Man pages for akeyel/spatialdemography
A Spatially Explicit Metacommunity Model
| absorbing.edge | Absorbing edge |
| absorbing.lookup | Lookup function, absorbing edge |
| as.num | As number |
| assign.loop | Assign loop |
| assign.spp.v2 | Assign species to the landscape (v2) |
| assign.spp.v3 | Assign species to the landscape (v3) |
| calc.beta | Calculate Beta Values |
| calc.delta.metrics | Calculate metric change |
| calc.delta.metrics.v2 | Calculate metric change |
| calc.fd | Calculate model functional diversity |
| calc.metrics | Calculate output metrics |
| calc.metrics.v2 | Calculate output metrics |
| calculate.traits | Calculate traits (stochastic plants) |
| cell.occupancy | Cell Occupancy |
| cell.size | Cell Size The size of the cell is determined by the... |
| change.check | Check for environmental change |
| change.cover.my.env | Update my.env settings |
| change.lookup | Change Lookup |
| change.transition.rates | Change Transition Rates |
| check.coords | Check coordinates |
| check.cum | Check that cumulative probabilities are correctly made |
| check.inputs | Check inputs |
| check.outputs | Check outputs |
| check.packages | Check for required packages |
| check.spp | Check species |
| chk.file | Check file |
| compile.log.lambdas | Write log lambdas to file |
| compute.diagnostics | Compute Diagnostics |
| compute.funct | Implement standard functions |
| compute.microsites | Compute number of available microsites |
| Connectance | Calculate distances between cells |
| CreateCompositeDemographyMatrix | Create a composite demography matrix |
| CreateCompositeDispersalMatrix | Create the composite dispersal matrix |
| CreatePermutationMatrix | Create Permutation Matrix |
| create.stochastic.landscape | Create stochastic landscape |
| cv.setup | Get conditioning layer |
| DFRF | Distribution and Response Functions |
| Digit | Digit |
| disp.lookup.v2 | Look up Dispersal Probabilities |
| do.competition | Implement seed competition |
| do.copula | Function to implement copula |
| do.env.change | Implement environmental change |
| do.input.rename | do.input.rename = Helper function to help with renaming |
| do.invasion | Implement invasion in MetaComeSE model |
| do.spot.chk | Spot check |
| do.standard.checks | Implement checks of data |
| do.thinning | Apply thinning law |
| do.warn | Issue warnings |
| do.z.transform | Calculate Z-transform |
| drop.partial | Drop fractional individuals |
| env.change.type | env.change.type & env.change.mag inputs |
| env.file | Environmental Layers File |
| env.param.file | Environmental Parameters File |
| env.type | env.type input |
| ethreshold | Simple function to apply an extinction threshold |
| extract.message | Give extraction message |
| extract.scale.cells | Extract Scale Cells |
| find.disp | Find Displacement |
| force.hibernate | Hibernate |
| ForEach | ForEach |
| gen.spp | Generate species |
| get.adj.pos | Get adjusted positions |
| get.base.env.lyr | Create base environmental layer |
| get.cond.env.lyr | Create conditional environmental layer |
| get.cors | Calculatae spearman correlations |
| get.cov | Calculate modified coefficient of varation |
| get.disp.prob | Get dispersal probabilities |
| get.env.lyr | Create environmental layer configuration |
| getfd | Calculate functional diversity (helper function to calc.fd) |
| get.log.lambda | Calculate log lambda and dispersion of log lambda |
| get.mod | Get Modifier |
| get.positions | get positions |
| gettime | Get Time |
| GetTimes | Get model timing |
| get.vrs | Get vital rates |
| get.x | Get x/y coordinate |
| IA.recode | Convert double T's to T, otherwise set to F |
| id.extract | ID Extract |
| import.env.lyr | Import environmental layer |
| initial.conditions.file | Initial Conditions File |
| is.ergodic | 2. TEST ERGODICITY OF A MATRIX |
| is.irreducible | 1. TEST REDUCIBILITY OF THE MATRIX |
| landscape.files | Landscape Files |
| landscape.object | The landscape object |
| landscape.wide.matrix | Landscape-wide Matrix |
| listtotext | List to text |
| load.seed | Load Seed |
| local.matrix.summary.info | Local Matrix Summary Info |
| local.transition.matrices | Local Transition Matrices |
| locations.file | Initial Species Locations File |
| make.cum | Make cumulative probabilities |
| make.disp.prob.v2 | Generate dispersal probabilities |
| make.species.locs | Make species locations element |
| markov.change | Markov change |
| matrix.as.vector | matrix.as.vector |
| OccSetup | Set up initial population sizes |
| old.style.locs | Original format for locations file |
| out.metrics | Calculated Metrics |
| overall.matrix.diagnostics | Overall Matrix Diagnostics |
| patch.assign.v2 | Patch level species assignment |
| prep.output | Prep diagnostic output |
| read.landscape.lyr | Read landscape layer |
| recode | Convert abundance to occupancy |
| results.file | Results File |
| Results.Outputs | Results Outputs |
| rl.cat | RunLog cat |
| s.a.check | Check species availability |
| sample.fixed | Sample (fixed) |
| save.seed | Save Seed |
| scale.vec | Setting the Scale of output results |
| scenario.timing | Scenario Timing |
| scl.subset | Create a subset for scale cells |
| sdr.lookup | Look up Seed Dispersal Ratio |
| settings.file | Settings File |
| setup.abund | Set up species abundances in the landscape |
| setup.copula | Function to set up copula |
| setup.env.change.mag | Setup env.change.mag |
| setup.env.info | Set up env.info variable |
| setup.inputs | Set up species and environmental inputs for stochastic plants... |
| setup.locations | Set up species locations in the landscape |
| setup.matrices | Set up model matrices |
| setup.results | Create results file |
| setup.results.v2 | Create results file in a new format |
| setup.rtd | Estimate Response Trait Diversity |
| Simulation | Function to run the simulation portion of SpatialDemography |
| SpatialDemography | SpatialDemography = Main function for running the spatially... |
| spatialdemography_package | MetaComeSE (package) |
| species.statistics | Species Statistics |
| sp.file | Species File |
| sp.instr.file | Species Instructions File |
| sp.param.file | Species Parameters File |
| spp.subset | Species subset |
| sp.resp.instr.file | Species Response Traits Instructions File |
| sp.vals | Species Values Input |
| stage.abundances | Stage Abundances |
| stoch.plant.setup | Stochastic Plants Setup |
| target.recode | Target recode |
| test.setup | Test Setup |
| torus.edge | Torus Edge |
| validity.check | Validity Check |
| write.env.lyr | Write environmental layer to file |
| write.sp.data | Write species locations to file |
| write.sp.hdr.data | Write header for species data |
| wrt | Write table for timing function |
| Ztrans | Z transform |
