Exposure #87

virgile-baudrot · 2021-02-05T11:15:54Z

Description

Add two rules of exposure to treatment:

ThresholdExposure: Exposure to a single treatment depending on a threshold layer
RotationExposure: Exposure by several treatments in rotation depending on a threshold layer

Changes (choose one only, with x or click after creating PR):

New formulation/rule
Documentation
Bug fix for existing rules (non-breaking syntax)
Major change to existing rules (breaking syntax, needs a breaking version bump)

Checklist:

My code follows the BlueStyle style guide
My code is commented with explanations of anything hard to understand
There are no unnecessary or unrelated code changes included in this PR
There are no depencecies added: if so, please consider if they are necessary and explain why they are required

For bugfixes

My PR addresses a single bug/connected group of bugs
I have included a test that will ensure the bug does not recur

For new `Rule`s

My PR is limited to a clear theme/cenceptual unit. (Otherwise make multiple PRs that can be discussed separately)
New rules have tests in a file of the same name as the rule file, e.g. /test/newrulename.jl
I have cited the source of the new formulation/s, if applicable
I have added a documentation string to formulation struct/s, and added an entry in the docs

rafaqz

Thanks Virgile, this code and the test are solid and clean. Mostly my comments are just BlueStyle changes, and some questions about naming.

src/exposure.jl

rafaqz · 2021-02-05T14:54:00Z

src/exposure.jl

+Base.:+(x::Number, rs::RotationStruct) = RotationStruct(x + rs.rotationStep, rs.timeStep)
+Base.:+(rs1::RotationStruct, rs2::RotationStruct) = RotationStruct(rs1.rotationStep + rs2.rotationStep, rs1.timeStep + rs2.timeStep)
+Base.:-(rs::RotationStruct, x::Number) = RotationStruct(rs.rotationStep - x, rs.timeStep) 
+Base.:-(x::Number, rs::RotationStruct) = RotationStruct(x - rs.rotationStep, rs.timeStep)


Do we need these methods for addition/subtraction of a scalar?

rafaqz · 2021-02-05T14:55:26Z

src/exposure.jl

+Base.:-(rs::RotationStruct, x::Number) = RotationStruct(rs.rotationStep - x, rs.timeStep) 
+Base.:-(x::Number, rs::RotationStruct) = RotationStruct(x - rs.rotationStep, rs.timeStep)
+Base.:-(rs1::RotationStruct, rs2::RotationStruct) = RotationStruct(rs1.rotationStep - rs2.rotationStep, rs1.timeStep - rs2.timeStep)
+


If you want you can make it convert to color for ImageOutput that would be good.

Add a method for oneunit - it's basically the same as zero - needed for normalising for RGB output.

Base.oneunit(::Type{<:RotationStruct{T1,T2}}) where {T1,T2} = RotationStruct(oneunit(T1), oneunit(T2))

And division by a scalar to normalise between 0 and 1 (limits for colors) using minval and maxval

Base.:/(rs::RotationStruct, x::Number) = RotationStruct(rs.rotationStep / x, rs.timeStep)

And method for converting to color - rotationstep will be between 0 and 1 at this point. Edit this to suit:

DynamicGrids.to_rgb(scheme::ObjectScheme, obj::RotationStruct) = ARGB32(RGB(make it a color somehow)) # For use with ColorSchemes.jl etc - `get` needs a single `Real` number DynamicGrids.to_rgb(scheme, obj::RotationStruct) = ARGB32(get(scheme, obj.rotationstep)) # ??

@rafaqz DynamicGrids.to_rgb is not avaible when doing in the instantiate of Dispersal.jl using JuliaHub release

Yeah I messed up the registration of the new version, hopefully it will all be register in a few hours.

