RP Meeting - 6 July 2021

[sarahcleary]

Review of Pinus Model - https://github.com/APSIMInitiative/ApsimX/issues/5147

@sme016 to present

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

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

Information for Developer

• Upload the presentation at least a week prior to the meeting to the relevant issue - https://github.com/APSIMInitiative/ApsimX/issues/5147

• 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.

[sarahcleary]

@JulianneLilley unable to attend meeting

[sarahcleary]

@sarchontoulis unable to attend meeting. Fernando Miguez has been invited to attend from ISU.

[sarahcleary]

@femiguez

[sarahcleary]

@APSIMInitiative/reference-panel - please see powerpoint - https://github.com/APSIMInitiative/ApsimX/issues/5147#issuecomment-869285925

[sarahcleary]

2021-07 Minutes

Attendees:

@LouisAK; @hol353; @peter-devoil; @yashvirchauhan; @sarahcleary; @jbrider; @HamishBrownPFR; @hut104; @sno036; @EnliWang; @kchenu; @Keith-Pembleton; @sme016

Tuesday 6th July 2021 - 9:30 am AEST

Meeting recorded – which can be accessed on Teams link for meeting attendees. Review of Pinus Model - https://github.com/APSIMInitiative/ApsimX/issues/5147 @sme016 ran through the powerpoint – PinusReviewSlidesSmethurst.pptx

Discussion can be found on recording. Please email apsim@csiro.au if you wish to have access.

Work required for Model to be accepted into Release

@jbrider - https://github.com/APSIMInitiative/ApsimX/issues/5147#issuecomment-874384128 @HamishBrownPFR requested that the simulations are allowed to continue but document why they are deviating. This will allow a baseline to be established for when improvements are made. Action: update simulations ** @sno036 requested a simulation is provided with Stock

Note no representative from ISU at meeting. @sarahcleary has forwarded recording to @femiguez and @sarchontoulis.

Awaiting ISU's sign off. All other parties comfortable with model going into release once the above issues have been addressed.

[sme016]

Update on Pinus

Requested changes and RESPONSES:

• Some of the memo fields in many of the generic organs refer to Leaf (copied I assume) DELETED

• Stem has a 2nd memo whose contents should replace the first memo within stem. DELETED

• The autodoc wasn't present on the website (apologies for not catching this before the meeting). NOW INCLUDED

• Example file has a broken graph (MineralNppm) FIXED

• Extend simulations for full range of observed – try to filter to show OvPs +/- this extension. THIS WAS NEEDED FOR TWO SITES. AS IT DIDN’T CHANGE THE OvP STATS MUCH, I DIDN’T ALTER GRAPHS. INSTEAD I ADDED A MEMO ABOUT THOSE DURATION OF SIMULATION FOR THOSE TWO SITES. This led to a minor deterioration in most OvP stats, but the important ones are still quite good.

• Mortality thinnings should take less proportionally of biomass and stem volume I MODIFIED THE THINNING SCRIPT TO ENABLE REMOVAL OF BIOMASS IN RELATION TO POPULATION THAT WAS BIASED TO REFLECT THINNING FROM ABOVE OR BELOW

• Test stock don’t eat Pinus. PINUS DID NOT INITIALLY RUN IN THE STOCK EXAMPLE DUE TO ROOT REMOVAL AND MASS BALANCE ISSUES. DREW FIXED THIS, BUT I AM STILL WAINTING TO TEST IT.

• Example: tidy up obs and graphs DONE

• Check Pinus runs in agroforestry A TEST OF PINUS IN AGROFORESTRY WORKED

• Update Validation and Example through GitHub DONE

• Include Pinus.json in Models/Resources I’LL LEAVE THIS TO AN EXPERT

Please let me know if more work is needed to address the review process. Otherwise, I look forward to seeing the full release of Pinus.

