META-X®-Software for Metapopulation Viability Analysis

197 Pages·2003·1.958 MB·English

by  Dr. Karin Frank, Professor Dr. Christian Wissel, Dr. Volker Grimm, Dr. Frank Köster, Dr. Helmut Lorek, Professor Dr. Michael Sonnenschein (auth.)

META-X®-Software for Metapopulation Viability Analysis
UFZ – Centre for Environmental Research Leipzig-Halle (Ed.)
Karin Frank Helmut Lorek Frank Köster Michael Sonnenschein
Christian Wissel Volker Grimm
Springer-Verlag Berlin Heidelberg GmbH
UFZ – Centre for Environmental Research Leipzig-Halle (Ed.)
Karin Frank Helmut Lorek Frank Köster
Michael Sonnenschein Christian Wissel Volker Grimm
META-X®-Software
for Metapopulation Viability
Analysis
123
Dr. Karin Frank
Professor Dr. Christian Wissel
Dr. Volker Grimm
UFZ – Centre for Environmental Research Leipzig-Halle
Dept. of Ecological Modelling
P.O. Box 500136
04301 Leipzig
Germany
Dr. Frank Köster
Carl von Ossietzky Universität Oldenburg
Fachbereich Informatik
Escherweg 2
26121 Oldenburg
Germany
Dr. Helmut Lorek
Math Consulting Group AG
Bahnhofsstrasse 17
6301 Zug
Switzerland
Professor Dr. Michael Sonnenschein
OFFIS – Oldenburg Research and Development Institute
for Computer Science Tools and Systems
Escherweg 2
26121 Oldenburg
Germany
Additional material to this book can be downloaded from http:// extras.springer.com.

ISBN 978-3-642-62906-8 ISBN 978-3-642-55723-1 (eBook)
DOI 10.1007/978-3-642-55723-1
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The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the
absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and
therefore free for general use.
Cover design: Erich Kirchner, Heidelberg
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Preface
The user-friendly META-X software for metapopulation viability analysis provided
with this handbook is the result of fruitful cooperation between the Department of
Ecological Modelling of the UFZ Centre for Environmental Research Leipzig-
Halle and the OFFIS Oldenburg Research Institute for the Development of Com-
puter Tools and Systems. The Department of Ecological Modelling has long expe-
rience of the development and analysis of standard models for population viability
analysis. Therefore, it made sense to seek out opportunities to make this knowl-
edge available and applicable for teaching, research as well as conservation prac-
tice and landscape management. At the same time, in 1996, the OFFIS-Institute
was looking for a partner with experience in ecology to help develop computer
tools for environmental management. This was the beginning of a five-year co-
operation project mainly funded by the UFZ (grant code UFZ-21/96). The idea
was to use the generic metapopulation model presented in Chapter 14 and the
standard procedure for determining population viability described in Chapter 13 as
the heart of the software and to develop a user interface geared to the workflow of
decision-making in the field of nature conservation and landscape management.
The aim was to come up with a tool that supports understanding, ranking man-
agement options and dealing with ecological uncertainty.
Throughout this time, the META-X team received much assistance from several
people who made essential contributions to the project’s success in several re-
spects. First of all, we would like to thank Michael Malachinski and Jens Finke
who programmed some key features of META-X such as the landscape editor and
the report generator. We are also grateful to Atte Moilanen from the University of
Helsinki who placed his method of parameterizing metapopulation models on the
basis of occupancy data at our disposal and adapted his procedure to the specific
requirements of META-X. This procedure provides the basis for the parameteriza-
tion tool which can be downloaded from the META-X homepage. All the pro-
gramming work on the corresponding user interface was done by Torsten Abels to
whom we express our gratitude. Many thanks also go to Ilse Storch who provided
the data, the expert knowledge and the questions to be answered by META-X re-
garding the example of the capercaillie presented in Chapter 16.
