Man pages for secr
Spatially Explicit Capture-Recapture
| addCovariates | Add Covariates to Mask or Traps |
| addSightings | Mark-resight Data |
| addTelemetry | Combine Telemetry and Detection Data |
| AICcompatible | Model Compatibility |
| AIC.secr | Compare SECR Models |
| as.data.frame | Coerce capthist to Data Frame or Array |
| as.mask | Coerce traps object to mask |
| as.popn | Coerce ppp object to popn |
| autoini | Initial Parameter Values for SECR |
| binCovariate | Add Binned Covariate |
| blackbear | Black Bear Hair Snag Dataset |
| capthist | Spatial Capture History Object |
| capthistfn | Dissect Spatial Capture History Object |
| chat | Overdispersion of Activity Centres |
| circular | Circular Probability |
| clone | Replicate Rows |
| closedN | Closed population estimates |
| closure | Closure tests |
| cluster | Detector Clustering |
| coef.secr | Coefficients of secr Object |
| collate | Array of Parameter Estimates |
| confint.secr | Profile Likelihood Confidence Intervals |
| contour | Contour Detection Probability |
| coulombe | House mouse live trapping data |
| covariates | Covariates Attribute |
| CV | Coefficient of Variation |
| DA | Convert Data To Or From BUGS Format |
| D.designdata | Construct Density Design Data |
| deermouse | Deermouse Live-trapping Datasets |
| deletemaskpoints | Edit Mask Points |
| DENSITY | Import or export data |
| derivedDsurface | Derived Absolute Density |
| derivedMS | Derived Parameters of Fitted SECR Model |
| details | Detail Specification for secr.fit |
| detectfn | Detection Functions |
| detector | Detector Type |
| deviance.secr | Deviance of fitted secr model and residual degrees of freedom |
| discretize | Rasterize Area Search or Transect Data |
| distancetotrap | Distance To Nearest Detector |
| Dsurface | Density Surfaces |
| ellipse.secr | Confidence Ellipses |
| empirical | Empirical Variance of H-T Density Estimate |
| esaPlot | Mask Buffer Diagnostic Plot |
| expected.n | Expected Number of Individuals |
| extractMoves | Simulated Movements |
| FAQ | Frequently Asked Questions, And Others |
| Fletcher.chat | Estimate overdispersion |
| fxi | Probability Density of Activity Centre |
| fxTotal | Activity Centres of Detected and Undetected Animals |
| gridcells | Construct Grid Cells |
| hcov | Hybrid Mixture Model |
| head | First or Last Part of an Object |
| homerange | Home Range Statistics |
| hornedlizard | Flat-tailed Horned Lizard Dataset |
| join | Combine or Split Sessions of capthist Object |
| kfn | Overlap Index |
| list.secr.fit | Fit Multiple SECR Models |
| LLsurface | Plot Likelihood Surface |
| logit | Logit Transformation |
| logmultinom | Multinomial Coefficient of SECR Likelihood |
| LRtest | Likelihood Ratio Test |
| make.capthist | Construct capthist Object |
| make.lacework | Construct Lacework Detector Design |
| make.mask | Build Habitat Mask |
| makeNewData | Create Default Design Data |
| make.spcosa | Construct Spatial Coverage Design |
| makeStart | Initial Parameter Values |
| make.systematic | Construct Systematic Detector Design |
| make.traps | Build Detector Array |
| make.tri | Build Detector Array on Triangular or Hexagonal Grid |
| manip | Work with Open Population data |
| mask | Mask Object |
| mask.check | Mask Diagnostics |
| MCgof | Monte Carlo Goodness-of-fit for SECR Models |
| MCgof.methods | Methods for MCgof Objects |
| modelAverage | Averaging of SECR Models Using Akaike's Information Criterion |
| ms | Multi-session Objects |
| nontarget | Non-target Data |
| occasionKey | Key to Petal Plot |
| ovenbird | Ovenbird Mist-netting Dataset |
| ovensong | Ovenbird Acoustic Dataset |
| OVpossum | Orongorongo Valley Brushtail Possums |
| Parallel | Multi-core Processing |
| pdot | Net Detection Probability |
