summary.md
In occumb: Site Occupancy Modeling for Environmental DNA Metabarcoding

summary() has known output for occumbData

Code
  summary(data)
Output
  Sequence read counts: 
   Number of species, I = 2 
   Number of sites, J = 2 
   Maximum number of replicates per site, K = 2 
   Number of missing observations = 0 
   Number of replicates per site: 2 (average), 0 (sd) 
   Sequencing depth: 9 (average), 2.9 (sd)

  Species covariates: 
   cov1 (continuous) 
  Site covariates: 
   cov2 (continuous), cov3 (categorical) 
  Replicate covariates: 
   cov4 (continuous)

  Labels for species: 
   (None) 
  Labels for sites: 
   (None) 
  Labels for replicates: 
   (None)

summary() has known output for occumbFit

Code
  summary(occumb:::internal_fit)
Output
  Summary for an occumbFit object

  Summary of data:
   Number of species, I = 2 
   Number of sites, J = 2 
   Maximum number of replicates per site, K = 2 
   Number of missing observations = 0 
   Number of replicates per site: 2 (average), 0 (sd) 
   Sequencing depth: 9 (average), 2.9 (sd)

  Model specification:
   formula_phi:          ~ 1 
   formula_theta:        ~ 1 
   formula_psi:          ~ 1 
   formula_phi_shared:   ~ 1 
   formula_theta_shared: ~ 1 
   formula_psi_shared:   ~ 1 
   prior_prec:           1e-04 
   prior_ulim:           10000

  Saved parameters:
   Mu sigma rho alpha beta gamma phi theta psi z pi deviance

  MCMC ran for 0.001 minutes at time 2024-10-22 14:00:01.027647:
   For each of 1 chains:
    Adaptation:            100 iterations (sufficient)
    Burn-in:               10 iterations
    Thin rate:             1 iterations
    Total chain length:    120 iterations
    Posterior sample size: 10 draws

  Summary of posterior samples: 
   Mu: 
    Number of parameters: 3 
    Rhat:  (not available) 
    n.eff: (not available) 
   sigma: 
    Number of parameters: 3 
    Rhat:  (not available) 
    n.eff: (not available) 
   rho: 
    Number of parameters: 3 
    Rhat:  (not available) 
    n.eff: (not available) 
   alpha: 
    Number of parameters: 2 
    Rhat:  (not available) 
    n.eff: (not available) 
   beta: 
    Number of parameters: 2 
    Rhat:  (not available) 
    n.eff: (not available) 
   gamma: 
    Number of parameters: 2 
    Rhat:  (not available) 
    n.eff: (not available) 
   phi: 
    Number of parameters: 2 
    Rhat:  (not available) 
    n.eff: (not available) 
   theta: 
    Number of parameters: 2 
    Rhat:  (not available) 
    n.eff: (not available) 
   psi: 
    Number of parameters: 2 
    Rhat:  (not available) 
    n.eff: (not available) 
   z: 
    Number of parameters: 4 
    Rhat:  (not available) 
    n.eff: (not available) 
   pi: 
    Number of parameters: 8 
    Rhat:  (not available) 
    n.eff: (not available) 
   deviance: 
    Rhat:  (not available) 
    n.eff: (not available)

  **WARNING** Set n.chains > 1 to monitor Rhat and n.eff values.