predsumspeciesRV: Compute predicted distributions of number species detected

In sustainablefarms/msod: Multispecies Occupancy Detection Models

Compute predicted distributions of number species detected

Description

Uses discreteRV to compute distribution of number of species

Usage

predsumspeciesRV(
  fit,
  chains = NULL,
  UseFittedLV = TRUE,
  nLVsim = 100,
  type = "marginal",
  cl = NULL
)

predsumspeciesRV_newdata(
  fit,
  Xocc,
  Xobs = NULL,
  ModelSiteVars = NULL,
  chains = NULL,
  nLVsim = 100,
  type = "marginal",
  cl = NULL
)

sumspeciesRV_raw(
  Xocc,
  Xobs = NULL,
  ModelSite = NULL,
  numspecies,
  nlv,
  draws,
  useLVindraws = TRUE,
  nLVsim = NULL,
  cl = NULL
)

Arguments

fit	A runjags fitted object
chains	The chains of MCMC to use. Default is all chains.
UseFittedLV	If TRUE the fitted LV variables are used, if false then 100 LV values are simulated.
type	If "draws" then a list of distributions for each site and draw is returned If "marginal" then a single distribution for each site is returned and this distribution is marginalised over the draws.
cl	A cluster object created by parallel::makeCluster. If NULL no cluster is used.
Xocc	A matrix of occupancy covariates. Must have a single row. Columns correspond to covariates.
Xobs	A matrix of detection covariates, each row is a visit. If NULL then expected number of species in occupation is returned
theta	A vector of model parameters, labelled according to the BUGS labelling convention seen in runjags
lv.v	A matrix of LV values. Each column corresponds to a LV. To condition on specific LV values, provide a matrix of row 1.

Functions

• predsumspeciesRV_newdata: Distribution of species numbers for new ModelSite

• sumspeciesRV_raw: For raw model information. Returns distributions per draw.

Examples

fit <- readRDS("./tmpdata/7_3_02_clim_someclimate_year_woody500m_msnm_det1stO.rds")
indata <- readRDS("./private/data/clean/7_2_10_input_data.rds")
det_dist_2060 <- predsumspeciesRV_newdata(fit,
                         Xocc = indata$holdoutdata$Xocc[indata$holdoutdata$Xocc$ModelSiteID == 2060, , drop = FALSE],
                         Xobs = indata$holdoutdata$yXobs[indata$holdoutdata$yXobs$ModelSiteID == 2060, , drop = FALSE],
                         ModelSiteVars = "ModelSiteID")

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