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Methods on a fitted gllvmTMB model

Source: R/methods-gllvmTMB.R
gllvmTMB_multi-methods.Rd

Standard model-object accessors for a multivariate fit returned by gllvmTMB(), whether the call started from wide traits(...) data or already-stacked long data. Internally the fit has class gllvmTMB_multi, which is what these S3 methods dispatch on, but you just call print(fit), summary(fit), logLik(fit) etc. as usual.

Usage

# S3 method for class 'gllvmTMB_multi'
print(x, ...)

# S3 method for class 'gllvmTMB_multi'
summary(object, ...)

# S3 method for class 'summary.gllvmTMB_multi'
print(x, digits = 3, ...)

# S3 method for class 'gllvmTMB_multi'
logLik(object, ...)

# S3 method for class 'gllvmTMB_multi'
nobs(object, ...)

Arguments

x, object

A fit returned by gllvmTMB().

...

Currently unused.

digits

Decimal digits in the printed summary. Default 3.

Details

  • print() shows the active covstructs, the number of fixed effects, and the converged log-likelihood.

  • summary() adds a fixed-effects table with SEs, the global and local trait correlation matrices, per-trait ICCs, and global / local communalities.

  • logLik() returns the converged maximum log-likelihood with df = length(opt$par) and nobs equal to the number of likelihood-contributing observed response cells, so AIC() and BIC() all work directly.

nobs() returns the number of likelihood-contributing observations – the observed-response cells. This equals fit$missing_data$counts$likelihood_rows and the nobs attribute of logLik(). Under the default miss_control(response = "drop") every fitted row is observed, so it equals length(fit$tmb_data$y); under response = "include" the masked rows are excluded. Original-row counts live in fit$missing_data, never in nobs().