fixNoFishNodes: Modify basic JAGS model

In mackerman44/DABOM: Dam Adult Branch Occupancy Model

Modify basic JAGS model

Description

Takes the basic JAGS model and modifies it based on particular observations. Specifically, it fixes the detection probability of all nodes that had no observations to 0.

Usage

fixNoFishNodes(
  init_file = NULL,
  file_name = NULL,
  filter_ch = NULL,
  parent_child = NULL,
  configuration = NULL,
  by_origin = FALSE,
  fish_origin = NULL
)

Arguments

init_file	name (with file path) of basic JAGS model.
file_name	name (with file path) to save the model as.
filter_ch	filtered capture history as returned by the 'filterDetections()' function in the 'PITcleanr' package, which has then been verified by a user and all blank or NA 'user_keep_obs' entries have been completed.
parent_child	data frame with at least 'parent' and 'child' columns. Can be created with 'buildParentChild()' function in the 'PITcleanr' package.
configuration	is a data frame which assigns node names to unique SiteID, AntennaID, and site configuration ID combinations. One example can be built with the function 'buildConfig'
by_origin	should Dirichlet vectors be created for each fish origin separately ('TRUE'), or be common to all origins ('FALSE')? Default is 'FALSE'
fish_origin	tibble containing 'tag_code' and origin ("W" or "H") of every tag. If not supplied, every tag will be assigned "W".

Author(s)

Kevin See

Examples

fixNoFishNodes()

mackerman44/DABOM documentation built on April 3, 2024, 6:51 a.m.