diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index e48d434be..2cbfc986f 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-10-08T12:28:19","documenter_version":"1.1.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-10-10T11:26:48","documenter_version":"1.1.0"}} \ No newline at end of file diff --git a/dev/assets/Manifest.toml b/dev/assets/Manifest.toml index 12c2b6252..f43b0d9bd 100644 --- a/dev/assets/Manifest.toml +++ b/dev/assets/Manifest.toml @@ -235,9 +235,9 @@ uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" [[deps.DiffEqBase]] deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "61c73769521e37d95a448528074a67fb3df5bcaf" +git-tree-sha1 = "d5a64797f46c37ea59da9e4dcc86b208cb150182" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.132.1" +version = "6.133.0" [deps.DiffEqBase.extensions] DiffEqBaseDistributionsExt = "Distributions" @@ -379,9 +379,9 @@ version = "200.900.7+0" [[deps.FastBroadcast]] deps = ["ArrayInterface", "LinearAlgebra", "Polyester", "Static", "StaticArrayInterface", "StrideArraysCore"] -git-tree-sha1 = "aa9925a229d45fe3018715238956766fa21804d1" +git-tree-sha1 = "9d77cb1caf03e67514ba60bcfc47c6e131b1950c" uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898" -version = "0.2.6" +version = "0.2.7" [[deps.FastClosures]] git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" @@ -525,9 +525,9 @@ uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" version = "0.1.1" [[deps.Inflate]] -git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" +git-tree-sha1 = "ea8031dea4aff6bd41f1df8f2fdfb25b33626381" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" -version = "0.1.3" +version = "0.1.4" [[deps.IntegerMathUtils]] git-tree-sha1 = "b8ffb903da9f7b8cf695a8bead8e01814aa24b30" @@ -803,9 +803,9 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.ModelingToolkit]] deps = ["AbstractTrees", "ArrayInterface", "Combinatorics", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "IfElse", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "LabelledArrays", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "MacroTools", "NaNMath", "OrdinaryDiffEq", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] -git-tree-sha1 = "43751c01aefb8f22a7ce6ac6a8f8fa332f00bbc7" +git-tree-sha1 = "90b0d8395c9a8d3fcb5838f7f4f54b3f26e6f17a" uuid = "961ee093-0014-501f-94e3-6117800e7a78" -version = "8.71.2" +version = "8.72.2" [deps.ModelingToolkit.extensions] MTKDeepDiffsExt = "DeepDiffs" @@ -864,9 +864,9 @@ version = "1.2.0" [[deps.NonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LineSearches", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "445a7ba86794e1f8ee9da3b3b7becf284e2625fd" +git-tree-sha1 = "b9a71b5bb35766e857cad2acfc86213608e69a24" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "2.1.0" +version = "2.2.0" [[deps.OffsetArrays]] deps = ["Adapt"] @@ -950,9 +950,9 @@ version = "0.4.4" [[deps.Polyester]] deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] -git-tree-sha1 = "c7dc9720390fcc296bf757b3f833f9e41c68a086" +git-tree-sha1 = "398f91235beaac50445557c937ecb0145d171842" uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" -version = "0.7.7" +version = "0.7.8" [[deps.PolyesterWeave]] deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] @@ -1020,9 +1020,9 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[deps.RandomExtensions]] deps = ["Random", "SparseArrays"] -git-tree-sha1 = "062986376ce6d394b23d5d90f01d81426113a3c9" +git-tree-sha1 = "b8a399e95663485820000f26b6a43c794e166a49" uuid = "fb686558-2515-59ef-acaa-46db3789a887" -version = "0.4.3" +version = "0.4.4" [[deps.RandomNumbers]] deps = ["Random", "Requires"] @@ -1118,9 +1118,9 @@ version = "0.6.39" [[deps.SciMLBase]] deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FillArrays", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "5454a829596e3c2d4df38c10a392bfcacf641cf6" +git-tree-sha1 = "317f77cb31f7a0275cdd045aa7b3526ebc15c817" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.3.1" +version = "2.4.0" [deps.SciMLBase.extensions] SciMLBasePyCallExt = "PyCall" @@ -1203,9 +1203,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SparseDiffTools]] deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] -git-tree-sha1 = "0a4538040f6eeae9016043104056dc6c13e1d8c1" +git-tree-sha1 = "336fd944a1bbb8873bfa8171387608ca93317d68" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.7.0" +version = "2.8.0" [deps.SparseDiffTools.extensions] SparseDiffToolsEnzymeExt = "Enzyme" @@ -1397,9 +1397,9 @@ uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" version = "0.1.19" [[deps.Tricks]] -git-tree-sha1 = "aadb748be58b492045b4f56166b5188aa63ce549" +git-tree-sha1 = "eae1bb484cd63b36999ee58be2de6c178105112f" uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.7" +version = "0.1.8" [[deps.TruncatedStacktraces]] deps = ["InteractiveUtils", "MacroTools", "Preferences"] diff --git a/dev/export/export/index.html b/dev/export/export/index.html index 540cb3025..509541b9f 100644 --- a/dev/export/export/index.html +++ b/dev/export/export/index.html @@ -3,4 +3,4 @@ function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-90474609-3', {'page_path': location.pathname + location.search + location.hash}); -
GitHub

Exporting to Other Systems

Here we put some helpful utilities to export your code to other identifiability software.

StructuralIdentifiability.print_for_maple — Function
print_for_maple(ode, package)

Prints the ODE in the format accepted by maple packages

  • SIAN (https://github.com/pogudingleb/SIAN) if package=:SIAN
  • DifferentialAlgebra if package=:DifferentialAlgebra
  • DifferentialThomas if package=:DifferentialThomas
source
+
GitHub

Exporting to Other Systems

Here we put some helpful utilities to export your code to other identifiability software.

StructuralIdentifiability.print_for_maple — Function
print_for_maple(ode, package)

Prints the ODE in the format accepted by maple packages

  • SIAN (https://github.com/pogudingleb/SIAN) if package=:SIAN
  • DifferentialAlgebra if package=:DifferentialAlgebra
  • DifferentialThomas if package=:DifferentialThomas
source
diff --git a/dev/identifiability/identifiability/index.html b/dev/identifiability/identifiability/index.html index 9409fcae4..e9963145c 100644 --- a/dev/identifiability/identifiability/index.html +++ b/dev/identifiability/identifiability/index.html @@ -3,12 +3,12 @@ function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-90474609-3', {'page_path': location.pathname + location.search + location.hash}); -
GitHub

ָFunctions to Assess Identifiability

Assessing All Types of Identifiability

StructuralIdentifiability.assess_identifiability — Function
assess_identifiability(ode; funcs_to_check = [], p=0.99)

Input:

  • ode - the ODE model
  • funcs_to_check - list of functions to check identifiability for; if empty, all parameters and states are taken
  • p - probability of correctness.

