zoon: Reproducible, Accessible & Shareable Species Distribution Modelling
Version 0.6

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.

Browse man pages Browse package API and functions Browse package files

AuthorTom August [aut, cre], Tim Lucas [aut], Nick Golding [aut], Emiel van Loon [ctb], Greg McInerny [aut]
Date of publication2017-01-12 15:13:42
MaintainerTom August <tomaug@ceh.ac.uk>
LicenseBSD_3_clause + file LICENSE
Version0.6
URL https://github.com/zoonproject/zoon
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("zoon")

Man pages

AplumbeusOcc: UK occurrence data for Anopheles plumbeus as taken from GBIF
BuildModule: BuildModule
cbindZoon: cbindZoon
Chain: Chain modules together
ChangeWorkflow: Change a workflow and rerun.
CombineRasters: Combine rasters
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.zoonCitation: A function to print zoonCitation
print.zoonWorkflow: A function to print a zoonWorkflow object
Replicate: Replicate a module multiple times
RerunWorkflow: Rerun a workflow object.
RunModels: RunModels
subsetColumnsZoon: subsetColumnsZoon
summary.zoonWorkflow: A function to summarize the output of a zoon workflow
TransformCRS: Change the CRS of occurrence data
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

Functions

AddDefaultParas Source code
AplumbeusOcc Man page
Boxed2 Source code
BuildModule Man page Source code
CWBZim Man page
CallLister Source code
Chain Man page Source code
ChangeWorkflow Man page Source code
CheckModList Source code
CombineRasters Man page Source code
Covariate Man page Source code
DisplayModuleHelp Source code
DoCovariateModule Source code
DoModelModules Source code
DoOccurrenceModule Source code
DoOutputModules Source code
DoProcessModules Source code
DownloadQuietly Source code
ErrorModule Source code
ExtractAndCombData Man page Source code
FormatModuleList Source code
FrescaloBias Man page
GetCex Source code
GetMaxEnt Man page Source code
GetModule Source code
GetModuleList Man page Source code
GetModuleVersion Source code
GetPackage Man page Source code
LapplyGetModule Source code
LoadModule Man page Source code
Model Man page Source code
ModuleHelp Man page Source code
ModuleLabels Source code
Occurrence Man page Source code
Output Man page Source code
PasteAndDep Source code
Process Man page Source code
Replicate Man page Source code
RerunWorkflow Man page Source code
RunModels Man page Source code
SortArgs Source code
SplitArgs Source code
SplitCall Source code
StringToCall Source code
TransformCRS Man page Source code
UKAirRas Man page
WriteWorkflowMetadata Source code
Writeable Source code
ZoonCitation Man page Source code
ZoonFigshare Man page Source code
ZoonModel Man page Source code
ZoonModuleParse Man page Source code
ZoonPredict Man page Source code
cbindZoon Man page Source code
covHTML Source code
covariateSummary Source code
htmlTable Source code
modHTML Source code
modelSummary Source code
occHTML Source code
occurrenceSummary Source code
onLoad Source code
outHTML Source code
outputSummary Source code
plot.zoonWorkflow Man page Source code
print.zoonCitation Man page Source code
print.zoonWorkflow Man page Source code
proHTML Source code
processSummary Source code
subsetColumnsZoon Man page Source code
summary.zoonWorkflow Man page Source code
summaryHTML Source code
test_module Source code
test_outputs Source code
test_parameters Source code
tryCatchModule Source code
tryCatchWorkflow Source code
workflow Man page Source code
zoon Man page
zoon-package Man page

