[27]:

from IPython.display import display, Markdown
import os
import json
from libcbm import resources
import pandas as pd
import numpy as np
from numpy.random import default_rng
from libcbm.model.cbm_exn import cbm_exn_model
from libcbm.model.cbm_exn import cbm_exn_spinup
from libcbm.model.cbm_exn import cbm_exn_step
from libcbm.model.cbm_exn.cbm_exn_parameters import parameters_factory
from libcbm.model.model_definition.model_variables import ModelVariables

[28]:

rng = default_rng()
n_stands = 10

[29]:

# load the default bundled parameters
parameters = parameters_factory(resources.get_cbm_exn_parameters_dir())

Fully dynamic modelling with cbm_exn¶

This document illustrates a scheme to simulate with fully dynamic pools, fluxes and flow in libcbm using the cbm_exn package.

This outlines a component of a highly efficient method for processing C flows in a CBM-Like model, producing outputs that are compatible with current reporting methods, and systems.

The approach makes the hard coded model pool, flow, flux in CBM-CFS3 fully dynamic, and definable via high level language in the cbm_exn package.

Prior to this improvement, using CBM-CFS3, it was only possible to modify parameters for the pool-flows withing the hard-coded model structure. This opens up opportunities to evaluate changes to model structure dynamically, in addition to modifiying pool flows.

In addition the architecture opens opportunities for using machine learning both for informing pool flow parameters and the model structure itself.

The document explains the basic structure of the default parameters and configuration in cbm_exn, and also shows the an example of the default pool flows generated in dataframe form, and describes their format.

While only the default pool flows (based on CBM-CFS3) are presented here, it’s important to note if the general format is followed it’s possible to alter model pool-flow-flux structure via high level programming language. The default values could potentially be used as a template to accomplish this.

Sections below are:

Operation DataFrame: a description of the storage scheme for mult-dimensional pool flow proportions within dataframe structures.
Default spinup operation dataframes: examples of spinup ops derived from the cbm_exn default parameters and example simulation area input
Default step operation dataframes: example of step ops also derived from the same inputs
Appendix1, Appendix2: the default parameters, and example simulation area used.

[30]:

# read some packaged net increments, derived from a
# simulation of the same growth curve used in CBM-CFS3
# tutorial 1
net_increments = pd.read_csv(
    os.path.join(
        resources.get_test_resources_dir(),
        "cbm_exn_net_increments",
        "net_increments.csv",
    )
)

[31]:

# the same set of increments are repeated for each stand in this example
n_stands = 1000
increments = None
for s in range(n_stands):
    s_increments = net_increments.copy()
    s_increments.insert(0, "row_idx", s)
    s_increments = s_increments.rename(
        columns={
            "SoftwoodMerch": "merch_inc",
            "SoftwoodFoliage": "foliage_inc",
            "SoftwoodOther": "other_inc",
        }
    )
    increments = pd.concat([increments, s_increments])

[32]:

# create the require inputs for spinup
spinup_input = {
    "parameters": pd.DataFrame(
        {
            # random age
            "age": rng.integers(low=0, high=60, size=n_stands, dtype="int"),
            "area": np.full(n_stands, 1, dtype="int"),
            "delay": np.full(n_stands, 0, dtype="int"),
            "return_interval": np.full(n_stands, 125, dtype="int"),
            "min_rotations": np.full(n_stands, 10, dtype="int"),
            "max_rotations": np.full(n_stands, 30, dtype="int"),
            "spatial_unit_id": np.full(
                n_stands, 17, dtype="int"
            ),  # ontario/mixedwood plains
            "species": np.full(n_stands, 20, dtype="int"),  # red pine
            "mean_annual_temperature": np.arange(
                0, 2, 2 / n_stands
            ),  # make a temperature ramp
            "historical_disturbance_type": np.full(n_stands, 1, dtype="int"),
            "last_pass_disturbance_type": np.full(n_stands, 1, dtype="int"),
        }
    ),
    "increments": increments,
}

[33]:

spinup_vars = cbm_exn_spinup.prepare_spinup_vars(
    ModelVariables.from_pandas(spinup_input),
    parameters,
)
spinup_op_list = cbm_exn_spinup.get_default_op_list()
spinup_ops = cbm_exn_spinup.get_default_ops(parameters, spinup_vars)

[34]:

spinup_op_list

[34]:

['growth',
 'snag_turnover',
 'biomass_turnover',
 'overmature_decline',
 'growth',
 'dom_decay',
 'slow_decay',
 'slow_mixing',
 'disturbance']

Operation dataframes¶

Operation dataframes are multi-dimensional sparse matrices, using column-name-formatting to denote the dimensions.

The rationale for this design apporach is that multi-dimensional arrays lack interoperable standards that would work with many different high level languages simulataneously. Dataframes however are well supported by several high level languages.

Each dataframe has pool flow columns, where the column name is of the form:

pool_source_name.pool_sink_name

Each row can be interpreted as a pool flow matrix (in sparse coordinate form). By default unspecified diagnal values (those where pool_source_name is equal to pool_sink_name) will be assigned a value of 1.

There are 4 basic types of dataframes with regards to mapping to simulation space. These are covered in the next section

Single row¶

The single row is a matrix that is applied to all simulation areas. See the slow_mixing dataframe in the following section.

Simulation-aligned¶

the dataframe has a row for each simulation area in subsequent spinup or step calls. Each row represents a matrix that is 1:1 with simulation areas This type is appropriate for processes that vary by simulation area. See the dom_decay dataframe in the followin section.

Property-indexed¶

A property-index dataframe has one or more values that correspond to values stored in the current simulation state. This type of dataframe contains 1 or more columns of the form:

[table_name.variable_name]

Where a simulation table, series name pair is surrounded by left and right brackets.

An example of this is if one flow matrix is defined for each spatial unit identifier. See the disturbance dataframe in the following section for an example.