Assesses identifiability of a given ODE model. The result is guaranteed to be correct with the probability at least p. The function returns a dictionary from the functions to check to their identifiability properties (one of :nonidentifiable, :locally, :globally).

source
assess_identifiability(ode::ModelingToolkit.ODESystem; measured_quantities=Array{ModelingToolkit.Equation}[], funcs_to_check=[], p = 0.99)

Input:

  • ode - the ModelingToolkit.ODESystem object that defines the model
  • measured_quantities - the output functions of the model
  • funcs_to_check - functions of parameters for which to check the identifiability
  • p - probability of correctness.

Assesses identifiability (both local and global) of a given ODE model (parameters detected automatically). The result is guaranteed to be correct with the probability at least p.

source

Assessing Local Identifiability

StructuralIdentifiability.assess_local_identifiability — Function
function assess_local_identifiability(ode::ModelingToolkit.ODESystem; measured_quantities=Array{ModelingToolkit.Equation}[], funcs_to_check=Array{}[], p::Float64=0.99, type=:SE)

Input:

  • ode - the ODESystem object from ModelingToolkit
  • measured_quantities - the measurable outputs of the model
  • funcs_to_check - functions of parameters for which to check identifiability
  • p - probability of correctness
  • type - identifiability type (:SE for single-experiment, :ME for multi-experiment)

Output:

  • for type=:SE, the result is a dictionary from each parameter to boolean;
  • for type=:ME, the result is a tuple with the dictionary as in :SE case and array of number of experiments.

The function determines local identifiability of parameters in funcs_to_check or all possible parameters if funcs_to_check is empty

The result is correct with probability at least p.

type can be either :SE (single-experiment identifiability) or :ME (multi-experiment identifiability). The return value is a tuple consisting of the array of bools and the number of experiments to be performed.

source
assess_local_identifiability(ode::ODE{P}; funcs_to_check::Array{<: Any, 1}, p::Float64=0.99, type=:SE) where P <: MPolyElem{Nemo.fmpq}

Checks the local identifiability/observability of the functions in funcs_to_check. The result is correct with probability at least p.

Call this function if you have a specific collection of parameters of which you would like to check local identifiability.

type can be either :SE (single-experiment identifiability) or :ME (multi-experiment identifiability). If the type is :ME, states are not allowed to appear in the funcs_to_check.

source
function assess_local_identifiability(
+
GitHub
ָFunctions to Assess Identifiability
Assessing All Types of Identifiability
StructuralIdentifiability.assess_identifiability — Function
assess_identifiability(ode; funcs_to_check = [], p=0.99)
Input:
  • ode - the ODE model
  • funcs_to_check - list of functions to check identifiability for; if empty, all parameters  and states are taken
  • p - probability of correctness.
Assesses identifiability of a given ODE model. The result is guaranteed to be correct with the probability at least p. The function returns a dictionary from the functions to check to their identifiability properties  (one of :nonidentifiable, :locally, :globally).
source
assess_identifiability(ode::ModelingToolkit.ODESystem; measured_quantities=Array{ModelingToolkit.Equation}[], funcs_to_check=[], p = 0.99)
Input:
  • ode - the ModelingToolkit.ODESystem object that defines the model
  • measured_quantities - the output functions of the model
  • funcs_to_check - functions of parameters for which to check the identifiability
  • p - probability of correctness.
Assesses identifiability (both local and global) of a given ODE model (parameters detected automatically). The result is guaranteed to be correct with the probability at least p.
source
Assessing Local Identifiability
StructuralIdentifiability.assess_local_identifiability — Function
function assess_local_identifiability(ode::ModelingToolkit.ODESystem; measured_quantities=Array{ModelingToolkit.Equation}[], funcs_to_check=Array{}[], p::Float64=0.99, type=:SE)
Input:
  • ode - the ODESystem object from ModelingToolkit
  • measured_quantities - the measurable outputs of the model
  • funcs_to_check - functions of parameters for which to check identifiability
  • p - probability of correctness
  • type - identifiability type (:SE for single-experiment, :ME for multi-experiment)
Output:
  • for type=:SE, the result is a dictionary from each parameter to boolean;
  • for type=:ME, the result is a tuple with the dictionary as in :SE case and array of number of experiments.
The function determines local identifiability of parameters in funcs_to_check or all possible parameters if funcs_to_check is empty
The result is correct with probability at least p.
type can be either :SE (single-experiment identifiability) or :ME (multi-experiment identifiability). The return value is a tuple consisting of the array of bools and the number of experiments to be performed.
source
assess_local_identifiability(ode::ODE{P}; funcs_to_check::Array{<: Any, 1}, p::Float64=0.99, type=:SE) where P <: MPolyElem{Nemo.fmpq}
Checks the local identifiability/observability of the functions in funcs_to_check. The result is correct with probability at least p.
Call this function if you have a specific collection of parameters of which you would like to check local identifiability.
type can be either :SE (single-experiment identifiability) or :ME (multi-experiment identifiability). If the type is :ME, states are not allowed to appear in the funcs_to_check.
source
function assess_local_identifiability(
     dds::ModelingToolkit.DiscreteSystem; 
     measured_quantities=Array{ModelingToolkit.Equation}[], 
     funcs_to_check=Array{}[], 
     known_ic=Array{}[],
-    p::Float64=0.99)
Input:
  • dds - the DiscreteSystem object from ModelingToolkit
  • measured_quantities - the measurable outputs of the model
  • funcs_to_check - functions of parameters for which to check identifiability (all parameters and states if not specified)
  • known_ic - functions (of states and parameter) whose initial conditions are assumed to be known
  • p - probability of correctness
Output:
  • the result is a dictionary from each function to to boolean;
The result is correct with probability at least p.
source
Assessing Global Identifiability
StructuralIdentifiability.assess_global_identifiability — Function
assess_global_identifiability(ode::ODE{P}, p::Float64=0.99; var_change=:default) where P <: MPolyElem{fmpq}
Input:
  • ode - the ODE model
  • known - a list of functions in states which are assumed to be known and generic
  • p - probability of correctness
  • var_change - a policy for variable change (:default, :yes, :no), affects only the runtime
Output:
  • a dictionary mapping each parameter to a boolean.
Checks global identifiability for parameters of the model provided in ode. Call this function to check global identifiability of all parameters automatically.
source
assess_global_identifiability(ode, [funcs_to_check, p=0.99, var_change=:default])
Input:
  • ode - the ODE model
  • funcs_to_check - rational functions in parameters
  • known - function in parameters that are assumed to be known and generic
  • p - probability of correctness
  • var_change - a policy for variable change (:default, :yes, :no),               affects only the runtime
Output:
  • array of length length(funcs_to_check) with true/false values for global identifiability       or dictionary param => Bool if funcs_to_check are not given
Checks global identifiability of functions of parameters specified in funcs_to_check.
source
Finding Identifiable Functions
StructuralIdentifiability.find_identifiable_functions — Function
find_identifiable_functions(ode::ODE; options...)
Finds all functions of parameters/states that are identifiable in the given ODE system.
Options
This functions takes the following optional arguments:
  • with_states: When true, also reports the identifiabile functions in the   ODE states. Default is false.
  • simplify: The extent to which the output functions are simplified. Stronger simplification may require more time. Possible options are:
    • :standard: Default simplification.
    • :weak: Weak simplification. This option is the fastest, but the output functions can be quite complex.
    • :strong: Strong simplification. This option is the slowest, but the output
    functions are nice and simple.
    • :absent: No simplification.
  • p: A float in the range from 0 to 1, the probability of correctness. Default is 0.99.
  • seed: The rng seed. Default value is 42.
Example
using StructuralIdentifiability
+    p::Float64=0.99)
Input:
  • dds - the DiscreteSystem object from ModelingToolkit
  • measured_quantities - the measurable outputs of the model
  • funcs_to_check - functions of parameters for which to check identifiability (all parameters and states if not specified)
  • known_ic - functions (of states and parameter) whose initial conditions are assumed to be known
  • p - probability of correctness
Output:
  • the result is a dictionary from each function to to boolean;
The result is correct with probability at least p.
source
Assessing Global Identifiability
StructuralIdentifiability.assess_global_identifiability — Function
assess_global_identifiability(ode::ODE{P}, p::Float64=0.99; var_change=:default) where P <: MPolyElem{fmpq}
Input:
  • ode - the ODE model
  • known - a list of functions in states which are assumed to be known and generic
  • p - probability of correctness
  • var_change - a policy for variable change (:default, :yes, :no), affects only the runtime
Output:
  • a dictionary mapping each parameter to a boolean.
Checks global identifiability for parameters of the model provided in ode. Call this function to check global identifiability of all parameters automatically.
source
assess_global_identifiability(ode, [funcs_to_check, p=0.99, var_change=:default])
Input:
  • ode - the ODE model
  • funcs_to_check - rational functions in parameters
  • known - function in parameters that are assumed to be known and generic
  • p - probability of correctness
  • var_change - a policy for variable change (:default, :yes, :no),               affects only the runtime
Output:
  • array of length length(funcs_to_check) with true/false values for global identifiability       or dictionary param => Bool if funcs_to_check are not given
Checks global identifiability of functions of parameters specified in funcs_to_check.
source
Finding Identifiable Functions
StructuralIdentifiability.find_identifiable_functions — Function
find_identifiable_functions(ode::ODE; options...)
Finds all functions of parameters/states that are identifiable in the given ODE system.
Options
This functions takes the following optional arguments:
  • with_states: When true, also reports the identifiabile functions in the   ODE states. Default is false.
  • simplify: The extent to which the output functions are simplified. Stronger simplification may require more time. Possible options are:
    • :standard: Default simplification.
    • :weak: Weak simplification. This option is the fastest, but the output functions can be quite complex.
    • :strong: Strong simplification. This option is the slowest, but the output
    functions are nice and simple.
    • :absent: No simplification.
  • p: A float in the range from 0 to 1, the probability of correctness. Default is 0.99.
  • seed: The rng seed. Default value is 42.
Example
using StructuralIdentifiability
 
