How to encode MAC Season 4 drought experiments

[dlebauer]

Breaking out this issue from #174 (comment)

from @NewcombMaria
... the Managements I entered for 2017-08-01 and 2017-08-15 describe the establishment and reversal of 'water-deficit' and 'well-watered' blocks as part of the Field Campaign Stress Effect on Photosynthesis. I entered them under the Treatment 'Control BAP 2017'. Is this correct? Or should the month of August be split into 2 separate treatments for the time intervals August 1-14 and August 15-30?

Update

I've calculated the irrigation levels for season 4
season_4_irrigation.csv

[dlebauer]

@NewcombMaria regarding the irrigation / water deficit treatment. It looks like there were two treatments, one that was put under water stress at Day 103 (Aug 1) and the other at day 116 (Aug 15).

In this case, I would create two treatments, for example _BAP 2017 drought 103 days after planting" and "BAP 2017 with drought at 117 days after planting"

Then we can link all of the existing managments (planting, tillage, fertilization, etc) to both of these and then add managements called 'irrigation' with level = 0 and date Aug 01 and link it just to the 103 dap drought treatment. Another management with irrigation level = 0 and date Aug 15 and link it to the 116 dap drought treatment. In addition, we can add managements with the same initial irrigation rates on these dates and attach them to the opposite treatment.

So the irrigation timeline for 103 dap would look like

Date	Management	Level	Units	Description
...
2017-04-20	planting
...
2017-07-30	irrigation	20	mm/d
2017-08-01	irrigation	0	mm / d
2017-08-15	irrigation	20	mm /d
2017-08-30	irrigation	20	mm / d
2017-09-11	harvest
...

So the irrigation timeline for 116 dap would have all of the same managements except the 8-01 and 08-15 dates:

Date	Management	Level	Units	Description
...
2017-08-01	irrigation	20	mm / d
2017-08-15	irrigation	0	mm /d
2017-08-30	irrigation	20	mm / d
...

The description / treatments can point to the raw irrigation data here: https://terraref.ncsa.illinois.edu/clowder/api/geostreams/datapoints?stream_id=3212

Which look like this:

(code here: https://gist.github.com/dlebauer/ff5826d9528b720bbd7a5129c25ad319)

---

However, this has uncovered an invalid assumption in our irrigation data stream: we have been assuming that the area irrigated is constant, at 4000 m2 in order to convert from galons / d to CF standard units of kg / m2 / s (= mm / s).

The code is here: https://github.com/terraref/extractors-environmental/blob/master/irrigation_datparser/parser.py#L10

So, we need to revisit this calculation. One way would be to create a new treatment named 'irrigated_area', and the value would be valid from the date of the treatment until a new value occurs.

@NewcombMaria could you or @Andrade-Pedro provide the values for irrigated area: is 4000 m2 a sensible default? Then, do you know what fraction of the field was in the drought treatments?

NB: we won't have time to fix this before Nov, but can make it high priority shortly thereafter

[NewcombMaria]

@dlebauer the irrigation timeline is correct (one part of the field at level 0 from 103 to 116 DAP and returning to level 20 after 116 DAP, while the opposite section of the field remains at level 20 until 116 DAP then drops to 0 . Thanks!

• I'll talk with Pedro and we'll figure out the proportion of the field (m2) in the water-restricted area for each of the time periods. Knowing the area (proportion of the field) will allow for correction of the irrigation data stream.

• Do we still need to link specific plots (sites) to the water-deficit time periods? If it's helpful I can share a spreadsheet with each site (plot) described by water-deficit or well-watered for each time period (103 - 116 DAP and 116 - 131 DAP). Let me know how to geo-reference the water-deficit areas.