Both Simulation-aligned, and Property-indexed¶

If a dataframe is both simulation aligned and property indexed each row corresponds to both a simulation area, and 1 or more properties within the simulation areas. The following pattern of columns is present in this type of dataframe:

[row_idx], [table_name_1.variable_name_1], ... [table_name_N.variable_name_N]

An example of this is a dataframe of matrices where each row corresponds to the simulation areas, and to simulation age. See the spinup growth dataframe in the following section.

Default spinup operation dataframes¶

The default spinup operation dataframes are generated as a function of the default parameters (see appendix 1) and the simulation area input (Appendix 2).

The libcbm.model.cbm_exn.cbm_exn_spinup.spinup function can directly ingest operations in this format via the ops parameter.

Within a spinup timestep these operations are applied in the following order by default. The order and naming of these operation is user-specifyable via passing a string list to the op_sequence parameter of the above linked function

growth
snag_turnover
biomass_turnover
overmature_decline
growth
dom_decay
slow_decay
slow_mixing
disturbance

[35]:

for op in spinup_ops:
    display(Markdown(f"## {op['name']}"))
    display(op["op_data"])

snag_turnover¶

	[parameters.spatial_unit_id]	[parameters.sw_hw]	StemSnag.StemSnag	StemSnag.MediumSoil	BranchSnag.BranchSnag	BranchSnag.AboveGroundFastSoil
0	1	0	0.968	0.032	0.9	0.1
1	3	0	0.968	0.032	0.9	0.1
2	4	0	0.968	0.032	0.9	0.1
3	5	0	0.968	0.032	0.9	0.1
4	6	0	0.968	0.032	0.9	0.1
...	...	...	...	...	...	...
91	52	1	0.968	0.032	0.9	0.1
92	53	1	0.968	0.032	0.9	0.1
93	54	1	0.968	0.032	0.9	0.1
94	58	1	0.968	0.032	0.9	0.1
95	59	1	0.968	0.032	0.9	0.1

96 rows × 6 columns

biomass_turnover¶

	[parameters.spatial_unit_id]	[parameters.sw_hw]	Merch.StemSnag	Foliage.AboveGroundVeryFastSoil	Other.BranchSnag	Other.AboveGroundFastSoil	CoarseRoots.AboveGroundFastSoil	CoarseRoots.BelowGroundFastSoil	FineRoots.AboveGroundVeryFastSoil	FineRoots.BelowGroundVeryFastSoil
0	1	0	0.0050	0.10	0.0100	0.0300	0.01	0.01	0.3205	0.3205
1	3	0	0.0060	0.05	0.0075	0.0225	0.01	0.01	0.3205	0.3205
2	4	0	0.0050	0.10	0.0100	0.0300	0.01	0.01	0.3205	0.3205
3	5	0	0.0067	0.15	0.0100	0.0300	0.01	0.01	0.3205	0.3205
4	6	0	0.0067	0.15	0.0100	0.0300	0.01	0.01	0.3205	0.3205
...	...	...	...	...	...	...	...	...	...	...
91	52	1	0.0050	0.95	0.0100	0.0300	0.01	0.01	0.3205	0.3205
92	53	1	0.0060	0.95	0.0100	0.0300	0.01	0.01	0.3205	0.3205
93	54	1	0.0045	0.95	0.0100	0.0300	0.01	0.01	0.3205	0.3205
94	58	1	0.0060	0.95	0.0075	0.0225	0.01	0.01	0.3205	0.3205
95	59	1	0.0050	0.95	0.0100	0.0300	0.01	0.01	0.3205	0.3205

96 rows × 10 columns

dom_decay¶

	AboveGroundVeryFastSoil.AboveGroundVeryFastSoil	AboveGroundVeryFastSoil.AboveGroundSlowSoil	AboveGroundVeryFastSoil.CO2	BelowGroundVeryFastSoil.BelowGroundVeryFastSoil	BelowGroundVeryFastSoil.BelowGroundSlowSoil	BelowGroundVeryFastSoil.CO2	AboveGroundFastSoil.AboveGroundFastSoil	AboveGroundFastSoil.AboveGroundSlowSoil	AboveGroundFastSoil.CO2	BelowGroundFastSoil.BelowGroundFastSoil	...	BelowGroundFastSoil.CO2	MediumSoil.MediumSoil	MediumSoil.AboveGroundSlowSoil	MediumSoil.CO2	StemSnag.StemSnag	StemSnag.AboveGroundSlowSoil	StemSnag.CO2	BranchSnag.BranchSnag	BranchSnag.AboveGroundSlowSoil	BranchSnag.CO2
0	0.866038	0.024783	0.109179	0.750000	0.042500	0.207500	0.928250	0.012198	0.059552	0.928250	...	0.059552	0.981300	0.003179	0.015521	0.990650	0.001590	0.007760	0.964125	0.006099	0.029776
1	0.866012	0.024788	0.109201	0.749965	0.042506	0.207529	0.928240	0.012199	0.059561	0.928240	...	0.059561	0.981297	0.003179	0.015523	0.990649	0.001590	0.007762	0.964120	0.006100	0.029780
2	0.865986	0.024793	0.109222	0.749931	0.042512	0.207558	0.928230	0.012201	0.059569	0.928230	...	0.059569	0.981295	0.003180	0.015525	0.990647	0.001590	0.007763	0.964115	0.006100	0.029785
3	0.865959	0.024798	0.109243	0.749896	0.042518	0.207586	0.928220	0.012203	0.059577	0.928220	...	0.059577	0.981292	0.003180	0.015527	0.990646	0.001590	0.007764	0.964110	0.006101	0.029789
4	0.865933	0.024802	0.109264	0.749861	0.042524	0.207615	0.928210	0.012204	0.059586	0.928210	...	0.059586	0.981290	0.003181	0.015530	0.990645	0.001590	0.007765	0.964105	0.006102	0.029793
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
995	0.837367	0.030087	0.132546	0.713024	0.048786	0.238190	0.917638	0.014002	0.068360	0.917638	...	0.068360	0.978534	0.003649	0.017817	0.989267	0.001825	0.008908	0.958819	0.007001	0.034180
996	0.837335	0.030093	0.132572	0.712985	0.048793	0.238223	0.917627	0.014003	0.068370	0.917627	...	0.068370	0.978531	0.003650	0.017819	0.989266	0.001825	0.008910	0.958813	0.007002	0.034185
997	0.837304	0.030099	0.132597	0.712945	0.048799	0.238256	0.917615	0.014005	0.068379	0.917615	...	0.068379	0.978528	0.003650	0.017822	0.989264	0.001825	0.008911	0.958808	0.007003	0.034190
998	0.837272	0.030105	0.132623	0.712905	0.048806	0.238289	0.917604	0.014007	0.068389	0.917604	...	0.068389	0.978525	0.003651	0.017824	0.989263	0.001825	0.008912	0.958802	0.007004	0.034194
999	0.837240	0.030111	0.132649	0.712865	0.048813	0.238322	0.917592	0.014009	0.068398	0.917592	...	0.068398	0.978522	0.003651	0.017826	0.989261	0.001826	0.008913	0.958796	0.007005	0.034199

