search

James-Thorson-NOAA / ATM

Advection-taxis movement model
GNU General Public License v3.0
6 stars 1 forks source link

ATM model error #3

Open robertbthorpe opened 1 year ago

robertbthorpe commented 1 year ago

A colleague and I would like to use this package to make a near-real time forecast in the Celtic Sea region. We are trying to familiarise ourselves with the method by running the cod demonstration provided, but cannot get it to fit in TMB. In particular I am getting the error in R-studio :- Error in as.data.frame.default(Cov_stars): cannot coerce class "stars" to a data.frame.

can you advise on what I am doing wrongly? Thanks

fit = fitTMB(

source("C:/ADT/ATM-1.0.0/R/demo.R") Using strata All_areas For the UTM conversion, automatically detected zone 2. Using strata All_areas For the UTM conversion, automatically detected zone 2. n_x greater than or equal to n_unique so no calculation necessary Error in as.data.frame.default(Cov_stars) : cannot coerce class ‘"stars"’ to a data.frame In addition: Warning messages: 1: PROJ support is provided by the sf and terra packages among others 2: PROJ support is provided by the sf and terra packages among others 3: PROJ support is provided by the sf and terra packages among others 4: In INLA:::inla.barrier.fem(mesh = anisotropic_mesh, barrier.triangles = anisotropic_mesh_triangles_over_land) : Using implementation from the INLAspacetime package 5: PROJ support is provided by the sf and terra packages among others

James-Thorson-NOAA commented 1 year ago

I'm not sure what might be happening and can't replicate your error message. What packageVersion("stars") do you have installed?

However, I was getting a separate compiler error (resulting from me having a local rtweedie that had a name-conflict with a function added to base TMB after ATM was released). I just merged dev branch into main, which fixes that. Could you you please try again using dev branch?

Ultimately, ATM is a research model and I doubt I can help much with tracking down syntax changes in stars or whatever is happening. I think options are:

robertbthorpe commented 1 year ago

Thanks for getting back to me Jim. I will try your suggestions and see what happens. The textbook sounds great as I think the methods you are pioneering have the potential to be really helpful for the near-real-time forecast we would like to make. Other options such as neural nets or correlative only models may not be mechanistic enough, whilst IBMs with data assimilation are likely to be too slow and not close enough to the state at t=0 to be useful.

From: Jim Thorson @.> Sent: Thursday, June 22, 2023 7:22 PM To: James-Thorson-NOAA/ATM @.> Cc: Robert Thorpe (Cefas) @.>; Author @.> Subject: Re: [James-Thorson-NOAA/ATM] ATM model error (Issue #3)

WARNING - This email originated from outside of the organisation. Do not click links , forward or open attachments unless you recognise the sender and have established the content is safe.

I'm not sure what might be happening and can't replicate your error message. What packageVersion("stars") do you have installed?

However, I was getting a separate compiler error (resulting from me having a local rtweedie that had a name-conflict with a function added to base TMB after ATM was released). I just merged dev branch into main, which fixes that. Could you you please try again using dev branch?

Ultimately, ATM is a research model and I doubt I can help much with tracking down syntax changes in stars or whatever is happening. I think options are:

— Reply to this email directly, view it on GitHubhttps://github.com/James-Thorson-NOAA/ATM/issues/3#issuecomment-1603121951, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUPIDLUIQNJPRQ2YCSH5EN3XMSEOHANCNFSM6AAAAAAZQARM2A. You are receiving this because you authored the thread.Message ID: @.**@.>>

This email and any attachments are intended for the named recipient only. Its unauthorised use, distribution, disclosure, storage or copying is not permitted. If you have received it in error, please destroy all copies and notify the sender. In messages of a non-business nature, the views and opinions expressed are the author's own and do not necessarily reflect those of Cefas. Communications on Cefas’ computer systems may be monitored and/or recorded to secure the effective operation of the system and for other lawful purposes. All messages sent and received by the Centre for Environment, Fisheries and Aquaculture Science may be monitored in line with relevant UK legislation . https://www.gov.uk/government/organisations/centre-for-environment-fisheries-and-aquaculture-science/about/personal-information-charter

robertbthorpe commented 1 year ago

Dear Jim,

Thanks, I’ve got it to run. I don’t know what made the difference, your dev branch or updating R about 500 times in a loop, or having to reinstall Rtools, but something did the job.

We would like to do the same sort of thing for the Celtic Sea and wondered if there was any documentation on the case study and the data that would be needed to transplant the approach to another region. Don’t worry if not, there’s always your course and maybe book!

Robert

From: Robert Thorpe (Cefas) Sent: Friday, June 23, 2023 10:48 AM To: James-Thorson-NOAA/ATM @.**@.>> Subject: RE: [James-Thorson-NOAA/ATM] ATM model error (Issue #3)

Thanks for getting back to me Jim. I will try your suggestions and see what happens. The textbook sounds great as I think the methods you are pioneering have the potential to be really helpful for the near-real-time forecast we would like to make. Other options such as neural nets or correlative only models may not be mechanistic enough, whilst IBMs with data assimilation are likely to be too slow and not close enough to the state at t=0 to be useful.

From: Jim Thorson @.**@.>> Sent: Thursday, June 22, 2023 7:22 PM To: James-Thorson-NOAA/ATM @.**@.>> Cc: Robert Thorpe (Cefas) @.**@.>>; Author @.**@.>> Subject: Re: [James-Thorson-NOAA/ATM] ATM model error (Issue #3)

WARNING - This email originated from outside of the organisation. Do not click links , forward or open attachments unless you recognise the sender and have established the content is safe.

I'm not sure what might be happening and can't replicate your error message. What packageVersion("stars") do you have installed?

However, I was getting a separate compiler error (resulting from me having a local rtweedie that had a name-conflict with a function added to base TMB after ATM was released). I just merged dev branch into main, which fixes that. Could you you please try again using dev branch?

Ultimately, ATM is a research model and I doubt I can help much with tracking down syntax changes in stars or whatever is happening. I think options are:

— Reply to this email directly, view it on GitHubhttps://github.com/James-Thorson-NOAA/ATM/issues/3#issuecomment-1603121951, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUPIDLUIQNJPRQ2YCSH5EN3XMSEOHANCNFSM6AAAAAAZQARM2A. You are receiving this because you authored the thread.Message ID: @.**@.>>

This email and any attachments are intended for the named recipient only. Its unauthorised use, distribution, disclosure, storage or copying is not permitted. If you have received it in error, please destroy all copies and notify the sender. In messages of a non-business nature, the views and opinions expressed are the author's own and do not necessarily reflect those of Cefas. Communications on Cefas’ computer systems may be monitored and/or recorded to secure the effective operation of the system and for other lawful purposes. All messages sent and received by the Centre for Environment, Fisheries and Aquaculture Science may be monitored in line with relevant UK legislation . https://www.gov.uk/government/organisations/centre-for-environment-fisheries-and-aquaculture-science/about/personal-information-charter

James-Thorson-NOAA commented 1 year ago

Robert,

There isn't any real documentation besides the code base there. Please email me if you want me to dig up the scripts I ran to format the inputs.