Description Usage Arguments Value Details Author(s) Examples

View source: R/stackedsdm_s3.R

Calculate residuals from a stackedsdm object

1 2 |

`object` |
An object of class |

`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 |

A matrix of residuals

Calculated the residuals from `stackedsdm`

object.

Francis K.C. Hui <francis.hui@anu.edu.au>.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ```
X <- as.data.frame(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)
``` |

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