Establishment behaviors
In this document:
Establishment parameters
Substrate Dependent Seed Survival No Gap Status
Substrate Dependent Seed Survival With Gap Status
Light Dependent Seed Survival
Density Dependent Seed Survival
Proportional Seed Survival
Seed Establishment
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 the Seed Establishment behavior.
- Beam Fraction of Global Radiation The fraction of total solar radiation that is direct beam radiation (as opposed to diffuse). Expressed as a value between 0 and 1. See Light Behaviors for more on GLI calculations. Used by the Light Dependent Seed Survival behavior.
- Clear Sky Transmission Coefficient Used to determine the amount of solar radiation seen at the plot location. See Light Behaviors for more on GLI calculations. Used by the Light Dependent Seed Survival behavior.
- First Day of Growing Season for GLI Light Calculations The first day of the growing season, as a Julian day (number between 1 and 365). Seeds only get light during the growing season. See Light Behaviors for more on GLI calculations. Used by the Light Dependent Seed Survival behavior.
- Fraction Seeds Germinating on Canopy Decayed Logs The proportion of those seeds that land on decayed logs under canopy conditions that survive to become seedlings. Expressed as a value between 0 and 1. Used by the Substrate Dependent Seed Survival No Gap Status and Substrate Dependent Seed Survival With Gap Status behaviors.
- Fraction Seeds Germinating on Canopy Fresh Logs The proportion of those seeds that land on fresh logs under canopy conditions that survive to become seedlings. Expressed as a value between 0 and 1. Used by the Substrate Dependent Seed Survival No Gap Status and Substrate Dependent Seed Survival With Gap Status behaviors.
- Fraction Seeds Germinating on Canopy Forest Floor The proportion of those seeds that land on forest floor under canopy conditions that survive to become seedlings. Expressed as a value between 0 and 1. Used by the Substrate Dependent Seed Survival No Gap Status and Substrate Dependent Seed Survival With Gap Status behaviors.
- Fraction Seeds Germinating on Canopy Scarified Soil The proportion of those seeds that land on scarified soil under canopy conditions that survive to become seedlings. Expressed as a value between 0 and 1. Used by the Substrate Dependent Seed Survival No Gap Status and Substrate Dependent Seed Survival With Gap Status behaviors.
- Fraction Seeds Germinating on Canopy Tip-Up The proportion of those seeds that land on tip-up mounds substrate under canopy conditions that survive to become seedlings. Expressed as a value between 0 and 1. Used by the Substrate Dependent Seed Survival No Gap Status and Substrate Dependent Seed Survival With Gap Status behaviors.
- Fraction Seeds Germinating on Gap Decayed Logs The proportion of those seeds that land on decayed logs under gap conditions that survive to become seedlings. Expressed as a value between 0 and 1. Used by the Substrate Dependent Seed Survival With Gap Status behavior.
- Fraction Seeds Germinating on Gap Fresh Logs The proportion of those seeds that land on fresh logs under gap conditions that survive to become seedlings. Expressed as a value between 0 and 1. Used by the Substrate Dependent Seed Survival With Gap Status behavior.
- Fraction Seeds Germinating on Gap Forest Floor The proportion of those seeds that land on forest floor under gap conditions that survive to become seedlings. Expressed as a value between 0 and 1. Used by the Substrate Dependent Seed Survival With Gap Status behavior.
- Fraction Seeds Germinating on Gap Scarified Soil The proportion of those seeds that land on scarified soil under gap conditions that survive to become seedlings. Expressed as a value between 0 and 1. Used by the Substrate Dependent Seed Survival With Gap Status behavior.
- Fraction Seeds Germinating on Gap Tip-Up The proportion of those seeds that land on tip-up mounds substrate under gap conditions that survive to become seedlings. Expressed as a value between 0 and 1. Used by the Substrate Dependent Seed Survival With Gap Status behavior.
- GLI of Optimum Establishment, 0-100 The GLI value of optimum survival for seeds, as a value between 0 and 100. Used by the Light Dependent Seed Survival behavior.
- Height in m At Which to Calculate GLI The height, in meters, at which to calculate GLI at the center of each grid cell. Used by Light Dependent Seed Survival behavior.
- Last Day of Growing Season for GLI Light Calculations The last day of the growing season, as a Julian day (number between 1 and 365). Seeds only get light during the growing season. See Light Behaviors for more on GLI calculations. Used by the Light Dependent Seed Survival behavior.
- Light Extinction Coeff of Complete Damage Trees (0-1) The fraction of light transmitted by the crowns of trees with complete Storm damage. Not required if storms are not used. Expressed as a value between 0 and 1. If storms are used, a value must be supplied for every species. See Light Behaviors for more on GLI calculations. Used by the Light Dependent Seed Survival behavior.
- Light Extinction Coeff of Medium Damage Trees (0-1) The fraction of light transmitted by the crowns of trees with medium Storm damage. Not required if storms are not used. Expressed as a value between 0 and 1. If storms are used, a value must be supplied for every species. See Light Behaviors for more on GLI calculations. Used by the Light Dependent Seed Survival behavior.
