Package: SpaDES.project 1.0.1.9364

Eliot J B McIntire

SpaDES.project: Project Templates Using 'SpaDES'

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

Authors:Eliot J B McIntire [aut, cre], Alex M Chubaty [ctb], Ian Eddy [ctb], Ceres Barros [ctb]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SpaDES.project/json (API)

# Install 'SpaDES.project' in R:
install.packages('SpaDES.project', repos = c('https://predictiveecology.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/predictiveecology/spades.project/issues

Pkgdown/docs site:https://spades-project.predictiveecology.org

On CRAN:

Conda:

7.57 score 4 stars 1 packages 43 scripts 4 mentions 90 exports 17 dependencies

Last updated from:a77288bf9c (on development). Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK205
source / vignettesOK281
linux-release-x86_64OK199
macos-release-arm64OK110
macos-oldrel-arm64OK113
windows-develOK172
windows-releaseOK175
windows-oldrelOK147
wasm-releaseOK127

Exports:.libPathDefault.teardownProjectas_pathas_scenarioas_tarnameawaitExperimentFutureawaitExperimentSBATCHexperimentexperiment2experimentFutureexperimentFutureListexperimentMonitorexperimentSBATCHexperimentTmuxfactorialDesignfdSelectLimitfindProjectNamefindProjectPathget_sim_year_heartbeatgetGithubFilegetModuleinitializekillExperimentFuturekillExperimentSBATCHlastTracebacklistModuleslocalHostLabelmachinemetadataInModulesmoduleDependenciesmoduleDependenciesToGraphnodeopenFdsopenFdsReportoutListoutSaveoutSaveTarUploadoutScenariosoutTaroutUploadpackagesInModulespathBuildpathParsepkgload2plotChangeOverTimePlotModuleGraphplotSAsplotSAsLeafletplotTimeSeriesLeafletpreRunSetupProjectqueueReadqueueUploadMissingreGetreGetUntarLoadregister_scenario_formatreLoadreUntarrunWorkerLoopFuturescenarioscenarioFieldsscenarioFieldsSetsetProjPkgDirsetupFilessetupFunctionssetupGitIgnoresetupModulessetupOptionssetupPackagessetupParamssetupPathssetupProjectsetupSideEffectssetupStudyAreashowsimInitAndExperimentspadesProjectOptionsstatusCalculate_FireSenseFitstatusCalculate_LandRteardownProjecttmuxActiveRunningPathtmuxFindDuplicatestmuxKillPanestmuxListPanestmuxPrepareQueueFromDFtmuxRefreshQueueStatustmuxRunNextWorkertmuxRunWorkerLooptmuxSetMousetmuxSetPaneTitleuser

Dependencies:callrcurldata.tablefilelockfsmagickmagrittrotelpakprocessxpsR6RcppRequirerprojrootrstudioapisys

Getting Started
Setting Up Prerequisites: Installing System Dependencies, R, and RStudio | Installing SpaDES.project | Understanding SpaDES.project's Main Function: setupProject() | Function objectives | Function Tasks | What Makes this Function so Special | 1. Versatile Argument Types | 2. Sequential Argument Processing | 3. Handling Missing Values | Relationship between setupProject() and SpaDES.core::simInit Call | See Also | Examples of usage of setupProject() | Get modules from GitHub | Paths | Default values | Arguments sourced sequentially | Arguments not sourced to .GlobalEnv | With options and params set | Arguments as values or urls | Setting arbitrary arguments, using defaultDots | Pass args from GlobalEnv | Mixing argument: a named list, a github file and local file | studyArea argument | Alberta and British Columbia, Canada | Specify an epsg | require and objects arguments | Passing named arguments as part of the ... | Make project-level change to .libPaths() that is persistent
Rendered fromi-getting-started.Rmdusingknitr::rmarkdown

Last update: 2026-03-27
Started: 2022-03-24

Finding other modules
Find other's modules | A small selection of SpaDES modules | Some Biomass_ modules* | FireSense modules | LandR modules | A larger selection of "known" SpaDES modules | All SpaDES modules in a set of known accounts
Rendered fromv-finding-other-modules.Rmdusingknitr::rmarkdown

Last update: 2024-05-31
Started: 2024-05-31

Installing R
Traditional installation | Windows | macOS | Linux | Alternate installation | Launching Rstudio using a specific version of R | Installing Rstudio
Rendered fromiv-Installing-R.Rmdusingknitr::rmarkdown

Last update: 2024-05-31
Started: 2024-05-31

Using git for project development
What is git? | Installation | Commandline tools | Desktop clients | Getting started with GitHub | Additonal commandline setup | Development workflow | Git submodules | Cloning a project with submodules | Adding submodules to a project | Updating submodules | Additional resources
Rendered fromiii-using-git-github.Rmdusingknitr::rmarkdown

