Substrate behaviors

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.

• Boundary Between Log Diam Classes (cm) DBH boundary between the "small" and "large" log size classes, in cm. Used by the Detailed Substrate behavior.
• Clear Cut Large Logs Mean Diameter (cm) After a clear cut harvest, the mean diameter of logs in the "large" size class, in cm. This is not required if the Harvest behavior is not used. Used by the Detailed Substrate behavior.
• Clear Cut Small Logs Mean Diameter (cm) After a clear cut harvest, the mean diameter of logs in the "small" size class, in cm. This is not required if the Harvest behavior is not used. Used by the Detailed Substrate behavior.
• 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 and Detailed Substrate behaviors.
• 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 and Detailed Substrate behaviors.
• Decayed Log Annual Decay Alpha The α exponent in the decay equation , as applied to decayed logs. Note that this is annual decay. Used by the Substrate behavior.
• Decayed Log Annual Decay Beta The β exponent in the decay equation , as applied to decayed logs. Note that this is annual decay. Used by the 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. 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. Used by the Substrate behavior.
• Gap Cut Small Logs Mean Diameter (cm) After a gap cut harvest, the mean diameter of logs in the "small" size class, in cm. This is not required if the Harvest behavior is not used. Used by the Detailed Substrate behavior.
• Gap Cut Large Logs Mean Diameter (cm) After a gap cut harvest, the mean diameter of logs in the "large" size class, in cm. This is not required if the Harvest behavior is not used. Used by the Detailed 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 and Detailed Substrate behaviors. Used by the Substrate and Detailed Substrate behaviors.
• 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 and Detailed Substrate behaviors.
• 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 and Detailed Substrate behaviors.
• 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 and Detailed Substrate behaviors.
• Initial Large Logs Mean Diameter (cm) For initial conditions, the mean diameter of logs in the "large" size class, in cm. Used by the Detailed Substrate behavior.
• Initial Small Logs Mean Diameter (cm) For initial conditions, the mean diameter of logs in the "small" size class, in cm. Used by the Detailed 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 and Detailed Substrate behaviors.
• Partial Cut Large Logs Mean Diameter (cm) After a partial cut harvest, the mean diameter of logs in the "large" size class, in cm. This is not required if the Harvest behavior is not used. Used by the Detailed Substrate behavior.
• Partial Cut Small Logs Mean Diameter (cm) After a partial cut harvest, the mean diameter of logs in the "small" size class, in cm. This is not required if the Harvest behavior is not used. Used by the Detailed 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 and Detailed Substrate behaviors.
• 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 and Detailed Substrate behaviors.
• Proportion of Dead that Fall The proportion of the total number of newly 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 and Detailed Substrate behaviors.
• Proportion of Forest Floor Litter/Moss Pool that is Moss The fixed proportion of the forest floor litter/moss pool that is moss. Expressed as a value between 0 and 1. Used by the Substrate and Detailed Substrate behaviors.
• 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 and Detailed Substrate behaviors.
• Prop. Live Trees Entering Decay Class X (0-1) The proportion of live trees entering each of the five decay classes. The proportion for all five classes together must add up to 1. Used by the Detailed Substrate behavior.
• Prop. Snags Entering Decay Class X (0-1) The proportion of snags entering each of the five decay classes. The proportion for all five classes together must add up to 1. Used by the Detailed 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. Used by the Substrate and Detailed Substrate behaviors.
• Scarified Soil Annual Decay Beta The β exponent in the decay equation , as applied to scarified soil. Note that this is annual decay. Used by the Substrate and Detailed Substrate behaviors.
• Species Group Which species group (1-3) each species is assigned to. Used by the Detailed Substrate behavior.
• Species Group X Large Class Y Clear Cut Log (0-1) After a clear cut harvest, the proportion of substrate area that is large logs of species group X, decay class Y. All clear cut values added together must be less than or equal to 1. This is not required if the Harvest behavior is not used. Used by the Detailed Substrate behavior.
• Species Group X Small Class Y Clear Cut Log (0-1) After a clear cut harvest, the proportion of substrate area that is small logs of species group X, decay class Y. All clear cut values added together must be less than or equal to 1. This is not required if the Harvest behavior is not used. Used by the Detailed Substrate behavior.
• Species Group X Large Class Y Gap Cut Log (0-1) After a gap cut harvest, the proportion of substrate area that is large logs of species group X, decay class Y. All gap cut values added together must be less than or equal to 1. This is not required if the Harvest behavior is not used. Used by the Detailed Substrate behavior.
• Species Group X Small Class Y Gap Cut Log (0-1) After a gap cut harvest, the proportion of substrate area that is small logs of species group X, decay class Y. All gap cut values added together must be less than or equal to 1. This is not required if the Harvest behavior is not used. Used by the Detailed Substrate behavior.
• Species Group X Large Class Y Initial Log Prop (0-1) For the initial conditions, the proportion of substrate area that is large logs of species group X, decay class Y. All initial conditions values added together must be less than or equal to 1. Used by the Detailed Substrate behavior.
• Species Group X Small Class Y Initial Log Prop (0-1) For the initial conditions, the proportion of substrate area that is small logs of species group X, decay class Y. All initial conditions values added together must be less than or equal to 1. Used by the Detailed Substrate behavior.
• Species Group X Large Class Y Log Decay Alpha The α exponent in the decay equation, as applied to large logs of species group X, decay class Y. This value must be a negative number. Used by the Detailed Substrate behavior.
• Species Group X Small Class Y Log Decay Alpha The α exponent in the decay equation, as applied to small logs of species group X, decay class Y. This value must be a negative number. Used by the Detailed Substrate behavior.
• Species Group X Large Class Y Log Decay Beta The β exponent in the decay equation, as applied to large logs of species group X, decay class Y. Used by the Detailed Substrate behavior.
• Species Group X Small Class Y Log Decay Beta The β exponent in the decay equation, as applied to small logs of species group X, decay class Y. Used by the Detailed Substrate behavior.
• Species Group X Large Class Y Partial Cut Log (0-1) After a partial cut harvest, the proportion of substrate area that is large logs of species group X, decay class Y. All partial cut values added together must be less than or equal to 1. This is not required if the Harvest behavior is not used. Used by the Detailed Substrate behavior.
• Species Group X Small Class Y Partial Cut Log (0-1) After a partial cut harvest, the proportion of substrate area that is small logs of species group X, decay class Y. All partial cut values added together must be less than or equal to 1. This is not required if the Harvest behavior is not used. Used by the Detailed 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. Used by the Substrate and Detailed Substrate behaviors.
• 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. Used by the Substrate and Detailed Substrate behaviors.
• 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 and Detailed Substrate behaviors.
• Use Directional Tree Fall If true, dead trees fall in a random direction and possibly contribute new fresh log across several Substrate grid cells. If false, dead trees collapse vertically and contribute all their fresh log area to the cell in which they are rooted. Used by the Substrate and Detailed Substrate behaviors.