1000 rows × 21 columns

slow_decay¶

	AboveGroundSlowSoil.AboveGroundSlowSoil	AboveGroundSlowSoil.CO2	BelowGroundSlowSoil.BelowGroundSlowSoil	BelowGroundSlowSoil.CO2
0	0.994340	0.005660	0.9967	0.0033
1	0.994339	0.005661	0.9967	0.0033
2	0.994337	0.005663	0.9967	0.0033
3	0.994336	0.005664	0.9967	0.0033
4	0.994335	0.005665	0.9967	0.0033
...	...	...	...	...
995	0.993128	0.006872	0.9967	0.0033
996	0.993127	0.006873	0.9967	0.0033
997	0.993126	0.006874	0.9967	0.0033
998	0.993124	0.006876	0.9967	0.0033
999	0.993123	0.006877	0.9967	0.0033

1000 rows × 4 columns

slow_mixing¶

	AboveGroundSlowSoil.BelowGroundSlowSoil	AboveGroundSlowSoil.AboveGroundSlowSoil
0	0.006	0.994

disturbance¶

	[parameters.spatial_unit_id]	[state.disturbance_type]	[parameters.sw_hw]	AboveGroundFastSoil.AboveGroundFastSoil	AboveGroundFastSoil.AboveGroundSlowSoil	AboveGroundFastSoil.BelowGroundFastSoil	AboveGroundFastSoil.CH4	AboveGroundFastSoil.CO	AboveGroundFastSoil.CO2	AboveGroundFastSoil.MediumSoil	...	Other.Other	Other.Products	Products.Products	StemSnag.AboveGroundSlowSoil	StemSnag.CH4	StemSnag.CO	StemSnag.CO2	StemSnag.MediumSoil	StemSnag.Products	StemSnag.StemSnag
0	1	0	0	1.000000	0.0	0.0	0.000000	0.000000	0.000000	0.0	...	1.0	0.0	1.0	0.0	0.0	0.0	0.0	0.0	0.0	1.0
1	3	0	0	1.000000	0.0	0.0	0.000000	0.000000	0.000000	0.0	...	1.0	0.0	1.0	0.0	0.0	0.0	0.0	0.0	0.0	1.0
2	4	0	0	1.000000	0.0	0.0	0.000000	0.000000	0.000000	0.0	...	1.0	0.0	1.0	0.0	0.0	0.0	0.0	0.0	0.0	1.0
3	5	0	0	1.000000	0.0	0.0	0.000000	0.000000	0.000000	0.0	...	1.0	0.0	1.0	0.0	0.0	0.0	0.0	0.0	0.0	1.0
4	6	0	0	1.000000	0.0	0.0	0.000000	0.000000	0.000000	0.0	...	1.0	0.0	1.0	0.0	0.0	0.0	0.0	0.0	0.0	1.0
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
12747	52	1	1	0.386657	0.0	0.0	0.006133	0.055201	0.552009	0.0	...	0.0	0.0	1.0	0.0	0.0	0.0	0.0	1.0	0.0	0.0
12748	53	1	1	0.444126	0.0	0.0	0.005559	0.050029	0.500287	0.0	...	0.0	0.0	1.0	0.0	0.0	0.0	0.0	1.0	0.0	0.0
12749	54	1	1	0.448397	0.0	0.0	0.005516	0.049644	0.496443	0.0	...	0.0	0.0	1.0	0.0	0.0	0.0	0.0	1.0	0.0	0.0
12750	58	1	1	0.338494	0.0	0.0	0.006615	0.059536	0.595355	0.0	...	0.0	0.0	1.0	0.0	0.0	0.0	0.0	1.0	0.0	0.0
12751	59	1	1	0.338494	0.0	0.0	0.006615	0.059536	0.595355	0.0	...	0.0	0.0	1.0	0.0	0.0	0.0	0.0	1.0	0.0	0.0

12752 rows × 101 columns

growth¶

	[row_idx]	[state.age]	Input.Merch	Input.Other	Input.Foliage	Input.CoarseRoots	Input.FineRoots
0	0	0	0.009449	0.009383	0.020006	0.004955	0.003667
1	0	1	0.041615	0.049833	0.040492	0.016929	0.012362
2	0	2	0.085850	0.094331	0.054661	0.030487	0.021648
3	0	3	0.138499	0.138077	0.066074	0.045285	0.030783
4	0	4	0.197727	0.179735	0.075630	0.061304	0.039282
...	...	...	...	...	...	...	...
70995	999	66	0.000000	0.000000	0.000000	0.000000	0.000000
70996	999	67	0.000000	0.000000	0.000000	0.000000	0.000000
70997	999	68	0.000000	0.000000	0.000000	0.000000	0.000000
70998	999	69	0.000000	0.000000	0.000000	0.000000	0.000000
70999	999	70	0.000000	0.000000	0.000000	0.000000	0.000000

