MetaIBM (Metacommunity Individual-based Modelling)

This is the formal released version.2.9.12

a python-based library for building a Individual-based model in Community Ecology

metacommunity_IBM.py is the source code of the library (version.2.9.12).

MetaIBM users mannual.docx is the user mannual of the library

we also provided four examples of how to use to library to built a IBMs by the users

Note that other versions of this library providing other advanced algorithms is also avaiable in the brance of the repository.

Table of contents (Details in Users Mannual)

1. INTRODUCTION ...... 2

2. INSTALLATION ...... 3

2.1 WINDOWS PLATFORM ...... 3

2.2 LINUX PLATFORM ...... 4

2.3 MACOS PLATFORM WITH APPLE SILICON 4

2.4 IMPORTING THE METAIBM MODULE IN PYTHON ...... 5

3.PROCESSES AND SUB-MODELS ...... 5

3.1 LANDSCAPE TOPOLOGY OF A METACOMMUNITY ...... 5

3.1.1 Habitat scales ...... 5

3.1.2 patch scales ...... 7

3.1.3 global scales or metacommunity scales ...... 9

3.2 SPECIES AND INDIVIDUALS’ ATTRIBUTES SETTING ...... 11

3.2.1 Individuals and attributes ...... 11

3.2.2 the data structure of metaIBM.individual.genotype_set ...... 14

3.2.3 the data structure of metaIBM.individual.phenotype_set ...... 14

3.3 ENVIRONMENT GRADIENTS AND FITNESS LANDSCAPE ...... 15

3.3.1 Environment gradients ...... 15

3.3.2 fitness landscape ...... 18

3.4 COLONIZATION PROCESS ...... 20

3.4.1 create an islands-mainland modelling system ...... 20

3.4.2 modelling the Colonization process ...... 23

3.5 NATURAL SELECTION OR ENVIRONMENTAL FILTERS PROCESS ...... 25

3.6 REPRODUCTION AND MUTATION PROCESSES ...... 26

3.6.1 asexual reproduction ...... 26

3.6.2 sexual reproduction ...... 27

3.6.3 mutation ...... 28

3.7 DISPERSAL PROCESS ...... 28

3.7.1 the dispersal of propagules ...... 28

3.7.2 Dispersal among patches ...... 28

3.7.3 Dispersal within a patch ...... 30

3.8 DORMANCY PROCESS ...... 31

3.9 DISTURBANCE PROCESS ...... 32

3.9.1 Disturbance in a habitat ...... 32

3.9.2 Disturbance in a patch ...... 32

4.INPUT ...... 33

5.OUTPUT ...... 33

5.1 THE GUI SYSTEM OF THE SOFTWARE ...... 33

5.1.1 showing environmental gradients ...... 34

5.1.2 showing species distribution ...... 35

5.1.3 showing species phenotype in the metacommunity ...... 36

5.2 OTHER FORM OF OUTPUT ...... 37

5.2.1 saving species distribution data into a csv file ...... 38

5.2.2 saving species phenotypes data into a csv file ...... 39

6.EXAMPLES OF SIMULATION ...... 41

7.HIGH PERFORMANCE COMPUTING (HPC) ...... 41

7.1 INSTALLATION OF MPI SOFTWARE AND MPI4PY PYTHON MODULE ...... 42

7.1.1 Windows platform ...... 42

7.1.2 Linux platform ...... 43

7.1.3 MacOS platform with Apple Silicon ...... 43

7.2 EXAMPLES OF PARALLEL-COMPUTING ...... 44

8.REFERENCES ...... 45

9.ACKNOWLEDGEMENTS ...... 46