This behavior keeps track of six kinds of substrate: forest floor litter, forest floor moss, scarified soil, tip-up mounds, decayed logs, and fresh logs. Forest floor litter and forest floor moss form a common pool in fixed relative proportion to each other. These six substrates form a cycle. Fresh logs decay into decayed logs. Decayed logs, scarified soil, and tip-up mounds decay into forest floor litter and moss. (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 litter and moss 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

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. For the purposes of adding new substrate, fallen logs are assumed to be cone-shaped. Since they land on their sides, the area of the cone is approximated to a triangle. Thus, each new fresh log contributes the following amount of new fresh log area:

• 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".

How new fresh log area is distributed depends on the value in the Use Directional Tree Fall parameter. If false, a dead 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. If true, a trees is 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

• 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.

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 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 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.

This behavior is a modification of the Substrate behavior that primarily incorporates greater detail in tracking log cover. In Detailed Substrate, the pool for logs is divided into up to 3 species groups, 2 size classes, and 5 decay classes, whereas the Substrate behavior has 1 species/size class and 2 decay classes for logs. Also, unlike Substrate, Detailed Substrate is designed to work with snag dynamics behaviors that assign data members representing fall or break heights of trees and snags. This way, the processes of tree (and snag) breakage and fall are separated from their input into the log substrate pool. There is also a change from Substrate to the way harvesting adds new substrate, and values for log volume are calculated in addition to projected area (cover).

Like Substrate, Detailed Substrate keeps track of the relative cover of forest floor litter, moss, scarified soil, tip-up mounds, and logs each timestep. Unless explained otherwise, the manner in which Detailed Substrate calculates and tracks these components is the same as for the Substrate behavior.

Detailed Substrate divides logs into species groups, size classes, and decay classes. Logs in each combination of species group, size class, and decay class can have different initial proportions, proportions after harvest, and decay parameters from all other types of logs. Each species to which this behavior is assigned belongs to one species group (assigned with the Species Group parameter). As saplings, adults, and snags enter the substrate pool, they are added to the logs for the appropriate species group. Log substrate belongs to one of two size classes defined by diameter. The threshold diameter separating the two size classes is defined by the Boundary Between Log Diam Classes (cm) parameter. When a sapling, adult, or snag enters the substrate pool, the area input to each size class is calculated separately. The species group and size class to which log substrate is added do not change over time.

