RP Meeting - 6 July 2021

[sarahcleary]

Review of Pinus Model - APSIMInitiative/ApsimX#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 - New Pinus Model for Apsim Next Gen ApsimX#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 - APSIMInitiative/ApsimX#5147 (comment)

[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 - APSIMInitiative/ApsimX#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 - APSIMInitiative/ApsimX#5147 (comment)
** @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: @LouisAK<https://github.com/LouisAK>; @hol353<https://github.com/hol353>; @peter-devoil<https://github.com/peter-devoil>; @yashvirchauhan<https://github.com/yashvirchauhan>; @sarahcleary<https://github.com/sarahcleary>; @jbrider<https://github.com/jbrider>; @HamishBrownPFR<https://github.com/HamishBrownPFR>; @hut104<https://github.com/hut104>; @sno036<https://github.com/sno036>; @EnliWang<https://github.com/EnliWang>; @kchenu<https://github.com/kchenu>; @Keith-Pembleton<https://github.com/Keith-Pembleton>; @sme016<https://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#5147<APSIMInitiative/ApsimX#5147> @sme016<https://github.com/sme016> ran through the powerpoint – PinusReviewSlidesSmethurst.pptx<https://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 ** @jbrider<https://github.com/jbrider> - APSIMInitiative/ApsimX#5147 (comment)<APSIMInitiative/ApsimX#5147 (comment)> ** @HamishBrownPFR<https://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 ** @sno036<https://github.com/sno036> requested a simulation is provided with Stock Note no representative from ISU at meeting. @sarahcleary<https://github.com/sarahcleary> has forwarded recording to @femiguez<https://github.com/femiguez> and @sarchontoulis<https://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 GitHub<#90 (comment)>, or unsubscribe<https://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: @LouisAK<https://github.com/LouisAK>; @hol353<https://github.com/hol353>; @peter-devoil<https://github.com/peter-devoil>; @yashvirchauhan<https://github.com/yashvirchauhan>; @sarahcleary<https://github.com/sarahcleary>; @jbrider<https://github.com/jbrider>; @HamishBrownPFR<https://github.com/HamishBrownPFR>; @hut104<https://github.com/hut104>; @sno036<https://github.com/sno036>; @EnliWang<https://github.com/EnliWang>; @kchenu<https://github.com/kchenu>; @Keith-Pembleton<https://github.com/Keith-Pembleton>; @sme016<https://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#5147<APSIMInitiative/ApsimX#5147> @sme016<https://github.com/sme016> ran through the powerpoint – PinusReviewSlidesSmethurst.pptx<https://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 ** @jbrider<https://github.com/jbrider> - APSIMInitiative/ApsimX#5147 (comment)<APSIMInitiative/ApsimX#5147 (comment)> ** @HamishBrownPFR<https://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 ** @sno036<https://github.com/sno036> requested a simulation is provided with Stock Note no representative from ISU at meeting. @sarahcleary<https://github.com/sarahcleary> has forwarded recording to @femiguez<https://github.com/femiguez> and @sarchontoulis<https://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 GitHub<#90 (comment)>, or unsubscribe<https://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.