In the second half of the project, the various versions of META-X were exten-
sively tested for correctness by comparing the results of the software with those of
the original model which was implemented as a Mathematica program. We are
most grateful to Alexander Singer for conducting this long-term test with enor-
mous patience and precision. He also implemented and analyzed all the examples
presented in this handbook. We would also like to thank Simone K. Heinz who
Preface VI
particularly tested the import routine of META-X. Many thanks to Ute Vogel from
the University of Oldenburg for fruitful discussions on the design of the user inter-
face of Meta-X and to Monika Schwager and Matthias Wichmann from the Uni-
versity of Potsdam who tested the software from the user’s point of view and who
also commented on earlier drafts of the entire handbook. Moreover, we would like
to thank Jürgen Groeneveld, Simone K. Heinz, Stephanie Schadt and Björn Rei-
neking for carefully reading and critically commenting on Chapter 13 of this book.
Last but not least, we are grateful to Chris Abbey for polishing the English and
Ursula Gramm from Springer Verlag for her vital hints concerning the handbook’s
layout.
We hope very much that you are satisfied with the results – and that META-X
lives up to your expectations!
The META-X team
Leipzig and Oldenburg, July 2002
Contents
1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1 What Is META-X? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Metapopulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
PVA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Ecological Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2 What Is so Special About META-X? . . . . . . . . . . . . . . . . . . . . . . . 3
1.3 In What Areas Can META-X Be Used? . . . . . . . . . . . . . . . . . . . . . 4
In Teaching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
In Empirical Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
In Biological Conservation and Planning . . . . . . . . . . . . . . . . . . . . . 5
1.4 What Do You Need to Use META-X? . . . . . . . . . . . . . . . . . . . . . . 5
1.5 What Cannot Be Done with META-X? . . . . . . . . . . . . . . . . . . . . . 6
1.6 News on META-X . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2 Contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
4 Basic Concepts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
4.1 The Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
4.2 Landscape Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Position of Patches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Initial Occupancy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Net of Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
4.3 Patch Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Local Extinction Rate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Number of Emigrants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Number of Immigrants Needed . . . . . . . . . . . . . . . . . . . . . . . . . . 17
4.4 Spatial Processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Dispersal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Correlated Extinctions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
4.5 Simulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Control Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Interactive Simulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Automatic Simulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
4.6 Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
VIII Contents
4.7 Organizing Projects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Scenarios . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Projects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
4.8 The META-X Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
5 Guided Tour . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
5.1 Your First META-X Experiment . . . . . . . . . . . . . . . . . . . . . . . . . 25
Defining a New Project . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Creating a New Project by Saving . . . . . . . . . . . . . . . . . . . . . . . . 26
Enter Project Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Creating and Documenting Your First Experiment . . . . . . . . . . . . . . . . 28
Naming the Species and Delineating the Landscape . . . . . . . . . . . . . . . 29
Defining Control Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Scenario: Documentation and Defining the Landscape . . . . . . . . . . . . . 30
Patch Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Connection Between Patches . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Correlation Length . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Dispersal Range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Main Model Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Saving the Project to Your Hard Disk . . . . . . . . . . . . . . . . . . . . . . . 38
5.2 Interactive Simulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Choosing a Scenario . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Interactive Simulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Check Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Pattern of Occupancy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Modifying the Scenario . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Mean Time to Extinction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Adding a Second Scenario . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
5.3 Automatic Simulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
5.4 Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
5.5 Generating a Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
5.6 Where Next? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
6 The Project Tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
6.1 The Elements of the Project Tree . . . . . . . . . . . . . . . . . . . . . . . . . 53
The Root of the Project Tree . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
The Experiments Branch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
The Scenarios Branch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
6.2 Working with the Project Tree . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Working with Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Working with Scenarios . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
7 Scenarios and Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
