Files in akeyel/spatialdemography
A Spatially Explicit Metacommunity Model
.Rbuildignore
.Rproj.user/B77A4777/build_options
.Rproj.user/B77A4777/pcs/files-pane.pper
.Rproj.user/B77A4777/pcs/source-pane.pper
.Rproj.user/B77A4777/pcs/windowlayoutstate.pper
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.Rproj.user/B77A4777/sdb/per/t/EAB1D106
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.Rproj.user/B77A4777/sdb/prop/378C62E2
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.Rproj.user/B77A4777/sdb/prop/F78FA8B5
.Rproj.user/B77A4777/sdb/prop/INDEX
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/.Rhistory
R/sdhelper.r
R/simulation.r
R/spatialdemography.r
README.md
inst/test/.Rhistory
inst/test/RunLog.csv
inst/test/SeedTokenTestRun1_1.RData
inst/test/SeedTokenTestRun1_2.RData
inst/test/SeedTokenTestRun1_3.RData
inst/test/SeedTokenTestRun2_1.RData
inst/test/SeedTokenTestRun2_2.RData
inst/test/SeedTokenTestRun2_3.RData
inst/test/dt/funct1_mean_0.14_sd_1_Nsim_1000000_Dispersal_Probabilities.csv
inst/test/dt/funct1_mean_0.14_sd_1_Nsim_1000_Dispersal_Probabilities.csv
inst/test/dt/funct1_mean_0.4_sd_0.4_Nsim_1000000_Dispersal_Probabilities.csv
inst/test/dt/test.txt
inst/test/functiontests.r
inst/test/test_spatialdemography.r
inst/test/testfiles/tr1/ENL_TestRun1.csv
inst/test/testfiles/tr1/INC_TestRun1.csv
inst/test/testfiles/tr1/SET_TestRun1.csv
inst/test/testfiles/tr1/SPI_TestRun1.csv
inst/test/testfiles/tr1/SRI_TestRun1.csv
inst/test/testfiles/tr2/ELF_grazing_scn1.csv
inst/test/testfiles/tr2/ELF_landcover_scn1.csv
inst/test/testfiles/tr2/ELF_mowing_scn1.csv
inst/test/testfiles/tr2/ENL_TestRun2.csv
inst/test/testfiles/tr2/INC_TestRun2.csv
inst/test/testfiles/tr2/LOC_TestRun2.csv
inst/test/testfiles/tr2/SET_TestRun2.csv
inst/test/testfiles/tr2/SPF_TestRun2.csv
inst/test/testfiles/tr3/Initial_conditions_TestRun3.csv
inst/test/testfiles/tr3/Settings_TestRun3.csv
man-roxygen/mycitation.R
man-roxygen/stochasticplants.R
man/Connectance.Rd
man/CreateCompositeDemographyMatrix.Rd
man/CreateCompositeDispersalMatrix.Rd
man/CreatePermutationMatrix.Rd
man/DFRF.Rd
man/Digit.Rd
man/ForEach.Rd
man/GetTimes.Rd
man/IA.recode.Rd
man/OccSetup.Rd
man/Results.Outputs.Rd
man/Simulation.Rd
man/SpatialDemography.Rd
man/Ztrans.Rd
man/absorbing.edge.Rd
man/absorbing.lookup.Rd
man/as.num.Rd
man/assign.loop.Rd
man/assign.spp.v2.Rd
man/assign.spp.v3.Rd
man/calc.beta.Rd
man/calc.delta.metrics.Rd
man/calc.delta.metrics.v2.Rd
man/calc.fd.Rd
man/calc.metrics.Rd
man/calc.metrics.v2.Rd
man/calculate.traits.Rd
man/cell.occupancy.Rd
man/cell.size.Rd
man/change.check.Rd
man/change.cover.my.env.Rd
man/change.lookup.Rd
man/change.transition.rates.Rd
man/check.coords.Rd
man/check.cum.Rd
man/check.inputs.Rd
man/check.outputs.Rd