71000 rows × 7 columns

overmature_decline¶

	[row_idx]	[state.age]	Merch.StemSnag	Other.BranchSnag	Other.AboveGroundFastSoil	Foliage.AboveGroundVeryFastSoil	CoarseRoots.AboveGroundFastSoil	CoarseRoots.BelowGroundFastSoil	FineRoots.AboveGroundVeryFastSoil	FineRoots.BelowGroundVeryFastSoil
0	0	0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
1	0	1	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
2	0	2	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
3	0	3	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
4	0	4	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
...	...	...	...	...	...	...	...	...	...	...
70995	999	66	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
70996	999	67	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
70997	999	68	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
70998	999	69	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
70999	999	70	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0

71000 rows × 10 columns

Run the spinup routine with the default operations passed as a parameter

[36]:

with cbm_exn_model.initialize() as model:
    cbm_vars = cbm_exn_spinup.spinup(
        model, spinup_vars, ops=spinup_ops, op_sequence=spinup_op_list
    )

[37]:

# initialize parameters for stepping (values for illustration)
cbm_vars["parameters"]["mean_annual_temperature"].assign(1.1)
cbm_vars["parameters"]["merch_inc"].assign(0.1)
cbm_vars["parameters"]["foliage_inc"].assign(0.01)
cbm_vars["parameters"]["other_inc"].assign(0.05)
cbm_vars["parameters"]["disturbance_type"].assign(
    rng.choice([0, 1, 4], n_stands, p=[0.98, 0.01, 0.01])
)

[38]:

step_ops_sequence = cbm_exn_step.get_default_annual_process_op_sequence()
step_disturbance_ops_sequence = (
    cbm_exn_step.get_default_disturbance_op_sequence()
)
step_ops = cbm_exn_step.get_default_ops(parameters, cbm_vars)

[39]:

step_disturbance_ops_sequence

[39]:

['disturbance']

[40]:

step_ops_sequence

[40]:

['growth',
 'snag_turnover',
 'biomass_turnover',
 'overmature_decline',
 'growth',
 'dom_decay',
 'slow_decay',
 'slow_mixing']

Step processes¶

With the exception of growth and overmature decline, the default step processes use an identical process for generation as the spinup processes, and so only growth and overmature decline are shown below.

The difference is that by default in stepping, growth and overmature decline dataframes are both Simulation-aligned.

The libcbm.model.cbm_exn.cbm_exn_step.step function can directly ingest operations in this format via the ops parameter

[41]:

for op in step_ops:
    name = op["name"]
    if name in ["growth", "overmature_decline"]:
        display(Markdown(f"## {name}"))
        display(op["op_data"])

growth¶

	Input.Merch	Input.Other	Input.Foliage	Input.CoarseRoots	Input.FineRoots
0	0.05	0.025	0.005	0.017196	0.000564
1	0.05	0.025	0.005	0.013941	0.003819
2	0.05	0.025	0.005	0.017014	0.000746
3	0.05	0.025	0.005	0.017046	0.000714
4	0.05	0.025	0.005	0.017068	0.000692
...	...	...	...	...	...
995	0.05	0.025	0.005	0.014380	0.003380
996	0.05	0.025	0.005	0.017109	0.000651
997	0.05	0.025	0.005	0.015855	0.001905
998	0.05	0.025	0.005	0.014380	0.003380
999	0.05	0.025	0.005	0.016869	0.000891

1000 rows × 5 columns

overmature_decline¶

	Merch.StemSnag	Other.BranchSnag	Other.AboveGroundFastSoil	Foliage.AboveGroundVeryFastSoil	CoarseRoots.AboveGroundFastSoil	CoarseRoots.BelowGroundFastSoil	FineRoots.AboveGroundVeryFastSoil	FineRoots.BelowGroundVeryFastSoil
0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
1	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
2	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
3	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
4	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
...	...	...	...	...	...	...	...	...
995	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
996	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
997	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
998	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
999	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0

1000 rows × 8 columns

run a timestep with the specified parameters

[42]:

with cbm_exn_model.initialize() as model:
    cbm_vars = cbm_exn_step.step(
        model,
        cbm_vars,
        ops=step_ops,
        step_op_sequence=step_ops_sequence,
        disturbance_op_sequence=step_disturbance_ops_sequence,
    )

[43]:

cbm_vars["pools"].to_pandas()

[43]:

	Input	Merch	Foliage	Other	CoarseRoots	FineRoots	AboveGroundVeryFastSoil	BelowGroundVeryFastSoil	AboveGroundFastSoil	BelowGroundFastSoil	MediumSoil	AboveGroundSlowSoil	BelowGroundSlowSoil	StemSnag	BranchSnag	CO2	CH4	CO	NO2	Products
0	1.0	73.280370	7.178385	21.031789	20.379709	2.151192	9.947479	1.968485	10.564232	2.449042	57.708379	38.779972	127.722972	22.150185	1.350400	7723.799871	8.475443	76.277752	0.0	0.0
1	1.0	7.774118	1.920598	5.284176	2.297170	1.028144	2.180844	0.769231	14.300553	6.267484	59.129590	34.133895	129.648400	54.009079	3.155953	7608.867436	8.474532	76.269556	0.0	0.0
2	1.0	89.648104	8.665880	25.289823	25.107673	2.332372	12.248857	2.156594	13.017832	2.845668	52.095064	41.999048	127.418286	18.394004	1.710146	7789.726276	8.473622	76.261360	0.0	0.0
3	1.0	86.794134	8.390010	24.485410	24.270207	2.296434	11.722687	2.114842	12.323974	2.721871	53.695097	41.024695	127.446422	19.127702	1.623961	7770.320595	8.472711	76.253165	0.0	0.0
4	1.0	84.872181	8.204230	23.943693	23.705336	2.273127	11.412086	2.089355	11.959022	2.658248	54.497336	40.548368	127.473572	19.574634	1.574184	7760.799934	8.471801	76.244972	0.0	0.0
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
995	1.0	9.338820	2.147632	6.058011	2.751865	1.143006	2.266580	0.757995	11.935299	4.905127	53.628358	32.404702	124.955399	50.929667	2.618341	7638.111865	7.617916	68.560102	0.0	0.0
996	1.0	81.277491	7.856761	22.930502	22.646881	2.231494	9.202949	1.790814	9.963568	2.183926	48.055328	37.770128	122.998702	19.467886	1.445742	7774.280777	7.617101	68.552767	0.0	0.0
997	1.0	17.020424	3.072825	9.243063	4.991417	1.521245	3.487677	1.076058	10.145725	3.619583	54.966027	32.991306	124.594030	43.196613	1.716888	7654.197317	7.616286	68.545434	0.0	0.0
998	1.0	9.338820	2.147632	6.058011	2.751865	1.143006	2.265884	0.757736	11.929870	4.902391	53.611115	32.398762	124.940633	50.926692	2.617775	7638.186920	7.615472	68.538101	0.0	0.0
999	1.0	29.410534	3.937428	11.838268	8.248054	1.783289	4.867150	1.355955	8.783199	2.640505	55.291161	33.722775	124.187274	35.563809	1.235053	7674.474894	7.614657	68.530769	0.0	0.0

