Simulate from covariate/metadata in the absence of a real data set (EXPERIMENTAL)

See vignette("sim", package = "glmmTMB") for more details and examples, and vignette("covstruct", package = "glmmTMB") for more information on the parameterization of different covariance structures.

Usage

simulate_new(
  object,
  nsim = 1,
  seed = NULL,
  family = gaussian,
  newdata,
  newparams = NULL,
  ...,
  return_val = c("sim", "pars", "object")
)

Arguments

object: a one-sided model formula (e.g. ~ a + b + c (peculiar naming is for consistency with the generic function, which typically takes a fitted model object)
nsim: number of simulations
seed: random-number seed
family: a family function, a character string naming a family function, or the result of a call to a family function (variance/link function) information. See family for a generic discussion of families or family_glmmTMB for details of glmmTMB-specific families.
newdata: a data frame containing all variables listed in the formula, including the response variable (which needs to fall within the domain of the conditional distribution, and should probably not be all zeros, but whose value is otherwise irrelevant)
newparams: a list of parameters containing sub-vectors (beta, betazi, betadisp, theta, etc.) to be used in the model. If b is specified in this list, then the conditional modes/BLUPs will be set to these values; otherwise they will be drawn from the appropriate Normal distribution. See vignette("covstruct", package = "glmmTMB") for details on the parameterizations used for various random-effects models (i.e., theta).
...: other arguments to glmmTMB (e.g. family)
return_val: what information to return: "sim" (the default) returns a list of vectors of simulated outcomes; "pars" returns the default parameter vector (this variant does not require newparams to be specified, and is useful for figuring out the appropriate dimensions of the different parameter vectors); "object" returns a fake glmmTMB object (useful, e.g., for retrieving the Z matrix (getME(simulate_new(...), "Z")) or covariance matrices (VarCorr(simulate_new(...))) implied by a particular set of input data and parameter values)

Details

Use the weights argument to set the size/number of trials per observation for binomial-type models; the default is 1 for every observation (i.e., Bernoulli trials)

Examples

## use Salamanders data for observational design and covariate values
## parameters used here are sensible, but do not fit the original data
params <- list(beta = c(2, 1),
               betazi = c(-0.5, 0.5), ## logit-linear model for zi
               betadisp = log(2), ## log(NB dispersion)
               theta = log(1)) ## log(among-site SD)
sim_count <- simulate_new(~ mined + (1|site),
             newdata = Salamanders,
             zi = ~ mined,
             family = nbinom2,
             seed = 101,
             newparams = params
)
## simulate_new with return="sim" always returns a list of response vectors
Salamanders$sim_count <- sim_count[[1]]    
summary(glmmTMB(sim_count ~ mined + (1|site), data=Salamanders, ziformula=~mined, family=nbinom2))
#>  Family: nbinom2  ( log )
#> Formula:          sim_count ~ mined + (1 | site)
#> Zero inflation:             ~mined
#> Data: Salamanders
#> 
#>       AIC       BIC    logLik -2*log(L)  df.resid 
#>    3324.1    3350.9   -1656.0    3312.1       638 
#> 
#> Random effects:
#> 
#> Conditional model:
#>  Groups Name        Variance Std.Dev.
#>  site   (Intercept) 0.669    0.8179  
#> Number of obs: 644, groups:  site, 23
#> 
#> Dispersion parameter for nbinom2 family (): 1.69 
#> 
#> Conditional model:
#>             Estimate Std. Error z value Pr(>|z|)    
#> (Intercept)   1.6481     0.2572   6.407 1.48e-10 ***
#> minedno       1.3861     0.3550   3.904 9.44e-05 ***
#> ---
#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
#> 
#> Zero-inflation model:
#>             Estimate Std. Error z value Pr(>|z|)    
#> (Intercept)  -0.7164     0.1510  -4.745 2.08e-06 ***
#> minedno       0.6331     0.1864   3.397 0.000682 ***
#> ---
#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
## return a glmmTMB object
sim_obj <- simulate_new(~ mined + (1|site),
            return_val = "object",
             newdata = Salamanders,
             zi = ~ mined,
             family = nbinom2,
             newparams = params)
## simulate Gaussian data, multivariate random effect
data("sleepstudy", package = "lme4")
sim_obj <- simulate_new(~ 1 + (1|Subject) + ar1(0 + factor(Days)|Subject),
             return_val = "pars",
             newdata = sleepstudy,
             family = gaussian,
             newparams = list(beta = c(280, 1),
                         betad = log(2), ## log(residual std err)
                         theta = c(log(2), ## log(SD(subject))
                                   log(2), ## log(SD(slope))
                                   ## AR1 correlation = 0.2
                                   put_cor(0.2, input_val = "vec"))
                         )
)
#> Warning: unmatched parameter names: betad
#> Warning: length mismatch in component beta (1 != 2); not setting
#> Warning: unmatched parameter names: betad
#> Warning: length mismatch in component beta (1 != 2); not setting
#> Warning: length mismatch in component betad (0 != 1); not setting

Simulate from covariate/metadata in the absence of a real data set (EXPERIMENTAL)

Usage

Arguments

Details

See also

Examples