Substrate behaviors
In this document:
Substrate parameters
Substrate behavior
NZ Substrate behavior
Substrate is what seedlings germinate in - soil, rock, and the organic layers on top. The quality of the substrate can make a big difference in a seedling's ability to survive and establish. The substrate composition in any one place is constantly shifting and changing as new substrate is added to the forest floor and as existing substrate decays. These behaviors keep track of the substrate conditions at different locations through time.
Substrate parameters
- Clear Cut Proportion of Decayed Logs The proportion of substrate that is decayed logs in areas that had a clear cut harvest event, as a value between 0 and 1. This is not required if the Harvest behavior is not used. Used by the Substrate behavior.
- Clear Cut Proportion of Fresh Logs The proportion of substrate that is fresh logs in areas that had a clear cut harvest event, as a value between 0 and 1. This is not required if the Harvest behavior is not used. Used by the Substrate behavior.
- Clear Cut Proportion of Scarified Soil The proportion of substrate that is scarified soil in areas that had a clear cut harvest event, as a value between 0 and 1. This is not required if the Harvest behavior is not used. Used by the Substrate behavior.
- Clear Cut Proportion of Tip-Up Mounds The proportion of substrate that is tip-up mounds substrate in areas that had a clear cut harvest event, as a value between 0 and 1. This is not required if the Harvest behavior is not used. Used by the Substrate behavior.
- Decayed Log to Forest Floor Annual Decay The proportion of decayed logs converted to forest floor per year, as a value between 0 and 1. Used by the Substrate behavior.
- Decayed Log to Litter/Moss Annual Decay The proportion of decayed logs converted to the litter/moss pool per year, as a value between 0 and 1. Used by the NZ Substrate behavior.
- Fresh Log Annual Decay Alpha The α exponent in the decay equation
, as applied to fresh logs. Note that this is annual decay. Parameter files for old SORTIE versions are for five-year decay. Used by the Substrate behavior.
- Fresh Log Annual Decay Beta The β exponent in the decay equation
, as applied to fresh logs. Note that this is annual decay. Parameter files for old SORTIE versions are for five-year decay. Used by the Substrate behavior.
- Gap Cut Proportion of Decayed Logs The proportion of substrate that is decayed logs in areas that had a gap cut harvest event, as a value between 0 and 1. This is not required if the Harvest behavior is not used. Used by the Substrate behavior.
- Gap Cut Proportion of Fresh Logs The proportion of substrate that is fresh logs in areas that had a gap cut harvest event, as a value between 0 and 1. This is not required if the Harvest behavior is not used. Used by the Substrate behavior.
- Gap Cut Proportion of Scarified Soil The proportion of substrate that is scarified soil in areas that had a gap cut harvest event, as a value between 0 and 1. This is not required if the Harvest behavior is not used. Used by the Substrate behavior.
- Gap Cut Proportion of Tip-Up Mounds The proportion of substrate that is tip-up mounds substrate in areas that had a gap cut harvest event, as a value between 0 and 1. This is not required if the Harvest behavior is not used. Used by the Substrate behavior.
- Initial Conditions Proportion of Decayed Logs The proportion of plot substrate that is decayed logs when the run starts, as a value between 0 and 1. If a map of substrate values is included in the parameter file (see Adding to a parameter file for information on how to do this), then the map values will be used for the initial conditions and this number will be ignored. Used by the Substrate behavior.
- Initial Conditions Proportion of Fresh Logs The proportion of plot substrate that is fresh logs when the run starts, as a value between 0 and 1. If a map of substrate values is included in the parameter file (see Adding to a parameter file for information on how to do this), then the map values will be used for the initial conditions and this number will be ignored. Used by the Substrate behavior.
- Initial Conditions Proportion of Scarified Soil The proportion of plot substrate that is scarified soil when the run starts, as a value between 0 and 1. If a map of substrate values is included in the parameter file (see Adding to a parameter file for information on how to do this), then the map values will be used for the initial conditions and this number will be ignored. Used by the Substrate behavior.
- Initial Conditions Proportion of Tip-Up Mounds The proportion of plot substrate that is tip-up mounds substrate when the run starts, as a value between 0 and 1. If a map of substrate values is included in the parameter file (see Adding to a parameter file for information on how to do this), then the map values will be used for the initial conditions and this number will be ignored. Used by the Substrate behavior.
- Maximum Number of Years that Decay Occurs The number of years that a substrate disturbance event has effect before it is deleted - the lifetime of a substrate cohort. Used by the Substrate behavior.
- NZ Fresh Log Annual Decay Alpha The α exponent in the decay equation y = e-αtβ, as applied to fresh logs. Used by the NZ Substrate behavior.
