This package contains MCMC algorithms in R and Rcpp for various SCR models, including the spatial partial identification model.

build.data | Format encounter data for SPIM or regular SCR. Open SPIM to... |

mcmc.2side | Spatial partial identity MCMC algorithm. |

mcmc.2side.ind | Run MCMC algorithm for the naive independence estimator. |

mcmc.2side.SCRIPP | Spatial partial identity MCMC algorithm with inhomogenous... |

mcmc.CatSPIM | Fit the categorical spatial partial identity model (catSPIM) |

mcmc.conCatSMR | Fit the conventional (marking process not modeled)... |

mcmc.conCatSMR.df | Fit the categorical spatial mark resight model with detection... |

mcmc.conCatSMR.natural | Fit the categorical spatial mark resight model for natural... |

mcmc.genCatSMR | Fit the generalized categorical spatial mark resight model |

mcmc.genCatSMR.df | Fit the generalized categorical spatial mark resight model... |

mcmc.genCatSMR.move | Fit the generalized categorical spatial mark resight model... |

mcmc.SCR | Run MCMC algorithm for basic SCR model. |

mcmc.SCRIPP | Run MCMC algorithm for SCR model with inhomogenous density... |

pID | Produce the posteriors for P(ID_L_i = ID_R_j) from the... |

SCR2DNAmcmc | Run MCMC algorithm for basic SCR model with 2 observation... |

SCR2DNAPPcheck | Calculate goodness of fit statistics for a model fit by... |

SCRPPcheck | Calculate goodness of fit statistics for a model fit by... |

sim2side | Simulate data from camera trap SCR study with partial... |

sim2side.plot | Plot trapping array and realized capture results of simulated... |

sim2sideSCRIPP | Simulate data from camera trap SCR study with inhomogenous... |

sim2sidetf | Simulate data from camera trap SCR study with partial... |

simCatSPIM | Simulate data from the categorical spatial partial identity... |

sim.conCatSMR | Simulate data from the conventional (no marking process)... |

sim.conCatSMR.df | Simulate data from the conventional (no marking process)... |

sim.genCatSMR | Simulate data from the generalized categorical spatial mark... |

sim.genCatSMR.df | Simulate data from the generalized categorical spatial mark... |

sim.genCatSMR.move | Simulate data from the generalized categorical spatial mark... |

simgenSPIM | Simulate data with potentially partial individual indentities |

simOpenAsySCR | Simulate data from a Open population SCR study. Update help... |

simOpenSPIM | Simulate data from open population SPIM. Update help file... |

simSCR | Simulate data from a SCR study |

simSCR2DNA | Simulate data from a SCR study with DNA collected from scat... |

simSCRIPP | Simulate data from camera trap SCR study with inhomogenous... |

simSCRtf | Simulate data from a SCR study and simulate a random trap... |

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