Last update: 2022-03-24
Started: 2022-03-24

Readme and manuals

Help Manual

Help pageTopics
Project templates using 'SpaDES'SpaDES.project-package SpaDES.project
SpaDES.project default .libPaths() directory.libPathDefault
Render a scenario (or list of them) as the canonical output path.as_path
Coerce any scenario representation to a canonical record.as_scenario
Render a scenario as an upload tar filename.as_tarname
Coerce elements of a 'simLists' object to a 'data.table'as.data.table.simLists
Assess simulation status from PNG outputsassessDoneInFigure
Wait for all workers in an experimentFuture to finishawaitExperimentFuture
Wait for all SBATCH workers to finishawaitExperimentSBATCH
Run an experiment using 'SpaDES.core::spades()'experiment
Experiment functions: five ways to run a SpaDES experimentexperiment_family
Run experiment, algorithm 2, using 'SpaDES.core::spades()'experiment2
Run parallel R jobs using background processes (tmux-free)experimentFuture
Find (and optionally kill) live experimentFuture workersexperimentFutureList
Monitor live workers across an experiment (tmux panes or callr/cluster futures)experimentMonitor
Run parallel R jobs on a Slurm cluster (SBATCH-based)experimentSBATCH
Spawn tmux worker panes and process a job queueexperimentTmux
Build a factorial experiment designfactorialDesign
FD_SETSIZE on this platform (the 'select()' ceiling).fdSelectLimit
Find the project root directoryfindProjectName findProjectPath
Heartbeat for year-checkpoint SpaDES simulationsget_sim_year_heartbeat
A simple way to get a Github file, authenticatedgetGithubFile
Simple function to download a SpaDES module as GitHub repositorygetModule
Generate a 'simLists' objectinitialize,simLists-method
Stop workers launched by experimentFuturekillExperimentFuture
Stop SBATCH workers launched by experimentSBATCHkillExperimentSBATCH
Inspect the call stack from the most recent worker errorlastTraceback
Tools for examining modules on known repositorieslistModules moduleDependencies moduleDependenciesToGraph PlotModuleGraph
Short friendly name for the local machinelocalHostLabel
Make DESCRIPTION file(s) from SpaDES module metadatamakeDESCRIPTION makeDESCRIPTIONproject
Inspect open file descriptors.openFds
Printable summary of open file descriptors.openFdsReport
List uploaded scenario output archives.outList
Save a SpaDES simulation to an RDS fileoutSave
Save, tar, and upload a SpaDES simulation to Google DriveoutSaveTarUpload
Uploaded outputs as scenario records.outScenarios
Bundle a sim file and output files into a tar.gz archiveoutTar
Upload a file to Google DriveoutUpload
Extract element from SpaDES module metadatametadataInModules packagesInModules
Default scenario path builder.pathBuild
Default scenario path parser.pathParse
An alternative to 'pkgload::load_all' with cachingpkgload2
Difference between two layers of a time-series, as a leaflet mapplotChangeOverTime
Plot studyArea** and rasterToMatch** with ggplot2 or leafletplotSAs plotSAsLeaflet
Time-series of 'SpatRaster' layers as an interactive leaflet map with a sliderplotTimeSeriesLeaflet
Partially or Fully Run 'setupProject'preRunSetupProject
Read the driver queue (local RDS or Google Sheet).queueRead
Queue rows whose tarball is missing from the upload folder.queueUploadMissing
Download tarballs from Google DrivereGet
Download, untar, and load SpaDES sims from Google DrivereGetUntarLoad
Register a project-specific path builder / parser.register_scenario_format
Load saved SpaDES simListsreLoad
Extract sim tarballs, optionally remapping a path prefixreUntar
Worker loop for future/cluster-based remote executionrunWorkerLoopFuture
Construct a scenario record.scenario
Scenario records: one canonical form, multiple representationsscenario_family
Active scenario field labels.scenarioFields scenarioFieldsSet
Set the package directory for a projectsetProjPkgDir
Parse a list of (possibly remote) R / config filessetupFiles
Source user-supplied helper functions into the project environmentsetupFunctions
Add 'packagePath' and/or 'modulePath' to the project's '.gitignore'setupGitIgnore
Download (or git clone) SpaDES modules into the project's 'modulePath'setupModules
Apply (and stage) project optionssetupOptions
Install module + user-supplied R packages into the project librarysetupPackages
Prepare module parameter lists for 'simInit()'setupParams
Set up project, module, and scratch pathssetupPaths
Sets up a new or existing SpaDES projectsetupProject
Run side-effect scripts (e.g., authentication, custom package options)setupSideEffects
Resolve a study area from a 'studyArea' spec via 'geodata::gadm()'setupStudyArea
Show method for 'simLists'show,simLists-method
Run 'simInit' and 'experiment' in one stepsimInitAndExperiment
The 'simLists' classsimLists simLists-class
'SpaDES.project' optionsspadesProjectOptions
Pre-built statusCalculate expressions for experimentTmux / experimentFuturestatusCalculate_family statusCalculate_FireSenseFit statusCalculate_LandR
Tear down a project created by 'setupProject()'.teardownProject teardownProject
Log path for default tmux statustmuxActiveRunningPath
Find duplicate worker panes running the same jobtmuxFindDuplicates
Kill a set of tmux panes (e.g., those spawned by experimentTmux)tmuxKillPanes
List all tmux panes on this machine across every tmux servertmuxListPanes
Mirror local queue to Google SheetstmuxMirrorQueueToSheets
Initialize a file-backed queue from a data.frametmuxPrepareQueueFromDF
Refresh and Assess Queue Status from Simulation OutputstmuxRefreshQueueStatus
Run one queued job (claim-next semantics) in the current R session.tmuxRunNextWorker
Run queued jobs repeatedly (pane-local loop).tmuxRunWorkerLoop
Enable or disable tmux mouse interactiontmuxSetMouse
Set a tmux pane's title by matching its current titletmuxSetPaneTitle
Helpers to develop easier to understand code.machine node user