 ode = @ODEmodel(
     x0'(t) = -(a01 + a21) * x0(t) + a12 * x1(t),
@@ -21,7 +21,7 @@
 # prints
 3-element Vector{AbstractAlgebra.Generic.Frac{Nemo.fmpq_mpoly}}:
  a12 + a01 + a21
- a12*a01
source
find_identifiable_functions(ode::ModelingToolkit.ODESystem; measured_quantities=[], options...)
Finds all functions of parameters/states that are identifiable in the given ODE system.
Options
This functions takes the following optional arguments:
  • measured_quantities - the output functions of the model.
Example
using StructuralIdentifiability
+ a12*a01
source
find_identifiable_functions(ode::ModelingToolkit.ODESystem; measured_quantities=[], options...)
Finds all functions of parameters/states that are identifiable in the given ODE system.
Options
This functions takes the following optional arguments:
  • measured_quantities - the output functions of the model.
Example
using StructuralIdentifiability
 using ModelingToolkit
 
 @parameters a01 a21 a12
@@ -39,4 +39,4 @@
 # prints
 2-element Vector{Num}:
          a01*a12
- a01 + a12 + a21
source

+ a01 + a12 + a21
source
diff --git a/dev/index.html b/dev/index.html index b4c14038b..ed07761ab 100644 --- a/dev/index.html +++ b/dev/index.html @@ -16,7 +16,7 @@ }

Feature Summary

StructuralIdentifiability.jl can assess local and global identifiability of ODE models. In addition to these straightforward identifiability queries on individual parameters, the package can distinguish between single- and multi-experiment identifiability.