- Light Extinction Coeff of Undamaged Trees (0-1) The fraction of light transmitted by the crowns of regular live trees (and if storms are being used, trees with no Storm damage). Expressed as a value between 0 and 1. A value must be supplied for every species. See Light Behaviors for more on GLI calculations. Used by the Light Dependent Seed Survival behavior.
- Minimum Solar Angle for GLI Calculations, in rad This is the minimum angle at which sunlight is seen, in radians. Below this value the sky is assumed to be dark due to shading neighbors. See Light Behaviors for more on GLI calculations. Used by the Light Dependent Seed Survival behavior.
- Number of Altitude Sky Divisions for GLI Light Calculations Number of grid cells into which the sky is divided from horizon to zenith, for the purpose of calculating light direction. See Light Behaviors for more on GLI calculations. Used by the Light Dependent Seed Survival behavior.
- Number of Azimuth Sky Divisions for GLI Light Calculations Number of grid cells into which the sky is divided around the horizon, for the purpose of calculating light direction. See Light Behaviors for more on GLI calculations. Used by the Light Dependent Seed Survival behavior.
- Proportion Germinating Between 0 and 1 The proportion of seeds of a species that survive germination, as a value between 0 and 1. Used by the Proportional Seed Survival behavior.
- Slope of Density Dependence The slope of the density dependence function for determining how many seedlings establish (c in the equations below). Used by the Density Dependent Seed Survival behavior.
- Slope of Dropoff Above the Optimum GLI The slope of the line describing the drop off in seedling survival as a function of GLI above the optimum GLI. Used by the Light Dependent Seed Survival behavior.
- Slope of Dropoff Below Optimum GLI The slope of the line describing the dropoff in seedling survival as a function of GLI below the optimum GLI. Used by the Light Dependent Seed Survival behavior.
- Steepness of Density Dependence The steepness of the density dependence function for determining how many seedlings establish (δ in the equations below). Used by the Density Dependent Seed Survival behavior.
- Snag Age Class 1 Light Extinction Coefficient (0-1) Fraction of light transmitted through the snag tree crown for each species. Applies to those snags whose age is less than or equal to "Upper age (yrs) of snag light extinction class 1". Expressed as a fraction between 0 and 1. If your run does not work with snags, you can ignore this. Otherwise, a value must be provided for all species. Used by the Light Dependent Seed Survival behavior.
- Snag Age Class 2 Light Extinction Coefficient (0-1) Fraction of light transmitted through the snag tree crown for each species. Applies to those snags whose age is greater than "Upper age (yrs) of snag light extinction class 1", but is less than or equal to "Upper age (yrs) of snag light extinction class 2". Expressed as a fraction between 0 and 1. If your run does not work with snags, you can ignore this. Otherwise, a value must be provided for all species. Used by the Light Dependent Seed Survival behavior.
- Snag Age Class 3 Light Extinction Coefficient (0-1) Fraction of light transmitted through the snag tree crown for each species. Applies to those snags whose age is greater than "Upper age (yrs) of snag light extinction class 2". Expressed as a fraction between 0 and 1. If your run does not work with snags, you can ignore this. Otherwise, a value must be provided for all species. Used by the Light Dependent Seed Survival behavior.
- Upper Age (Yrs) of Snag Light Extinction Class 1 The upper age limit, in years, defining the first age class of snag light extinction. Snags with an age less than or equal to this age have a light extinction coefficient matching "Snag age class 1 light extinction coefficient". If your run does not work with snags, you can ignore this. Used by the Light Dependent Seed Survival behavior.
- Upper Age (Yrs) of Snag Light Extinction Class 2 The upper age limit, in years, defining the second age class of snag light extinction. Snags with an age greater than the upper limit for size class 1, but less than or equal to this age, have a light extinction coefficient matching "Snag age class 2 light extinction coefficient". Snags with an age greater than this value are in age class three. If your run does not work with snags, you can ignore this. Used by the Light Dependent Seed Survival behavior.
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.
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:
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:
- If GLI < GLIopt, LE = 1 - (Slo(GLIopt - GLI))
- If GLI = GLIopt, LE = 1
- If GLI > GLIopt, LE = 1 - (Shi(GLI - GLIopt))
where
- GLI is the GLI at the center of the Dispersed Seeds grid cell at the height in the Height in m At Which to Calculate GLI parameter
- GLIopt is the GLI of Optimum Establishment, 0-100 parameter
- Slo is the Slope of Dropoff Below Optimum GLI parameter
- Shi is the Slope of Dropoff Above the Optimum GLI parameter
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.
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 * Sspδ)
where:
- Rsp is the number of surviving seeds of a given species in the seed grid cell
- Ssp is the original number of seeds of that species in that grid cell
- c is the Slope of Density Dependence parameter
- δ is the Steepness of Density Dependence parameter
Once the number of surviving seeds has been determined, the behavior assigns that number back to the Dispersed Seeds grid cell.
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.
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.
Last updated: 21-Apr-2005 12:02 PM