Package: SpaDES.project 1.0.1.9340

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✨
card.svg |card.png
SpaDES.project/json (API)
NEWS

# 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:

7.32 score 4 stars 1 packages 27 scripts 4 mentions 88 exports 16 dependencies

Last updated from:bea8eae40b (on development). Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	202
source / vignettes	OK	315
linux-release-x86_64	OK	203
macos-release-arm64	OK	143
macos-oldrel-arm64	OK	176
windows-devel	OK	230
windows-release	OK	263
windows-oldrel	OK	238
wasm-release	OK	166

Exports:.libPathDefault .teardownProject as_path as_scenario as_tarname awaitExperimentFuture awaitExperimentSBATCH experiment experiment2 experimentFuture experimentFutureList experimentMonitor experimentSBATCH experimentTmux factorialDesign fdSelectLimit findProjectName findProjectPath get_sim_year_heartbeat getGithubFile getModule initialize killExperimentFuture killExperimentSBATCH lastTraceback listModules localHostLabel machine metadataInModules moduleDependencies moduleDependenciesToGraph node openFds openFdsReport outList outSave outSaveTarUpload outScenarios outTar outUpload packagesInModules pathBuild pathParse pkgload2 PlotModuleGraph plotSAs plotSAsLeaflet preRunSetupProject queueRead queueUploadMissing reGet reGetUntarLoad register_scenario_format reLoad reUntar runWorkerLoopFuture scenario scenarioFields scenarioFieldsSet setProjPkgDir setupFiles setupFunctions setupGitIgnore setupModules setupOptions setupPackages setupParams setupPaths setupProject setupSideEffects setupStudyArea show simInitAndExperiment spadesProjectOptions statusCalculate_FireSenseFit statusCalculate_LandR teardownProject tmuxActiveRunningPath tmuxFindDuplicates tmuxKillPanes tmuxListPanes tmuxPrepareQueueFromDF tmuxRefreshQueueStatus tmuxRunNextWorker tmuxRunWorkerLoop tmuxSetMouse tmuxSetPaneTitle user

Dependencies:callr curl data.table filelock fs magick magrittr pak processx ps R6 Rcpp Require rprojroot rstudioapi sys

Finding other modules

Eliot McIntire

Rendered fromv-finding-other-modules.Rmdusingknitr::rmarkdownon Jun 03 2026.

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

Getting Started

Eliot McIntire

Rendered fromi-getting-started.Rmdusingknitr::rmarkdownon Jun 03 2026.

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

Installing R

Alex M. Chubaty

Rendered fromiv-Installing-R.Rmdusingknitr::rmarkdownon Jun 03 2026.

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

Using git for project development

Alex M. Chubaty

Rendered fromiii-using-git-github.Rmdusingknitr::rmarkdownon Jun 03 2026.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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 outputs	assessDoneInFigure
Wait for all workers in an experimentFuture to finish	awaitExperimentFuture
Wait for all SBATCH workers to finish	awaitExperimentSBATCH
Run an experiment using 'SpaDES.core::spades()'	experiment
Experiment functions: five ways to run a SpaDES experiment	experiment_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 workers	experimentFutureList
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 queue	experimentTmux
Build a factorial experiment design	factorialDesign
FD_SETSIZE on this platform (the 'select()' ceiling).	fdSelectLimit
Find the project root directory	findProjectName findProjectPath
Heartbeat for year-checkpoint SpaDES simulations	get_sim_year_heartbeat
A simple way to get a Github file, authenticated	getGithubFile
Simple function to download a SpaDES module as GitHub repository	getModule
Generate a 'simLists' object	initialize,simLists-method
Stop workers launched by experimentFuture	killExperimentFuture
Stop SBATCH workers launched by experimentSBATCH	killExperimentSBATCH
Inspect the call stack from the most recent worker error	lastTraceback
Tools for examining modules on known repositories	listModules moduleDependencies moduleDependenciesToGraph PlotModuleGraph
Short friendly name for the local machine	localHostLabel
Make DESCRIPTION file(s) from SpaDES module metadata	makeDESCRIPTION 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 file	outSave
Save, tar, and upload a SpaDES simulation to Google Drive	outSaveTarUpload
Uploaded outputs as scenario records.	outScenarios
Bundle a sim file and output files into a tar.gz archive	outTar
Upload a file to Google Drive	outUpload
Extract element from SpaDES module metadata	metadataInModules packagesInModules
Default scenario path builder.	pathBuild
Default scenario path parser.	pathParse
An alternative to 'pkgload::load_all' with caching	pkgload2
Plot studyArea and rasterToMatch with ggplot2 or leaflet	plotSAs plotSAsLeaflet
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 Drive	reGet
Download, untar, and load SpaDES sims from Google Drive	reGetUntarLoad
Register a project-specific path builder / parser.	register_scenario_format
Load saved SpaDES simLists	reLoad
Extract sim tarballs, optionally remapping a path prefix	reUntar
Worker loop for future/cluster-based remote execution	runWorkerLoopFuture
Construct a scenario record.	scenario
Scenario records: one canonical form, multiple representations	scenario_family
Active scenario field labels.	scenarioFields scenarioFieldsSet
Set the package directory for a project	setProjPkgDir
Parse a list of (possibly remote) R / config files	setupFiles
Source user-supplied helper functions into the project environment	setupFunctions
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 options	setupOptions
Install module + user-supplied R packages into the project library	setupPackages
Prepare module parameter lists for 'simInit()'	setupParams
Set up project, module, and scratch paths	setupPaths
Sets up a new or existing SpaDES project	setupProject
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 step	simInitAndExperiment
The 'simLists' class	simLists simLists-class
'SpaDES.project' options	spadesProjectOptions
Pre-built statusCalculate expressions for experimentTmux / experimentFuture	statusCalculate_family statusCalculate_FireSenseFit statusCalculate_LandR
Tear down a project created by 'setupProject()'	.teardownProject teardownProject
Log path for default tmux status	tmuxActiveRunningPath
Find duplicate worker panes running the same job	tmuxFindDuplicates
Kill a set of tmux panes (e.g., those spawned by experimentTmux)	tmuxKillPanes
List all tmux panes on this machine across every tmux server	tmuxListPanes
Mirror local queue to Google Sheets	tmuxMirrorQueueToSheets
Initialize a file-backed queue from a data.frame	tmuxPrepareQueueFromDF
Refresh and Assess Queue Status from Simulation Outputs	tmuxRefreshQueueStatus
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 interaction	tmuxSetMouse
Set a tmux pane's title by matching its current title	tmuxSetPaneTitle
Helpers to develop easier to understand code.	machine node user