Establishment behaviors

In this document:
Establishment parameters
Substrate Dependent Seed Survival No Gap Status
Substrate Dependent Seed Survival With Gap Status
Substrate Based Seed Survival With Microtopography
Light Dependent Seed Survival
Storm Light Dependent Seed Survival
Density Dependent Seed Survival
Proportional Seed Survival
Seed Establishment
Establishment with Microtopography

Establishment behaviors assess seed survival and create new seedlings from seeds. Establishment behaviors do not create or distribute the seeds. The Disperse behaviors perform that function.

The seed survival behaviors act to reduce the number of seeds based on various environmental effects. They can be used alone or in combination. Once they have completed their work, the number of surviving seeds can be turned into seedlings by either the Seed Establishment or Establishment with Microtopography behaviors.

Establishment parameters

Substrate Dependent Seed Survival No Gap Status

This behavior assesses seed survival based on substrate conditions.

How it works

The behavior takes the substrate composition of each grid cell in the Substrate grid and converts it into a single number for each species, called the substrate favorability index. The favorability index is the sum of the proportions of each substrate multiplied by the proportion of seeds that germinate on that substrate. This index represents the proportion of total seeds of that species that are expected to survive in that area of the plot. This index is stored in the grid Substrate Favorability. (In the parameters list, above, the proportions used are the canopy proportions.)

The behavior then goes through each grid cell in the Dispersed Seeds grid and assesses the survival for the seeds of those species to which it applies. This behavior starts by giving each seed a random temporary location within the Dispersed Seeds grid cell. Then, it retrieves the substrate favorability at that point from the Substrate Favorability grid. It then compares a random number to the substrate favorability to determine whether the seed lives. This method ensures that we can assess substrate favorabilities correctly when the Dispersed Seeds and Substrate grids have different grid cell resolutions.

Once this process is complete, the number of surviving seeds for each species is assigned back to the Dispersed Seeds grid.

How to apply it

This behavior may be applied to seeds of any species. A species to which this is applied must also have a Disperse behavior applied. Also, the Substrate behavior must be used in the run.

Substrate Dependent Seed Survival With Gap Status

This behavior assesses seed survival as a function of both the substrate composition of the grid cells in which seeds land and the cells' forest cover (gap or canopy). This behavior allows for different germination favorability for substrates under the two forest covers.

How it works

The behavior takes the substrate composition of each grid cell in the Substrate grid and converts it into a single number for each species, called the substrate favorability index. The favorability index is the sum of the proportions of each substrate multiplied by the proportion of seeds that germinate on that substrate under that cell's cover (canopy or gap). This index represents the proportion of total seeds of that species that are expected to survive in that area of the plot. This index is stored in the grid Substrate Favorability.

The behavior then goes through each grid cell in the Dispersed Seeds grid and assesses the survival for the seeds of those species to which it applies. This behavior starts by giving each seed a random temporary location within the Dispersed Seeds grid cell. Then, it retrieves the substrate favorability at that point from the Substrate Favorability grid. It then compares a random number to the substrate favorability to determine whether the seed lives. This method ensures that we can assess substrate favorabilities correctly when the Dispersed Seeds and Substrate grids have different grid cell resolutions.

Once this process is complete, the number of surviving seeds for each species is assigned back to the Dispersed Seeds grid.

How to apply it

This behavior may be applied to seeds of any species. A species to which this is applied must also have the Gap spatial disperse behavior applied. Also, the Substrate behavior must be used in the run.

Substrate Based Seed Survival With Microtopography

This behavior assesses seed survival based on substrate conditions, allowing for site microtopography to influence seed survival. In this scenario, the plot is divided into small-scale mounds. The portion of the plot that is slightly elevated is "mound". The portion of the plot between the mounds, at lower elevation, is "ground". The size of the mounds and their height is not important.

