Calculate summary statistics for 'nomad_model' class

This function takes a nomad_model object and calculates summary statistics for the underlying mobility::mobility(). This is a wrapper function of MCMCvis::MCMCsummary that calculates summary statistics for each parameter in a mobility::mobility() object.

# S3 method for nomad_model
summary(object, probs = c(0.025, 0.975), ac_lags = c(5, 10), ...)

Arguments

object

a nomad_model() object containing the fitted mobility

probs

numeric vector giving the quantiles to calculate for each parameter (default = c(0.025, 0.5, 0.975))

ac_lags

numeric vector of lags over which to calculate autocorrelation of samples within chains (default = c(2,5,10))

...

further arguments passed to or from other methods

Value

a dataframe with summary statistics

Details

Summary statistics are calculated for all parameters across each chain along with convergance diagnosics like the Gelman-Rubin convergence diagnostic and (Rhat) and samples auto-correlation foreach parameter. If the model object contains deviance and penalty parameters, then Deviance Information Criterion (DIC) is calculated and appended to the summary.

See also

Other model: check(), compare(), fit_jags(), fit_prob_travel(), mobility(), predict(), residuals()

Author

John Giles

Examples

# Get nomad_model object
nmd_model <- nomad::model_db$zmb_cdr_2020_mod_dd_exp

# Check model fit
summary(nmd_model)
#>                  mean           sd         Q2.5        Q97.5 Rhat n.eff   AC5
#> delta    5.938836e+04 1.549880e+01 5.935755e+04 5.941836e+04 1.00  1899 -0.01
#> omega    9.111981e-01 2.835149e-04 9.106320e-01 9.117415e-01 1.00  1418 -0.01
#> tau      6.560246e-02 1.776256e-05 6.556752e-02 6.563678e-02 1.01  1239  0.02
#> theta    1.197415e+01 8.497188e-04 1.197248e+01 1.197584e+01 1.00  2256  0.00
#> DIC      7.632874e+07 5.146209e+01 7.632864e+07 7.632884e+07 1.00  1877 -0.01
#> deviance 7.632873e+07 5.146209e+01 7.632863e+07 7.632883e+07 1.00  1877 -0.01
#> pD       3.933670e+00           NA           NA           NA   NA    NA    NA
#>           AC10
#> delta     0.02
#> omega    -0.02
#> tau      -0.02
#> theta     0.01
#> DIC       0.02
#> deviance  0.02
#> pD          NA