DunnSmythResiduals: Dunn-Smyth Residuals for Detection and Occupancy for Fitted...

In sustainablefarms/linking-data: OBSOLETE: Linking Data Project R Package

Description

Dunn-Smyth Residuals for Detection and Occupancy for Fitted Models

Usage

ds_detection_residuals.fit(fit, type = "median", seed = NULL)

ds_occupancy_residuals.fit(
  fit,
  type = "median",
  seed = NULL,
  conditionalLV = TRUE
)

Arguments

fit	A fitted occupancy-detection model.
type	The type of point estimate to use for parameter estimates. See get_theta
seed	A seed to fix randomness of Dunn-Smyth residual jitter.

Value

A matrix, each row is a ModelSite and each column is a species. Detection residuals are only computed for species and sites that have at least one detection. Other values are NA.

A matrix, each row is a ModelSite and each column is a species.

Functions

• ds_detection_residuals.fit: Given a fitted occupancy detection model (variable names must match). Computes Dunn-Smyth residuals for detection, marginalising the latent variables.

• ds_occupancy_residuals.fit: Given a fitted occupancy detection model (variable names must match). Computes Dunn-Smyth residuals for occupancy, marginalising the latent variables.

References

D. I. Warton, J. Stoklosa, G. Guillera-Arroita, D. I. MacKenzie, and A. H. Welsh, "Graphical diagnostics for occupancy models with imperfect detection," Methods in Ecology and Evolution, vol. 8, no. 4, pp. 408-419, 2017, doi: 10.1111/2041-210X.12761.

Examples

fit <- readRDS("./tmpdata/7_2_10_clim_year.rds")
detection_resids <- ds_detection_residuals.fit(fit, type = "median")
occupancy_resids <- ds_occupancy_residuals.fit(fit, type = "median", conditionalLV = FALSE)

sustainablefarms/linking-data documentation built on Oct. 28, 2020, 2:41 a.m.