rgdal' will be retired during October 2023, plan transition to sf/stars/'terra' functions using 'GDAL' and 'PROJ' at your earliest convenience (see <https://r-spatial.org/r/2023/05/15/evolution4.html> and earlier blogs for guidance). Use is made of classes defined in the 'sp' package. Raster and vector map data can be imported into R, and raster and vector 'sp' objects exported. The 'GDAL' and 'PROJ' libraries are external to the package, and, when installing the package from source, must be correctly installed first; it is important that 'GDAL' < 3 be matched with 'PROJ' < 6. From 'rgdal' 1.5-8, installed with to 'GDAL' >=3, 'PROJ' >=6 and 'sp' >= 1.4, coordinate reference systems use 'WKT2_2019' strings, not 'PROJ' strings. 'Windows' and 'macOS' binaries (including 'GDAL', 'PROJ' and their dependencies) are provided on 'CRAN'.

Last updated 2 years ago

gdalprojcpp

8.99 score 10 stars 1 dependents 33k scripts 3.3k downloads

quickPlot - A System of Plotting Optimized for Speed and Modularity

A high-level plotting system, compatible with `ggplot2` objects, maps from `sf`, `terra`, `raster`, `sp`. It is built primarily on the 'grid' package. The objective of the package is to provide a plotting system that is built for speed and modularity. This is useful for quick visualizations when testing code and for plotting multiple figures to the same device from independent sources that may be independent of one another (i.e., different function or modules the create the visualizations). The suggested package 'fastshp' can be installed from the repository (<https://PredictiveEcology.r-universe.dev>).

Last updated 30 days ago

plottingvisualization

8.05 score 6 stars 12 dependents 129 scripts 663 downloads

SpaDES.tools - Additional Tools for Developing Spatially Explicit Discrete Event Simulation (SpaDES) Models

Provides GIS and map utilities, plus additional modeling tools for developing cellular automata, dynamic raster models, and agent based models in 'SpaDES'. Included are various methods for spatial spreading, spatial agents, GIS operations, random map generation, and others. See '?SpaDES.tools' for an categorized overview of these additional tools. The suggested package 'NLMR' can be installed from the following repository: (<https://PredictiveEcology.r-universe.dev>).

Last updated 30 days ago

cpp

7.53 score 4 stars 6 dependents 67 scripts 970 downloads

NetLogoR - Build and Run Spatially Explicit Agent-Based Models

Build and run spatially explicit agent-based models using only the R platform. 'NetLogoR' follows the same framework as the 'NetLogo' software (Wilensky (1999) <http://ccl.northwestern.edu/netlogo/>) and is a translation in R of the structure and functions of 'NetLogo'. 'NetLogoR' provides new R classes to define model agents and functions to implement spatially explicit agent-based models in the R environment. This package allows benefiting of the fast and easy coding phase from the highly developed 'NetLogo' framework, coupled with the versatility, power and massive resources of the R software. Examples of two models from the NetLogo software repository (Ants <http://ccl.northwestern.edu/netlogo/models/Ants>) and Wolf-Sheep-Predation (<http://ccl.northwestern.edu/netlogo/models/WolfSheepPredation>), and a third, Butterfly, from Railsback and Grimm (2012) <https://www.railsback-grimm-abm-book.com/>, all written using 'NetLogoR' are available. The 'NetLogo' code of the original version of these models is provided alongside. A programming guide inspired from the 'NetLogo' Programming Guide (<https://ccl.northwestern.edu/netlogo/docs/programming.html>) and a dictionary of 'NetLogo' primitives (<https://ccl.northwestern.edu/netlogo/docs/dictionary.html>) equivalences are also available. NOTE: To increment 'time', these functions can use a for loop or can be integrated with a discrete event simulator, such as 'SpaDES' (<https://cran.r-project.org/package=SpaDES>). The suggested package 'fastshp' can be installed with 'install.packages("fastshp", repos = ("<https://rforge.net>"), type = "source")'.

