new_set: Create new parameter set

Description Usage Arguments

View source: R/main.R

Description

Create a new parameter set within an rgeoprofile_project. The new parameter set becomes the active set once created.

Usage

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new_set(
  project,
  spatial_prior = NULL,
  source_model = "uniform",
  name = "(no name)",
  sigma_model = "single",
  dispersal_model = "normal",
  sigma_prior_mean = 1,
  sigma_prior_sd = 1,
  expected_popsize_model = "single",
  expected_popsize_prior_mean = 1000,
  expected_popsize_prior_sd = 20,
  sentinel_radius = 0.2,
  n_binom = FALSE,
  alpha_prior_mean = 1,
  alpha_prior_sd = 100,
  weight_prior = 1
)

Arguments

project

an rgeoprofile_project, as produced by the function rgeoprofile_project().

spatial_prior

a raster file defining the spatial prior. Precision values are taken from this raster if it is defined.

source_model

choose prior type for source locations. Pick from "uniform" (default), "normal" (bivariate normal), "kernel" (KDE based on positive data) or "manual" (the current value of the raster)

name

an optional name for the parameter set.

sigma_model

set as "single" to assume the same dispersal distance for all sources, or "independent" to assume an independently drawn dispersal distance for each source.

dispersal_model

distribute points via a "normal", "cauchy" or "laplace" model

sigma_prior_mean

the prior mean of the parameter sigma (km).

sigma_prior_sd

the prior standard deviation of the parameter sigma (km). Set to 0 to use a fixed value for sigma (fixed at sigma_prior_mean).

expected_popsize_model

set as "single" to assume the same number of events for all sources, or "independent" to assume an independently drawn number of events for each source.

expected_popsize_prior_mean

the prior mean of the expected total population size.

expected_popsize_prior_sd

the prior standard deviation of the expected total population size. Set to 0 to use a fixed value (fixed at expected_popsize_prior_mean).

sentinel_radius

the observation radius of sentinel sites.

n_binom

set to true or false, decide if a negative binomial model should be run for a set of over-dispersed count data.

alpha_prior_mean

the prior mean alpha.

alpha_prior_sd

the prior standard deviation of alpha.

weight_prior

control the prior on weights for a point-pattern model


Michael-Stevens-27/silverblaze documentation built on May 28, 2021, 5:47 p.m.