But you can checkout master of both DynamicGrids.jl and Dispersal.jl

rafaqz · 2021-02-05T22:42:16Z

test/exposure.jl

+            crop=Aux(:crop), rotationsize=3, rotationindex= 2,
+            pulselevel=20.0, popthreshold = 1000.0,degradationrate=0.5, timestep = 1
+        )
+        ruleTreatment3 = RotationExposure{Tuple{:pesticide3,:population,:rotation}, Tuple{:pesticide3,:rotation}}(


no space in type params

rafaqz · 2021-02-05T23:33:22Z

src/exposure.jl

+# Keyword Arguments
+
+- `crop`: Crop field. May be a `Number`, an [`Aux`](@ref) array or another [`Grid`](@ref).
+Treatment is applied when `crop > zero(crop) || return zero(pesticide) `.


probably delete this bit || return zero(pesticide) and just say "when crop is above zero"

rafaqz · 2021-02-05T23:47:55Z

src/exposure.jl

+    )
+Exposure by treatment depending on a threshold layer (population size) set with
+`popthreshold`.
+Treatment is applied only on `crop` fields (value of `crop` cell > 0).


Is crop always about crops? Or is it a more generic switch like active?

agree this may be more generic than crop (e.g. in biosecurity responses)

rafaqz · 2021-02-05T23:49:00Z

src/exposure.jl

+Abstract supertype of `CellRule` for rules of exposure dynamics
+"""
+
+abstract type Exposure{R,W} <: CellRule{R,W} end


I'm not sure I understand this enough, but Exposure seems like it should be about insect populations being exposed and the effect of that on their population? But this is calculating the treatment application rates and decay time, in response to population. Is it really like:

abstract type Treatment end struct ThreasholdTreatment <: Treatment end struct RotatingTreatment <: Treatment end

and should the files be caled exposure.jl or something else?

@jamesmaino you might have some input here too

The types you have suggested might not work because the threshold concept and rotating concept are not mutually exclusive. But I would suggest rotation by default because no rotation is just a special case of rotation where the series is just (treatment1, treatment1, treatment1,...)

Ok. FYI these are just renames of the types already in this PR.

I'm also wondering if these actually just ExponentialGrowth with this rotation/threshold/rotation+threshol treatment regime as separate, very simple rules? Should the degradation be a separate rule from the means of applying the pesticide?

Oh, very good point.
The assumption is that treatment always degradates. So we should consider the degradation rule as separate (which is the same as the exponential growth with a negative rate).

Then we would have the pulse rule which would be very simple based on theshold, And a rotation+pulsethreshold rule...

rafaqz · 2021-02-05T23:52:56Z

src/exposure.jl

+`popthreshold`.
+Treatment is applied only on `crop` fields (value of `crop` cell > 0).
+The amount of treatment `pulselevel` is applied once this threshold is passed.
+At every time step the pesticide is degradated at rate `degradationrate`


Should this say treatment instead of pesticide, as above?

or "chemical" as not all treatments will decay.

"not all treatments will decay" seems like decay should be in a separate rule to treatment application then.

Ok for separating degradation rule.
I would prefere something like "exposon": a thing to which the population is exposed to... but maybe "exposure" works?
Their is the idea of "exposome" https://en.wikipedia.org/wiki/Environmental_factor#Exposome

Exposure doesn't work... exposon would be great but we can't really do that in english!

arff ok. Science should be in a more playable language :-D (no worry, french is worst!)

rafaqz reviewed Feb 6, 2021

View reviewed changes

virgile-baudrot added 8 commits February 8, 2021 17:27

add rules for exposure to treatment

e718c2f

test of exposure

99a8071

export exposure functions

e4bda63

signature for the constructor in the doc string

a475ed8

change InitRotation to initrotation

a0745b3

add entry to docs for Exposure rules

21ee58c

fix InitRotation to initrotation in test

c8ffd93

update PR cesaraustralia#87

fcfbd24

virgile-baudrot force-pushed the exposure branch from 03494a8 to fcfbd24 Compare February 9, 2021 08:38

add to_rgb

c816046

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Exposure #87

Exposure #87

virgile-baudrot commented Feb 5, 2021

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Exposure #87

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Exposure #87

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virgile-baudrot commented Feb 5, 2021

Description

Changes (choose one only, with x or click after creating PR):

Checklist:

For bugfixes

For new Rules

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rafaqz Feb 5, 2021 • edited Loading

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For new `Rule`s

rafaqz Feb 5, 2021 •

edited

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