- NZ Fresh Log Annual Decay Beta The β exponent in the decay equation y = e-αtβ, as applied to fresh logs. Used by the NZ Substrate behavior.
- NZ Initial Conditions Proportion of Decayed Logs The proportion of plot substrate that is decayed logs when the run starts, as a value between 0 and 1. If a map of substrate values is included in the parameter file (see Adding to a parameter file for information on how to do this), then the map values will be used for the initial conditions and this number will be ignored. Used by the NZ Substrate behavior.
- NZ Initial Conditions Proportion of Fresh Logs The proportion of plot substrate that is fresh logs when the run starts, as a value between 0 and 1. If a map of substrate values is included in the parameter file (see Adding to a parameter file for information on how to do this), then the map values will be used for the initial conditions and this number will be ignored. Used by the NZ Substrate behavior.
- NZ Initial Conditions Proportion of Tip-Up Mounds The proportion of plot substrate that is tip-up mounds when the run starts, as a value between 0 and 1. If a map of substrate values is included in the parameter file (see Adding to a parameter file for information on how to do this), then the map values will be used for the initial conditions and this number will be ignored. Used by the NZ Substrate behavior.
- NZ Maximum Number of Years that Decay Occurs The number of years that a substrate disturbance event has effect before it is deleted - the lifetime of a substrate cohort. Used by the NZ Substrate behavior.
- NZ Proportion of Dead that Fall The proportion of the total number of dead trees that fall each year, as a value between 0 and 1. This does not apply to snags. Used by the NZ Substrate behavior.
- NZ Proportion of Fallen that Uproot The proportion of fallen trees that uproot to create new tip-up mounds substrate, as a value between 0 and 1. Used by the NZ Substrate behavior.
- NZ Tip-Up Mounds Annual Decay Alpha The α exponent in the decay equation y = e-αtβ, as applied to tip-up mounds. Used by the NZ Substrate behavior.
- NZ Tip-Up Mounds Annual Decay Beta The β exponent in the decay equation y = e-αtβ, as applied to tip-up mounds. Used by the NZ Substrate behavior.
- NZ Uprooted Tree Radius Increase Factor for Root Rip-Out The amount by which to multiply the tree's radius when calculating the size of the new tip-up mounds exposed by fallen trees (see equation below). This is meant to allow for the effects of roots. Used by the NZ Substrate behavior.
- Partial Cut Proportion of Decayed Logs The proportion of substrate that is decayed logs in areas that had a partial cut harvest event, as a value between 0 and 1. This is not required if the Harvest behavior is not used. Used by the Substrate behavior.
- Partial Cut Proportion of Fresh Logs The proportion of substrate that is fresh logs in areas that had a partial cut harvest event, as a value between 0 and 1. This is not required if the Harvest behavior is not used. Used by the Substrate behavior.
- Partial Cut Proportion of Scarified Soil The proportion of substrate that is scarified soil in areas that had a partial cut harvest event, as a value between 0 and 1. This is not required if the Harvest behavior is not used. Used by the Substrate behavior.
- Partial Cut Proportion of Tip-Up Mounds The proportion of substrate that is tip-up mounds substrate in areas that had a partial cut harvest event, as a value between 0 and 1. This is not required if the Harvest behavior is not used. Used by the Substrate behavior.
- Proportion of Dead that Fall The proportion of the total number of dead trees that fall each year, as a value between 0 and 1. This does not apply to snags. Used by the Substrate behavior.
- Proportion of Fallen that Uproot The proportion of fallen trees that uproot to create new tip-up mound substrate, as a value between 0 and 1. Used by the Substrate behavior.
- Proportion of Litter/Moss Pool that is Moss The fixed proportion of the litter/moss pool that is moss. Expressed as a value between 0 and 1. Used by the NZ Substrate behavior.
- Proportion of Snags that Uproot The proportion of "dead" snags that uproot to create new tip-up mound substrate, as a value between 0 and 1. Not required if snags are not used in the run. Used by the Substrate behavior.
- Scarified Soil Annual Decay Alpha The α exponent in the decay equation
, as applied to scarified soil. Note that this is annual decay. Parameter files for old SORTIE versions are for five-year decay. Used by the Substrate behavior.
- Scarified Soil Annual Decay Beta The β exponent in the decay equation
, as applied to scarified soil. Note that this is annual decay. Parameter files for old SORTIE versions are for five-year decay. Used by the Substrate behavior.
- Tip-Up Mounds Annual Decay Alpha The α exponent in the decay equation
, as applied to tip-up mounds substrate. Note that this is annual decay. Parameter files for old SORTIE versions are for five-year decay. Used by the Substrate behavior.
- Tip-Up Mounds Annual Decay Beta The β exponent in the decay equation
, as applied to tip-up mounds substrate. Note that this is annual decay. Parameter files for old SORTIE versions are for five-year decay. Used by the Substrate behavior.
