getLVcorrMat {AHMbook} | R Documentation |

## Compute results of a Joint Species Distribution Model (JSDM)

### Description

Compute pairwise residual correlation in occurrence or abundance in a Joint Species Distribution Model (JSDM) with latent variables.

`getLVcorrMat`

computes the correlation matrix in residual occurrence or abundance in an latent-variable multi-species occupancy or N-mixture model which has been fit using MCMC (eg, in JAGS or WinBUGS). See Tobler et al. (2019) and Kéry & Royle (2021) chapter 8.

`getEcorrMat`

computes the correlation matrix for the coefficients of the observed environmental covariates.

### Usage

```
getLVcorrMat(lv.coef, type=c("occupancy", "Nmix"), stat=mean)
getEcorrMat(beta, stat=mean)
```

### Arguments

`lv.coef` |
MCMC chains for the coefficients of the latent variables, typically from the |

`beta` |
MCMC chains for the coefficients of the environment variables (excluding the intercept), typically from the |

`type` |
Indication of whether the model fit was for occupancy data (with a probit link) or an N-mixture model based on count data. |

`stat` |
The function used to summarize the MCMC chains for the correlations; if |

### Value

The relevant correlation matrix, species x species; if `stat = NULL`

, an array, iterations x species x species, with the MCMC chains.

### Author(s)

Mathias Tobler.

### References

Tobler, M. et al. (2019) Joint species distribution models with species correlations and imperfect detection. *Ecology*, 100(8), e02754.

Kéry, M. & Royle, J.A. (2021) *Applied Hierarchical Modeling in Ecology* AHM2 - 8.4.2 and 8.5.4.

*AHMbook*version 0.2.9 Index]