Feature List

Contributing

Reproducibility

The documentation of this SciML package was built using these direct dependencies,
Status `~/work/StructuralIdentifiability.jl/StructuralIdentifiability.jl/docs/Project.toml`
   [6e4b80f9] BenchmarkTools v1.3.2
   [e30172f5] Documenter v1.1.0
-  [961ee093] ModelingToolkit v8.71.2
+  [961ee093] ModelingToolkit v8.72.2
   [220ca800] StructuralIdentifiability v0.4.11 `~/work/StructuralIdentifiability.jl/StructuralIdentifiability.jl`
and using this machine and Julia version.
Julia Version 1.9.3
 Commit bed2cd540a1 (2023-08-24 14:43 UTC)
 Build Info:
@@ -57,7 +57,7 @@
   [9a962f9c] DataAPI v1.15.0
   [864edb3b] DataStructures v0.18.15
   [e2d170a0] DataValueInterfaces v1.0.0
-  [2b5f629d] DiffEqBase v6.132.1
+  [2b5f629d] DiffEqBase v6.133.0
   [459566f4] DiffEqCallbacks v2.33.0
   [163ba53b] DiffResults v1.1.0
   [b552c78f] DiffRules v1.15.1
@@ -65,14 +65,14 @@
   [31c24e10] Distributions v0.25.102
   [ffbed154] DocStringExtensions v0.9.3
   [e30172f5] Documenter v1.1.0
-  [5b8099bc] DomainSets v0.6.7
+⌅ [5b8099bc] DomainSets v0.6.7
   [fa6b7ba4] DualNumbers v0.6.8
   [7c1d4256] DynamicPolynomials v0.5.3
   [4e289a0a] EnumX v1.0.4
   [f151be2c] EnzymeCore v0.6.0
   [d4d017d3] ExponentialUtilities v1.25.0
   [e2ba6199] ExprTools v0.1.10
-  [7034ab61] FastBroadcast v0.2.6
+  [7034ab61] FastBroadcast v0.2.7
   [9aa1b823] FastClosures v0.3.2
   [29a986be] FastLapackInterface v2.0.0
   [1a297f60] FillArrays v1.6.1
@@ -92,7 +92,7 @@
   [34004b35] HypergeometricFunctions v0.3.23
   [b5f81e59] IOCapture v0.2.3
   [615f187c] IfElse v0.1.1
-  [d25df0c9] Inflate v0.1.3
+  [d25df0c9] Inflate v0.1.4
   [18e54dd8] IntegerMathUtils v0.1.2
   [8197267c] IntervalSets v0.7.7
   [92d709cd] IrrationalConstants v0.2.2
@@ -120,7 +120,7 @@
   [d125e4d3] ManualMemory v0.1.8
   [d0879d2d] MarkdownAST v0.1.2
   [e1d29d7a] Missings v1.1.0
-  [961ee093] ModelingToolkit v8.71.2
+  [961ee093] ModelingToolkit v8.72.2
   [46d2c3a1] MuladdMacro v0.2.4
   [102ac46a] MultivariatePolynomials v0.5.2
   [d8a4904e] MutableArithmetics v1.3.3
@@ -128,7 +128,7 @@
   [2774e3e8] NLsolve v4.5.1
   [77ba4419] NaNMath v1.0.2
 ⌅ [2edaba10] Nemo v0.35.3
-  [8913a72c] NonlinearSolve v2.1.0
+  [8913a72c] NonlinearSolve v2.2.0
   [6fe1bfb0] OffsetArrays v1.12.10
   [bac558e1] OrderedCollections v1.6.2
   [1dea7af3] OrdinaryDiffEq v6.58.0
@@ -138,7 +138,7 @@
   [d96e819e] Parameters v0.12.3
   [69de0a69] Parsers v2.7.2
   [e409e4f3] PoissonRandom v0.4.4
-  [f517fe37] Polyester v0.7.7
+  [f517fe37] Polyester v0.7.8
   [1d0040c9] PolyesterWeave v0.2.1
   [d236fae5] PreallocationTools v0.4.12
   [aea7be01] PrecompileTools v1.2.0
@@ -146,7 +146,7 @@
   [27ebfcd6] Primes v0.5.4
   [92933f4c] ProgressMeter v1.9.0
   [1fd47b50] QuadGK v2.9.1
-  [fb686558] RandomExtensions v0.4.3
+  [fb686558] RandomExtensions v0.4.4
   [e6cf234a] RandomNumbers v1.5.3
   [3cdcf5f2] RecipesBase v1.3.4
   [731186ca] RecursiveArrayTools v2.38.10
@@ -159,7 +159,7 @@
   [fdea26ae] SIMD v3.4.5
   [94e857df] SIMDTypes v0.1.0
   [476501e8] SLEEFPirates v0.6.39
-  [0bca4576] SciMLBase v2.3.1
+  [0bca4576] SciMLBase v2.4.0
   [e9a6253c] SciMLNLSolve v0.1.9
   [c0aeaf25] SciMLOperators v0.3.6
   [efcf1570] Setfield v1.1.1
@@ -168,7 +168,7 @@
   [ce78b400] SimpleUnPack v1.1.0
   [66db9d55] SnoopPrecompile v1.0.3
   [a2af1166] SortingAlgorithms v1.1.1
-  [47a9eef4] SparseDiffTools v2.7.0
+  [47a9eef4] SparseDiffTools v2.8.0
   [e56a9233] Sparspak v0.3.9
   [276daf66] SpecialFunctions v2.3.1
   [aedffcd0] Static v0.8.8
@@ -178,7 +178,7 @@
   [82ae8749] StatsAPI v1.7.0
   [2913bbd2] StatsBase v0.34.2
   [4c63d2b9] StatsFuns v1.3.0
-  [7792a7ef] StrideArraysCore v0.4.17
+⌅ [7792a7ef] StrideArraysCore v0.4.17
   [220ca800] StructuralIdentifiability v0.4.11 `~/work/StructuralIdentifiability.jl/StructuralIdentifiability.jl`
   [2efcf032] SymbolicIndexingInterface v0.2.2
   [d1185830] SymbolicUtils v1.4.0
@@ -190,7 +190,7 @@
   [0796e94c] Tokenize v0.5.25
   [a2a6695c] TreeViews v0.3.0
   [d5829a12] TriangularSolve v0.1.19
-  [410a4b4d] Tricks v0.1.7
+  [410a4b4d] Tricks v0.1.8
   [781d530d] TruncatedStacktraces v1.4.0
   [5c2747f8] URIs v1.5.0
   [3a884ed6] UnPack v1.0.2
@@ -259,4 +259,4 @@
   [3f19e933] p7zip_jll v17.4.0+0
 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
You can also download the manifest file and the -project file. +project file. diff --git a/dev/input/input/index.html b/dev/input/input/index.html index cd5529bb0..b52f113b0 100644 --- a/dev/input/input/index.html +++ b/dev/input/input/index.html @@ -9,4 +9,4 @@ x1'(t) = a * x1(t) + u(t), x2'(t) = b * x2(t) + c*x1(t)*x2(t), y(t) = x1(t) -)

Here,

source
StructuralIdentifiability.ODE — Type

The main structure that represents input ODE system.

Stores information about states (x_vars), outputs (y_vars), inputs (u_vars), parameters (parameters) and the equations.

This structure is constructed via @ODEmodel macro.

source
StructuralIdentifiability.set_parameter_values — Function
set_parameter_values(ode, param_values)

Input:

  • ode - an ODE as above
  • param_values - values for (possibly, some of) the parameters as dictionary parameter => value

Output:

  • new ode with the parameters in param_values plugged with the given numbers
source

Create Compartmental Model

StructuralIdentifiability.linear_compartment_model — Function
linear_compartment_model(graph, inputs, outputs, leaks)

Input: defines a linear compartment model with nodes numbered from 1 to n by

  • graph - and array of integer arrays representing the adjacency lists of the graph
  • inputs - array of input nodes
  • outputs - array of output nodes
  • leaks - array of sink nodes

Output:

  • the corresponding ODE system in the notation of https://doi.org/10.1007/s11538-015-0098-0
source
+)

Here,

source
StructuralIdentifiability.ODE — Type

The main structure that represents input ODE system.

Stores information about states (x_vars), outputs (y_vars), inputs (u_vars), parameters (parameters) and the equations.

This structure is constructed via @ODEmodel macro.

source
StructuralIdentifiability.set_parameter_values — Function
set_parameter_values(ode, param_values)

Input:

  • ode - an ODE as above
  • param_values - values for (possibly, some of) the parameters as dictionary parameter => value

Output:

  • new ode with the parameters in param_values plugged with the given numbers
source

Create Compartmental Model

StructuralIdentifiability.linear_compartment_model — Function
linear_compartment_model(graph, inputs, outputs, leaks)

Input: defines a linear compartment model with nodes numbered from 1 to n by

  • graph - and array of integer arrays representing the adjacency lists of the graph
  • inputs - array of input nodes
  • outputs - array of output nodes
  • leaks - array of sink nodes

Output:

  • the corresponding ODE system in the notation of https://doi.org/10.1007/s11538-015-0098-0
source
diff --git a/dev/ioequations/ioequations/index.html b/dev/ioequations/ioequations/index.html index a23b02757..3f9d4796c 100644 --- a/dev/ioequations/ioequations/index.html +++ b/dev/ioequations/ioequations/index.html @@ -3,4 +3,4 @@ function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-90474609-3', {'page_path': location.pathname + location.search + location.hash}); -
GitHub

Finding Input-Output Equations

StructuralIdentifiability.find_ioequations — Function
find_ioequations(ode, [var_change_policy=:default])

Finds the input-output equations of an ODE system Input:

  • ode - the ODE system
  • var_change_policy - whether to perform automatic variable change, can be one of :default, :yes, :no

Output:

