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terraref / reference-data

Coordination of Data Products and Standards for TERRA reference data
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Traits package to download data from BETYdb #261

Closed zhenbinHU closed 5 years ago

zhenbinHU commented 5 years ago

I try to download the date from BETYdb using traits package, for season 1, 2, 5 the code work well. For season 3, I got

canopy_height_all <- betydb_query(table = 'search', trait = "canopy_height", sitename = "~Season 3", limit = 'none') canopy_height_all NULL

For season 4, I got

canopy_height_all <- betydb_query(table = 'search', trait = "canopy_height", method = "~Laser 3d", sitename = "~Season 4", limit = 'none') Error in betydb_http(url, args, key, user, pwd, ...) : Gateway Timeout (HTTP 504).

dlebauer commented 5 years ago

There are no canopy height data for season 3. For season 4, the method name is 'Scanner 3d ply data to height' - you should get 63,900 records.

Try 

canopy_height_all <- betydb_query(table = 'search',
                                  trait = "canopy_height",
                                  method = "~Scanner 3d",
                                  sitename = "~Season 4",
                                  limit = 'none')
zhenbinHU commented 5 years ago

Thanks, it works. Obtained a 70,401 x 38 dataframe.

dlebauer commented 5 years ago

Great - closing since the issue is solved

zhenbinHU commented 5 years ago

@dlebauer I used the traits package to download the plant height data. However, how can get a list for traits names for sorghum in betydb. So I can use the traits names to download other trait's data.

dlebauer commented 5 years ago

You can find a list of all of the variables at terraref.ncsa.illinois.edu/bety/variables or, equivalently, 

betydb_query(table = 'variables')

Though note that the existence of a variable does not mean that there are actually data ...

To see what is actually in the database, you can browse traitvis.workbench.terraref.org and here is a current snapshot of the number of records we have for each variable: https://gist.github.com/dlebauer/5db33c5c54781069ff58302b3313dfd1