man/check.packages.Rd
man/check.spp.Rd
man/chk.file.Rd
man/compile.log.lambdas.Rd
man/compute.diagnostics.Rd
man/compute.funct.Rd
man/compute.microsites.Rd
man/create.stochastic.landscape.Rd
man/cv.setup.Rd
man/disp.lookup.v2.Rd
man/do.competition.Rd
man/do.copula.Rd
man/do.env.change.Rd
man/do.input.rename.Rd
man/do.invasion.Rd
man/do.spot.chk.Rd
man/do.standard.checks.Rd
man/do.thinning.Rd
man/do.warn.Rd
man/do.z.transform.Rd
man/drop.partial.Rd
man/env.change.type.Rd
man/env.file.Rd
man/env.param.file.Rd
man/env.type.Rd
man/ethreshold.Rd
man/extract.message.Rd
man/extract.scale.cells.Rd
man/find.disp.Rd
man/force.hibernate.Rd
man/gen.spp.Rd
man/get.adj.pos.Rd
man/get.base.env.lyr.Rd
man/get.cond.env.lyr.Rd
man/get.cors.Rd
man/get.cov.Rd
man/get.disp.prob.Rd
man/get.env.lyr.Rd
man/get.log.lambda.Rd
man/get.mod.Rd
man/get.positions.Rd
man/get.vrs.Rd
man/get.x.Rd
man/getfd.Rd
man/gettime.Rd
man/id.extract.Rd
man/import.env.lyr.Rd
man/initial.conditions.file.Rd
man/is.ergodic.Rd
man/is.irreducible.Rd
man/landscape.files.Rd
man/landscape.object.Rd
man/landscape.wide.matrix.Rd
man/listtotext.Rd
man/load.seed.Rd
man/local.matrix.summary.info.Rd
man/local.transition.matrices.Rd
man/locations.file.Rd
man/make.cum.Rd
man/make.disp.prob.v2.Rd
man/make.species.locs.Rd
man/markov.change.Rd
man/matrix.as.vector.Rd
man/old.style.locs.Rd
man/out.metrics.Rd
man/overall.matrix.diagnostics.Rd
man/patch.assign.v2.Rd
man/prep.output.Rd
man/read.landscape.lyr.Rd
man/recode.Rd
man/results.file.Rd
man/rl.cat.Rd
man/s.a.check.Rd
man/sample.fixed.Rd
man/save.seed.Rd
man/scale.vec.Rd
man/scenario.timing.Rd
man/scl.subset.Rd
man/sdr.lookup.Rd
man/settings.file.Rd
man/setup.abund.Rd
man/setup.copula.Rd
man/setup.env.change.mag.Rd
man/setup.env.info.Rd
man/setup.inputs.Rd
man/setup.locations.Rd
man/setup.matrices.Rd
man/setup.results.Rd
man/setup.results.v2.Rd
man/setup.rtd.Rd
man/sp.file.Rd
man/sp.instr.file.Rd
man/sp.param.file.Rd
man/sp.resp.instr.file.Rd
man/sp.vals.Rd
man/spatialdemography_package.Rd
man/species.statistics.Rd
man/spp.subset.Rd
man/stage.abundances.Rd
man/stoch.plant.setup.Rd
man/target.recode.Rd
man/test.setup.Rd
man/torus.edge.Rd
man/validity.check.Rd
man/write.env.lyr.Rd
man/write.sp.data.Rd
man/write.sp.hdr.data.Rd
man/wrt.Rd
spatialdemography.Rproj
vignettes/.RData
vignettes/.Rhistory
vignettes/Example1.Rmd
vignettes/Example1.html
vignettes/Example1.pdf
vignettes/Example2.Rmd
vignettes/Example2.html
vignettes/LifeCycleGraph_small.tif
vignettes/Timing.R
vignettes/Timing.Rmd
vignettes/Timing.html
vignettes/Timing.md
vignettes/dt/funct1_mean_0.14_sd_1_Nsim_1000000_Dispersal_Probabilities.csv
vignettes/dt/funct1_mean_0.4_sd_0.4_Nsim_1000000_Dispersal_Probabilities.csv
vignettes/spdem_ex1/Example1/.Rhistory