Regards, Philip

From: sarahcleary @.> Sent: Tuesday, 6 July 2021 12:22 PM To: APSIMInitiative/ReferencePanel @.> Cc: Smethurst, Philip (L&W, Sandy Bay) @.>; Mention @.> Subject: Re: [APSIMInitiative/ReferencePanel] RP Meeting - 6 July 2021 (#90)

2021-07 Minutes Attendees:

@LouisAKhttps://github.com/LouisAK; @hol353https://github.com/hol353; @peter-devoilhttps://github.com/peter-devoil; @yashvirchauhanhttps://github.com/yashvirchauhan; @sarahclearyhttps://github.com/sarahcleary; @jbriderhttps://github.com/jbrider; @HamishBrownPFRhttps://github.com/HamishBrownPFR; @hut104https://github.com/hut104; @sno036https://github.com/sno036; @EnliWanghttps://github.com/EnliWang; @kchenuhttps://github.com/kchenu; @Keith-Pembletonhttps://github.com/Keith-Pembleton; @sme016https://github.com/sme016

Tuesday 6th July 2021 - 9:30 am AEST

Meeting recorded – which can be accessed on Teams link for meeting attendees. Review of Pinus Model - APSIMInitiative/ApsimX#5147https://github.com/APSIMInitiative/ApsimX/issues/5147 @sme016https://github.com/sme016 ran through the powerpoint – PinusReviewSlidesSmethurst.pptxhttps://github.com/APSIMInitiative/ApsimX/files/6722884/PinusReviewSlidesSmethurst.pptx

Discussion can be found on recording. Please email @.**@.> if you wish to have access.

Work required for Model to be accepted into Release

@jbriderhttps://github.com/jbrider - APSIMInitiative/ApsimX#5147 (comment)https://github.com/APSIMInitiative/ApsimX/issues/5147#issuecomment-874384128 @HamishBrownPFRhttps://github.com/HamishBrownPFR requested that the simulations are allowed to continue but document why they are deviating. This will allow a baseline to be established for when improvements are made. Action: update simulations ** @sno036https://github.com/sno036 requested a simulation is provided with Stock

Note no representative from ISU at meeting. @sarahclearyhttps://github.com/sarahcleary has forwarded recording to @femiguezhttps://github.com/femiguez and @sarchontoulishttps://github.com/sarchontoulis.

Awaiting ISU's sign off. All other parties comfortable with model going into release once the above issues have been addressed.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/APSIMInitiative/ReferencePanel/issues/90#issuecomment-874412815, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ALYXHJAP5YW77JXNHEUJJYTTWJSFLANCNFSM46LDGKSA.

[sme016]

Hi Jason,

I am anxious to soon have the Pinus model fully released, as I am running training on the Eucalyptus and Pinus models on the 15th October. Is there anything more I should do to complete this release?

Full release appears close, as a recently updated version of Pinus is now in the example in the GUI, and documentation of the validation is up-to-date – thanks.

However:

1. I assume someone needs to add Pinus.json in Models/Resources, and
2. At the documentation page (https://apsimnextgeneration.netlify.app/modeldocumentation/) someone need to remove (Under Review) from Pinus.

Further update on a review question:

• Drew had fixed documentation of stock, but there remains a mass balance issue that Drew, Dean and Val are aware of but which I don’t think has yet been resolved.

Regards, Philip

From: Smethurst, Philip (L&W, Sandy Bay) Sent: Friday, 27 August 2021 3:30 PM To: APSIMInitiative/ReferencePanel @.>; APSIMInitiative/ReferencePanel @.> Cc: Mention @.***> Subject: RE: [APSIMInitiative/ReferencePanel] RP Meeting - 6 July 2021 (#90)

Update on Pinus

Requested changes and RESPONSES:

• Some of the memo fields in many of the generic organs refer to Leaf (copied I assume) DELETED

• Stem has a 2nd memo whose contents should replace the first memo within stem. DELETED

• The autodoc wasn't present on the website (apologies for not catching this before the meeting). NOW INCLUDED

• Example file has a broken graph (MineralNppm) FIXED

• Extend simulations for full range of observed – try to filter to show OvPs +/- this extension. THIS WAS NEEDED FOR TWO SITES. AS IT DIDN’T CHANGE THE OvP STATS MUCH, I DIDN’T ALTER GRAPHS. INSTEAD I ADDED A MEMO ABOUT THOSE DURATION OF SIMULATION FOR THOSE TWO SITES. This led to a minor deterioration in most OvP stats, but the important ones are still quite good.