How it works

The area of the plot that is "mound" and the area that is "ground" are in fixed relative proportion to each other. This fixed proportion is entered in the Proportion of Plot Area that is Mound parameter. Each grid cell in the Substrate grid has been divided by the Substrate behavior into six substrate types; each of those types is further divided into "mound" and "ground" according to the fixed proportion, making twelve total substrate types. For example, if 20% of a grid cell's area is forest floor litter, and 60% of the plot area is mound, then the area of the grid cell that is forest floor litter mound substrate is 12% and the area of grid cell that is forest floor litter ground substrate is 8%.

The behavior takes the substrate composition of each grid cell in the Substrate grid, calculates the amount of the twelve substrate types, and converts it into a single number for each species, called the substrate favorability index. The favorability index is the sum of the proportions of each substrate multiplied by the proportion of seeds that germinate on that substrate. This index represents the proportion of total seeds of that species that are expected to survive in that area of the plot. This index is stored in the grid Substrate Favorability.

The behavior then goes through each grid cell in the Dispersed Seeds grid and assesses the survival for the seeds of those species to which it applies. This behavior starts by giving each seed a random temporary location within the Dispersed Seeds grid cell. Then, it retrieves the substrate favorability at that point from the Substrate Favorability grid. It then compares a random number to the substrate favorability to determine whether the seed lives. This method ensures that we can assess substrate favorabilities correctly when the Dispersed Seeds and Substrate grids have different grid cell resolutions.

Once this process is complete, the number of surviving seeds for each species is assigned back to the Dispersed Seeds grid.

How to apply it

This behavior may be applied to seeds of any species. A species to which this is applied must also have a Disperse behavior applied. Also, the Substrate behavior must be used in the run.

Light Dependent Seed Survival

This behavior assesses seed survival as a function of the Global Light Index (GLI) of the location in which a seed lands. Light level calculations can take into account the change in light blocking by snags and trees with storm damage, if desired.

The effects of light levels on seed survival is graphed as:

Light dependent seed survival GLI diagram

How it works

To assess the effects of light level on the number of seeds that survive, this behavior calculates the GLI at the center of each grid cell in the Dispersed Seeds grid at the height specified in the Height in m At Which to Calculate GLI parameter (value is in meters). The calculation proceeds exactly as described in the Light Behaviors. In order to perform these GLI calculations, this behavior requires its own copy of the key GLI setup parameters.

If you wish to use storms in your run, this behavior can take into account the fact that storm-damaged trees may have different light extinction coefficients. These light extinction coefficients are specified in the Light Extinction Coeff of Complete Damage Trees (0-1) and Light Extinction Coeff of Medium Damage Trees (0-1) parameters.

Once GLI has been calculated, the proportion of seeds that survive for a given species is calculated as:

where

Once the proportion of seeds that survive at the given GLI has been calculated, this value is multiplied by the number of seeds to reduce them by the proper amount. The new reduced number of seeds is put back in the Dispersed Seeds grid.

How to apply it

Apply this behavior to seeds of your desired species. Any species to which it is applied must also have a Disperse behavior applied. Storm damage is optional.

Storm Light Dependent Seed Survival

This behavior assesses seed survival as a function of the light level of the location in which a seed lands. Light level calculations are performed by the Storm Light behavior. (This behavior is exactly like Light Dependent Seed Survival except for the method of light level calculation.)

The effects of light levels on seed survival is graphed as:

Light dependent seed survival GLI diagram

How it works

To assess the effects of light level on the number of seeds that survive, this behavior retrieves the light level from the Storm Light grid that corresponds to the point in the center of each Dispersed Seeds grid cell.

The proportion of seeds that survive for a given species is calculated as:

where

Once the proportion of seeds that survive at the given light level has been calculated, this value is multiplied by the number of seeds to reduce them by the proper amount. The new reduced number of seeds is put back in the Dispersed Seeds grid.

How to apply it

Apply this behavior to seeds of your desired species. Any species to which it is applied must also have a Disperse behavior and the Storm Light behavior applied.

Density Dependent Seed Survival

This behavior assesses seed survival as a function of the local density of conspecific seeds.