[NewcombMaria]

@dlebauer here are the values for area irrigated by time that @Andrade-Pedro and I worked out. Sorghum season4 irrigated area was slightly larger compared to previous seasons because we added an additional buffer row in the narrow spaces on the West and East edges (outside of the scan-able area but inside the rails, and at narrower row spacing). I don't know the history of when/how the value 4000 m2 irrigated area originated. In previous seasons I think the irrigated area would have been 5267 m2, (216 m x 24.384 m)but perhaps there's an explanation for 4000 m2 that I don't know about.

Full-field area (including buffer rows) that was irrigated from the start of the season to August 1 (103 dap): 5486.4 m2 (=216 m x 25.4 m)

Well-watered treatment zones from August 1 to 15 (103 to 116 dap): 2522.88 m2 (=216 m x 11.68 m) in total, combined areas of non-contiguous blocks

Well-watered treatment zones from August 15 - 30 (116 to 131 dap): 3181.68 m2 (=216 m x 14.73 m), again in total as the combined areas of non-contiguous blocks

[dlebauer]

but perhaps there's an explanation for 4000 m2 that I don't know about.

I've always thought the field dimensions were 200 x 20m but I can see that this was just an approximation.

• If you provide the list of plot names in each treatment, I can match the plots with specific treatments in the database. Then in future uploads it will be easiest if each file contains both a site and treatment column.

Do you or Pedro have polygons representing the irrigation zones? I am wondering if 1) computing the area is gis operation that could be automated and 2) if we can record irrigation zones as 'sites' so that we can easily query all plots within an irrigation zone and compute areas irrigated.

[NewcombMaria]

@dlebauer I added 2 spreadsheets to the directory https://drive.google.com/drive/folders/0B1OR5-zeXagnUGdLb0dVUFRYc1k
with the site names at the plot-level matched to WW (well-watered or irrigated) or D (dry or not irrigated). These irrigation treatments only are associated with data collected in August, not for any data collected from April 20 to July 31. One spreadsheet is for the irrigation blocks from 2017-08-01 to 2017-08-15; the other spreadsheet has the irrigation blocks from 2017-08-16 to 2017-08-30. (Could have merged them into one spreadsheet with different columns but this is how I have the treatments for now).

[NewcombMaria]

We don't have GIS polygons for the irrigation blocks in August. The areas in previous comments are accurate, based on row widths and range lengths. We could create polygons for the experimental and border plots based on the descriptions in the Management list:
https://terraref.ncsa.illinois.edu/bety/managements/6000000079
https://terraref.ncsa.illinois.edu/bety/managements/6000000080

[dlebauer]

@NewcombMaria indeed we should be able to create polygons for a given management thus:

water-deficit blocks with restricted irrigation starting Aug 01

select st_astext(st_union(geometry)) as geometry 
     from sites 
     where sitename ~ 'Column (5|6|7|12|13|14|15)$' 
              and sitename like 'MAC Field Scanner Season 4%'

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water-deficit blocks with restricted irrigation starting Aug 14

select st_astext(st_union(geometry)) as geometry 
      from sites 
     where sitename ~ 'Column (2|3|4|9|10|11)$' 
           and sitename like 'MAC Field Scanner Season 4%'

MULTIPOLYGON Z (((-111.974924758217 33.0745634177791 0,-111.974908389131 33.074563423097 0,-111.974892020044 33.0745634284128 0,-111.974875650957 33.0745634337264 0,-111.974875636484 33.0745318660188 0,-111.974892005565 33.0745318607053 0,-111.974908374646 33.0745318553897 0,-111.974924743727 33.0745318500719 0,-111.974924758217 33.0745634177791 0)),((-111.975039341823 33.0745633805837 0,-111.975022972736 33.0745633859167 0,-111.97500660365 33.0745633912475 0,-111.974990234564 33.0745633965761 0,-111.974990220049 33.0745318287791 0,-111.975006589131 33.0745318235408 0,-111.975022958211 33.0745318182101 0,-111.975039327291 33.0745318128772 0,-111.975039341823 33.0745633805837 0)),((-111.975039358223 33.0745993226679 0,-111.975022989237 33.0745993280001 0,-111.975006620145 33.0745993333311 0,-111.974990251052 33.0745993386599 0,-111.974990236538 33.0745677709532 0,-111.975006605625 33.0745677656246 0,-111.975022974712 33.0745677602937 0,-111.975039343799 33.0745677549608 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[NewcombMaria]

