geodata - Access 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.

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agricultureclimatedataecologysoilspatial

11.96 score 193 stars 13 dependents 2.3k scripts 19k 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.

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discrete-events-simulationssimulation-frameworksimulation-modeling

10.56 score 11 stars 6 dependents 144 scripts 698 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()'.

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reproducibilityreproducible-research

10.13 score 39 stars 15 dependents 110 scripts 2.5k 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.

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10.10 score 24 stars 14 dependents 151 scripts 2.4k 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.

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simulation-frameworksimulation-toolkitspatially-explicit-models

8.23 score 55 stars 260 scripts 247 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).

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plottingvisualization

8.14 score 6 stars 10 dependents 129 scripts 821 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.

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cpp

7.64 score 4 stars 6 dependents 68 scripts 485 downloads

NLMR - Simulating Neutral Landscape Models

Provides neutral landscape models (<doi:10.1007/BF02275262>, <https://sci-hub.in/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.

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landscape-ecologyneutral-landscape-modelpeer-reviewedspatialcpp

7.53 score 68 stars 228 scripts 5 downloads

SpaDES.project - Project Templates Using 'SpaDES'

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

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7.32 score 4 stars 1 dependents 27 scripts

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) <https://www.netlogo.org>) 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 <https://ccl.northwestern.edu/netlogo/models/Ants>) and Wolf-Sheep-Predation (<https://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://docs.netlogo.org/programming.html>) and a dictionary of 'NetLogo' primitives (<https://docs.netlogo.org/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>).

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6.93 score 44 stars 24 scripts 248 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.

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ecological-modellinglandscape-ecosystem-modellingspadescpp

6.14 score 19 stars 3 dependents 13 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).

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4.99 score 3 scripts

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

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

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4.64 score 3 stars 1 dependents 194 scripts

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

Provides wrappers for working with 'libcbm_py' in R.

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4.38 score 3 stars 5 scripts

pemisc - Miscellaneous Utilities Developed by the Predictive Ecology Group

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

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landscape-ecologysimulation-modeling

3.83 score 1 stars 5 dependents 3 scripts

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

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

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3.70 score 1 stars 3 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.

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3.58 score 26 stars 29 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.

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3.56 score 728 scripts 56 downloads

amc - Alex's Miscellaneous Code

A collection of variously useful functions and utilities.

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3.50 score 1 stars 7 dependents 8 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.

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3.30 score 1 stars 33 downloads

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.

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3.26 score 1 scripts

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).

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2.95 score 6 dependents

LandWebUtils - Helper functions for the LandWeb project

Additional utilities for LandWeb analyses.

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landscape-ecologysimulation-modeling

2.85 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>.

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2.70 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.

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2.65 score 3 stars 6 scripts

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.

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2.64 score 22 scripts 3 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'.

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2.54 score 1 stars

clusters - Utilities to manage, estimate speed, optimize use of parallel clusters

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

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2.48 score 1 stars 1 dependents 5 scripts

SpaDES.experiment - Simulation Experiments Within The SpaDES Ecosystem (Deprecated)

DEPRECATED and no longer maintained: this functionality has moved to the 'SpaDES.project' package, which is now its maintained home. The experiment functions here (experiment(), experiment2(), simInitAndExperiment()) forward to 'SpaDES.project'. Historically, this package provided tools to do simulation experiments within the SpaDES ecosystem, including replication, parameter sweeps, scenario analysis, pattern oriented modeling, and simulation experiments, and introduced the simLists class (an environment that contains many simList class objects) plus tools to do post hoc analyses of such objects.

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simulation-experiments

2.30 score 1 stars 2 scripts

usefulFuns - Useful functions for my modules and packages

A few functions and wrappers around useful code.

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1.70 score 1 scripts

pedev - Predictive Ecology Development Tools

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

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1.70 score 1 stars

mpbutils - Utilities for Mountain Pine Beetle Simulation Modelling

Utilities for mountain pine beetle (MPB) simulation modelling.

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1.70 score