trace_asco example failing

[PaulMelloy]

The trace_asco example is failing https://github.com/IhsanKhaliq/ascotraceR/blob/15b2fc3464e85185b13a10063c45c82ec06fa6cc/R/trace_asco.R#L95-L106

This is because the primary_infection_intensity = 1000 while the seeding rate is 40

This means in the model susceptible_gps get rationalised in the following manner susceptible_gps - sporulating_gps When the user inputs a primary_infection_intensity more than the number of growing points this causes a negative number of susceptible_gps to be calculated. Also, a warning is generated stating "This may cause an overestimation of disease spread".

This needs to be corrected Note: Historically there was no use for having a larger primary_infection_intensity than the number of growing points because this model was estimated from either infected seeds or infected plants. A higher primary_infection_intensity was allowed to suit circumstances where stubble was present or added via experimentation which increased the inoculum contributing to an epidemic in the field.

I will add a dependent statement for when primary_infection_intensity is higher than susceptible_gps not to subtract.

[IhsanKhaliq]

Does primary_infection_intensity occur on infested stubble (primary infection foci) or chickpea? In the model you're referring that primary_infection_intensity can only occur on infested stubble.

[IhsanKhaliq]

If primary_infection_intensity occur on infested stubble, then it has absolutely no association with the number of growing points on chickpea or seeding_rate

[PaulMelloy]

primary_infection_intensity The intensity of the starting epidemic is described by the number of sporulating growing points (from seed infection and/or volunteers) and/or sporulating lesions from crop debris.

[IhsanKhaliq]

What does it mean? Is it on chickpea or stubble?

[IhsanKhaliq]

primary_infection_intensity occur on chickpea or stubble?

[PaulMelloy]

It can be either or both

[IhsanKhaliq]

How are the number of infected growing points/primary_infection_intensity` on stubble related to the number of growing points on chickpea seedling? There is no comparison

[PaulMelloy]

they are not. It is up to the user to decide what the intensity of the primary infections are at each coordinate. Those primary infections could come from a variety of sources.

[IhsanKhaliq]

Now you're coming to my point. It's not up to the user. To me the correct definition of primary_infection_intensity is the number of infected growing points produced on chickpea seedlings when conidia are splashed dispersed on chickpea seedling from a source (source doesn't matter, it can be infected seed or infested stubble). Then you can say that the number of infected growing points on chickpea cannot be greater than the total number of growing points on chickpea. It doesn't make sense to say that number of infected growing points on stubble are more/less than growing points on chickpea because there is no association

[IhsanKhaliq]

primary_infection_intensity can only occur on chickpea

[PaulMelloy]

What you have described is how the model was originally programmed. _"primary_infectionintensity is the number of infected growing points produced on chickpea seedlings when conidia are splashed dispersed on chickpea seedling from a source (source doesn't matter, it can be infected seed or infested stubble)."

However as you requested in issues #71 and #72 I changed the model to allow primary_infection_intensity to be greater than the number of growing points.

Perhaps what you want is an extra parameter stubble_infection_intensity or something that can be used explicitly in this context?

[IhsanKhaliq]

I you want to quantify the amount of inoculum on infested stubble then perhaps call it primary_inoculum_intensity. Infection would mean spore dispersal, germination and penetration and subsequent infection on host after latent period. But it will have no association with the number of infected growing points on chickpea (can be more or less)

[IhsanKhaliq]

But you can say that MORE primary_inoculum_intensity will result in MORE SEVERE disease and vice versa

[PaulMelloy]

Ok do you want to open a new issue to discuss primary_infection_intensity vs primary_inoculum_intensity ect further? Examples are passing now and I have amended the model so susceptible_gps are not made negative by high primary_inoculum intensity. So I think this issue can be closed, but I will leave it up to you.

[IhsanKhaliq]

Yes I can open a new issue to explain these

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From: Paul Melloy @.> Sent: Thursday, November 4, 2021 12:50:11 PM To: IhsanKhaliq/ascotraceR @.> Cc: Ihsan Khaliq @.>; Comment @.> Subject: Re: [IhsanKhaliq/ascotraceR] trace_asco example failing (Issue #104)

Ok do you want to open a new issue to discuss primary_infection_intensity vs primary_inoculum_intensity ect further? Examples are passing now and I have amended the model so susceptible_gps are not made negative by high primary_inoculum intensity. So I think this issue can be closed, but I will leave it up to you.

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