7.1 The Experiment Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Compile Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Specify the Species and the Study Area . . . . . . . . . . . . . . . . . . . . . 63
Specify Control Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Contents IX
Specify New Scenario (Based on ) . . . . . . . . . . . . . . . . . . . . . . . 63
Modify Existing Scenario . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Complete Definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
7.2 The Scenario Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Documentation of the Scenario . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Number of Patches for a Scenario . . . . . . . . . . . . . . . . . . . . . . . . 65
Position of Patches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Patch Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Connection of Patches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Correlation Length . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Correlation Length (Direct) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Correlation Length (Indirect) . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Mean Dispersal Range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Mean Dispersal Range (Direct) : . . . . . . . . . . . . . . . . . . . . . . . . . 68
Mean Dispersal Range (Indirect) : . . . . . . . . . . . . . . . . . . . . . . . . 68
Rates of Colonization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Main Model Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Control Parameters for the Whole Experiment . . . . . . . . . . . . . . . . . . 70
End of the Scenario Specification . . . . . . . . . . . . . . . . . . . . . . . . 70
7.3 Homogeneous Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
7.4 User-Defined Scenarios and the Parameter Hierarchy of META-X . . . . . . . 72
Submodels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
The Standard Submodels of META-X . . . . . . . . . . . . . . . . . . . . . . 73
User-Defined . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Parameter Hierarchy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Update Matrix: Warning Message . . . . . . . . . . . . . . . . . . . . . . . . 74
8 Simulation and Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
8.1 Interactive Simulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Metapopulation Dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Recorded Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Diagrams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Control Unit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Further Analysis – FD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Further Analysis – TM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Change Scenario . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
8.2 Simulation and Evaluation of Scenarios . . . . . . . . . . . . . . . . . . . . . 80
Automatic Simulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
8.3 Simulation and Evaluation of Experiments . . . . . . . . . . . . . . . . . . . . 81
Select Experiments and Scenarios . . . . . . . . . . . . . . . . . . . . . . . . 81
Check Control Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Batch Simulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
What to Evaluate? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
9 The Landscape Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
9.1 Elements of the Landscape Editor . . . . . . . . . . . . . . . . . . . . . . 85
9.2 Visualization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
X Contents
9.3 Modifying Existing Scenarios . . . . . . . . . . . . . . . . . . . . . . . . . 89
9.4 Saving Your Work with the Apply Button . . . . . . . . . . . . . . . . . . . . 91
9.5 Creating New Scenarios . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
10 Parameter Variation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
10.1 Variation Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Creating Variation Experiments (1) . . . . . . . . . . . . . . . . . . . . . . . 95
Creating Variation Experiments (2) . . . . . . . . . . . . . . . . . . . . . . . 97
Modify Variation Experiments . . . . . . . . . . . . . . . . . . . . . . . . . 98
Resetting Variation Experiments . . . . . . . . . . . . . . . . . . . . . . . . 98
10.2 Simulation, Evaluation and Reports . . . . . . . . . . . . . . . . . . . . . . 99
11 Import,Export and Report . . . . . . . . . . . . . . . . . . . . . . . . . . 101
11.1 Import of Model Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Format of Import Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
11.2 Export of Simulation Results . . . . . . . . . . . . . . . . . . . . . . . . . . 103
11.3 Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Report of Scenarios . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Report of Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Report of Projects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
11.4 Exporting Graphs to the Clipboard . . . . . . . . . . . . . . . . . . . . . . . 106
12 Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
12.1 The META-X Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
The File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
The Edit Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
The View Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
The Experiment Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
The Scenario Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
The Parameter Variation Menu . . . . . . . . . . . . . . . . . . . . . . . . . 111
The Editor Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
The Tools Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
The Window Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
The Help Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
12.3 Context Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Project Tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Landscape Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
12.4 Warning Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
Scenario Wizard Warning Messages . . . . . . . . . . . . . . . . . . . . . . 117
Landscape Editor Warning Messages . . . . . . . . . . . . . . . . . . . . . . 117
Interactive Simulation Warning Messages . . . . . . . . . . . . . . . . . . . 118
13 Goals,Methods,and Concepts of PVA . . . . . . . . . . . . . . . . . . . . 119
13.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
13.2 Goals of PVA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
13.3 Ecological Models for PVA . . . . . . . . . . . . . . . . . . . . . . . . . . . 121