Last updated 30 days ago

7.06 score 38 stars 19 scripts 312 downloads

rgeos - Interface to Geometry Engine - Open Source ('GEOS')

Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. Please note that 'rgeos' will be retired during October 2023, plan transition to 'sf' or 'terra' functions using 'GEOS', or the 'geos' package, at your earliest convenience (see <https://r-spatial.org/r/2023/05/15/evolution4.html> and earlier blogs for guidance). The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'. ('rgeos' >= 0.5-1): Up to and including 'GEOS' 3.7.1, topological operations succeeded with some invalid geometries for which the same operations fail from and including 'GEOS' 3.7.2. The 'checkValidity=' argument defaults and structure have been changed, from default FALSE to integer default '0L' for 'GEOS' < 3.7.2 (no check), '1L' 'GEOS' >= 3.7.2 (check and warn). A value of '2L' is also provided that may be used, assigned globally using 'set_RGEOS_CheckValidity(2L)', or locally using the 'checkValidity=2L' argument, to attempt zero-width buffer repair if invalid geometries are found. The previous default (FALSE, now '0L') is fastest and used for 'GEOS' < 3.7.2, but will not warn users of possible problems before the failure of topological operations that previously succeeded. From 'GEOS' 3.8.0, repair of geometries may also be attempted using 'gMakeValid()', which may, however, return a collection of geometries of different types.

Last updated 1 years ago

geos

6.84 score 7 stars 2 dependents 11k scripts 1.5k downloads

NLMR - Simulating Neutral Landscape Models

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

Last updated 4 months ago

landscape-ecologyneutral-landscape-modelpeer-reviewedspatialcpp

6.74 score 65 stars 194 scripts 101 downloads

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.

Last updated 2 days ago

ecological-modellinglandscape-ecosystem-modellingspades

5.93 score 17 stars 3 dependents 12 scripts

SpaDES.project - Project Templates Using 'SpaDES'

Quickly setup a 'SpaDES' project directories and add modules using templates.

Last updated 5 days ago

4.86 score 3 stars 20 scripts

libcbmr - Interface to the Carbon Budget Model Library Based on CBM-CFS3

Provides wrappers for working with 'libcbm_py' in R.

Last updated 1 months ago

4.68 score 3 stars 5 scripts

RandomFields - Simulation and Analysis of Random Fields

Methods for the inference on and the simulation of Gaussian fields are provided. Furthermore, methods for the simulation of extreme value random fields are provided. Main geostatistical parts are based among others on the books by Christian Lantuejoul <doi:10.1007/978-3-662-04808-5>.

Last updated 3 years ago

openblascppopenmp

4.66 score 7 stars 696 scripts 1.3k downloads

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

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

Last updated 5 days ago

4.41 score 1 stars 2 scripts

map - Defines a meta class of geographical objects, the 'map' class, and associated tools

The map class is a collection of map objects ('sp', 'raster', 'sf'), with a number of metadata additions to enable powerful methods, e.g., for leaflet, reproducible GIS etc.

Last updated 30 days ago

4.00 score 2 stars 1 dependents 166 scripts

pemisc - Miscellaneous Utilities Developed by the Predictive Ecology Group

Miscellaneous utilities developed by the Predictive Ecology Group (<http://predictiveecology.org>).

Last updated 9 days ago

landscape-ecologysimulation-modeling

3.95 score 1 stars 5 dependents 3 scripts

CBMutils - Utilities for modelling carbon based on CBM-CFS3

Implementation of several components of the Carbon Budget Model of the Canadian Forest Service (v3).

Last updated 30 days ago

cpp

3.85 score 3 scripts

SpaDES.addins - Development Tools for 'SpaDES' and 'SpaDES' Modules

Provides 'RStudio' addins for 'SpaDES' packages and 'SpaDES' module development. See '?SpaDES.addins' for an overview of the tools provided.

Last updated 30 days ago

3.64 score 1 stars 11 scripts 79 downloads

SpaDES.experiment - Simulation Experiments Within The SpaDES Ecosystem

Tools to do simulation experiments within the SpaDES ecosystem. This includes replication, parameter sweeps, scenario analysis, pattern oriented modeling, and simulation experiments. The package introduces a new object class, the simLists, which is an environment that contains many simList class objects. This package also includes tools to do post hoc analyses of such simLists objects.

Last updated 30 days ago

simulation-experiments

3.60 score 1 stars 7 scripts

visualTest - Perform Fuzzy Image Matching

Extract and match fingerprints, characteristic signal in plot files. It can be used for testing packages or other R code with graphical output. It is possible to set the level of fuzzyness when comparing the target and the tested images.