vignettes/spdem_ex1/Example1/Cells_occupied.csv
vignettes/spdem_ex1/Example1/Diagnostics/AMatrices.csv
vignettes/spdem_ex1/Example1/Diagnostics/AMatricesSummaries.csv
vignettes/spdem_ex1/Example1/Diagnostics/MatrixDiagnostics.csv
vignettes/spdem_ex1/Example1/Diagnostics/TransitionMatrices.csv
vignettes/spdem_ex1/Example1/LogLambda.csv
vignettes/spdem_ex1/Example1/SpeciesData.csv
vignettes/spdem_ex1/Example1/SpeciesStats_Adults_v2.csv
vignettes/spdem_ex1/Example1/SpeciesStats_All_v2.csv
vignettes/spdem_ex1/Example1/SpeciesStats_Juvs.csv
vignettes/spdem_ex1/Example1/SpeciesStats_Seeds.csv
vignettes/spdem_ex1/Example1/change_count_lookup.csv
vignettes/spdem_ex1/Species/Species_spdem_ex1.csv
vignettes/spdem_ex1/inputs/Environmental_layers_spdem_ex1.csv
vignettes/spdem_ex1/inputs/Initial_conditions_spdem_ex1.csv
vignettes/spdem_ex1/inputs/Settings_spdem_ex1.csv
vignettes/spdem_ex1/inputs/locations_spdem_ex1.csv
vignettes/spdem_ex1/landscape/herbicide_scn1.csv
vignettes/spdem_ex1/landscape/landcover_.csv
vignettes/spdem_ex1/landscape/landcover__Example1.csv
vignettes/spdem_ex1/landscape/landcover_scn1.csv
vignettes/spdem_ex1/outputs/Results_spdem_ex1.csv
vignettes/spdem_ex1/outputs/Timefile_Example1.csv
vignettes/spdem_ex2/Example2_1/Cells_occupied.csv
vignettes/spdem_ex2/Example2_1/Diagnostics/AMatrices.csv
vignettes/spdem_ex2/Example2_1/Diagnostics/AMatricesSummaries.csv
vignettes/spdem_ex2/Example2_1/Diagnostics/MatrixDiagnostics.csv
vignettes/spdem_ex2/Example2_1/Diagnostics/TransitionMatrices.csv
vignettes/spdem_ex2/Example2_1/LogLambda.csv
vignettes/spdem_ex2/Example2_1/SpeciesData.csv
vignettes/spdem_ex2/Example2_1/SpeciesStats_Adults_v2.csv
vignettes/spdem_ex2/Example2_1/SpeciesStats_All_v2.csv
vignettes/spdem_ex2/Example2_1/SpeciesStats_Juvs.csv
vignettes/spdem_ex2/Example2_1/SpeciesStats_Seeds.csv
vignettes/spdem_ex2/Example2_1/change_count_lookup.csv
vignettes/spdem_ex2/Example2_10/Cells_occupied.csv
vignettes/spdem_ex2/Example2_10/Diagnostics/AMatrices.csv
vignettes/spdem_ex2/Example2_10/Diagnostics/AMatricesSummaries.csv
vignettes/spdem_ex2/Example2_10/Diagnostics/MatrixDiagnostics.csv
vignettes/spdem_ex2/Example2_10/Diagnostics/TransitionMatrices.csv
vignettes/spdem_ex2/Example2_10/LogLambda.csv
vignettes/spdem_ex2/Example2_10/SpeciesData.csv
vignettes/spdem_ex2/Example2_10/SpeciesStats_Adults_v2.csv
vignettes/spdem_ex2/Example2_10/SpeciesStats_All_v2.csv
vignettes/spdem_ex2/Example2_10/SpeciesStats_Juvs.csv
vignettes/spdem_ex2/Example2_10/SpeciesStats_Seeds.csv
vignettes/spdem_ex2/Example2_10/change_count_lookup.csv
vignettes/spdem_ex2/Example2_2/Cells_occupied.csv
vignettes/spdem_ex2/Example2_2/Diagnostics/AMatrices.csv
vignettes/spdem_ex2/Example2_2/Diagnostics/AMatricesSummaries.csv
