Program ATLAS 1.4: Active Tag Life Adjusted Survival

106 Pages·2012·2.02 MB·English

Program ATLAS 1.4:
Active Tag Life Adjusted Survival
James M. Lady, Peter Westhagen, John R. Skalski
Columbia Basin Research
School of Aquatic and Fishery Sciences
University of Washington
1325 4th Avenue, Suite 1820
Seattle, WA 98101-2509
Prepared for
U.S. Department of Energy
Bonneville Power Administration
Department of Fish and Wildlife
P.O. Box 3621
Portland, OR 97208-3621
Project No. 1989-107-00
Contract No. 00055454
and
U.S. Army Corps of Engineers
P.O. Box 2946
Portland, OR 97208-2946
Contract No. W9127N-06-D-0005 08
February 2012
ii
Contents
1 Introduction 1
2 ATLAS User Interface 3
2.1 File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.2 Edit Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.2.1 Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.2.2 Optimizer Settings . . . . . . . . . . . . . . . . . . . . . . . . 9
2.3 View Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3 Analysis With ATLAS 11
3.1 Capture History Data . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3.1.1 Define Release Groups . . . . . . . . . . . . . . . . . . . . . . 12
3.1.2 View Mixing . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
3.1.3 Select Downstream Sites . . . . . . . . . . . . . . . . . . . . . 12
3.1.4 Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3.1.5 Attribute Grouping . . . . . . . . . . . . . . . . . . . . . . . . 17
3.2 Tag Life Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.2.1 Fit Tag-Life Curves . . . . . . . . . . . . . . . . . . . . . . . . 19
3.2.2 Map Tag Life Data to Bins . . . . . . . . . . . . . . . . . . . . 25
3.2.3 Calculate Tag Correction Table . . . . . . . . . . . . . . . . . 26
3.2.4 View Tag Life Correction Table . . . . . . . . . . . . . . . . . 26
3.3 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
iii
iv CONTENTS
3.3.1 Closed Form Estimates . . . . . . . . . . . . . . . . . . . . . . 28
3.3.2 Modeled Survival Estimates . . . . . . . . . . . . . . . . . . . 28
3.3.3 Estimate Full Variance . . . . . . . . . . . . . . . . . . . . . . 37
3.3.4 Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
3.4 Multi-Run Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
4 Single-Release Study Design 45
4.1 Load Capture History Data . . . . . . . . . . . . . . . . . . . . . . . 45
4.2 Actual Single-Release Study Design . . . . . . . . . . . . . . . . . . . 47
4.2.1 Tag Corrections . . . . . . . . . . . . . . . . . . . . . . . . . . 47
4.3 Virtual Single-Release Study Design . . . . . . . . . . . . . . . . . . . 48
4.3.1 Closed Form Parameter Report . . . . . . . . . . . . . . . . . 53
4.3.2 Equate Parameters Across Releases . . . . . . . . . . . . . . . 53
4.3.3 Creating a Virtual Release . . . . . . . . . . . . . . . . . . . . 54
5 Paired-Release Study Design 59
5.1 Define Release Groups . . . . . . . . . . . . . . . . . . . . . . . . . . 59
5.2 Tag Corrections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
5.3 View Mixing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
5.4 Closed Form Parameter Report . . . . . . . . . . . . . . . . . . . . . 60
6 Virtual/Paired-Release Study Design 65
6.1 Define Release Groups . . . . . . . . . . . . . . . . . . . . . . . . . . 65
6.2 Tag Corrections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
6.3 View Mixing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
6.4 Closed Form Parameter Report . . . . . . . . . . . . . . . . . . . . . 66
6.5 Parameter Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
CONTENTS v
A Input Data Files 71
A.1 Capture History Data File . . . . . . . . . . . . . . . . . . . . . . . . 71
A.2 Attribute Group File . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
A.3 Tag-Life Data File . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
B Statistical Methods used in ATLAS 75
B.1 Tag-Life Analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
B.1.1 Parametric Failure-Time Distributions . . . . . . . . . . . . . 75
B.1.2 Nonparametric Method . . . . . . . . . . . . . . . . . . . . . . 77
B.1.3 Right-Censored Tag-Life Analyses . . . . . . . . . . . . . . . . 78
B.2 Tag-Life Adjusted Estimates of Survival . . . . . . . . . . . . . . . . 79
B.2.1 Single Release-Recapture Design . . . . . . . . . . . . . . . . . 80
B.2.2 Paired Release-Recapture Design . . . . . . . . . . . . . . . . 84
B.2.3 Virtual/Paired Release-Recapture Design . . . . . . . . . . . . 86
Glossary 91
Acronyms 93
References 96
vi CONTENTS
List of Figures
2.1 Initial dialog for study design selection . . . . . . . . . . . . . . . . . 3
2.2 Program ATLAS at initial startup in single-release mode . . . . . . . 5
2.3 The File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.4 The Edit Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.5 The General Settings dialog . . . . . . . . . . . . . . . . . . . . . . . 8
2.6 The Bootstrapping Settings dialog . . . . . . . . . . . . . . . . . . . . 8
2.7 The Optimizer Setup dialog . . . . . . . . . . . . . . . . . . . . . . . 9
2.8 The View Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3.1 Site Selection Dialog for a single-release study with four downstream
sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3.2 A portion of a Capture History Report . . . . . . . . . . . . . . . . . 14
3.3 Cormack-Jolly-Seber Report for a single-release study . . . . . . . . . 15
3.4 Cumulative CJS Report for a single-release study . . . . . . . . . . . 16
3.5 CJS Covariance Report . . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.6 Attribute Group Selection dialog for an attribute file with two attributes 18