  • a dictionary from “leaders” to the corresponding input-output equations; if an extra projection is needed, it will be the value corresponding to rand_proj_var
source

Reducing with respect to Input-Output Equations

StructuralIdentifiability.PBRepresentation — Type

The structure for storing a projection-based representation of differential ideal (see Section 2.3 https://arxiv.org/abs/2111.00991). Contains the following fields:

  • y_names - the names of the variables with finite order in the profile (typically, outputs)
  • u_names - the names of the variables with infinite order in the profile (typically, inputs)
  • param_names - the names of the parameters
  • profile - the profile of the PB-representation (see Definition 2.13) as a dict from y_names with finite orders to the orders
  • projections - the corresponding projections (see Definition 2.15) as a dict from y_names to the projections
source
StructuralIdentifiability.pseudodivision — Function
pseudodivision(f, g, x)

Computes the result of pseudodivision of f by g as univariate polynomials in x Input:

  • f - the polynomial to be divided
  • g - the polynomial to divide by
  • x - the variable for the division

Output: the pseudoremainder of f divided by g w.r.t. x

source
StructuralIdentifiability.diffreduce — Function
diffreduce(diffpoly, pbr)

Computes the result of differential reduction of a differential polynomial diffpoly with respect to the charset defined by a PB-representation pbr Input:

  • diffpoly - a polynomial representing a differential polynomial to be reduced
  • pbr - a projection-based representation

Output: the result of differential reduction of diffpoly by pbr considered as a characteristic set (see Remark 2.20 in the paper)

source
+
GitHub

Finding Input-Output Equations

StructuralIdentifiability.find_ioequations — Function
find_ioequations(ode, [var_change_policy=:default])

Finds the input-output equations of an ODE system Input:

  • ode - the ODE system
  • var_change_policy - whether to perform automatic variable change, can be one of :default, :yes, :no

Output:

  • a dictionary from “leaders” to the corresponding input-output equations; if an extra projection is needed, it will be the value corresponding to rand_proj_var
source

Reducing with respect to Input-Output Equations

StructuralIdentifiability.PBRepresentation — Type

The structure for storing a projection-based representation of differential ideal (see Section 2.3 https://arxiv.org/abs/2111.00991). Contains the following fields:

  • y_names - the names of the variables with finite order in the profile (typically, outputs)
  • u_names - the names of the variables with infinite order in the profile (typically, inputs)
  • param_names - the names of the parameters
  • profile - the profile of the PB-representation (see Definition 2.13) as a dict from y_names with finite orders to the orders
  • projections - the corresponding projections (see Definition 2.15) as a dict from y_names to the projections
source
StructuralIdentifiability.pseudodivision — Function
pseudodivision(f, g, x)

Computes the result of pseudodivision of f by g as univariate polynomials in x Input:

  • f - the polynomial to be divided
  • g - the polynomial to divide by
  • x - the variable for the division

Output: the pseudoremainder of f divided by g w.r.t. x

source
StructuralIdentifiability.diffreduce — Function
diffreduce(diffpoly, pbr)

Computes the result of differential reduction of a differential polynomial diffpoly with respect to the charset defined by a PB-representation pbr Input:

  • diffpoly - a polynomial representing a differential polynomial to be reduced
  • pbr - a projection-based representation

Output: the result of differential reduction of diffpoly by pbr considered as a characteristic set (see Remark 2.20 in the paper)

source
diff --git a/dev/tutorials/creating_ode/index.html b/dev/tutorials/creating_ode/index.html index 2b9f5b369..d1085d9b8 100644 --- a/dev/tutorials/creating_ode/index.html +++ b/dev/tutorials/creating_ode/index.html @@ -57,4 +57,4 @@ chi2 => :globally x1(t) => :globally c1 => :globally - u(t) => :globally
+ u(t) => :globally
diff --git a/dev/tutorials/identifiability/index.html b/dev/tutorials/identifiability/index.html index ba6f329cf..7e1a30a43 100644 --- a/dev/tutorials/identifiability/index.html +++ b/dev/tutorials/identifiability/index.html @@ -48,4 +48,4 @@ alpha => :nonidentifiable x3 => :nonidentifiable

As a result, each parameter/state is assigned one of the labels :globally (globally identifiable), :locally (locally but not globally identifiable), or :nonidentifiable (not identifiable, even locally). The algorithm behind this computation follows [4].

Similarly to assess_local_identifiability, this function has optional parameters:

Using funcs_to_check parameter, one can further inverstigate the nature of the lack of identifiability in the model at hand. For example, for the Goodwin oscillator, we can check if beta + delta and beta * delta are identifiable:

assess_identifiability(ode, funcs_to_check = [beta + delta, beta * delta])
Dict{Any, Symbol} with 2 entries:
   delta*beta   => :globally
-  delta + beta => :globally

And we see that they indeed are. This means, in particular, that the reason why beta and delta are not identifiable is because their values can be exchanged. One may wonder how could we guess these functions beta + delta, beta * delta. In fact, they can be just computed using find_identifiable_functions function as we will explain in the next tutorial. Stay tuned!

+ delta + beta => :globally

And we see that they indeed are. This means, in particular, that the reason why beta and delta are not identifiable is because their values can be exchanged. One may wonder how could we guess these functions beta + delta, beta * delta. In fact, they can be just computed using find_identifiable_functions function as we will explain in the next tutorial. Stay tuned!

diff --git a/dev/tutorials/identifiable_functions/index.html b/dev/tutorials/identifiable_functions/index.html index 5e4de3711..687a42521 100644 --- a/dev/tutorials/identifiable_functions/index.html +++ b/dev/tutorials/identifiable_functions/index.html @@ -22,4 +22,4 @@ p2*p4 p3 + p1 p2*x2 + p4*x1 - (p2*x2 - p4*x1)//(p3 - p1)

By default, find_identifiable_functions tries to simplify the output functions as much as possible, and it has simplify keyword responsible for the degree of simplification. The default value is :standard but one could use :string to try to simplify further (at the expense of heavier computation) or use :weak to simplify less (but compute faster).

+ (p2*x2 - p4*x1)//(p3 - p1)

By default, find_identifiable_functions tries to simplify the output functions as much as possible, and it has simplify keyword responsible for the degree of simplification. The default value is :standard but one could use :string to try to simplify further (at the expense of heavier computation) or use :weak to simplify less (but compute faster).

diff --git a/dev/utils/elimination/index.html b/dev/utils/elimination/index.html index 6fc13f8d0..20b8119b4 100644 --- a/dev/utils/elimination/index.html +++ b/dev/utils/elimination/index.html @@ -3,4 +3,4 @@ function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-90474609-3', {'page_path': location.pathname + location.search + location.hash}); -
GitHub

Elimination

StructuralIdentifiability.Bezout_matrix — Method
Bezout_matrix(f, g, var_elim)

Compute the Bezout matrix of two polynomials f, g with respect to var_elim

Inputs:

  • f - first polynomial
  • g - second polynomial
  • var_elim - variable, of which f and g are considered as polynomials

Output:

  • M::MatrixElem - The Bezout matrix
source
StructuralIdentifiability.Sylvester_matrix — Method
Sylvester_matrix(f, g, var_elim)