vignettes/spdem_ex2/Example2_2/Diagnostics/MatrixDiagnostics.csv
vignettes/spdem_ex2/Example2_2/Diagnostics/TransitionMatrices.csv
vignettes/spdem_ex2/Example2_2/LogLambda.csv
vignettes/spdem_ex2/Example2_2/SpeciesData.csv
vignettes/spdem_ex2/Example2_2/SpeciesStats_Adults_v2.csv
vignettes/spdem_ex2/Example2_2/SpeciesStats_All_v2.csv
vignettes/spdem_ex2/Example2_2/SpeciesStats_Juvs.csv
vignettes/spdem_ex2/Example2_2/SpeciesStats_Seeds.csv
vignettes/spdem_ex2/Example2_2/change_count_lookup.csv
vignettes/spdem_ex2/Example2_3/Cells_occupied.csv
vignettes/spdem_ex2/Example2_3/Diagnostics/AMatrices.csv
vignettes/spdem_ex2/Example2_3/Diagnostics/AMatricesSummaries.csv
vignettes/spdem_ex2/Example2_3/Diagnostics/MatrixDiagnostics.csv
vignettes/spdem_ex2/Example2_3/Diagnostics/TransitionMatrices.csv
vignettes/spdem_ex2/Example2_3/LogLambda.csv
vignettes/spdem_ex2/Example2_3/SpeciesData.csv
vignettes/spdem_ex2/Example2_3/SpeciesStats_Adults_v2.csv
vignettes/spdem_ex2/Example2_3/SpeciesStats_All_v2.csv
vignettes/spdem_ex2/Example2_3/SpeciesStats_Juvs.csv
vignettes/spdem_ex2/Example2_3/SpeciesStats_Seeds.csv
vignettes/spdem_ex2/Example2_3/change_count_lookup.csv
vignettes/spdem_ex2/Example2_4/Cells_occupied.csv
vignettes/spdem_ex2/Example2_4/Diagnostics/AMatrices.csv
vignettes/spdem_ex2/Example2_4/Diagnostics/AMatricesSummaries.csv
vignettes/spdem_ex2/Example2_4/Diagnostics/MatrixDiagnostics.csv
vignettes/spdem_ex2/Example2_4/Diagnostics/TransitionMatrices.csv
vignettes/spdem_ex2/Example2_4/LogLambda.csv
vignettes/spdem_ex2/Example2_4/SpeciesData.csv
vignettes/spdem_ex2/Example2_4/SpeciesStats_Adults_v2.csv
vignettes/spdem_ex2/Example2_4/SpeciesStats_All_v2.csv
vignettes/spdem_ex2/Example2_4/SpeciesStats_Juvs.csv
vignettes/spdem_ex2/Example2_4/SpeciesStats_Seeds.csv
vignettes/spdem_ex2/Example2_4/change_count_lookup.csv
vignettes/spdem_ex2/Example2_5/Cells_occupied.csv
vignettes/spdem_ex2/Example2_5/Diagnostics/AMatrices.csv
vignettes/spdem_ex2/Example2_5/Diagnostics/AMatricesSummaries.csv
vignettes/spdem_ex2/Example2_5/Diagnostics/MatrixDiagnostics.csv
vignettes/spdem_ex2/Example2_5/Diagnostics/TransitionMatrices.csv
vignettes/spdem_ex2/Example2_5/LogLambda.csv
vignettes/spdem_ex2/Example2_5/SpeciesData.csv
vignettes/spdem_ex2/Example2_5/SpeciesStats_Adults_v2.csv
vignettes/spdem_ex2/Example2_5/SpeciesStats_All_v2.csv
vignettes/spdem_ex2/Example2_5/SpeciesStats_Juvs.csv
vignettes/spdem_ex2/Example2_5/SpeciesStats_Seeds.csv
vignettes/spdem_ex2/Example2_5/change_count_lookup.csv
vignettes/spdem_ex2/Example2_6/Cells_occupied.csv
vignettes/spdem_ex2/Example2_6/Diagnostics/AMatrices.csv
vignettes/spdem_ex2/Example2_6/Diagnostics/AMatricesSummaries.csv
vignettes/spdem_ex2/Example2_6/Diagnostics/MatrixDiagnostics.csv
