Initial inoculum intensity parameter not used

[IhsanKhaliq]

I think the Initial inoculum intensity need to included in the ascotraceR so the valascotraceR can recognise it. Getting an error Error in { : task 1 failed - "unused argument (initial_inoculum_intensity = 1)"

https://github.com/IhsanKhaliq/valascotraceR/blob/f69e838f3899e59156669cb9aebe9d3624b18c78/example_trace_ascoRun.Rmd#L93

[adamhsparks]

I thought this was removed from ascotraceR for submission to CRAN. Why on earth are we putting it back after all the discussion we had on the topic?

[IhsanKhaliq]

[adamhsparks]

What does it even mean? The model just runs starting from the initial number of infective sites. AFAIK it doesn't distinguish between inoculum sources.

[IhsanKhaliq]

It's not related to inoculum sources. It's related to the number of infected quadrats on the date of initial infection. We have currently have an open issue #7

[adamhsparks]

then why is it called initial_inoculum_intensity? That's related to inoculum.

I thought you could have the number of foci specified in the model as it exists?

[IhsanKhaliq]

We can call it initial_infection_intensity instead, but it's still not used. We have the same number of foci. It's not about the number of foci. It's about the number of infected quadrats at the time of initial infection

[PaulMelloy]

Have you reinstalled the latest version?

[IhsanKhaliq]

Yes, I Install and Restart package locally before visiting valascotraceR.

[PaulMelloy]

do you mean primary_inoculum_intensity

[PaulMelloy]

as you mention initial_infection_intensity is not a argument in the model, the argument you might be looking for is primary_inoculum_intensity

[IhsanKhaliq]

No primary_inoculum_intensity works (these are lesions on infested stubble). I am talking about issue #7 (number of infected quadrats at the time of initial infection)

[PaulMelloy]

We decided to remove that as per the email. You agreed on it. See the documentation for what primary_inoculum_intensity means

#' primary_inoculum_intensity Refers to the amount of primary infection
#'   as lesions on chickpea plants at the time of `initial_infection`. On the
#'   date of initial infection in the experiment. The sources of primary
#'   inoculum can be infected seed, volunteer chickpea plants or infested
#'   stubble from the previous seasons. Defaults to `1`.

[IhsanKhaliq]

Do I put this back this back there? https://github.com/IhsanKhaliq/ascotraceR/commit/a3754c6ac843a12e7cd88536f285975103f98658

Please disregard. Changing back definitions is not going to work, and neither is Paul's current definition going to work. I changed value of primary_infection_intensity to 1 and 3 for Billa Billa and Tosari, respectively to represent 1 and 3 quadrats infections at these locations, but we're getting very low spread. So the value has to be around 200 as we currently have, and should indicate the number of lesions on stubble

Initially, the definition of primary_inoculum_intensity indicated the number of lesions on infested stubble. The argument was made that the model requires quantifying the amount of initial inoculum. This sort of make sense, and we have the same amount of primary inoculum.
The current definition primar_inoculum_intensity suggests infection, not inoculum, indicating the number of lesions on chickpea seedlings at the time of initial infection. I counted two lesions at Billa Billa as only one seedling was infected. At Tosari, 16 plants were infected, and the number of lesions were impossible to count. It will be impossible to count the number of lesions on chickpea seedlings under field conditions, and this is not a parameter in the original model either. As discussed in the above email, I thought we're sticking to the old definition of primary_inoculum_intensity indicating 200 lesions on stubble and removing the sources of inoculum (stubble inoculum intensity etc.) So the solution seems to be stick to the old defintion of primary_inoculum_intensity as 200 lesions on stubble (not infection on seedling).

[IhsanKhaliq]

Issue #7 will still remain though

[IhsanKhaliq]

Closed by changing the definition of primary_inoculum_intensity to represent primary inoculum not primary infection. We still need to introduce a parameter primary_infection_intensity to include the number of infected quadrats (primary infection) at the time of initial infection, as discussed issue #7