AdjSurv.fn {cbrATLAS} | R Documentation |
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.
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 )
taghist.file |
Required. Dataframe or a filename of .csv file with detection histories |
taghist.format |
Required. Format of tag detection histories
|
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 |
All date-times are assumed to be character vector with format: "%m/%d/%Y %H:%M"
Returns a list "out" with (if provided):
tagfile filename
table of unadjusted survival estimates
tag life filename
taglife model name
expect proportion tags active to each site
adjusted survival estimates