AdjSurv.fn: Active Tag Life Adjusted Survival Model Fitting

In Columbia-Basin-Research-West/cbrATLAS: Active Tag Life Adjusted Survival Modeling

Active Tag Life Adjusted Survival Model Fitting

Description

This function analyzes release-recapture data from a study that uses active-tag technology. It estimates survival and detection probabilities and, if provided with tag-life data, the average probability a tag is active at each detection site. These estimates are then used to adjust estimated survival for potential tag-failure that may otherwise be interpreted as mortality. Methods are documented in Program ATLAS 1.4:Active Tag Life Adjusted Survival.

Usage

AdjSurv.fn(
  taghist.file,
  taghist.format = "atlas",
  taglife.file = NULL,
  taglife.model = NULL,
  num.release = 1,
  num.bootstrap = 250,
  adjust.cjs = T,
  rounding = 4,
  plot.taglife = T
)

Arguments

taghist.file	Required. Dataframe or a filename of .csv file with detection histories
taghist.format	Required. Format of tag detection histories "atlas" format based on Program ATLAS input files. Eight columns. Each tag has one line per possible detection site. "flat" format has one line per tag: tag.code, activation date, release date, and one column per detection site filled with first detection times at that site
taglife.file	Optional. Name of .csv file with taglife times in first column. Other columns ignored. Header expected
taglife.model	fc_obj. Failure time model object. (default = NULL). If no fc_obj is provided, function will try models available in failCompare and select best fit
num.release	(default = 1) If more than one release group, first column will be added to flat format file to denote group name (not implemented in this version)
num.bootstrap	(default = 1000) Number of resample iterations to estimate additional variance on survival estimates
adjust.cjs	(T|F) (default = T) adjust CJS estimates for estimated tag-life
rounding	(default = 4) Number of decimal places on estimate
plot.taglife	(T|F) (default = T) Plot the estimated tag-life curve

Details

All date-times are assumed to be character vector with format: "%m/%d/%Y %H:%M"

Value

Returns a list "out" with (if provided):

taghist

tagfile filename

unadjusted.cjs

table of unadjusted survival estimates

tagfile

tag life filename

taglife.model

taglife model name

mean.tag.pLive

expect proportion tags active to each site

adjust.cjs

adjusted survival estimates

Columbia-Basin-Research-West/cbrATLAS documentation built on April 1, 2022, 1:52 p.m.