zoon: Reproducible, Accessible & Shareable Species Distribution Modelling

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Reproducible and remixable species distribution modelling. The package reads user submitted modules from an online repository, runs full SDM workflows and returns output that is fully reproducible.

Author
Tim Lucas, Nick Golding, Tom August, Greg McInerny, Emiel van Loon
Date of publication
2016-06-07 16:36:21
Maintainer
Tom August <tomaug@ceh.ac.uk>
License
BSD_3_clause + file LICENSE
Version
0.5
URLs

View on CRAN

Man pages

AplumbeusOcc
UK occurrence data for Anopheles plumbeus as taken from GBIF
BuildModule
BuildModule
Chain
Chain modules together
ChangeWorkflow
Change a workflow and rerun.
CWBZim
Presence/absence of the coffee white stem borer in Zimbabwe...
ExtractAndCombData
ExtractAndCombData
FrescaloBias
Example bias raster for plants in England
GetMaxEnt
Get MaxEnt
GetModuleList
GetModuleList
GetPackage
Helper to install (if needed) and load a package
LoadModule
A function to load a module function from url or disk.
ModuleHelp
ModuleHelp
Occurrence
Accessor functions for getting module outputs from a workflow...
plot.zoonWorkflow
Plot a schematic illustration of a zoon workflow structure.
print.Summary
A function to print zoon workflow summaries
print.zoonCitation
A function to print zoonCitation
print.zoonWorkflow
A function to print a zoonWorkflow object
Replicate
A function to replicate a module multiple times
RerunWorkflow
Rerun a workflow object.
RunModels
RunModels
summary.zoonWorkflow
A function to summarize the output of a zoon workflow
UKAirRas
UK Air temperature raster layer.
workflow
Run a full workflow.
zoon
Zoon: A package for comparing multple SDM models, good model...
ZoonCitation
ZoonCitation
ZoonFigshare
ZoonFigshare
ZoonModel
ZoonModel
ZoonModuleParse
Parse a module file to read roxygen tags
ZoonPredict
ZoonPredict