1000 rows × 20 columns

[44]:

cbm_vars["flux"].to_pandas()

[44]:

	DisturbanceCO2Production	DisturbanceCH4Production	DisturbanceCOProduction	DisturbanceBioCO2Emission	DisturbanceBioCH4Emission	DisturbanceBioCOEmission	DecayDOMCO2Emission	DisturbanceProduction	DisturbanceDOMProduction	DeltaBiomass_AG	...	DisturbanceFineLitterInput	DisturbanceVFastAGToAir	DisturbanceVFastBGToAir	DisturbanceFastAGToAir	DisturbanceFastBGToAir	DisturbanceMediumToAir	DisturbanceSlowAGToAir	DisturbanceSlowBGToAir	DisturbanceStemSnagToAir	DisturbanceBranchSnagToAir
0	0.0	0.0	0.0	0.0	0.0	0.0	4.819715	0.0	0.0	0.16	...	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
1	0.0	0.0	0.0	0.0	0.0	0.0	4.199927	0.0	0.0	0.16	...	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
2	0.0	0.0	0.0	0.0	0.0	0.0	5.308425	0.0	0.0	0.16	...	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
3	0.0	0.0	0.0	0.0	0.0	0.0	5.188081	0.0	0.0	0.16	...	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
4	0.0	0.0	0.0	0.0	0.0	0.0	5.118937	0.0	0.0	0.16	...	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
995	0.0	0.0	0.0	0.0	0.0	0.0	3.784433	0.0	0.0	0.16	...	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
996	0.0	0.0	0.0	0.0	0.0	0.0	4.391971	0.0	0.0	0.16	...	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
997	0.0	0.0	0.0	0.0	0.0	0.0	3.772003	0.0	0.0	0.16	...	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
998	0.0	0.0	0.0	0.0	0.0	0.0	3.783260	0.0	0.0	0.16	...	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
999	0.0	0.0	0.0	0.0	0.0	0.0	3.819926	0.0	0.0	0.16	...	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0

1000 rows × 47 columns

Appendix 1: CBM EXN Default parameters¶

[45]:

for k, v in parameters._data.items():
    display(Markdown(f"## {k}"))
    if isinstance(v, list):
        display(Markdown(f"```json\n{json.dumps(v, indent=4)}\n```"))
    else:
        display(v)

pools¶

[
    "Input",
    "Merch",
    "Foliage",
    "Other",
    "CoarseRoots",
    "FineRoots",
    "AboveGroundVeryFastSoil",
    "BelowGroundVeryFastSoil",
    "AboveGroundFastSoil",
    "BelowGroundFastSoil",
    "MediumSoil",
    "AboveGroundSlowSoil",
    "BelowGroundSlowSoil",
    "StemSnag",
    "BranchSnag",
    "CO2",
    "CH4",
    "CO",
    "NO2",
    "Products"
]