| PG | Telemetry Fixes in Polygons |
| plot.capthist | Plot Detection Histories |
| plot.mask | Plot Habitat Mask, Density or Resource Surface |
| plotmaskedge | Outline Around Mask Cells |
| plot.popn | Plot Population Object |
| plot.secr | Plot Detection Functions |
| plot.traps | Plot traps Object |
| pmixProfileLL | Mixture Model Check |
| pointsInPolygon | Points Inside Polygon |
| polyarea | Area of Polygon(s) |
| popn | Population Object |
| possum | Brushtail Possum Trapping Dataset |
| predictDsurface | Predict Density Surface |
| predict.secr | SECR Model Predictions |
| print.capthist | Print Detections |
| print.secr | Print or Summarise secr Object |
| print.traps | Print Detectors |
| randomHabitat | Random Landscape |
| raster2 | Create a RasterLayer Object from Mask or Dsurface |
| rbind.capthist | Combine capthist Objects |
| rbind.popn | Combine popn Objects |
| rbind.traps | Combine traps Objects |
| read.mask | Read Habitat Mask From File |
| read.telemetry | Import Telemetry Fixes |
| read.traps | Read Detector Data From File |
| rectangularMask | Rectangular Mask |
| reduce | Combine Columns |
| reduce.capthist | Combine Occasions Or Detectors |
| region.N | Population Size |
| RMarkInput | Convert Data to RMark Input Format |
| RSE | RSE from Fitted Model |
| Rsurface | Smoothed Resource Surface |
| score.test | Score Test for SECR Models |
| secr-defunct | Defunct Functions in Package 'secr' |
| secrdemo | SECR Models Fitted to Demonstration Data |
| secr-deprecated | Deprecated Functions in Package 'secr' |
| secr.design.MS | Construct Detection Model Design Matrices and Lookups |
| secr.fit | Spatially Explicit Capture-Recapture |
| secr-internal | Internal Functions |
| secr-package | Spatially Explicit Capture-Recapture Models |
| secr.refit | Repeat or Resume Model Fit |
| secrRNG | Random Number Seed |
| secrtest | Goodness-of-fit Test Results |
| secr.test | Goodness-of-Fit Test |
| secr-version5 | Changes in 'secr' 5.0 |
| session | Session Vector |
| setNumThreads | Number of Threads |
| sharefactorlevels | Fix Inconsistent Covariates |
| sighting | Sighting Attributes |
| signal | Signal Fields |
| signalmatrix | Reformat Signal Data |
| sim.capthist | Simulate Detection Histories |
| sim.popn | Simulate 2-D Population |
| sim.secr | Simulate From Fitted secr Model |
| skink | Skink Pitfall Data |
| smooths | Smooth Terms in SECR Models |
| snip | Slice Transect Into Shorter Sections |
| sort | Sort Rows of capthist or mask Object |
| spacing | Detector or Mask Spacing |
| speed | Speed Tips |
| stoatDNA | Stoat DNA Data |
| strip.legend | Colour Strip Legend |
| subset.capthist | Subset or Split capthist Object |
| subset.mask | Subset, Split or Combine Mask Objects |
| subset.popn | Subset popn Object |
| subset.traps | Subset traps Object |
| suggest.buffer | Mask Buffer Width |
| summary.capthist | Summarise Detections |
| summary.mask | Summarise Habitat Mask |
| summary.popn | Summarise Simulated Population |
| summary.traps | Summarise Detector Array |
| timevaryingcov | Time-varying Covariates |
| transformations | Transform Point Array |
| trap.builder | Complex Detector Layouts |
| traps | Detector Array |
| trapsfn | Detector Attributes |
| trend | Density Trend |
| trim | Drop Unwanted List Components |
| troubleshooting | Problems in Fitting SECR Models |
| turnover | Specifying a Dynamic Population |
| updateCH | Update Old capthist Format |
| usage | Detector Usage |
| usagePlot | Plot usage, detections or sightings. |
| userdist | Non-Euclidean Distances |
| utility | Utility Functions |
| vcov.secr | Variance - Covariance Matrix of SECR Parameters |
| verify | Check SECR Data |
| write | Write Data to Text File |
| writeGPS | Upload to GPS |