Compute the Sylvester matrix of two polynomials f, g with respect to var_elim Inputs:

  • f - first polynomial
  • g - second polynomial
  • var_elim - variable, of which f and g are considered as polynomials

Output:

  • M::MatrixElem - The Sylvester matrix
source
StructuralIdentifiability.choose — Method
choose(polys, generic_point_generator)

Input:

  • polys - an array of distinct irreducible polynomials in the same ring
  • generic_point_generator - a generic point generator as described above for one of polys

Output:

  • the polynomial that vanishes at the generic_point_generator
source
StructuralIdentifiability.eliminate_var — Method
eliminate_var(f, g, var_elim, generic_point_generator)

Eliminate a variable from a pair of polynomials

Input:

  • f and g - polynomials
  • var_elim - variable to be eliminated
  • generic_point_generator - a generic point generator object for the factor of the resultant of f and g of interest

Output:

  • polynomial - the desired factor of the resultant of f and g
source
StructuralIdentifiability.simplify_matrix — Method
simplify_matrix(M)

Eliminate GCD of entries of every row and column

Input:

  • M::MatrixElem - matrix to be simplified

Output:

  • M::MatrixElem - Simplified matrix
  • extra_factors::Vector{AbstractAlgebra.MPolyElem} - array of GCDs eliminated from M.
source
+
GitHub

Elimination

StructuralIdentifiability.Bezout_matrix — Method
Bezout_matrix(f, g, var_elim)

Compute the Bezout matrix of two polynomials f, g with respect to var_elim

Inputs:

  • f - first polynomial
  • g - second polynomial
  • var_elim - variable, of which f and g are considered as polynomials

Output:

  • M::MatrixElem - The Bezout matrix
source
StructuralIdentifiability.Sylvester_matrix — Method
Sylvester_matrix(f, g, var_elim)

Compute the Sylvester matrix of two polynomials f, g with respect to var_elim Inputs:

  • f - first polynomial
  • g - second polynomial
  • var_elim - variable, of which f and g are considered as polynomials

Output:

  • M::MatrixElem - The Sylvester matrix
source
StructuralIdentifiability.choose — Method
choose(polys, generic_point_generator)

Input:

  • polys - an array of distinct irreducible polynomials in the same ring
  • generic_point_generator - a generic point generator as described above for one of polys

Output:

  • the polynomial that vanishes at the generic_point_generator
source
StructuralIdentifiability.eliminate_var — Method
eliminate_var(f, g, var_elim, generic_point_generator)

Eliminate a variable from a pair of polynomials

Input:

  • f and g - polynomials
  • var_elim - variable to be eliminated
  • generic_point_generator - a generic point generator object for the factor of the resultant of f and g of interest

Output:

  • polynomial - the desired factor of the resultant of f and g
source
StructuralIdentifiability.simplify_matrix — Method
simplify_matrix(M)

Eliminate GCD of entries of every row and column

Input:

  • M::MatrixElem - matrix to be simplified

Output:

  • M::MatrixElem - Simplified matrix
  • extra_factors::Vector{AbstractAlgebra.MPolyElem} - array of GCDs eliminated from M.
source
diff --git a/dev/utils/global_identifiability/index.html b/dev/utils/global_identifiability/index.html index 59f2b15e6..9f3463360 100644 --- a/dev/utils/global_identifiability/index.html +++ b/dev/utils/global_identifiability/index.html @@ -12,4 +12,4 @@ rff = RationalFunctionField([x // y, y // z]) # Constructs a subfield generated by y / x, 1 / x, z / y -rff = RationalFunctionField([[x, y, R(1)], [y, z]])source
StructuralIdentifiability.field_contains — Function
field_contains(field, ratfuncs, p)

Checks whether given rational function field field contains given rational functions ratfuncs (represented as a list of lists). The result is correct with probability at least p

Inputs:

  • field - a rational function field
  • ratfuncs - a list of lists of polynomials. Each of the lists, say, [f1, ..., fn], defines generators f2/f1, ..., fn/f1.
  • p real number from (0, 1)

Output:

  • a list L[i] of bools of length length(rat_funcs) such that L[i] is true iff the i-th function belongs to field
source
StructuralIdentifiability.get_degree_and_coeffsize — Function
get_degree_and_coeffsize(f)

for f being a polynomial/rational function over rationals (QQ) returns a tuple (degree, max_coef_size)

source
+rff = RationalFunctionField([[x, y, R(1)], [y, z]])source
StructuralIdentifiability.field_contains — Function
field_contains(field, ratfuncs, p)

Checks whether given rational function field field contains given rational functions ratfuncs (represented as a list of lists). The result is correct with probability at least p

Inputs:

  • field - a rational function field
  • ratfuncs - a list of lists of polynomials. Each of the lists, say, [f1, ..., fn], defines generators f2/f1, ..., fn/f1.
  • p real number from (0, 1)

Output:

  • a list L[i] of bools of length length(rat_funcs) such that L[i] is true iff the i-th function belongs to field
source
StructuralIdentifiability.get_degree_and_coeffsize — Function
get_degree_and_coeffsize(f)

for f being a polynomial/rational function over rationals (QQ) returns a tuple (degree, max_coef_size)

source
diff --git a/dev/utils/local_identifiability/index.html b/dev/utils/local_identifiability/index.html index c0a4d1b74..18ab14a8d 100644 --- a/dev/utils/local_identifiability/index.html +++ b/dev/utils/local_identifiability/index.html @@ -3,4 +3,4 @@ function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-90474609-3', {'page_path': location.pathname + location.search + location.hash}); -
GitHub

Local Identifiability Tools

StructuralIdentifiability.differentiate_solution — Function
differentiate_solution(ode, params, ic, inputs, prec)

Input:

  • the same as for power_series_solutions

Output:

  • a tuple consisting of the power series solution and a dictionary of the form (u, v) => power series, where u is a state variable v is a state or parameter, and the power series is the partial derivative of the function u w.r.t. v evaluated at the solution
source
StructuralIdentifiability.differentiate_output — Function
differentiate_output(ode, params, ic, inputs, prec)

Similar to differentiate_solution but computes partial derivatives of prescribed outputs returns a dictionary of the form y_function => Dict(var => dy/dvar) where dy/dvar is the derivative of y_function with respect to var.

source
+
GitHub

Local Identifiability Tools

StructuralIdentifiability.differentiate_solution — Function
differentiate_solution(ode, params, ic, inputs, prec)

Input:

  • the same as for power_series_solutions

Output:

  • a tuple consisting of the power series solution and a dictionary of the form (u, v) => power series, where u is a state variable v is a state or parameter, and the power series is the partial derivative of the function u w.r.t. v evaluated at the solution
source
StructuralIdentifiability.differentiate_output — Function
differentiate_output(ode, params, ic, inputs, prec)

Similar to differentiate_solution but computes partial derivatives of prescribed outputs returns a dictionary of the form y_function => Dict(var => dy/dvar) where dy/dvar is the derivative of y_function with respect to var.

