RP Meeting - 1/6/21

[sarahcleary]

Review of Chickpea Model - APSIMInitiative/ApsimX#158

@AllanPeake to present.

@APSIMInitiative/reference-panel - Please let me know if you have suggestions for additional attendees.

[sarahcleary]

@APSIMInitiative/steering-committee - FYI. If you would like to attend, please let me know and I'll forward the meeting invitation.

[yashvirchauhan]

Will the presentation be available in advance?

[sarahcleary]

I'm currently putting together
** information for developers
** information for RP/reviewers
which will include timing expectations.
I will be asking for the presenter to forward their presentation for review a week in advance of the meeting as well as putting the model "under review" at the same time.

[sarahcleary]

As per request from @peter-devoil - invited @jwhish and @uqdrodri

[uqghamme]

Hi Sarah If possible I wouldn’t mind sitting in on chickpea model review Regards Graeme Hammer Professor in Crop Science Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation The University of Queensland, Brisbane, Qld 4072, Australia Tel: +61 7 3346 9463 Mob: 0412 189 757 Email: ***@***.******@***.***> Web: http://www.qaafi.uq.edu.au/ https://orcid.org/0000-0002-1180-7374 From: sarahcleary ***@***.***> Sent: Tuesday, 11 May 2021 9:23 AM To: APSIMInitiative/ReferencePanel ***@***.***> Cc: Graeme Hammer ***@***.***>; Team mention ***@***.***> Subject: Re: [APSIMInitiative/ReferencePanel] RP Meeting - 1/6/21 (#88) I'm currently putting together ** information for developers ** information for RP/reviewers which will include timing expectations. I will be asking for the presenter to forward their presentation for review a week in advance of the meeting as well as putting the model "under review" at the same time. — You are receiving this because you are on a team that was mentioned. Reply to this email directly, view it on GitHub<#88 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ANMBBGEKBGZY6FB77XZTV4LTNBTEPANCNFSM44S3EMRA>.

[sarahcleary]

Information for Developer

• Upload the presentation at least a week prior to the meeting to the relevant issue - New Chickpea Model
• An example of a presentation can be found here, however, structure and content need not follow this form
• Ideally presentation should be approximately 30 min
  • Model to be moved into “Under Review” and upload the Model Documentation to APSIM Next Generation
  • At the end of the meeting, it is anticipated that the AI RP will provide a list of tasks if complete will allow for the Model to move into Release and be available as part of the APSIM download.

Information for Reviewers

• Please review presentation and the Model prior to the meeting.
• Any key issues or relevant papers, please provide via this issue prior to the meeting for consideration by the Developer.

[sno036]

@AllanPeake, @hut104 some early comments.

The validation graphs are much better than most! Exception is HI (harvest index I assume?) but I gather that is not unusual with the crop models?

Section 4.1 has some sort of issue (documentation unless there is something wrong with the supplied coordinates) with the map

Section 5.1 is really useful but could do with some interpretation/narrative of the results against the experimental trends.

What should be section 5.2 (detailed dynamics) is not showing in the documentation

The test needs a grazing simulation to make sure that the stock eat the things they should and don't eat the things they should not.

It looks like the validation dataset is from a limited geographic range. Should add some geographic transects ranging across climates where you would and would not expect the crop to thrive.

Also need to see a good example simulation before it is ready for release. This should not be the chickpea version of "Continuous Wheat" but should include a simple simulation and then a series of more complex set ups, probably including some experiments. Add some explanatory memos so that it begins to act as a tutorial. See AgPasture for one that is not fantastic but heading in the right direction - this is something that we are trying to get all models in release to do better. These examples might include skip row (if applicable to chickpea) and grazing (again if applicable - but note that still need the grazing in the validation simulation to continually test that the interaction with Stock is as it should be).

[AllanPeake]

Hi All, here is the presentation I will be giving next week. We will discuss Val's comments (and any others) after the presentation.
Chickpea Peake Reference Panel Presentation May 2021.pptx

[sarahcleary]

@APSIMInitiative/reference-panel - any further comments for @AllanPeake prior to the meeting/presentation tomorrow?

[sarahcleary]

@jwhish; @uqdrodri - please note @AllanPeake's presentation provided

[uqdrodri]

Sarah I’ve got to do some training at this time though will try to follow up the seminar with my left eye,… d From: sarahcleary ***@***.***> Date: Monday, 31 May 2021 at 9:26 am To: APSIMInitiative/ReferencePanel ***@***.***> Cc: Daniel Rodriguez ***@***.***>, Mention ***@***.***> Subject: Re: [APSIMInitiative/ReferencePanel] RP Meeting - 1/6/21 (#88) @jwhish<https://github.com/jwhish>; @uqdrodri<https://github.com/uqdrodri> - please note @AllanPeake<https://github.com/AllanPeake>'s presentation provided — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#88 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/APMHY7N2MUOJDR2EAHKJ7HTTQLCS3ANCNFSM44S3EMRA>.

