defineCapHistCols: Define Column Names for Capture History Matrix
In KevinSee/PITcleanr: Cleans up PIT tag capture histories

defineCapHistCols

R Documentation

Define Column Names for Capture History Matrix

Description

Based on a parent-child table, this returns a vector of column names to help create a consistent capture history matrix. By default, it will sort using the paths constructed from 'buildNodeOrder()'. If river kilometer ('rkm') is included as a column in the configuration file, this function could use that to help determine the column order.

Usage

defineCapHistCols(
  parent_child = NULL,
  configuration = NULL,
  use_rkm = FALSE,
  bottom_sites = NULL,
  incl_all_nodes = TRUE
)

Arguments

`parent_child`	parent-child table. Could be created from 'buildParentChild()' from 'PITcleanr' package.
`configuration`	configuration file. Could be created from 'buildConfig()' from 'PITcleanr' package.
`use_rkm`	if the river kilometer code exists in the configuration file (in a column named 'rkm'), use those codes to help establish the order of capture history columns. Default value is 'FALSE'.
`bottom_sites`	If provided, represents a character vector of sites to use as "bottom sites". All upstream sites of each bottom site will be grouped just after that bottom site in the capture history matrix.
`incl_all_nodes`	if some 'bottom_sites' are supplied, should all the nodes in the parent-child table be included (default is 'TRUE'), or only nodes upstream of those bottom sites be returned ('FALSE'). The initial site will always be returned. If no 'bottom_sites' are supplied, this is set to 'TRUE'.