source
diff --git a/dev/utils/power_series_utils/index.html b/dev/utils/power_series_utils/index.html index d829a30b8..77f23ef99 100644 --- a/dev/utils/power_series_utils/index.html +++ b/dev/utils/power_series_utils/index.html @@ -3,4 +3,4 @@ function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-90474609-3', {'page_path': location.pathname + location.search + location.hash}); -
GitHub

Power Series Utilities

StructuralIdentifiability.ps_matrix_homlinear_de — Method
ps_matrix_homlinear_de(A, Y0, prec)

Input:

  • A - a square matrix with entries in a univariate power series ring
  • Y0 - a square invertible matrix over the base field

Output:

  • matrix Y such that Y' = AY up to precision of A - 1 and Y(0) = Y0
source
StructuralIdentifiability.ps_matrix_inv — Function
ps_matrix_inv(M, prec)

Input:

  • M - a square matrix with entries in a univariate power series ring it is assumed that M(0) is invertible and all entries having the same precision
  • prec - an integer, precision, if -1 then defaults to precision of M

Output:

  • the inverse of M computed up to prec
source
StructuralIdentifiability.ps_matrix_linear_de — Method
ps_matrix_linear_de(A, B, Y0, prec)

Input:

  • A, B - square matrices with entries in a univariate power series ring
  • Y0 - a matrix over the base field with the rows number the same as A

Output:

  • matrix Y such that Y' = AY + B up to precision of A - 1 and Y(0) = Y0
source
StructuralIdentifiability.ps_ode_solution — Method
ps_ode_solution(equations, ic, inputs, prec)

Input:

  • equations - a system of the form $A(x, u, mu)x' - B(x, u, mu) = 0$, where A is a generically nonsingular square matrix. Assumption: A is nonzero at zero
  • ic - initial conditions for x's (dictionary)
  • inputs - power series for inputs represented as arrays (dictionary)
  • prec - precision of the solution

Output:

  • power series solution of the system
source
+
GitHub

Power Series Utilities

StructuralIdentifiability.ps_matrix_homlinear_de — Method
ps_matrix_homlinear_de(A, Y0, prec)

Input:

  • A - a square matrix with entries in a univariate power series ring
  • Y0 - a square invertible matrix over the base field

Output:

  • matrix Y such that Y' = AY up to precision of A - 1 and Y(0) = Y0
source
StructuralIdentifiability.ps_matrix_inv — Function
ps_matrix_inv(M, prec)

Input:

  • M - a square matrix with entries in a univariate power series ring it is assumed that M(0) is invertible and all entries having the same precision
  • prec - an integer, precision, if -1 then defaults to precision of M

Output:

  • the inverse of M computed up to prec
source
StructuralIdentifiability.ps_matrix_linear_de — Method
ps_matrix_linear_de(A, B, Y0, prec)

Input:

  • A, B - square matrices with entries in a univariate power series ring
  • Y0 - a matrix over the base field with the rows number the same as A

Output:

  • matrix Y such that Y' = AY + B up to precision of A - 1 and Y(0) = Y0
source
StructuralIdentifiability.ps_ode_solution — Method
ps_ode_solution(equations, ic, inputs, prec)

Input:

  • equations - a system of the form $A(x, u, mu)x' - B(x, u, mu) = 0$, where A is a generically nonsingular square matrix. Assumption: A is nonzero at zero
  • ic - initial conditions for x's (dictionary)
  • inputs - power series for inputs represented as arrays (dictionary)
  • prec - precision of the solution

Output:

  • power series solution of the system
source
diff --git a/dev/utils/primality/index.html b/dev/utils/primality/index.html index 49ed9a200..9ec58e115 100644 --- a/dev/utils/primality/index.html +++ b/dev/utils/primality/index.html @@ -3,4 +3,4 @@ function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-90474609-3', {'page_path': location.pathname + location.search + location.hash}); -
GitHub

Primality Checks

StructuralIdentifiability.check_primality — Function
check_primality(polys::Dict{fmpq_mpoly, fmpq_mpoly}, extra_relations::Array{fmpq_mpoly, 1})

The function checks if the ideal generated by the polynomials and saturated at the leading coefficient with respect to the corresponding variables is prime over rationals.

The extra_relations allows adding more polynomials to the generators (not affecting the saturation).

source
check_primality(polys::Dict{fmpq_mpoly, fmpq_mpoly})

The function checks if the ideal generated by the polynomials and saturated at the leading coefficient with respect to the corresponding variables is prime over rationals.

source
+
GitHub

Primality Checks

StructuralIdentifiability.check_primality — Function
check_primality(polys::Dict{fmpq_mpoly, fmpq_mpoly}, extra_relations::Array{fmpq_mpoly, 1})

The function checks if the ideal generated by the polynomials and saturated at the leading coefficient with respect to the corresponding variables is prime over rationals.

The extra_relations allows adding more polynomials to the generators (not affecting the saturation).

source
check_primality(polys::Dict{fmpq_mpoly, fmpq_mpoly})

The function checks if the ideal generated by the polynomials and saturated at the leading coefficient with respect to the corresponding variables is prime over rationals.

source
diff --git a/dev/utils/reparametrization/index.html b/dev/utils/reparametrization/index.html index 68b778ae2..ea4f25379 100644 --- a/dev/utils/reparametrization/index.html +++ b/dev/utils/reparametrization/index.html @@ -3,4 +3,4 @@ function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-90474609-3', {'page_path': location.pathname + location.search + location.hash}); -
GitHub
+
GitHub
diff --git a/dev/utils/util/index.html b/dev/utils/util/index.html index e05d527bf..d3e0feadc 100644 --- a/dev/utils/util/index.html +++ b/dev/utils/util/index.html @@ -3,5 +3,5 @@ function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-90474609-3', {'page_path': location.pathname + location.search + location.hash}); -
GitHub

Other Helpful Functions

StructuralIdentifiability.dennums_to_fractions — Method
dennums_to_fractions(dennums)

Returns the field generators represented by fractions.

Input: an array of arrays of polynomials, as in [[f1, f2, f3, ...], [g1, g2, g3, ...], ...]

Output: an array of fractions [f2/f1, f3/f1, ..., g2/g1, g3/g1, ...]

source
StructuralIdentifiability.extract_coefficients — Method
extract_coefficients(poly, variables)

Input:

  • poly - multivariate polynomial
  • variables - a list of variables from the generators of the ring of p

Output:

  • dictionary with keys being tuples of length lenght(variables) and values being polynomials in the variables other than those which are the coefficients at the corresponding monomials (in a smaller polynomial ring)
source
StructuralIdentifiability.fractions_to_dennums — Method
fractions_to_dennums(fractions)

Returns the field generators represented by lists of denominators and numerators.

Input: an array of fractions, as in [f2/f1, f3/f1, ..., g2/g1, g3/g1, ...]

Output: an array of arrays of polynomials, [[f1, f2, f3, ...], [g1, g2, g3, ...], ...]

source
StructuralIdentifiability.gen_tag_name — Function
gen_tag_name(base; stop_words)
-gen_tag_names(n, base; stop_words)

Generates a string which will not collide with the words in stop_words.