• Mortality thinnings should take less proportionally of biomass and stem volume I MODIFIED THE THINNING SCRIPT TO ENABLE REMOVAL OF BIOMASS IN RELATION TO POPULATION THAT WAS BIASED TO REFLECT THINNING FROM ABOVE OR BELOW

• Test stock don’t eat Pinus. PINUS DID NOT INITIALLY RUN IN THE STOCK EXAMPLE DUE TO ROOT REMOVAL AND MASS BALANCE ISSUES. DREW FIXED THIS, BUT I AM STILL WAINTING TO TEST IT.

• Example: tidy up obs and graphs DONE

• Check Pinus runs in agroforestry A TEST OF PINUS IN AGROFORESTRY WORKED

• Update Validation and Example through GitHub DONE

• Include Pinus.json in Models/Resources I’LL LEAVE THIS TO AN EXPERT

Please let me know if more work is needed to address the review process. Otherwise, I look forward to seeing the full release of Pinus.

Regards, Philip

From: sarahcleary @.**@.>> Sent: Tuesday, 6 July 2021 12:22 PM To: APSIMInitiative/ReferencePanel @.**@.>> Cc: Smethurst, Philip (L&W, Sandy Bay) @.**@.>>; Mention @.**@.>> Subject: Re: [APSIMInitiative/ReferencePanel] RP Meeting - 6 July 2021 (#90)

2021-07 Minutes Attendees:

@LouisAKhttps://github.com/LouisAK; @hol353https://github.com/hol353; @peter-devoilhttps://github.com/peter-devoil; @yashvirchauhanhttps://github.com/yashvirchauhan; @sarahclearyhttps://github.com/sarahcleary; @jbriderhttps://github.com/jbrider; @HamishBrownPFRhttps://github.com/HamishBrownPFR; @hut104https://github.com/hut104; @sno036https://github.com/sno036; @EnliWanghttps://github.com/EnliWang; @kchenuhttps://github.com/kchenu; @Keith-Pembletonhttps://github.com/Keith-Pembleton; @sme016https://github.com/sme016

Tuesday 6th July 2021 - 9:30 am AEST

Meeting recorded – which can be accessed on Teams link for meeting attendees. Review of Pinus Model - APSIMInitiative/ApsimX#5147https://github.com/APSIMInitiative/ApsimX/issues/5147 @sme016https://github.com/sme016 ran through the powerpoint – PinusReviewSlidesSmethurst.pptxhttps://github.com/APSIMInitiative/ApsimX/files/6722884/PinusReviewSlidesSmethurst.pptx

Discussion can be found on recording. Please email @.**@.> if you wish to have access.

Work required for Model to be accepted into Release

@jbriderhttps://github.com/jbrider - APSIMInitiative/ApsimX#5147 (comment)https://github.com/APSIMInitiative/ApsimX/issues/5147#issuecomment-874384128 @HamishBrownPFRhttps://github.com/HamishBrownPFR requested that the simulations are allowed to continue but document why they are deviating. This will allow a baseline to be established for when improvements are made. Action: update simulations ** @sno036https://github.com/sno036 requested a simulation is provided with Stock

Note no representative from ISU at meeting. @sarahclearyhttps://github.com/sarahcleary has forwarded recording to @femiguezhttps://github.com/femiguez and @sarchontoulishttps://github.com/sarchontoulis.

Awaiting ISU's sign off. All other parties comfortable with model going into release once the above issues have been addressed.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/APSIMInitiative/ReferencePanel/issues/90#issuecomment-874412815, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ALYXHJAP5YW77JXNHEUJJYTTWJSFLANCNFSM46LDGKSA.

[sno036]

@sme016 - given that @hol353 is working on the generic method for Stock (I think nearing merging) I am OK with this proceeding Can you disable the particular simulation that throws the mass balance error for now with the understanding that it will be re-enabled once Dean's method in merged? I think Dean is on leave this week.