poccupancy_margotherspecies.jsodm_lv: Prediction Summaries for jsodm_lv Model for New Sites

In sustainablefarms/msod: Multispecies Occupancy Detection Models

Prediction Summaries for jsodm_lv Model for New Sites

Description

Interesting summaries of predictions made by a fitted jsodm_lv. Includes occupancy probability of species independent of all other species, for each site, with error bars; expected species richness for single site;

Usage

poccupancy_margotherspecies.jsodm_lv(fit)

Arguments

Xocc	A matrix of unprocessed occupancy covariates. Each row is a site, each column a covariate.
occ.b	An array of occupancy covariate loadings. Each row is a species, each column a covariate, and each layer a draw from the posterior.

Examples

fit <- readRDS("../sflddata/private/data/testdata/cutfit_7_4_11_2LV.rds")
fit <- readRDS("../Experiments/7_4_modelrefinement/fittedmodels/7_4_13_model_2lv_e13.rds")
fit <- translatefit(fit)
Xocc <- sflddata::unstandardise.designmatprocess(fit$XoccProcess, fit$data$Xocc[1:5, , drop = FALSE])
fittmp <- supplant_new_data(fit, Xocc)
pocc <- poccupancy_margotherspecies.jsodm_lv(fittmp)
pocc <- poccupancy_margotherspeciespmaxsite.jsodm_lv(fittmp)
pocc <- poccupancy_mostfavourablesite.jsodm_lv(fittmp)
pocc <- poccupancy_randomsite.jsodm_lv(fittmp)
sprich1 <- occspecrichness.jsodm_lv(fittmp)
sprich <- occspecrichnessRV.jsodm_lv(fittmp)
system.time(sprich <- occspecrichness_avsite.jsodm_lv(fittmp))

sustainablefarms/msod documentation built on March 6, 2023, 7:17 a.m.