Files

inst
inst/extdata
inst/extdata/data_PO.rdata
inst/extdata/data_PB.rdata
inst/extdata/myData.csv
inst/extdata/myRaster.grd
inst/extdata/myRaster.gri
inst/extdata/data_PA.rdata
inst/doc
inst/doc/basic-zoon-usage.html
inst/doc/interactive_zoon_usage.html
inst/doc/basic-zoon-usage.Rmd
inst/doc/interactive_zoon_usage.Rmd
inst/doc/Building_a_module.Rmd
inst/doc/Building_a_module.html
tests
tests/testthat
tests/testthat/testExtractAndCombData.R
tests/testthat/testWholeWorkflows.R
tests/testthat/testGetModule.R
tests/testthat/Rplots.pdf
tests/testthat/testCombineRasters.R
tests/testthat/testSortArgs.R
tests/testthat/testplot.zoonWorkflow.r
tests/testthat/testBuildModule.R
tests/testthat/testRunModules.R
tests/testthat/testTransformCRS.R
tests/testthat/testLoadModule.R
tests/testthat/testFormatModuleList.R
tests/testthat/testsubsetColumnsZoon.R
tests/testthat/testSplitCall.R
tests/testthat/testplot.zoonCitation.R
tests/testthat/testcbindZoon.R
tests/testthat/testaccessors.R
tests/testthat/testprint.zoonWorkflow.R
tests/testthat/testCheckModList.R
tests/testthat/testZoonCitation.R
tests/testthat/testErrorModule.R
tests/testthat/testChangeWorkflow.R
tests/testthat/testLapplyGetModule.R
tests/testthat/testGetModuleList.R
tests/testthat/testGetPackage.R
tests/testthat/testPasteAndDep.R
tests/testthat/testcall_path.R
tests/testthat/testSplitArgs.R
tests/testthat/testChain.R
tests/testthat/testsummary.zoonWorkflow.R
tests/testthat/testWriteWorkflowMetadata.R
tests/testthat/testGetMaxEnt.R
tests/testthat/testModuleHelp.R
tests/testthat/testReplicate.R
tests/testthat/testRerunWorkflow.R
tests/testthat/testtestModule.R
tests/test-all.R
NAMESPACE
data
data/CWBZim.rda
data/UKAir.rda
data/AplumbeusOcc.rda
data/FrescaloBias.rda
R
R/test_outputs.R
R/HelpFunctions.R
R/test_parameters.R
R/accessors.R
R/GetPackage.R
R/ZoonModuleParse.R
R/zoon.R
R/zoonPredict.R
R/SearchFunctions.R
R/ChangeWorkflow.R
R/plot.zoonWorkflow.R
R/test_module.R
R/WriteWorkflowMetadata.R
R/ZoonFigshare.R
R/zoonHelpers.R
R/Replicate.R
R/print.zoonCitation.R
R/ZoonCitation.R
R/print.zoonWorkflow.R
R/workflow.R
R/DoModuleFunctions.R
R/RerunWorkflow.R
R/attributeFunctions.R
R/CombineRasters.R
R/summary.zoonWorkflow.R
R/DataDocumentation.R
R/BuildModule.R
R/TransformCRS.R
R/zzz.R
vignettes
vignettes/building_occ6-1.png
vignettes/building_cov4-1.png
vignettes/building_pro6-7.png
vignettes/building_pro7-1.png
vignettes/building_mod6-4.png
vignettes/building_out9-2.png
vignettes/basic_5-1.png
vignettes/occurrenceInOut.svg
vignettes/building_cov5-1.png
vignettes/building_out8-2.png
vignettes/building_pro6-6.png
vignettes/buliding_pro1a-1.png
vignettes/building_occ7-1.png
vignettes/building_pro1-1.png
vignettes/building_out7-2.png
vignettes/modelInOut.svg
vignettes/basic_12-2.png
vignettes/building_pro6-8.png
vignettes/building_cov5-4.png
vignettes/building_out8-1.png
vignettes/building_mod6-1.png
vignettes/covariateInOut.svg
vignettes/building_mod6-2.png
vignettes/building_pro6-2.png
vignettes/building_out8-3.png
vignettes/interactive_output-1.png
vignettes/building_cov5-2.png
vignettes/basic-zoon-usage.Rmd
vignettes/building_pro5-1.png
vignettes/building_mod7-1.png
vignettes/basic_11-1.png
vignettes/basic_11-2.png
vignettes/building_occ7-2.png
vignettes/processInOut.svg
vignettes/building_out7-1.png
vignettes/building_mod6-3.png
vignettes/building_pro6-9.png
vignettes/building_pro6-4.png
vignettes/building_cov5-3.png
vignettes/basic_12-3.png
vignettes/basic_15-1.png
vignettes/interactive_zoon_usage.Rmd
vignettes/building_pro6-3.png
vignettes/building_pro6-5.png
vignettes/interactive_noninteractive-1.png
vignettes/building_pro6-1.png
vignettes/Building_a_module.Rmd
vignettes/outputInOut.svg
vignettes/building_out9-1.png
vignettes/interactive_cross_validation-1.png
vignettes/basic_12-1.png
MD5
build
build/vignette.rds
DESCRIPTION
man
man/Chain.Rd
man/FrescaloBias.Rd
man/workflow.Rd
man/AplumbeusOcc.Rd
man/UKAirRas.Rd
man/ChangeWorkflow.Rd
man/zoon.Rd
man/TransformCRS.Rd
man/plot.zoonWorkflow.Rd
man/GetPackage.Rd
man/cbindZoon.Rd
man/print.zoonWorkflow.Rd
man/print.zoonCitation.Rd
man/ModuleHelp.Rd
man/BuildModule.Rd
man/ZoonModuleParse.Rd
man/RunModels.Rd
man/Replicate.Rd
man/GetMaxEnt.Rd
man/RerunWorkflow.Rd
man/ZoonPredict.Rd
man/ZoonModel.Rd
man/CombineRasters.Rd
man/ZoonCitation.Rd
man/CWBZim.Rd
man/Occurrence.Rd
man/LoadModule.Rd
man/summary.zoonWorkflow.Rd
man/ExtractAndCombData.Rd
man/subsetColumnsZoon.Rd
man/GetModuleList.Rd
man/ZoonFigshare.Rd
LICENSE
zoon documentation built on May 19, 2017, 7:49 a.m.