Introduction to SECR | State and observation models | Distribution of home-range centres | Detection functions | Detector types | Outline of the package secr | How secr works | Model fitting and estimation | Habitat masks | Input | Output | Documentation | References | Appendix 1. Core functions of secr | Appendix 2. Classified index to secr functions

Introduction | Text formats - general | Capture data format | Detector layout format | Using read.capthist | When read.capthist is inadequate... | Reading Excel files | Other detector types | Count detectors | Signal detectors | Polygon and transect detectors | Telemetry | Mark--resight | Troubleshooting | References | Appendix: Glossary | Covariate | Detector | Identifier | Occasion | SECR | Session

Inverse prediction for capture--recapture estimation | Simple example | Proxy functions | Multi-session models | Fitting a density gradient | Non-target interference | Conditioning to minimise the effect of ghost individuals | Tuning the algorithm | Fractional designs | Models with extra parameters | Relationship to package secr | Troubleshooting and limitations | Sparse data | "simulations for box 1 did not reach target for proxy SE 0.002 " | "solution not found after 5 attempts" | References

Introduction | Dependence on other packages | Setup | Define populations | Unconditional (Poisson N(A)) | Conditional (fixed N(A)) | Examples using defined populations | Code for simulations in paper | Sampling only | Full model fits (suffix M) | Conditional model fits (suffix MCL) | Summaries | Cohesion | References | Appendix 1. Example | No model fit | Model fit | Appendix 2. Simulation summaries | No model | Model fitted | Model fitted, conditional likelihood | Complete cohesion | Finally...

Introduction | Theory | Simple example | Generating functions | randomDensity | randomGaussian | randomParents | Parameter combinations | Scaling to constant expected number | References

Introductory example | Linear habitat masks | Input from a polyline shapefile | Input from a SpatialLinesDataFrame | Input from a dataframe of coordinates | Input from a text file of coordinates | Network distance | Detector layouts | Simulating detection data | Model fitting | Advanced topics | Population size and effective sampling area | Linear habitat covariates | Discontinuities and traversable non-habitat | Linear home-range size | Evaluating study designs | Limitations, tips and troubleshooting | References | Appendix. Extended water vole example.

Outline | Model types | Data | Model specification and fitting | Parameterization | Features and limitations | Dipper example | A brief survey of open population capture--recapture models | CJS vs JS | Parameterization of recruitment in JSSA models | Conditional (PLB) vs full likelihood JSSA | Sufficient statistics vs capture histories | Robust design | Spatial vs nonspatial | Home-range shifts between primary sessions | Data structure and input | Stratification | Non-spatial openCR models | Parameters and model types | Non-spatial models using sufficient statistics | Spatial openCR models | Model formulae | Built-in predictors | User-provided covariates | More on modelling | Closed populations | Finite mixtures | Age | Sampling intervals | Custom design data | Transience | Factor coding | Mean of a parameter across levels of a factor | Movement models | Movement kernels | Zero-inflated kernels | User-defined kernel | Sparse kernels | Edge effects | Plotting and summary | Warnings | Settlement models | Derived parameters | Simulating open-population data | Troubleshooting | Nonidentifiability | Failure of numerical maximization | Starting values | Boundary estimates | Alternative algorithms | Step into infeasible parameter space | Number of iterations | Factor coding | Speed | Extras | Sampling variance warning | Example datasets | Testing assumptions | Limitations of openCR | Differences from secr | Relationship to other software | References | Appendix 1. Code for figures.