Log substrate is also divided into 5 decay classes. Over time, decay class 1 logs decay into decay class 2 logs, then decay class 3 logs, then decay class 4 logs, then decay class 5 logs, then forest floor litter and moss. The relationship among these states, as well as tip-up mounds and scarified soil, is depicted in the figure below.

Like in Substrate, decay among the log decay classes and for tip-up mounds and scarified soil (relationships 1-5, 7, and 9), is a function of substrate age according to the equation:

where t is time in years since the last decay transition. Decay calculations for the 5 log decay classes are performed on an annual basis so it is possible to advance by more than one decay class in a single multi-year timestep. At the end of each timestep, the age of all logs is rounded to the nearest multiple of the timestep duration. This is necessary to keep memory requirements manageable.

Log substrate is created by the processes of tree fall and breakage along the bole (relationship 6). Detailed Substrate looks at flags set by mortality and snag dynamics behaviors to determine whether a sapling, adult tree, or snag has either fallen or broken to a certain height in the current timestep. If so, it adds the appropriate area to the log substrate pool. Like in Substrate, tree boles are modeled as cones. The projected horizontal area is therefore a triangle if the top of the tree is included, or a trapezoid if only considering the lower section of a tree. New log substrate does not need to enter in decay class 1: the Prop. Live Trees Entering Decay Class X (0-1) and Prop. Snags Entering Decay Class X (0-1) parameters determine the probability of entering the substrate pool in each of the 5 decay classes for both snags and dead saplings/adults.

Detailed Substrate allows new substrate proportions to be specified following clear cut, gap, and partial harvesting. If the total proportion of substrate after harvesting specified by parameters is less than 1, the remainder will be distributed in proportion to pre-harvest substrate values. In comparison, remaining substrate after harvest is assigned to moss and litter pools in the Substrate behavior. This change is designed to allow legacy substrates, such as logs and tip-up mounds, to persist after a harvest event.

In addition to tracking log area, Detailed Substrate also stores the volume of each type of log substrate in each grid cell. For new inputs, log volume is calculated as:

where:

• LV is new log volume, in m³
• DBH is the DBH of the fallen tree, in m
• h is the height of the fallen tree, in m

For initial volume and volume added after harvest:

where:

• LV is initial log volume or volume added after harvest, in m³/ha
• PLA is the proportional log area in the grid cell, from 0 to 1
• MDBH is the mean DBH of logs of that type (either initial or added by harvest). These are set with parameters. A reasonable default is values of 0.5 and 1.5 of the diameter boundary are used for small and large size classes, respectively

Log volume differs from log area proportions in that it does not have an upper bound. Each time new substrate is added, existing log substrate proportions are reduced so that the total of all substrate proportions is still less than or equal to 1. However, new inputs from tree fall and breakage do not reduce existing log volume (that is, logs can be on top of each other and still contribute to volume but not area). The volume of logs is reduced after harvesting when scarified soil is added (that is, log volume is destroyed in the area that is scarified). Log volume also decreases as pieces decay from decay class 5 to forest floor litter and moss.

How it works

The relative proportions of each kind of substrate are tracked in the Detailed Substrate grid. Within each cell, the grid keeps track of each substrate's area as a proportion of the total area, as well as volume for each type of log substrate in m³/ha. The behavior also summarizes and copies values into the Substrate grid for compatibility with other behaviors that use that grid.

Each timestep, Detailed Substrate looks for harvest events and new tree inputs. It finds harvest events by looking in the Harvest grid. Harvest events add new scarified soil, tip-up, and log substrate. The behavior finds fallen and broken trees by looking for the flags set by mortality and snag dynamics behaviors. Each fallen and broken tree (or snag) "rolls the dice" with a random number to determine the log decay class it will enter as substrate. Fallen adult trees and snags also use a random number to determine whether they expose tip-up mound substrate. All the new substrate created by harvest and tree inputs is then totaled up. When there is new substrate in a grid cell, Detailed Substrate reduces the other substrate amounts in the cell to make way for the amount of new substrate.

All existing substrates are decayed each timestep as they age. After they reach their maximum lifespan, which is set by parameters, they are deleted. The final proportions of scarified soil, tip-up, and logs are found by adding up the values representing each substrate age. 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 fixed proportions of each in the pool, as specified by the Proportion of Forest Floor Litter/Moss Pool that is Moss parameter.

How to apply it

Apply Detailed Substrate to all trees which can create substrate by becoming fallen logs. This generally means that it should be applied to saplings, adults, and snags of all species. Substrate cannot be applied to seedlings. Any tree species/type combination to which it is applied must also have a mortality and snag dynamics behavior applied.