- Uprooted Tree Radius Increase Factor for Root Rip-Out The amount by which to multiply the tree's radius when calculating the size of the new tip-up mounds soil exposed by fallen trees (see equation below). This is meant to allow for the effects of roots. Used by the Substrate behavior.
Substrate
This behavior keeps track of five kinds of substrate: forest floor, scarified soil, tip-up mounds, decayed logs, and fresh logs. These five substrates form a cycle. Fresh logs decay into decayed logs. Decayed logs, scarified soil, and tip-up mounds decay into forest floor. (If no new substrate were created, eventually the whole forest would be uniformly covered in "forest floor" substrate.) The creation of new substrate decreases the amount of forest floor and starts the process over again.
There are two ways in which new substrate is added: harvest treatments and tree fall. Each kind of harvest treatment (partial cut, gap cut, and clear cut) has its own substrate signature, which you set in the parameters. The existing substrate proportions after a harvest are erased and replaced with this signature.
The other type of substrate change event, tree fall, allows SORTIE to account for small-scale dynamics by allowing some dead trees to fall and create tip-up mounds. When a live tree dies, there is a certain probability that the tree will fall at death to create new fresh log substrate. Snags marked as "dead" always contribute new fresh log substrate. For both dead snags and live trees, there is a certain probability that the tree will expose an area of tip-up mounds substrate. Any new substrate created this way is added in to the existing substrate, but does not completely replace it like harvest does.
Substrate relationships
Relationships 1, 4, and 6 represent the decay of the different substrates as a function of substrate age according to the equation
where t is time in years. Graphed, this equation looks like this:
In this diagram, there are two kinds of substrate, A and B. A decays into B according to the equation above. The amount of A and B together sum to 1 for this diagram. The curve for "% Remaining" is the amount of A. The curve for "% Lost/yr" is the amount of B. When β > 1, the rate of loss/time step increases over time (giving an initial lag period when there is little loss of the substrate). When β < 1 the substrate disappears most rapidly immediately after substrate creation (less likely). β = 1 gives a constant % loss per time step (i.e. exponential decline). (In this example, α = 0.0002 and β = 4.)
Relationship 3 governs the amount of fresh logs created each time step as a result of tree mortality. Each new fresh log contributes the following amount of new fresh log area:
FL = (DBH + h)/2
where:
- FL is new fresh log area, in square meters
- DBH is the DBH of the fallen tree, in m
- h is the height of the fallen tree, in m
A dead adult or sapling as a certain probability of contributing fresh log substrate; this probability is specified in the Proportion of Dead that Fall parameter. Snags always add fresh log substrate upon their "death". A tree contributes all of its fresh log area into the grid cell where it was rooted. In other words, it doesn't fall over so much as vertically collapse.
Relationship 5 governs the amount of newly exposed tip-up mounds created by fallen dead trees. For each fallen tree, the amount of new tip-up mounds area is calculated as
OA = π * (r*F)2
where
- OA is the new tip-up mounds area in square meters
- r is the tree trunk radius in meters
- F is the Uprooted Tree Radius Increase Factor for Root Rip-Out parameter, which accounts for the effects of root disturbance
A tree contributes all of its new tip-up mounds area to the grid cell where it was rooted. Saplings never create tip-up mounds. Fallen adults create new tip-ups with the probability specified in the Proportion of Fallen that Uproot parameter; snags contribute at the probability in Proportion of Fallen that Uproot.
Relationship 7 results from harvests only. Scarified soil creation results from the use of machinery and skidding during a harvest.
Relationship 2 specifies the fixed rate at which decayed logs are converted to forest floor each time step.
How it works
The relative proportions of each kind of substrate are tracked in the Substrate grid. You can change this grid's cell resolution. Within each cell, the grid keeps track of each substrate's area as a proportion of the total area.
Each timestep, Substrate looks for harvest events and tree death. It finds harvest events by looking in the Harvest grid; it finds dead trees by looking for the flag set by the Mortality behaviors. Harvest events completely replace existing substrate with their substrate signatures. Each dead tree "rolls the dice" with a random number to determine if it falls, and, if it falls, if it exposes tip-up mounds substrate. All the new substrate created by harvest and tree fall is then totaled up.
When there is new substrate in a grid cell, Substrate reduces the other substrate amounts in the cell to make way for the amount of new substrate. Then Substrate creates a record of the substrate change, called a "cohort." The substrates in a cohort decay as the cohort ages. Cohorts have a set lifetime of a certain number of years, which you set in the parameters. After this they are deleted. This means that the effects of a substrate change event linger, with decreasing intensity, for a number of years after the event occurs.
