sigma.glmmTMB {glmmTMB} | R Documentation |
Extract residual standard deviation or dispersion parameter
Description
For Gaussian models, sigma
returns the value of the residual
standard deviation; for other families, it returns the
dispersion parameter, however it is defined for that
particular family. See details for each family below.
Usage
## S3 method for class 'glmmTMB'
sigma(object, ...)
Arguments
object |
a “glmmTMB” fitted object |
... |
(ignored; for method compatibility) |
Details
The value returned varies by family:
- gaussian
returns the maximum likelihood estimate of the standard deviation (i.e., smaller than the results of
sigma(lm(...))
by a factor of (n-1)/n)- nbinom1
returns a dispersion parameter (usually denoted
as in Hardin and Hilbe (2007)): such that the variance equals
.
- nbinom2
returns a dispersion parameter (usually denoted
or
); in contrast to most other families, larger
corresponds to a lower variance which is
.
- Gamma
Internally, glmmTMB fits Gamma responses by fitting a mean and a shape parameter; sigma is estimated as (1/sqrt(shape)), which will typically be close (but not identical to) that estimated by
stats:::sigma.default
, which uses sqrt(deviance/df.residual)- beta
returns the value of
, where the conditional variance is
(i.e., increasing
decreases the variance.) This parameterization follows Ferrari and Cribari-Neto (2004) (and the
betareg
package):- betabinomial
This family uses the same parameterization (governing the Beta distribution that underlies the binomial probabilities) as
beta
.- genpois
returns the index of dispersion
, where the variance is
(Consul & Famoye 1992)
- compois
returns the value of
; when
, compois is equivalent to the Poisson distribution. There is no closed form equation for the variance, but it is approximately underdispersed when
and approximately overdispersed when
. In this implementation,
is exactly equal to the mean (Huang 2017), which differs from the COMPoissonReg package (Sellers & Lotze 2015).
- tweedie
returns the value of
, where the variance is
. The value of
can be extracted using
family_params
The most commonly used GLM families
(binomial
, poisson
) have fixed dispersion parameters which are
internally ignored.
References
Consul PC, and Famoye F (1992). "Generalized Poisson regression model. Communications in Statistics: Theory and Methods" 21:89–109.
Ferrari SLP, Cribari-Neto F (2004). "Beta Regression for Modelling Rates and Proportions." J. Appl. Stat. 31(7), 799-815.
Hardin JW & Hilbe JM (2007). "Generalized linear models and extensions." Stata press.
Huang A (2017). "Mean-parametrized Conway–Maxwell–Poisson regression models for dispersed counts. " Statistical Modelling 17(6), 1-22.
Sellers K & Lotze T (2015). "COMPoissonReg: Conway-Maxwell Poisson (COM-Poisson) Regression". R package version 0.3.5. https://CRAN.R-project.org/package=COMPoissonReg