Files in this package

zoon
zoon/inst
zoon/inst/extdata
zoon/inst/extdata/data_PO.rdata
zoon/inst/extdata/data_PB.rdata
zoon/inst/extdata/myData.csv
zoon/inst/extdata/myRaster.grd
zoon/inst/extdata/myRaster.gri
zoon/inst/extdata/data_PA.rdata
zoon/inst/doc
zoon/inst/doc/basic-zoon-usage.html
zoon/inst/doc/interactive_zoon_usage.html
zoon/inst/doc/basic-zoon-usage.Rmd
zoon/inst/doc/interactive_zoon_usage.Rmd
zoon/inst/doc/Building_a_module.Rmd
zoon/inst/doc/Building_a_module.html
zoon/tests
zoon/tests/testthat
zoon/tests/testthat/testExtractAndCombData.R
zoon/tests/testthat/testWholeWorkflows.R
zoon/tests/testthat/testGetModule.R
zoon/tests/testthat/Rplots.pdf
zoon/tests/testthat/testSortArgs.R
zoon/tests/testthat/testplot.zoonWorkflow.r
zoon/tests/testthat/testBuildModule.R
zoon/tests/testthat/testRunModules.R
zoon/tests/testthat/testLoadModule.R
zoon/tests/testthat/testFormatModuleList.R
zoon/tests/testthat/testSplitCall.R
zoon/tests/testthat/testplot.zoonCitation.R
zoon/tests/testthat/testaccessors.R
zoon/tests/testthat/testprint.zoonWorkflow.R
zoon/tests/testthat/testprint.zoonSummary.R
zoon/tests/testthat/testCheckModList.R
zoon/tests/testthat/testZoonCitation.R
zoon/tests/testthat/testErrorModule.R
zoon/tests/testthat/testChangeWorkflow.R
zoon/tests/testthat/testLapplyGetModule.R
zoon/tests/testthat/testGetModuleList.R
zoon/tests/testthat/testGetPackage.R
zoon/tests/testthat/testPasteAndDep.R
zoon/tests/testthat/testcall_path.R
zoon/tests/testthat/testSplitArgs.R
zoon/tests/testthat/testChain.R
zoon/tests/testthat/testsummary.zoonWorkflow.R
zoon/tests/testthat/testGetMaxEnt.R
zoon/tests/testthat/testModuleHelp.R
zoon/tests/testthat/testReplicate.R
zoon/tests/testthat/testRerunWorkflow.R
zoon/tests/testthat/testtestModule.R
zoon/tests/test-all.R
zoon/NAMESPACE
zoon/data
zoon/data/CWBZim.rda
zoon/data/UKAir.rda
zoon/data/AplumbeusOcc.rda
zoon/data/FrescaloBias.rda
zoon/R
zoon/R/test_outputs.R
zoon/R/HelpFunctions.R
zoon/R/test_parameters.R
zoon/R/accessors.R
zoon/R/GetPackage.R
zoon/R/ZoonModuleParse.R
zoon/R/zoon.R
zoon/R/zoonPredict.R
zoon/R/SearchFunctions.R
zoon/R/ChangeWorkflow.R
zoon/R/plot.zoonWorkflow.R
zoon/R/test_module.R
zoon/R/print.zoonSummary.R
zoon/R/WriteWorkflowMetadata.R
zoon/R/ZoonFigshare.R
zoon/R/zoonHelpers.R
zoon/R/Replicate.R
zoon/R/print.zoonCitation.R
zoon/R/ZoonCitation.R
zoon/R/print.zoonWorkflow.R
zoon/R/workflow.R
zoon/R/DoModuleFunctions.R
zoon/R/RerunWorkflow.R
zoon/R/summary.zoonWorkflow.R
zoon/R/DataDocumentation.R
zoon/R/BuildModule.R
zoon/R/zzz.R
zoon/vignettes
zoon/vignettes/building_occ6-1.png
zoon/vignettes/building_cov4-1.png
zoon/vignettes/building_pro6-7.png
zoon/vignettes/building_pro7-1.png
zoon/vignettes/building_mod6-4.png
zoon/vignettes/building_out9-2.png
zoon/vignettes/basic_5-1.png
zoon/vignettes/occurrenceInOut.svg
zoon/vignettes/building_cov5-1.png
zoon/vignettes/building_out8-2.png
zoon/vignettes/building_pro6-6.png
zoon/vignettes/buliding_pro1a-1.png
zoon/vignettes/building_occ7-1.png
zoon/vignettes/building_pro1-1.png
zoon/vignettes/building_out7-2.png
zoon/vignettes/modelInOut.svg
zoon/vignettes/basic_12-2.png
zoon/vignettes/building_pro6-8.png
zoon/vignettes/building_cov5-4.png
zoon/vignettes/building_out8-1.png
zoon/vignettes/building_mod6-1.png
zoon/vignettes/covariateInOut.svg
zoon/vignettes/building_mod6-2.png
zoon/vignettes/building_pro6-2.png
zoon/vignettes/building_out8-3.png
zoon/vignettes/interactive_output-1.png
zoon/vignettes/building_cov5-2.png
zoon/vignettes/basic-zoon-usage.Rmd
zoon/vignettes/building_pro5-1.png
zoon/vignettes/building_mod7-1.png
zoon/vignettes/basic_11-1.png
zoon/vignettes/basic_11-2.png
zoon/vignettes/building_occ7-2.png
zoon/vignettes/processInOut.svg
zoon/vignettes/building_out7-1.png
zoon/vignettes/building_mod6-3.png
zoon/vignettes/building_pro6-9.png
zoon/vignettes/building_pro6-4.png
zoon/vignettes/building_cov5-3.png
zoon/vignettes/basic_12-3.png
zoon/vignettes/basic_15-1.png
zoon/vignettes/interactive_zoon_usage.Rmd
zoon/vignettes/building_pro6-3.png
zoon/vignettes/building_pro6-5.png
zoon/vignettes/interactive_noninteractive-1.png
zoon/vignettes/building_pro6-1.png
zoon/vignettes/Building_a_module.Rmd
zoon/vignettes/outputInOut.svg
zoon/vignettes/building_out9-1.png
zoon/vignettes/interactive_cross_validation-1.png
zoon/vignettes/basic_12-1.png
zoon/MD5
zoon/build
zoon/build/vignette.rds
zoon/DESCRIPTION
zoon/man
zoon/man/Chain.Rd
zoon/man/FrescaloBias.Rd
zoon/man/workflow.Rd
zoon/man/AplumbeusOcc.Rd
zoon/man/UKAirRas.Rd
zoon/man/ChangeWorkflow.Rd
zoon/man/zoon.Rd
zoon/man/plot.zoonWorkflow.Rd
zoon/man/GetPackage.Rd
zoon/man/print.zoonWorkflow.Rd
zoon/man/print.zoonCitation.Rd
zoon/man/ModuleHelp.Rd
zoon/man/BuildModule.Rd
zoon/man/ZoonModuleParse.Rd
zoon/man/RunModels.Rd
zoon/man/print.Summary.Rd
zoon/man/Replicate.Rd
zoon/man/GetMaxEnt.Rd
zoon/man/RerunWorkflow.Rd
zoon/man/ZoonPredict.Rd
zoon/man/ZoonModel.Rd
zoon/man/ZoonCitation.Rd
zoon/man/CWBZim.Rd
zoon/man/Occurrence.Rd
zoon/man/LoadModule.Rd
zoon/man/summary.zoonWorkflow.Rd
zoon/man/ExtractAndCombData.Rd
zoon/man/GetModuleList.Rd
zoon/man/ZoonFigshare.Rd
zoon/LICENSE