[sarahcleary]

Apologies from @MarkLieffering and @Keith-Pembleton

[yashvirchauhan]

Questions for Alan Peake:
I would appreciate if Alan could enlighten me and others on the following points.
In chickpea flowering and pod set is strongly modulated by soil water and we now have evidence for this. Is the APSIM Chickpea (Next Gen) model able to handle soil water effect on flowering and pod set well? In one of the GRDC updates you mentioned that the model is able to predict phenology well in drier years but not in wetter years. Is it correct?
What do you think of the paper by Chauhan et al. (2019) in Scientific Reports being relevant to improving phenology prediction by the model?
Is the model able to account for frost impacts on yield (both positive and negatives)?
Is the model able to account for temperature threshold of 15oC for pod set? Have you been able to collect data or get reference from literature that demonstrates that 15oC threshold for pod set is real as it appears strange for a crop with a base temperature of oC to have such a high threshold. At Kingaroy chickpea can set pod at much lower temperatures than 15oC

[jbrider]

@AllanPeake, @hut104 some early comments after going through the simulations file not the documentation.

• Extra memo in [Phenology].EarlyGrainFilling (accidental copy)

[Phenology].StartBudSoilTT, StartBudding_PhotoPeriod, PoddingDAS and EndJuv_PhotoPeriod all have the same memo. If intentional then would help to say where they are all referenced from.

Nodule - many of the constants have empty memo's - there are a few instances for constants in other organs as well.

Not chickpea specific
[Root].RootShape doesn't have any description on the right when clicked - RootshapeCylindre (correct spelling?)

StorageNDemandFunction that is implemented in generic organ (NDemands.Storage) is implemented the same way every time - referencing an NitrogenDemandSwitch that is always at the base level of the organ and he 2nd parameter is always maximumNConc. Can the NitrogenDemandSwitch be moved to be inside the StorageNDemandFunction as it does not appear to be referenced from anywhere else. The documentation refers to it as The demand for N is reduced by a factor specified by the NitrogenDemandSwitch but it is always used as a switch - either 1 or 0.
NitrogenDemandSwitch also seems to have an empty memo by default.

AvailableDMRetranslocation in GenericOrgan calls RetranslocateNitrogen.CalculateBiomass - which in most instances is implemented by RetranslocateNonStructural.cs. RetranslocateNitrogen seems to be doing more than just Nitrogen?
RetranslocateNonStructural also has nothing displayed in the presenter when selected.

GenericOrgan.DMSupply.Fixation has a default reference to PhotoSynthesis - and is usually implemented using a constant function that returns 0. Should GenericOrgan fixing dry matter?

Missing Charts in the chickpea.apsimx file:
Validation.2019_PulseAdaptation.Emerald19_.BiomassByCvv - Genesis90 chart is not in the factors list
Validation.2019_PulseAdaptation.GT_HatTrick_WU_2019_.YieldByCvv.HatTrickIrr - incorrect filter
Validation.2019_PulseAdaptation.GT_HatTrick_WU_2019_.ProfileWater.ProfileWater_Genesis90 - cultivar not in this experiment
Validation.SE Queensland.FloweringDate - no observed data maybe?
Validation.SE Queensland.Lawes1991 - large number of charts with repetitions/missing/bad configuration
Validation.SE Queensland.Lawes1995.Stress1 - shouldn't be there?
Validation.SE Queensland.Bremar_2003_.SW_Layers.Function - wrong name?
Validation.SE Queensland.Bremar_2003_.SW_Layers1 - different to SW_Layers.
Validation.ICRISAT.ICRISAT_18_19_BM8_.Transpiration
Validation.ICRISAT.ICRISAT_18_19_BM8_.PhotoperBranch

Charts Referencing incorrect variables
Every earlyVEGBranch and lateVEGBrach chart looks to have bad references.
Also check EarlyVeg and LateVeg charts for similar issue.
Validation.2019_PulseAdaptation.Greenethorpe_2019_.NStress.Predicted: Selected Y field name 'Lentil.Leaf.Fn'
Validation.2019_PulseAdaptation.GT_HatTrick_WU_2019_.DMSupplyDemand.Demand: Selected Y field name 'Lentil.Arbitrator.DM.TotalPlantDemand'
Validation.2019_PulseAdaptation.Narrabri19_.DMSupplyDemand.Demand: Selected Y field name 'Lentil.Arbitrator.DM.TotalPlantDemand'
Validation.SE Queensland.Bremar_2003_.rowspace.Predicted: Selected Y field name 'Chickpea.SowingData.RowSpacing'
Validation.ICRISAT.ICRISAT_18_19_BM8_.rowspace.Predicted: Selected Y field name 'Chickpea.SowingData.RowSpacing'

Charts that don't look to be configured correctly
Validation.2019_PulseAdaptation.Greenethorpe_2019_.DMSupplyDemand
Validation.2019_PulseAdaptation.Greenethorpe_2019_.DMDemands
Validation.2019_PulseAdaptation.Greenethorpe_2019_.Partitioning
Validation.2019_PulseAdaptation.Greenethorpe_2019_.LeafPartitioning
Validation.2019_PulseAdaptation.Greenethorpe_2019_.PartitioningSenesced
Validation.2019_PulseAdaptation.Greenethorpe_2019_.StemPartitioning
Validation.SE Queensland.Bremar_2003_.OrganDemand
Validation.ICRISAT.Leaf Mass
Validation.ICRISAT.Stem Mass
Validation.ICRISAT.Dead Leaf Mass
Validation.ICRISAT.ICRISAT_18_19_BM8_. - many charts near the bottom

Repeated Charts?
Validation.2019_PulseAdaptation.Narrabri19_.BiomassByCvv1
Validation.ICRISAT.ICRISAT_18_19_BM8_.SW_Layers1
Validation.ICRISAT.ICRISAT_18_19_BM8_.SW_Layers2