residuals.stackedsdm: Calculate residuals from a stackedsdm object

In ecoCopula: Graphical Modelling and Ordination using Copulas

Calculate residuals from a stackedsdm object

Description

Calculate residuals from a stackedsdm object

Usage

## S3 method for class 'stackedsdm'
residuals(object, type = "dunnsmyth", seed = NULL, ...)

Arguments

object	An object of class stackedsdm;
type	Determined what type of residuals to calculate. The current options include Dunn-Smyth residuals (default; "dunnsmyth"), raw response residuals ("response") or probability integral transform residuals ("PIT");
seed	For Dunn-Smyth and PIT residuals applied to discrete responses, random jittering is added, and the seed can be used to seed to jittering.
...	not used

Value

A matrix of residuals

Details

Calculated the residuals from stackedsdm object.

Author(s)

Francis K.C. Hui <[e-mail]>.

Examples

X <- spider$x
abund <- spider$abund

# Example 1: Simple example
myfamily <- "negative.binomial"
# Example 1: Funkier example where Species are assumed to have different distributions
# Fit models including all covariates are linear terms, but exclude for bare sand
fit0 <- stackedsdm(abund, formula_X = ~. -bare.sand, data = X, family = myfamily, ncores=2) 
residuals(fit0)

# Example 2: Funkier example where Species are assumed to have different distributions
abund[,1:3] <- (abund[,1:3]>0)*1 # First three columns for presence absence
myfamily <- c(rep(c("binomial"), 3),
              rep(c("negative.binomial"), (ncol(abund)-3)))
fit0 <- stackedsdm(abund, formula_X = ~ bare.sand, data = X, family = myfamily, ncores=2)
residuals(fit0)

ecoCopula documentation built on March 18, 2022, 6:56 p.m.