Arguments

  • n: Generates a sequence of unique strings of length n
  • base: A string or a vector of strings, the base for the generated sequence
  • stop_words: A vector of strings, stop words
source
StructuralIdentifiability.make_substitution — Method
make_substitution(f, var_sub, val_numer, val_denom)

Substitute a variable in a polynomial with an expression

Input:

  • f - the polynomial
  • var_sub - the variable to be substituted
  • var_numer - numerator of the substitution expression
  • var_denom - denominator of the substitution expression

Output:

  • polynomial - result of substitution
source
StructuralIdentifiability.parent_ring_change — Method
parent_ring_change(poly, new_ring)

Converts a polynomial to a different polynomial ring Input

  • poly - a polynomial to be converted
  • new_ring - a polynomial ring such that every variable name appearing in poly appears among the generators

Output:

  • a polynomial in new_ring “equal” to poly
source
StructuralIdentifiability.uncertain_factorization — Method
uncertain_factorization(f)

Input:

  • f - polynomial with rational coefficients

Output:

  • list of pairs (div, certainty) where
    • div's are divisors of f such that f is their product with certain powers
    • if certainty is true, div is $Q$-irreducible
source
+
GitHub

Other Helpful Functions

StructuralIdentifiability.dennums_to_fractions — Method
dennums_to_fractions(dennums)

Returns the field generators represented by fractions.

Input: an array of arrays of polynomials, as in [[f1, f2, f3, ...], [g1, g2, g3, ...], ...]

Output: an array of fractions [f2/f1, f3/f1, ..., g2/g1, g3/g1, ...]

source
StructuralIdentifiability.extract_coefficients — Method
extract_coefficients(poly, variables)

Input:

  • poly - multivariate polynomial
  • variables - a list of variables from the generators of the ring of p

Output:

  • dictionary with keys being tuples of length lenght(variables) and values being polynomials in the variables other than those which are the coefficients at the corresponding monomials (in a smaller polynomial ring)
source
StructuralIdentifiability.fractions_to_dennums — Method
fractions_to_dennums(fractions)

Returns the field generators represented by lists of denominators and numerators.

Input: an array of fractions, as in [f2/f1, f3/f1, ..., g2/g1, g3/g1, ...]

Output: an array of arrays of polynomials, [[f1, f2, f3, ...], [g1, g2, g3, ...], ...]

source
StructuralIdentifiability.gen_tag_name — Function
gen_tag_name(base; stop_words)
+gen_tag_names(n, base; stop_words)

Generates a string which will not collide with the words in stop_words.

Arguments

  • n: Generates a sequence of unique strings of length n
  • base: A string or a vector of strings, the base for the generated sequence
  • stop_words: A vector of strings, stop words
source
StructuralIdentifiability.make_substitution — Method
make_substitution(f, var_sub, val_numer, val_denom)

Substitute a variable in a polynomial with an expression

Input:

  • f - the polynomial
  • var_sub - the variable to be substituted
  • var_numer - numerator of the substitution expression
  • var_denom - denominator of the substitution expression

Output:

  • polynomial - result of substitution
source
StructuralIdentifiability.parent_ring_change — Method
parent_ring_change(poly, new_ring)

Converts a polynomial to a different polynomial ring Input

  • poly - a polynomial to be converted
  • new_ring - a polynomial ring such that every variable name appearing in poly appears among the generators

Output:

  • a polynomial in new_ring “equal” to poly
source
StructuralIdentifiability.uncertain_factorization — Method
uncertain_factorization(f)

Input:

  • f - polynomial with rational coefficients

Output:

  • list of pairs (div, certainty) where
    • div's are divisors of f such that f is their product with certain powers
    • if certainty is true, div is $Q$-irreducible
source
diff --git a/dev/utils/wronskian/index.html b/dev/utils/wronskian/index.html index ac83ce127..7c8e2c7d6 100644 --- a/dev/utils/wronskian/index.html +++ b/dev/utils/wronskian/index.html @@ -3,4 +3,4 @@ function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-90474609-3', {'page_path': location.pathname + location.search + location.hash}); -
GitHub

Wronskian Tools

StructuralIdentifiability.get_max_below — Method
get_max_below(t, vect)

Input:

  • t - a trie with exponent vectors
  • vect - yet another exponent vector

Output:

  • a pair (d, v) where v is a vector in the trie which is componentwise ≤ vect and the difference d is as small as possible
source
StructuralIdentifiability.massive_eval — Method
massive_eval(polys, eval_dict)

Input:

  • polys - a list of polynomials
  • eval_dict - dictionary from variables to the values. Missing values are treated as zeroes

Output:

  • a list of values of the polynomials

Evaluates a list of polynomials at a point. Assumes that multiplications are relatively expensive (like in truncated power series) so all the monomials are precomputed first and the values of monomials of lower degree are cached and used to compute the values of the monomials of higher degree

source
StructuralIdentifiability.monomial_compress — Method
monomial_compress(io_equation, ode)

Compresses an input-output equation for the rank computation Input:

  • io_equation - input-output equation
  • ode - the corresponding ODE model

Output:

  • pair (coeffs, terms) such that:
    • sum of coeffs[i] * terms[i] = io_equation
    • coeffs involve only parameters, terms involve only inputs and outputs
    • length of the representation is the smallest possible
source
StructuralIdentifiability.wronskian — Method
wronskian(io_equations, ode)

Input:

  • io_equations - a set of io-equations in the form of the Dict as returned by find_ioequations
  • ode - the ODE object

Output:

  • a list of Wronskians evaluated at a point modulo prime

Computes the Wronskians of io_equations

source
+
GitHub

Wronskian Tools

StructuralIdentifiability.get_max_below — Method
get_max_below(t, vect)

Input:

  • t - a trie with exponent vectors
  • vect - yet another exponent vector

Output:

  • a pair (d, v) where v is a vector in the trie which is componentwise ≤ vect and the difference d is as small as possible
source
StructuralIdentifiability.massive_eval — Method
massive_eval(polys, eval_dict)

Input:

  • polys - a list of polynomials
  • eval_dict - dictionary from variables to the values. Missing values are treated as zeroes

Output:

  • a list of values of the polynomials

Evaluates a list of polynomials at a point. Assumes that multiplications are relatively expensive (like in truncated power series) so all the monomials are precomputed first and the values of monomials of lower degree are cached and used to compute the values of the monomials of higher degree

source
StructuralIdentifiability.monomial_compress — Method
monomial_compress(io_equation, ode)

Compresses an input-output equation for the rank computation Input:

  • io_equation - input-output equation
  • ode - the corresponding ODE model

Output:

  • pair (coeffs, terms) such that:
    • sum of coeffs[i] * terms[i] = io_equation
    • coeffs involve only parameters, terms involve only inputs and outputs
    • length of the representation is the smallest possible
source
StructuralIdentifiability.wronskian — Method
wronskian(io_equations, ode)

Input:

  • io_equations - a set of io-equations in the form of the Dict as returned by find_ioequations
  • ode - the ODE object

Output:

  • a list of Wronskians evaluated at a point modulo prime

Computes the Wronskians of io_equations

source