vignettes/spdem_ex2/Example2_6/Diagnostics/TransitionMatrices.csv
vignettes/spdem_ex2/Example2_6/LogLambda.csv
vignettes/spdem_ex2/Example2_6/SpeciesData.csv
vignettes/spdem_ex2/Example2_6/SpeciesStats_Adults_v2.csv
vignettes/spdem_ex2/Example2_6/SpeciesStats_All_v2.csv
vignettes/spdem_ex2/Example2_6/SpeciesStats_Juvs.csv
vignettes/spdem_ex2/Example2_6/SpeciesStats_Seeds.csv
vignettes/spdem_ex2/Example2_6/change_count_lookup.csv
vignettes/spdem_ex2/Example2_7/Cells_occupied.csv
vignettes/spdem_ex2/Example2_7/Diagnostics/AMatrices.csv
vignettes/spdem_ex2/Example2_7/Diagnostics/AMatricesSummaries.csv
vignettes/spdem_ex2/Example2_7/Diagnostics/MatrixDiagnostics.csv
vignettes/spdem_ex2/Example2_7/Diagnostics/TransitionMatrices.csv
vignettes/spdem_ex2/Example2_7/LogLambda.csv
vignettes/spdem_ex2/Example2_7/SpeciesData.csv
vignettes/spdem_ex2/Example2_7/SpeciesStats_Adults_v2.csv
vignettes/spdem_ex2/Example2_7/SpeciesStats_All_v2.csv
vignettes/spdem_ex2/Example2_7/SpeciesStats_Juvs.csv
vignettes/spdem_ex2/Example2_7/SpeciesStats_Seeds.csv
vignettes/spdem_ex2/Example2_7/change_count_lookup.csv
vignettes/spdem_ex2/Example2_8/Cells_occupied.csv
vignettes/spdem_ex2/Example2_8/Diagnostics/AMatrices.csv
vignettes/spdem_ex2/Example2_8/Diagnostics/AMatricesSummaries.csv
vignettes/spdem_ex2/Example2_8/Diagnostics/MatrixDiagnostics.csv
vignettes/spdem_ex2/Example2_8/Diagnostics/TransitionMatrices.csv
vignettes/spdem_ex2/Example2_8/LogLambda.csv
vignettes/spdem_ex2/Example2_8/SpeciesData.csv
vignettes/spdem_ex2/Example2_8/SpeciesStats_Adults_v2.csv
vignettes/spdem_ex2/Example2_8/SpeciesStats_All_v2.csv
vignettes/spdem_ex2/Example2_8/SpeciesStats_Juvs.csv
vignettes/spdem_ex2/Example2_8/SpeciesStats_Seeds.csv
vignettes/spdem_ex2/Example2_8/change_count_lookup.csv
vignettes/spdem_ex2/Example2_9/Cells_occupied.csv
vignettes/spdem_ex2/Example2_9/Diagnostics/AMatrices.csv
vignettes/spdem_ex2/Example2_9/Diagnostics/AMatricesSummaries.csv
vignettes/spdem_ex2/Example2_9/Diagnostics/MatrixDiagnostics.csv
vignettes/spdem_ex2/Example2_9/Diagnostics/TransitionMatrices.csv
vignettes/spdem_ex2/Example2_9/LogLambda.csv
vignettes/spdem_ex2/Example2_9/SpeciesData.csv
vignettes/spdem_ex2/Example2_9/SpeciesStats_Adults_v2.csv
vignettes/spdem_ex2/Example2_9/SpeciesStats_All_v2.csv
vignettes/spdem_ex2/Example2_9/SpeciesStats_Juvs.csv
vignettes/spdem_ex2/Example2_9/SpeciesStats_Seeds.csv
vignettes/spdem_ex2/Example2_9/change_count_lookup.csv
vignettes/spdem_ex2/Species/Species_spdem_ex2.csv
vignettes/spdem_ex2/inputs/Environmental_layers_spdem_ex2.csv
vignettes/spdem_ex2/inputs/Initial_conditions_spdem_ex2.csv
vignettes/spdem_ex2/inputs/Settings_spdem_ex2.csv
vignettes/spdem_ex2/inputs/locations_spdem_ex2.csv
