pyMANGA.PopulationLib

Description

Library of population modules.

A population consists of one or more groups, which in turn consist of individual plants. These groups may or may not be of different species. For each group, separate growth, mortality and establishment modules can be defined.

The establishment process is divided in four parts:

definition of the initial population (see pyMANGA.PopulationLib.InitialPop)
seed or seedling production (see pyMANGA.PopulationLib.Production)
seed or seedling dispersal (see pyMANGA.PopulationLib.Dispersal)
(optional) seed or seedling recruitment (see pyMANGA.PopulationLib.Recruitment)

flowchart TB;
    id1[[InitialPop]]-->Random;
    id1[[InitialPop]]-->...;
    id2[[Production]]-->FixedRate;
    id2[[Production]]-->....;
    id3[[Dispersal]]-->Uniform;
    id3[[Dispersal]]-->..;
    id4[[Recruitment]]-->Weighted;

Usage

<population>
    <group>
        <name> Group_B </name>
        <species> Rhizophora </species>
        <vegetation_model_type> Bettina </vegetation_model_type>
        <mortality>NoGrowth</mortality>
        <domain>
            <x_1> 0 </x_1>
            <y_1> 0 </y_1>
            <x_2> 22 </x_2>
            <y_2> 22 </y_2>
        </domain>
        <initial_population>
            <type>Random</type>
            <n_individuals> 1 </n_individuals>
        </initial_population>
        <production>
            <type>FixedRate</type>
            <per_individual>False</per_individual>
            <per_ha>False</per_ha>
            <n_individuals> 1 </n_individuals>
        </production>
        <dispersal>
            <type> Uniform </type>
        </dispersal>
    </group>
</population>

Attributes

group (string): Nesting tag to define a group
name (string): Name of the group (can be chosen freely and does not affect the simulation)
species (string): see pyMANGA.PopulationLib.Species
vegetation_model_type (string): see pyMANGA.PlantModelLib
mortality (string): see pyMANGA.PlantModelLib.Mortality
domain (nesting-tag): coordinates to define the model domain (as mesh)
- x_1 (float): x-coordinate of left bottom border of grid
- x_2 (float): x-coordinate of right bottom border of grid
- y_1 (float): x-coordinate of left top border of grid
- y_2 (float): x-coordinate of right top border of grid
initial_population (nesting-tag): Defines initial population of a group, see pyMANGA.PopulationLib.InitialPop
production (nesting-tag): Defines seed or seedling production of a group, see pyMANGA.PopulationLib.Production
dispersal (nesting-tag): Defines seed or seedling dispersal of a group, see pyMANGA.PopulationLib.Dispersal

Value

An array containing separate dictionaries for each group.

Author(s)

Marie-Christin Wimmler

Examples

2 species example

Two species (groups), Avicennia and Rhizophora, grow in a model domain of 22x22m. Tree growth follows the Bettina approach. Species parameters and annual mortality are different. Avicennia starts with 50 trees and 2 new trees are recruited in each time step per existing Acivennia tree, while Rhizophora starts with 20 trees and 8 are recruited in each time step.

<population>
    <group>
        <name> Group_A </name>
        <species> Avicennia </species>
        <vegetation_model_type> Bettina </vegetation_model_type>
        <mortality>NoGrowth Random</mortality>
        <probability>0.0016</probability>
        <domain>
            <x_1> 0 </x_1>
            <y_1> 0 </y_1>
            <x_2> 22 </x_2>
            <y_2> 22 </y_2>
        </domain>
        <initial_population>
            <type>Random</type>
            <n_individuals> 50 </n_individuals>
        </initial_population>
        <production>
            <type>FixedRate</type>
            <per_individual>True</per_individual>
            <per_ha>False</per_ha>
            <n_individuals> 2 </n_individuals>
        </production>
        <dispersal>
            <type> Uniform </type>
        </dispersal>
    </group>
    <group>
        <name> Group_B </name>
        <species> Rhizophora </species>
        <vegetation_model_type> Bettina </vegetation_model_type>
        <mortality>NoGrowth Random</mortality>
        <probability>0.001</probability>
        <domain>
            <x_1> 0 </x_1>
            <y_1> 0 </y_1>
            <x_2> 22 </x_2>
            <y_2> 22 </y_2>
        </domain>
        <initial_population>
            <type>Random</type>
            <n_individuals> 20 </n_individuals>
        </initial_population>
        <production>
            <type>FixedRate</type>
            <per_individual>True</per_individual>
            <per_ha>False</per_ha>
            <n_individuals> 8 </n_individuals>
        </production>
        <dispersal>
            <type> Uniform </type>
        </dispersal>
    </group>
</population>

Example with recruitment

Avicennia trees grow in a model domain of 22x10m. Tree growth follows the Bettina approach. Trees die when maintenance > resource uptake (NoGrowth) and randomly with an annual probability of 0.16% (Random). The initial population of 50 trees is randomly generated. At each time step, 100 seedlings per hectare are produced and uniformly distributed over the model area. The success of germination, i.e. recruitment, is defined in the ``weights.csv'' file, which has the following form: where xy are the coordinates of each cell in the model and weight is a number between 0 and 1 indicating the probability of germination.

x,y,weight,idx
0,0,1,1
0.25,0,1,2

<population>
    <group>
        <name> Group_A </name>
        <species> Avicennia </species>
        <vegetation_model_type> Bettina </vegetation_model_type>
        <mortality>NoGrowth Random</mortality>
        <probability>0.0016</probability>
        <domain>
            <x_1> 0 </x_1>
            <y_1> 0 </y_1>
            <x_2> 22 </x_2>
            <y_2> 10 </y_2>
        </domain>
        <initial_population>
            <type>Random</type>
            <n_individuals> 50 </n_individuals>
        </initial_population>
        <production>
            <type>FixedRate</type>
            <per_individual>True</per_individual>
            <per_ha>False</per_ha>
            <n_individuals> 2 </n_individuals>
        </production>
        <dispersal>
            <type> Uniform </type>
        </dispersal>
        <recruitment>
            <type> Weighted </type>
            <weight_file> weights.csv </weight_file>
        </recruitment>
    </group>
</population>

View Source

1#!/usr/bin/env python3
2# -*- coding: utf-8 -*-
3"""
4.. include:: ./Population.md
5"""