search

mareframe / vat

Visualizing Atlantis Tool (vat)
5 stars 9 forks source link

gather dataframe #12

Closed mcgregorv closed 8 years ago

mcgregorv commented 8 years ago

When I ran it, create_vadt fell over unless I made everything 'gather' was to be used on a data.frame

cddesja commented 8 years ago

Can you share your model via Dropbox so I can take a peak?

cddesja commented 8 years ago

Are you getting a message that says "Error: unknown column 'X1'"?

mcgregorv commented 8 years ago

Hi Chris

Yes, I’ve put it here ftp://ftp.niwa.co.nz/os2020/ATLANTIS/TBGB_SendToChris

if you need a password it will be mcgregorv Let me know if you have any trouble getting it. It should have everything you need in it, including the Atlantis.exe and the output files. Also my R script and my version of your create_vadt.R

It’s nice to finally be using your shiny ap – it’s very good! Thanks ☺

And yes, it was Error: unknown column 'X1' which lead me to defining the object as a data.frame

Vidette

From: Christopher David Desjardins [mailto:notifications@github.com] Sent: Thursday, 28 January 2016 10:53 a.m. To: mareframe/vat Cc: Vidette McGregor Subject: Re: [vat] gather dataframe (#12)

Can you share your model via Dropbox so I can take a peak?

— Reply to this email directly or view it on GitHubhttps://github.com/mareframe/vat/issues/12#issuecomment-175877399.

Vidette McGregor Ecosystem Modeller

+64-4-386-0851 | 301 Evans Bay Parade, Greta Point, Wellington | www.niwa.co.nzhttp://www.niwa.co.nz [NIWA]http://www.niwa.co.nz To ensure compliance with legal requirements and to maintain cyber security standards, NIWA's IT systems are subject to ongoing monitoring, activity logging and auditing. This monitoring and auditing service may be provided by third parties. Such third parties can access information transmitted to, processed by and stored on NIWA's IT systems.

mcgregorv commented 8 years ago

yes

From: Christopher David Desjardins [mailto:notifications@github.com] Sent: Thursday, 28 January 2016 11:11 a.m. To: mareframe/vat Cc: Vidette McGregor Subject: Re: [vat] gather dataframe (#12)

Are you getting a message that says "Error: unknown column 'X1'"?

— Reply to this email directly or view it on GitHubhttps://github.com/mareframe/vat/issues/12#issuecomment-175886467.

Vidette McGregor Ecosystem Modeller

+64-4-386-0851 | 301 Evans Bay Parade, Greta Point, Wellington | www.niwa.co.nzhttp://www.niwa.co.nz [NIWA]http://www.niwa.co.nz To ensure compliance with legal requirements and to maintain cyber security standards, NIWA's IT systems are subject to ongoing monitoring, activity logging and auditing. This monitoring and auditing service may be provided by third parties. Such third parties can access information transmitted to, processed by and stored on NIWA's IT systems.

mcgregorv commented 8 years ago

Also, I see in the diets you’ve left the consumed units undefined. If the prey species is a vertebrate, Atlantis has output the amount consumed as individuals per second and if it is an invert it is mg N per second (at least I’m mostly sure that’s right!)

From: Christopher David Desjardins [mailto:notifications@github.com] Sent: Thursday, 28 January 2016 11:11 a.m. To: mareframe/vat Cc: Vidette McGregor Subject: Re: [vat] gather dataframe (#12)

Are you getting a message that says "Error: unknown column 'X1'"?

— Reply to this email directly or view it on GitHubhttps://github.com/mareframe/vat/issues/12#issuecomment-175886467.

Vidette McGregor Ecosystem Modeller

+64-4-386-0851 | 301 Evans Bay Parade, Greta Point, Wellington | www.niwa.co.nzhttp://www.niwa.co.nz [NIWA]http://www.niwa.co.nz To ensure compliance with legal requirements and to maintain cyber security standards, NIWA's IT systems are subject to ongoing monitoring, activity logging and auditing. This monitoring and auditing service may be provided by third parties. Such third parties can access information transmitted to, processed by and stored on NIWA's IT systems.

cddesja commented 8 years ago

Thanks. I see what you're referring to about the data.frame() command. Regarding diets, are you referring to the diets table or a diet plot or the Markdown file (the starting page)? I don't need your model.

mcgregorv commented 8 years ago

The Diet Data plots, which seem to be using the OutputDietCheck.txt data

From: Christopher David Desjardins [mailto:notifications@github.com] Sent: Thursday, 28 January 2016 11:23 a.m. To: mareframe/vat Cc: Vidette McGregor Subject: Re: [vat] gather dataframe (#12)

Thanks. I see what you're referring to about the data.frame() command. Regarding diets, are you referring to the diets table or a diet plot or the Markdown file (the starting page)? I don't need your model.

— Reply to this email directly or view it on GitHubhttps://github.com/mareframe/vat/issues/12#issuecomment-175891308.

Vidette McGregor Ecosystem Modeller

+64-4-386-0851 | 301 Evans Bay Parade, Greta Point, Wellington | www.niwa.co.nzhttp://www.niwa.co.nz [NIWA]http://www.niwa.co.nz To ensure compliance with legal requirements and to maintain cyber security standards, NIWA's IT systems are subject to ongoing monitoring, activity logging and auditing. This monitoring and auditing service may be provided by third parties. Such third parties can access information transmitted to, processed by and stored on NIWA's IT systems.

cddesja commented 8 years ago

OK. I'll take a look at this. Looks like either dplyr or tidyr is responsible for this bug. Thanks for fixing it for me.

cddesja commented 8 years ago

This has now been fixed in the mat-age-fix branch. If you want to test it, which Matteo has, you can do the following.

devtools::install_github(repo="mareframe/vat", ref = "mat-age-fix")

Regarding the y-axis label, I don't know what's the most elegant option. I could have a long y-axis label, but seems not so nice either. @mcgregorv, do you have a specific suggestion?

mcgregorv commented 8 years ago

Hey Chris Sorry, the units for diet check are just proportions. For a given predator/cohort, it gives the proportion of diet made up by each of the prey species over the given year. So the y-axis should be ‘Proportion of predator diet’ or something like that. Cheers, Vidette

From: Christopher David Desjardins [mailto:notifications@github.com] Sent: Friday, 29 January 2016 3:30 a.m. To: mareframe/vat Cc: Vidette McGregor Subject: Re: [vat] gather dataframe (#12)

This has now been fixed in the mat-age-fix branch. If you want to test it, which Matteo has, you can do the following.

devtools::install_github(repo="mareframe/vat", ref = "mat-age-fix")

Regarding the y-axis label, I don't know what's the most elegant option. I could have a long y-axis label, but seems not so nice either. @mcgregorvhttps://github.com/mcgregorv, do you have a specific suggestion?

— Reply to this email directly or view it on GitHubhttps://github.com/mareframe/vat/issues/12#issuecomment-176208587.

Vidette McGregor Ecosystem Modeller

+64-4-386-0851 | 301 Evans Bay Parade, Greta Point, Wellington | www.niwa.co.nzhttp://www.niwa.co.nz [NIWA]http://www.niwa.co.nz To ensure compliance with legal requirements and to maintain cyber security standards, NIWA's IT systems are subject to ongoing monitoring, activity logging and auditing. This monitoring and auditing service may be provided by third parties. Such third parties can access information transmitted to, processed by and stored on NIWA's IT systems.