flux¶

[
    {
        "name": "DisturbanceCO2Production",
        "process": "Disturbance",
        "source_pools": [
            "Merch",
            "Foliage",
            "Other",
            "CoarseRoots",
            "FineRoots",
            "AboveGroundVeryFastSoil",
            "BelowGroundVeryFastSoil",
            "AboveGroundFastSoil",
            "BelowGroundFastSoil",
            "MediumSoil",
            "AboveGroundSlowSoil",
            "BelowGroundSlowSoil",
            "StemSnag",
            "BranchSnag"
        ],
        "sink_pools": [
            "CO2"
        ]
    },
    {
        "name": "DisturbanceCH4Production",
        "process": "Disturbance",
        "source_pools": [
            "Merch",
            "Foliage",
            "Other",
            "CoarseRoots",
            "FineRoots",
            "AboveGroundVeryFastSoil",
            "BelowGroundVeryFastSoil",
            "AboveGroundFastSoil",
            "BelowGroundFastSoil",
            "MediumSoil",
            "AboveGroundSlowSoil",
            "BelowGroundSlowSoil",
            "StemSnag",
            "BranchSnag"
        ],
        "sink_pools": [
            "CH4"
        ]
    },
    {
        "name": "DisturbanceCOProduction",
        "process": "Disturbance",
        "source_pools": [
            "Merch",
            "Foliage",
            "Other",
            "CoarseRoots",
            "FineRoots",
            "AboveGroundVeryFastSoil",
            "BelowGroundVeryFastSoil",
            "AboveGroundFastSoil",
            "BelowGroundFastSoil",
            "MediumSoil",
            "AboveGroundSlowSoil",
            "BelowGroundSlowSoil",
            "StemSnag",
            "BranchSnag"
        ],
        "sink_pools": [
            "CO"
        ]
    },
    {
        "name": "DisturbanceBioCO2Emission",
        "process": "Disturbance",
        "source_pools": [
            "Merch",
            "Foliage",
            "Other",
            "CoarseRoots",
            "FineRoots"
        ],
        "sink_pools": [
            "CO2"
        ]
    },
    {
        "name": "DisturbanceBioCH4Emission",
        "process": "Disturbance",
        "source_pools": [
            "Merch",
            "Foliage",
            "Other",
            "CoarseRoots",
            "FineRoots"
        ],
        "sink_pools": [
            "CH4"
        ]
    },
    {
        "name": "DisturbanceBioCOEmission",
        "process": "Disturbance",
        "source_pools": [
            "Merch",
            "Foliage",
            "Other",
            "CoarseRoots",
            "FineRoots"
        ],
        "sink_pools": [
            "CO"
        ]
    },
    {
        "name": "DecayDOMCO2Emission",
        "process": "Decay",
        "source_pools": [
            "AboveGroundVeryFastSoil",
            "BelowGroundVeryFastSoil",
            "AboveGroundFastSoil",
            "BelowGroundFastSoil",
            "MediumSoil",
            "AboveGroundSlowSoil",
            "BelowGroundSlowSoil",
            "StemSnag",
            "BranchSnag"
        ],
        "sink_pools": [
            "CO2"
        ]
    },
    {
        "name": "DisturbanceProduction",
        "process": "Disturbance",
        "source_pools": [
            "Merch",
            "Foliage",
            "Other",
            "CoarseRoots",
            "FineRoots"
        ],
        "sink_pools": [
            "Products"
        ]
    },
    {
        "name": "DisturbanceDOMProduction",
        "process": "Disturbance",
        "source_pools": [
            "AboveGroundVeryFastSoil",
            "BelowGroundVeryFastSoil",
            "AboveGroundFastSoil",
            "BelowGroundFastSoil",
            "MediumSoil",
            "AboveGroundSlowSoil",
            "BelowGroundSlowSoil",
            "StemSnag",
            "BranchSnag"
        ],
        "sink_pools": [
            "Products"
        ]
    },
    {
        "name": "DeltaBiomass_AG",
        "process": "Growth and Turnover",
        "source_pools": [
            "Input"
        ],
        "sink_pools": [
            "Merch",
            "Foliage",
            "Other"
        ]
    },
    {
        "name": "DeltaBiomass_BG",
        "process": "Growth and Turnover",
        "source_pools": [
            "Input"
        ],
        "sink_pools": [
            "CoarseRoots",
            "FineRoots"
        ]
    },
    {
        "name": "TurnoverMerchLitterInput",
        "process": "Growth and Turnover",
        "source_pools": [
            "Merch"
        ],
        "sink_pools": [
            "StemSnag"
        ]
    },
    {
        "name": "TurnoverFolLitterInput",
        "process": "Growth and Turnover",
        "source_pools": [
            "Foliage"
        ],
        "sink_pools": [
            "AboveGroundVeryFastSoil"
        ]
    },
    {
        "name": "TurnoverOthLitterInput",
        "process": "Growth and Turnover",
        "source_pools": [
            "Other"
        ],
        "sink_pools": [
            "AboveGroundFastSoil",
            "BranchSnag"
        ]
    },
    {
        "name": "TurnoverCoarseLitterInput",
        "process": "Growth and Turnover",
        "source_pools": [
            "CoarseRoots"
        ],
        "sink_pools": [
            "AboveGroundFastSoil",
            "BelowGroundFastSoil"
        ]
    },
    {
        "name": "TurnoverFineLitterInput",
        "process": "Growth and Turnover",
        "source_pools": [
            "FineRoots"
        ],
        "sink_pools": [
            "AboveGroundVeryFastSoil",
            "BelowGroundVeryFastSoil"
        ]
    },
    {
        "name": "DecayVFastAGToAir",
        "process": "Decay",
        "source_pools": [
            "AboveGroundVeryFastSoil"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DecayVFastBGToAir",
        "process": "Decay",
        "source_pools": [
            "BelowGroundVeryFastSoil"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DecayFastAGToAir",
        "process": "Decay",
        "source_pools": [
            "AboveGroundFastSoil"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DecayFastBGToAir",
        "process": "Decay",
        "source_pools": [
            "BelowGroundFastSoil"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DecayMediumToAir",
        "process": "Decay",
        "source_pools": [
            "MediumSoil"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DecaySlowAGToAir",
        "process": "Decay",
        "source_pools": [
            "AboveGroundSlowSoil"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DecaySlowBGToAir",
        "process": "Decay",
        "source_pools": [
            "BelowGroundSlowSoil"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DecayStemSnagToAir",
        "process": "Decay",
        "source_pools": [
            "StemSnag"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DecayBranchSnagToAir",
        "process": "Decay",
        "source_pools": [
            "BranchSnag"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DisturbanceMerchToAir",
        "process": "Disturbance",
        "source_pools": [
            "Merch"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DisturbanceFolToAir",
        "process": "Disturbance",
        "source_pools": [
            "Foliage"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DisturbanceOthToAir",
        "process": "Disturbance",
        "source_pools": [
            "Other"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DisturbanceCoarseToAir",
        "process": "Disturbance",
        "source_pools": [
            "CoarseRoots"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DisturbanceFineToAir",
        "process": "Disturbance",
        "source_pools": [
            "FineRoots"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DisturbanceDOMCO2Emission",
        "process": "Disturbance",
        "source_pools": [
            "AboveGroundVeryFastSoil",
            "BelowGroundVeryFastSoil",
            "AboveGroundFastSoil",
            "BelowGroundFastSoil",
            "MediumSoil",
            "AboveGroundSlowSoil",
            "BelowGroundSlowSoil",
            "StemSnag",
            "BranchSnag"
        ],
        "sink_pools": [
            "CO2"
        ]
    },
    {
        "name": "DisturbanceDOMCH4Emission",
        "process": "Disturbance",
        "source_pools": [
            "AboveGroundVeryFastSoil",
            "BelowGroundVeryFastSoil",
            "AboveGroundFastSoil",
            "BelowGroundFastSoil",
            "MediumSoil",
            "AboveGroundSlowSoil",
            "BelowGroundSlowSoil",
            "StemSnag",
            "BranchSnag"
        ],
        "sink_pools": [
            "CH4"
        ]
    },
    {
        "name": "DisturbanceDOMCOEmission",
        "process": "Disturbance",
        "source_pools": [
            "AboveGroundVeryFastSoil",
            "BelowGroundVeryFastSoil",
            "AboveGroundFastSoil",
            "BelowGroundFastSoil",
            "MediumSoil",
            "AboveGroundSlowSoil",
            "BelowGroundSlowSoil",
            "StemSnag",
            "BranchSnag"
        ],
        "sink_pools": [
            "CO"
        ]
    },
    {
        "name": "DisturbanceMerchLitterInput",
        "process": "Disturbance",
        "source_pools": [
            "Merch"
        ],
        "sink_pools": [
            "StemSnag",
            "MediumSoil",
            "AboveGroundSlowSoil"
        ]
    },
    {
        "name": "DisturbanceFolLitterInput",
        "process": "Disturbance",
        "source_pools": [
            "Foliage"
        ],
        "sink_pools": [
            "AboveGroundVeryFastSoil",
            "BelowGroundVeryFastSoil"
        ]
    },
    {
        "name": "DisturbanceOthLitterInput",
        "process": "Disturbance",
        "source_pools": [
            "Other"
        ],
        "sink_pools": [
            "AboveGroundFastSoil",
            "BranchSnag",
            "BelowGroundFastSoil"
        ]
    },
    {
        "name": "DisturbanceCoarseLitterInput",
        "process": "Disturbance",
        "source_pools": [
            "CoarseRoots"
        ],
        "sink_pools": [
            "AboveGroundFastSoil",
            "BelowGroundFastSoil"
        ]
    },
    {
        "name": "DisturbanceFineLitterInput",
        "process": "Disturbance",
        "source_pools": [
            "FineRoots"
        ],
        "sink_pools": [
            "AboveGroundVeryFastSoil",
            "AboveGroundFastSoil",
            "BelowGroundFastSoil",
            "BelowGroundVeryFastSoil"
        ]
    },
    {
        "name": "DisturbanceVFastAGToAir",
        "process": "Disturbance",
        "source_pools": [
            "AboveGroundVeryFastSoil"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DisturbanceVFastBGToAir",
        "process": "Disturbance",
        "source_pools": [
            "BelowGroundVeryFastSoil"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DisturbanceFastAGToAir",
        "process": "Disturbance",
        "source_pools": [
            "AboveGroundFastSoil"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DisturbanceFastBGToAir",
        "process": "Disturbance",
        "source_pools": [
            "BelowGroundFastSoil"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DisturbanceMediumToAir",
        "process": "Disturbance",
        "source_pools": [
            "MediumSoil"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DisturbanceSlowAGToAir",
        "process": "Disturbance",
        "source_pools": [
            "AboveGroundSlowSoil"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DisturbanceSlowBGToAir",
        "process": "Disturbance",
        "source_pools": [
            "BelowGroundSlowSoil"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DisturbanceStemSnagToAir",
        "process": "Disturbance",
        "source_pools": [
            "StemSnag"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    },
    {
        "name": "DisturbanceBranchSnagToAir",
        "process": "Disturbance",
        "source_pools": [
            "BranchSnag"
        ],
        "sink_pools": [
            "CO2",
            "CH4",
            "CO",
            "NO2"
        ]
    }
]