How it works

This behavior takes the seeds that have been dispersed to each grid cell of the Dispersed Seeds grid and calculates how many will become survive. The number of seeds that survives is calculated as

Rsp = Ssp * exp(-c * Denspδ)

where:

Once the number of surviving seeds has been determined, the behavior assigns that number back to the Dispersed Seeds grid cell. If there is only one seed in a grid cell, it always survives.

How to apply it

Apply this behavior to seeds of your desired species. Any species to which it is applied must also have any disperse behavior applied.

Proportional Seed Survival

This behavior reduces the number of seeds by a set amount.

How it works

In each cell of the Dispersed Seeds grid, this multiples the number of seeds present by the Proportion Germinating Between 0 and 1 parameter, reducing the total number available. The new number of seeds is placed back in the Dispersed Seeds grid.

How to apply it

Apply this behavior to seeds of any species. Any species to which this is applied must have a Disperse behavior applied as well.

Seed Establishment

This behavior converts seeds into seedlings.

How it works

This behavior goes through each grid cell in the Dispersed Seeds grid and, for each species to which this behavior applies, converts each seed into a seedling. The seedlings are randomly placed within the grid cell area and have a slightly randomized value of New seedling diameter at 10 cm.

How to apply it

Apply this behavior to seeds of any species. A species to which this is applied must also have a Disperse behavior applied.

Establishment with Microtopography

This behavior germinates seeds into seedlings. It simulates microtopography in the plot and assigns new seedlings a rooting height as a function of the type of substrate on which they land (from the Substrate behavior). This behavior is designed to work with both the Substrate and the Beer's law light filter behaviors to simulate shading by ferns. The rooting height that seedlings get influences the amount of light they receive. Seeds that land on fresh logs, in addition, are eligible for a respite from the Beer's law light filter behavior.

How it works

Each timestep, the behavior starts by getting the substrate proportions for each cell of the Dispersed Seeds grid. The six substrate types are further divided into mound and non-mound types of each according to the Proportion of Ground Area that is Mound parameter. The relative proportions of the different kinds of substrate are thus the same on mound and non-mound areas.

The seeds in the Dispersed Seeds grid cell are then divided up among the substrate types in that cell according to their proportions relative to each other (so if 60% of the cell area is mound forest floor moss, that's the substrate type that 60% of the seeds land on). A seedling is created from each seed. Seedlings are randomly placed within their seed grid cell area and have a slightly randomized value of New seedling diameter at 10 cm.

Each seedling then gets a rooting height according to the substrate type upon which it has germinated. If it has germinated on fresh logs, its rooting height is a random number drawn from a normal distribution controlled by the Mean Height of Fresh Log Substrate, in m and Standard Deviation of Fresh Log Substrate Height, in m parameters (no distinction is made between mound and non-mound fresh logs). If it's on a mound substrate, its rooting height is a random number drawn from a normal distribution controlled by the Mean Height of Mounds, in m and Standard Deviation of Mound Height, in m parameters. If it's on a non-mound substrate, its rooting height is zero.

If a seedling germinates on fresh log, it has the chance of getting a respite from the effects of the Beer's law light filter behavior, which it expects to simulate fern shading. Fallen logs crash through the fern layer, and it takes a while for the ferns to grow back over the top of the log. This length of time is the maximum possible respite length, and is set in the # Years Respite from Fern Shading for Seeds on Fresh Logs parameter. Substrate keeps track of the age of its fresh log cohorts, so that it is possible to randomly assign the seedling to a fresh log of a specific age, given the relative proportions of various-aged fresh log cohorts. The age of the log is subtracted from the maximum respite length, and this value is assigned to the seedling. Thus a log that fell this timestep would give a seedling the maximum respite, whereas a much older log may not give any respite at all.

How to apply it

Apply this behavior to seeds of your desired species. Any species to which it is applied must also satisfy the following requirements:



Last updated: 16-Nov-2005 09:40 AM