Last updated 9 years ago

3.59 score 27 stars 29 scripts

LandWebUtils - Helper functions for the LandWeb project

Additional utilities for LandWeb analyses.

Last updated 30 days ago

landscape-ecologysimulation-modeling

2.78 score 2 stars 2 scripts

scfmutils - Tools and Utilities for Working With the SCFM Wildfire Simulation Model

The original fire model is described by Cumming et al. (1998), and more accessibly in Armstrong and Cumming (2003). It has recently been implemented as a collection of 'SpaDES' modules by Cumming, McIntire, Eddy, and Chubaty, available from <https://github.com/PredictiveEcology/scfm>.

Last updated 5 days ago

2.74 score

amc - Alex's Miscellaneous Code

A collection of variously useful functions and utilities.

Last updated 11 months ago

3.80 score 1 stars 7 dependents 8 scripts

SDMTools - Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises

This packages provides a set of tools for post processing the outcomes of species distribution modeling exercises. It includes novel methods for comparing models and tracking changes in distributions through time. It further includes methods for visualizing outcomes, selecting thresholds, calculating measures of accuracy and landscape fragmentation statistics, etc.. This package was made possible in part by financial support from the Australian Research Council & ARC Research Network for Earth System Science.

Last updated 5 years ago

3.52 score 5 stars 666 scripts 378 downloads

peutils - Utilities Developed by the Predictive Ecology Group

Dependency-free utilities developed by the Predictive Ecology Group (<http://predictiveecology.org>). (Do not depend on contributed R packages).

Last updated 11 months ago

2.95 score 6 dependents

J4R - Create 'Java' Objects and Execute 'Java' Methods

Makes it possible to create 'Java' objects and to execute 'Java' methods from the 'R' environment. The 'Java' Virtual Machine is handled by a gateway server. Commands are sent to the server through a socket connection from the 'R' environment. Calls to 'Java' methods allow for vectors so that a particular method is iteratively run on each element of the vector. A score algorithm also makes the calls to 'Java' methods less restrictive. The gateway server relies on the runnable 'Java' library 'j4r.jar'. This library is licensed under the LGPL-3. Its sources are included in the jar file.

Last updated 2 months ago

2.62 score 21 scripts 27 downloads

LandR.CS - Climate-sensitive Growth and Mortality in LandR

This package contains climate-sensitive growth and mortality function for LandR. Some flexibility exists in how climate-sensitivity is derived, however the simplest and most robust method is to use the SpaDES module 'gmcsDataPrep' and R package 'PSPclean'.

Last updated 30 days ago

2.40 score 1 stars

PSPclean - Sources and standardizes permanent sample plot data

Converts all data into two keyed tables. One is for tree measurements, and the other is for plot data. Some arguments exist for handling disturbance agents.

Last updated 6 months ago

2.30 score

BioSIM - 'BioSIM' Client for 'BioSIM' Web API

Provide a client that retrieves the climate variables from the original 'BioSIM' application hosted on a server. The 'BioSIM' application is being developed and maintained by the Canadian Forest Service.

Last updated 5 months ago

2.18 score 3 stars 4 scripts

usefulFuns - Useful functions for my modules and packages

A few functions and wrappers around useful code.

Last updated 30 days ago

2.00 score 1 scripts

pedev - Predictive Ecology Development Tools

Miscellaneous development tools developed by the Predictive Ecology Group (<https://predictiveecology.org>).

Last updated 30 days ago

2.00 score 1 stars

RandomFieldsUtils - Utilities for the Simulation and Analysis of Random Fields and Genetic Data

Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used.

Last updated 3 years ago

fortranopenblascppopenmp

1.95 score 90 scripts 309 downloads

fastshp - Fast routines for hanlding large ESRI shapefiles (.shp)

Routines for handling of large ESRI shapefiles (.shp). This includes reading, thinning of points and matching of points to containing shapes. The main aim for this package is to provide the speed to support large shapefiles (millions of points). It is several orders of maginute faster than some other shapefile packages.

Last updated 7 years ago

cpp

1.95 score 9 stars 8 scripts

mpbutils - Utilities for Mountain Pine Beetle Simulation Modelling

Utilities for mountain pine beetle (MPB) simulation modelling.

Last updated 5 months ago

1.70 score