@dlebauer if I'm understanding correctly, I should create 4 new treatments? So far there is one treatment for Season 4 named as 'Control BAP 2017' which is irrigated for optimal growth and was implemented from 2017-04-20 to 2017-07-31. Should I create 4 new treatments?:

Irrigation=0 BAP 2017-08-01 to 2017-08-15
Irrigation=1 BAP 2017-08-01 to 2017-08-15
Irrigation=0 BAP 2017-08-16 to 2017-08-30
Irrigation=1 BAP 2017-08-16 to 2017-08-30

See for example the treatment column (L) in the spreadsheet with August data from the MultispeQ device at the Google directory
https://drive.google.com/drive/folders/1MVkQpJ8f_gCHZP17j63tXaAGCT1R5tAO
Will this work for defining the August irrigation treatments?

[dlebauer]

I think there should be two treatments that cover two cases: one begins drought Aug 1 and the other begins drought Aug 15, All plots fall into one of these two, correct?

…

On Sun, Nov 12, 2017 at 2:12 PM MariaNewcomb ***@***.***> wrote: @dlebauer <https://github.com/dlebauer> if I'm understanding correctly, I should create 4 new treatments? So far there is one treatment for Season 4 named as 'Control BAP 2017' which is irrigated for optimal growth and was implemented from 2017-04-20 to 2017-07-31. Should I create 4 new treatments?: Irrigation=0 BAP 2017-08-01 to 2017-08-15 Irrigation=1 BAP 2017-08-01 to 2017-08-15 Irrigation=0 BAP 2017-08-16 to 2017-08-30 Irrigation=1 BAP 2017-08-16 to 2017-08-30 See for example the treatment column (L) in the spreadsheet with August data from the MultispeQ device at the Google directory https://drive.google.com/drive/folders/1MVkQpJ8f_gCHZP17j63tXaAGCT1R5tAO Will this work for defining the August irrigation treatments? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#196 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAcX50J20OY9HC0aa5o_hWXhLpCniU40ks5s11EvgaJpZM4P-Zww> .

[NewcombMaria]

With two new treatments [1) drought Aug 1-15 and 2) drought Aug 16-30], then do the non-drought plots that were irrigated during those times fall under 'Control BAP 2017' treatment?

[dlebauer]

Yes.

…

On Sun, Nov 12, 2017 at 2:31 PM MariaNewcomb ***@***.***> wrote: With two new treatments [1) drought Aug 1-15 and 2) drought Aug 16-30], then do the non-drought plots that were irrigated during those times fall under 'Control BAP 2017' treatment? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#196 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAcX51iXUBPY8ZFR2j1N48vy_oSBBaqvks5s11WZgaJpZM4P-Zww> .

[dlebauer]

Were there plots that were never droughted?

…

On Sun, Nov 12, 2017 at 4:21 PM David LeBauer ***@***.***> wrote: Yes. On Sun, Nov 12, 2017 at 2:31 PM MariaNewcomb ***@***.***> wrote: > With two new treatments [1) drought Aug 1-15 and 2) drought Aug 16-30], > then do the non-drought plots that were irrigated during those times fall > under 'Control BAP 2017' treatment? > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#196 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AAcX51iXUBPY8ZFR2j1N48vy_oSBBaqvks5s11WZgaJpZM4P-Zww> > . >

[NewcombMaria]

All plots were drought-stressed either during Aug 1 to 15 or Aug 16 to 30. Plots that were drought-stressed in early August and then returned to normal irrigation latter August were considered to be in 'recovery' from water-deficit stress. This Recovery status could be considered a 'Stress Recovery' treatment different from continuous well-watered status. The goal was to compare accessions for abilities to recover after drought.