slow_mixing_rate¶

	id	rate
0	1	0.006

turnover_parameters¶

	spatial_unit_id	sw_hw	FoliageFallRate	StemAnnualTurnoverRate	BranchTurnoverRate	CoarseRootTurnProp	FineRootTurnProp	OtherToBranchSnagSplit	CoarseRootAGSplit	FineRootAGSplit	StemSnag	BranchSnag
0	1	0	0.10	0.0050	0.04	0.02	0.641	0.25	0.5	0.5	0.032	0.1
1	3	0	0.05	0.0060	0.03	0.02	0.641	0.25	0.5	0.5	0.032	0.1
2	4	0	0.10	0.0050	0.04	0.02	0.641	0.25	0.5	0.5	0.032	0.1
3	5	0	0.15	0.0067	0.04	0.02	0.641	0.25	0.5	0.5	0.032	0.1
4	6	0	0.15	0.0067	0.04	0.02	0.641	0.25	0.5	0.5	0.032	0.1
...	...	...	...	...	...	...	...	...	...	...	...	...
91	52	1	0.95	0.0050	0.04	0.02	0.641	0.25	0.5	0.5	0.032	0.1
92	53	1	0.95	0.0060	0.04	0.02	0.641	0.25	0.5	0.5	0.032	0.1
93	54	1	0.95	0.0045	0.04	0.02	0.641	0.25	0.5	0.5	0.032	0.1
94	58	1	0.95	0.0060	0.03	0.02	0.641	0.25	0.5	0.5	0.032	0.1
95	59	1	0.95	0.0050	0.04	0.02	0.641	0.25	0.5	0.5	0.032	0.1

96 rows × 12 columns

species¶

	species_id	species_name	genus_id	genus_name	forest_type_id	forest_type_name
0	1	Spruce	1	Spruce	1	Softwood
1	2	Black spruce	1	Spruce	1	Softwood
2	3	Red spruce	1	Spruce	1	Softwood
3	4	Norway spruce	1	Spruce	1	Softwood
4	5	Engelmann spruce	1	Spruce	1	Softwood
...	...	...	...	...	...	...
189	191	Other broadleaved species - Genus type	12	Other broad-leaved species	3	Hardwood
190	192	Unspecified broadleaved species - Genus type	13	Unspecified broad-leaved species	3	Hardwood
191	193	Missing value - Genus type	14	Missing Value	1	Softwood
192	194	Softwood forest type	14	Missing Value	1	Softwood
193	195	Hardwood forest type	14	Missing Value	3	Hardwood