The final proportions of scarified soil, tip-up mounds, and fresh logs are found by adding up the decayed values in the cohorts. The final proportion of decayed logs is found by adding up the amount by which fresh logs have decayed in each cohort. The final proportion of forest floor is whatever grid cell area is left over.
How to apply it
Apply Substrate to all trees which can create substrate by becoming fallen logs. This generally means that it should be applied to saplings and adults of all species. Substrate cannot be applied to seedlings. Any tree species/type combination to which it is applied must also have a mortality behavior applied.
NZ substrate
This behavior theoretically keeps track of six kinds of substrate: tip-up mounds, fresh logs, decayed logs, litter, moss, and tree fern bark. The relationships for tree fern bark have not been fully worked out at this time, so it is currently omitted. The other five substrates form a cycle. Litter and moss form a common substrate pool in fixed proportion to each other. Fresh logs decay into decayed logs. Decayed logs and tip-up mounds decay into litter/moss. (If no new substrate were created, eventually the whole forest would be uniformly covered in litter and moss.) The creation of new substrate decreases the amount of litter and moss and starts the process over again.
There is one way in which new substrate is added: tree fall. Tree fall allows SORTIE to account for small-scale dynamics by allowing some dead trees to fall and create tip-up mounds. When a live tree dies, there is a certain probability that the tree will fall at death. Snags marked as "dead" are considered to have fallen over no matter what. For fallen trees, there is a certain probability that the tree will expose an area of tip-up mounds substrate.
Substrate relationships
Relationships 1, 4, and 6 represent the decay of the different substrates as a function of substrate age according to the equation
Graphed, this equation looks like this:
In this diagram, there are two kinds of substrate, A and B. A decays into B according to the equation above. The amount of A and B together sum to 1 for this diagram. The curve for "% Remaining" is the amount of A. The curve for "% Lost/yr" is the amount of B. When β > 1, the rate of loss/time step increases over time (giving an initial lag period when there is little loss of the substrate). When β < 1 the substrate disappears most rapidly immediately after substrate creation (less likely). β = 1 gives a constant % loss per time step (i.e. exponential decline). (In this example, α = 0.0002 and β = 4.)
Relationship 3 governs the amount of fresh logs created each time step as a result of tree mortality. Each new fresh log contributes the following amount of new fresh log area:
FL = (DBH + h)/2
where:
- FL is new fresh log area, in square meters
- DBH is the DBH of the fallen tree, in m
- h is the height of the fallen tree, in m
Trees are allowed to fall in a random direction. The amount of new fresh log area is distributed over the grid cells that the log overlays.
Relationship 5 governs the amount of newly exposed tip-up mounds created by fallen dead trees. For each fallen tree, the amount of new tip-up mounds area is calculated as
MS = π * (r*F)2
where
MS is the new tip-up mounds area in square meters
r is the tree radius in meters
F is the NZ Uprooted Tree Radius Increase Factor for Root Rip-Out parameter, which accounts for the effects of root disturbance
A tree contributes all of its new tip-up mounds area to the grid cell where it was rooted. Saplings never create tip-up mounds.
Relationship 7 is currently not included in the behavior but may be added at a later date.
Relationship 2 specifies the fixed rate at which decayed logs are converted to the litter/moss pool each time step.
How it works
The relative proportions of each kind of substrate are tracked in the NZ Substrate grid. You can change this grid's cell resolution. Within each cell, the grid keeps track of each substrate's area as a proportion of the total area.
Each timestep, NZ Substrate looks for tree death. It finds dead trees by looking for the flag set by the Mortality behaviors. Each dead tree "rolls the dice" with a random number to determine if it falls, and, if it falls, if it exposes tip-up mounds. All the new substrate created by tree fall is then totaled up. NZ Substrate reduces other substrate proportions to make way for the amount of new fresh log and tip-up mounds substrate. Then NZ Substrate creates a record of the substrate change, called a "cohort." The amount of substrate in a cohort decays as the cohort ages. Cohorts have a set lifetime of a certain number of years, which you set in the parameters. After this they are deleted. This means that the effects of a substrate change event linger, with decreasing intensity, for a number of years after the event occurs.
The final proportions of tip-up mounds and fresh logs are found by adding up the decayed values in the cohorts. The final proportion of decayed logs is found by adding up the amount by which fresh logs have decayed in each cohort. The final proportion of the moss/litter pool is whatever grid cell area is left over. The pool is further split into moss and litter by using the fixed proportion of each in the pool.
How to apply it
Apply NZ Substrate to all trees which can create substrate by becoming fallen logs. This generally means that it should be applied to saplings and adults of all species. NZ Substrate cannot be applied to seedlings. Any tree species/type combination to which it is applied must also have a mortality behavior applied.
Last updated: 22-Apr-2005 11:14 AM