3.7 The Navigation Panel after loading two tag-life files . . . . . . . . . . 19
3.8 Tag-Life Curve selection dialog . . . . . . . . . . . . . . . . . . . . . 20
3.9 Tag-Life Curve with arrival time distributions at a selected site . . . . 21
3.10 Tag-Life Curve with arrival time distributions for a selected release group 22
3.11 Tag-Life Curve with simulated data with outliers . . . . . . . . . . . 23
vii
viii LIST OF FIGURES
3.12 Tag-Life Curve after outliers have been excluded from the truncated
analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
3.13 Dialog for mapping tag-life curves to tag lots . . . . . . . . . . . . . . 25
3.14 Example of a Tag Correction Table for a virtual/paired-release study 27
3.15 Example of a Closed-Form Parameter Report for a single-release study 29
3.16 Equate parameter dialog for a paired-release study . . . . . . . . . . 31
3.17 Parameter Report with default configuration of no parameters equated
across releases for a paired-release study . . . . . . . . . . . . . . . . 32
3.18 Parameter Report with all possible parameters equated across releases
for a paired-release study. . . . . . . . . . . . . . . . . . . . . . . . . 33
3.19 Output window showing covariance estimation error after “Compute”
action. Note that the Direction Set (Powell’s) optimizer was used in
this example. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
3.20 Parameter Report after failure to estimate the covariance matrix . . . 34
3.21 Constrain Parameters with the Detection tab selected . . . . . . . . . 35
3.22 Output window after constraining parameters . . . . . . . . . . . . . 35
3.23 Parameter Report after successfully estimating the parameters and the
covariance matrix. Compare to Figure 3.20 . . . . . . . . . . . . . . . 36
3.24 Parameter Report after “Estimate Full Variance” action . . . . . . . 38
3.25 A portion of a Cumulative Parameter Report for a single-release study 39
3.26 A portion of a Parameter Covariance Report for a single-release study 40
3.27 Dialog for selecting the desired attributes in multi-run mode with a
subset of attrubutes selected . . . . . . . . . . . . . . . . . . . . . . . 41
3.28 Dialog for selecting desired output in multi-run mode . . . . . . . . . 43
3.29 Output files created in Multi-Run Mode . . . . . . . . . . . . . . . . 44
4.1 Actual single-release study with K detection sites . . . . . . . . . . . 45
4.2 Virtual single-release study with K detection sites . . . . . . . . . . . 46
4.3 Select Release Type dialog in single-release mode . . . . . . . . . . . 46
4.4 Dialog for selecting release(s) to be used in single-release study . . . . 47
4.5 Dialog for reviewing single-release study setup . . . . . . . . . . . . . 48
LIST OF FIGURES ix
4.6 Status Report after loading data with only one release for an actual
single-release study . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
4.7 Tag Correction Table for an actual single-release study . . . . . . . . 50
4.8 Status Report for a virtual single-release study. All three releases are
used in forming the virtual release V . . . . . . . . . . . . . . . . . . . 51
1
4.9 Example of a Tag Correction Table for a virtual single-release study . 52
4.10 ClosedFormParameterReportforasingle-releasestudyusingavirtual
release . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
4.11 Equate Parameters Across Releases with a virtual single-release with
three releases, default setting . . . . . . . . . . . . . . . . . . . . . . 54
4.12 Example of a Parameter Report for a single-release study, no parame-
ters equated across releases . . . . . . . . . . . . . . . . . . . . . . . . 55
4.13 Equate Parameters Across Releases for a virtual single-release study
with three releases, all parameters equated . . . . . . . . . . . . . . . 56
4.14 Example of a Parameter Report for a single-release study, all
parameters equated across releases . . . . . . . . . . . . . . . . . . . 57
5.1 Define Release Groups dialog for a paired-release study . . . . . . . . 60
5.2 Example of a Status Report for a paired-release study . . . . . . . . . 61
5.3 Example of a Tag Correction Table for a paired-release study . . . . . 62
5.4 View Mixing dialog for a paired-release study . . . . . . . . . . . . . 63
5.5 Example of a Closed Form Parameter Report for a paired-release study 64
6.1 Define Release Groups dialog for a virtual/paired-release study . . . . 66
6.2 Example of a Status Report for a virtual/paired-release study . . . . 67
6.3 Example of a Tag Correction Table for a virtual/paired-release study 68
6.4 View Mixing dialog for a virtual/paired-release study . . . . . . . . . 68
6.5 Example of a Closed Form Parameter Report for a virtual/paired-
release study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
6.6 Example of a Parameter Report for a virtual/paired-release study . . 70
A.1 Portion of a capture history data file . . . . . . . . . . . . . . . . . . 72
x LIST OF FIGURES
A.2 Top Portion of an Attribute Group File . . . . . . . . . . . . . . . . . 73
A.3 Portion of the tag-life data file . . . . . . . . . . . . . . . . . . . . . . 73
B.1 Schematic of a paired release-recapture design . . . . . . . . . . . . . 85
B.2 Schematic of the minimum design configuration to estimate dam pas-
sage survival based on a virtual release (i.e., V ), a paired release (R
1 2
and R ), and three downriver hydrophone arrays (shown as dotted
3
lines). At the dam face, a 3D hydrophone array is used to construct
the virtual release of fish known to have arrived at the dam. . . . . . 87