194 rows × 6 columns

root_parameters¶

	id	hw_a	sw_a	hw_b	frp_a	frp_b	frp_c	biomass_to_carbon_rate
0	1	1.576	0.222	0.615	0.072	0.354	-0.060212	0.5

decay_parameters¶

	pool	base_decay_rate	reference_temp	q10	prop_to_atmosphere	max_rate
0	AboveGroundVeryFastSoil	0.35500	10.0	2.65	0.815	1.0
1	BelowGroundVeryFastSoil	0.50000	10.0	2.00	0.830	1.0
2	AboveGroundFastSoil	0.14350	10.0	2.00	0.830	1.0
3	BelowGroundFastSoil	0.14350	10.0	2.00	0.830	1.0
4	MediumSoil	0.03740	10.0	2.00	0.830	1.0
5	AboveGroundSlowSoil	0.01500	10.0	2.65	1.000	1.0
6	BelowGroundSlowSoil	0.00330	10.0	1.00	1.000	1.0
7	StemSnag	0.01870	10.0	2.00	0.830	1.0
8	BranchSnag	0.07175	10.0	2.00	0.830	1.0

disturbance_matrix_value¶

	disturbance_matrix_id	source_pool	sink_pool	proportion
0	2	Merch	StemSnag	0.68624
1	2	Merch	CO2	0.28102
2	2	Merch	CH4	0.00316
3	2	Merch	CO	0.02842
4	2	Foliage	CO2	0.85570
...	...	...	...	...
14788	960	MediumSoil	MediumSoil	1.00000
14789	960	AboveGroundSlowSoil	AboveGroundSlowSoil	1.00000
14790	960	BelowGroundSlowSoil	BelowGroundSlowSoil	1.00000
14791	960	StemSnag	StemSnag	1.00000
14792	960	BranchSnag	BranchSnag	1.00000

14793 rows × 4 columns

disturbance_matrix_association¶

	spatial_unit_id	disturbance_type_id	sw_hw	disturbance_matrix_id
0	1	0	0	27
1	3	0	0	27
2	4	0	0	27
3	5	0	0	27
4	6	0	0	27
...	...	...	...	...
12747	52	1	1	850
12748	53	1	1	862
12749	54	1	1	845
12750	58	1	1	888
12751	59	1	1	880

12752 rows × 4 columns

Appendix 2: simulation parameters used to generate op-dataframes¶

Net C increments¶

These are derived from Tutorial 1 of the CBM-CFS3 Operational-Scale toolbox. Each simulation area is assigned the same set of increments.

[46]:

display(increments)

	row_idx	age	merch_inc	foliage_inc	other_inc
0	0	1	0.018897	0.040012	0.018766
1	0	2	0.083230	0.080984	0.099667
2	0	3	0.171700	0.109322	0.188663
3	0	4	0.276997	0.132148	0.276154
4	0	5	0.395454	0.151260	0.359470
...	...	...	...	...	...
65	999	66	0.000000	0.000000	0.000000
66	999	67	0.000000	0.000000	0.000000
67	999	68	0.000000	0.000000	0.000000
68	999	69	0.000000	0.000000	0.000000
69	999	70	0.000000	0.000000	0.000000

70000 rows × 5 columns

Simulation areas¶

[47]:

display(spinup_input["parameters"])

	sw_hw	age	area	delay	return_interval	min_rotations	max_rotations	spatial_unit_id	species	mean_annual_temperature	historical_disturbance_type	last_pass_disturbance_type
0	0	41	1	0	125	10	30	17	20	0.000	1	1
1	0	13	1	0	125	10	30	17	20	0.002	1	1
2	0	55	1	0	125	10	30	17	20	0.004	1	1
3	0	51	1	0	125	10	30	17	20	0.006	1	1
4	0	49	1	0	125	10	30	17	20	0.008	1	1
...	...	...	...	...	...	...	...	...	...	...	...	...
995	0	14	1	0	125	10	30	17	20	1.990	1	1
996	0	46	1	0	125	10	30	17	20	1.992	1	1
997	0	18	1	0	125	10	30	17	20	1.994	1	1
998	0	14	1	0	125	10	30	17	20	1.996	1	1
999	0	23	1	0	125	10	30	17	20	1.998	1	1

1000 rows × 12 columns

[ ]:

Fully dynamic modelling with cbm_exn¶

Operation dataframes¶

Single row¶

Simulation-aligned¶

Property-indexed¶

Both Simulation-aligned, and Property-indexed¶

Default spinup operation dataframes¶

snag_turnover¶

biomass_turnover¶

dom_decay¶

slow_decay¶

slow_mixing¶

disturbance¶

growth¶

overmature_decline¶

Step processes¶

growth¶

overmature_decline¶

Appendix 1: CBM EXN Default parameters¶

pools¶

flux¶

slow_mixing_rate¶

turnover_parameters¶

species¶

root_parameters¶

decay_parameters¶

disturbance_matrix_value¶

disturbance_matrix_association¶

Appendix 2: simulation parameters used to generate op-dataframes¶

Net C increments¶

Simulation areas¶

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	Merch.StemSnag	Other.BranchSnag	Other.AboveGroundFastSoil	Foliage.AboveGroundVeryFastSoil	CoarseRoots.AboveGroundFastSoil	CoarseRoots.BelowGroundFastSoil	FineRoots.AboveGroundVeryFastSoil	FineRoots.BelowGroundVeryFastSoil
0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
1	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
2	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
3	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
4	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
...	...	...	...	...	...	...	...	...
995	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
996	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
997	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
998	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
999	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0

	Merch.StemSnag	Other.BranchSnag	Other.AboveGroundFastSoil	Foliage.AboveGroundVeryFastSoil	CoarseRoots.AboveGroundFastSoil	CoarseRoots.BelowGroundFastSoil	FineRoots.AboveGroundVeryFastSoil	FineRoots.BelowGroundVeryFastSoil
0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
1	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
2	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
3	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
4	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
...	...	...	...	...	...	...	...	...
995	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
996	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
997	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
998	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
999	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0

	Merch.StemSnag	Other.BranchSnag	Other.AboveGroundFastSoil	Foliage.AboveGroundVeryFastSoil	CoarseRoots.AboveGroundFastSoil	CoarseRoots.BelowGroundFastSoil	FineRoots.AboveGroundVeryFastSoil	FineRoots.BelowGroundVeryFastSoil
0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
1	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
2	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
3	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
4	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
...	...	...	...	...	...	...	...	...
995	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
996	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
997	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
998	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
999	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0