vignettes/spdem_ex2/landscape/environmental_stochasticity__Example2_1.csv
vignettes/spdem_ex2/landscape/environmental_stochasticity__Example2_10.csv
vignettes/spdem_ex2/landscape/environmental_stochasticity__Example2_2.csv
vignettes/spdem_ex2/landscape/environmental_stochasticity__Example2_3.csv
vignettes/spdem_ex2/landscape/environmental_stochasticity__Example2_4.csv
vignettes/spdem_ex2/landscape/environmental_stochasticity__Example2_5.csv
vignettes/spdem_ex2/landscape/environmental_stochasticity__Example2_6.csv
vignettes/spdem_ex2/landscape/environmental_stochasticity__Example2_7.csv
vignettes/spdem_ex2/landscape/environmental_stochasticity__Example2_8.csv
vignettes/spdem_ex2/landscape/environmental_stochasticity__Example2_9.csv
vignettes/spdem_ex2/landscape/environmental_stochasticity_scn1.csv
vignettes/spdem_ex2/landscape/herbicide_scn1.csv
vignettes/spdem_ex2/landscape/landcover__Example2_1.csv
vignettes/spdem_ex2/landscape/landcover__Example2_10.csv
vignettes/spdem_ex2/landscape/landcover__Example2_2.csv
vignettes/spdem_ex2/landscape/landcover__Example2_3.csv
vignettes/spdem_ex2/landscape/landcover__Example2_4.csv
vignettes/spdem_ex2/landscape/landcover__Example2_5.csv
vignettes/spdem_ex2/landscape/landcover__Example2_6.csv
vignettes/spdem_ex2/landscape/landcover__Example2_7.csv
vignettes/spdem_ex2/landscape/landcover__Example2_8.csv
vignettes/spdem_ex2/landscape/landcover__Example2_9.csv
vignettes/spdem_ex2/landscape/landcover_scn1.csv
vignettes/spdem_ex2/landscape/microhabitat_stochasticity__Example2_1.csv
vignettes/spdem_ex2/landscape/microhabitat_stochasticity__Example2_10.csv
vignettes/spdem_ex2/landscape/microhabitat_stochasticity__Example2_2.csv
vignettes/spdem_ex2/landscape/microhabitat_stochasticity__Example2_3.csv
vignettes/spdem_ex2/landscape/microhabitat_stochasticity__Example2_4.csv
vignettes/spdem_ex2/landscape/microhabitat_stochasticity__Example2_5.csv
vignettes/spdem_ex2/landscape/microhabitat_stochasticity__Example2_6.csv
vignettes/spdem_ex2/landscape/microhabitat_stochasticity__Example2_7.csv
vignettes/spdem_ex2/landscape/microhabitat_stochasticity__Example2_8.csv
vignettes/spdem_ex2/landscape/microhabitat_stochasticity__Example2_9.csv
vignettes/spdem_ex2/landscape/microhabitat_stochasticity_scn1.csv
vignettes/spdem_ex2/outputs/Results_spdem_ex2.csv
vignettes/spdem_ex2/outputs/Timefile.csv
vignettes/spdem_timing/Species/species_file_spdem_timing_scn1.csv
vignettes/spdem_timing/Timing1/change_count_lookup.csv
vignettes/spdem_timing/inputs/Environmental_layers_spdem_timing.csv
vignettes/spdem_timing/inputs/Species_instructions_spdem_timing.csv
vignettes/spdem_timing/inputs/Species_response_instr_spdem_timing.csv
vignettes/spdem_timing/outputs/Results_spdem_timing.csv
vignettes/spdem_timing/outputs/Timefile.csv
