kaizadp/hysteresis_and_soil_carbon

hysteresis_and_soil_carbon's Issues

Missing data?

From #8 (comment) -

OK, let's see. The last Picarro files ends at 2019-11-11 19:58:32.154.
picarro_clean ends at 2019-11-11 19:58:32.
picarro_clean_matched ends at 2019-11-09 23:04:50.
The last entry in the valve_key is 155 2019-11-09 15:40:00 2019-11-10 15:55:00.

Maybe I'm tired at the moment, but not immediately seeing the problem.

NMR spectra

water suppression

• the peaks are not gaussian

• weird blip at the start of the peak that goes negative. phasing did not help.

• incomplete water suppression

• don't do WSUPP for future runs

we want WATERGATE W5

general track-keeping and experiment log

Analysis Summary

trt	cores	respiration	DOC	NMR
Soil_sat_W	16-20	x	x	16,17,19,20
Soil_sat_D	21-25	x	x	24,25
Soil_75_W	26-30	x	x	27,28,26,30
Soil_75_D	31-35	x	x	34,35
Soil_dry_W	36-40	x	x	36,37,38,40,39
Soil_dry_D	41-45	x	x	42,45,41,44
Soil_sand_sat_W	71-75	x	x	74
Soil_sand_sat_D	76-80	x	x	76,80
Soil_sand_75_W	81-85	x	x
Soil_sand_75_D	86-90	x	x	86,88
Soil_sand_dry_W	91-95	x	x	91
Soil_sand_dry_D	96-100	x	x	100,98,99,97,96
Soil_50_W	111-115	x	x	113, 115
Soil_50_D	116-120	x	x
Soil_sand_50_W	121-125	x	x
Soil_sand_50_D	126-130	x	x
Soil_fm	131-135	x	x
Soil_sand_fm	136-140	x	x
Soil_100_W	141-145	x	x	144,
Soil_100_D	146-150	x	x
Soil_sand_100_W	151-155	x	x
Soil_sand_100_D	156-160	x	x

DOING THIS WITHOUT F-ING DRAKE

😆

Do you want me to set up a drake pipeline for this project? As a demo; you wouldn't have to use it.

To-do

Initial set of analyses:

1. Picarro (respiration)
   2. TC [don't do on all samples, only initial characterization]
   3. TOC [don't do on all samples, only initial characterization]
2. WSOC concentrations
3. WSOC NMR: relative abundances
   6. Pore water WSOC concentrations
   7. Pore water NMR
4. Water retention curves

edit: not doing porewater because the damn pore plates aren't working.

Are timezones being handled correctly?

From #8 (comment) -

Re timestamps, there's time zone conversion:

In 1-moisture_tracking.R,

    dplyr::mutate(Start_datetime = mdy_hm(Start_datetime, tz = "America/Los_Angeles"),
                  Stop_datetime = mdy_hm(Stop_datetime, tz = "America/Los_Angeles"),

And for the Picarro data, in 3-picarro_data.R:

    clean_data(tz = "UTC") %>% 

NMR: next steps

discussion with @amyerspigg

• CH2/CH3 ratio
• compare presence/absence of peaks across treatments
• confirm what peaks are in the aromatic region
  • peaks at 6.7: lignin-like

Picarro data analysis

Fig. 1. by treatment

Fig. 2. individual cores

Fig. 3.

Fig. 4

Too few points to compute a flux

Currently there are 2,956 "samples" (periods where the Picarro was measuring a core). See the graph I posted over in #6 . Many (1,910) of these have only two data points, which currently is the below the minimum 3 that picarro.data requires to compute a flux. Thoughts? I can change the default minimum, but obviously a two-point regression line (from which the flux is computed) is pretty fragile. Thanks.

Visualization and normalization questions

I'm playing around with the best way to QC the computed fluxes, and wanted to get your feedback @kaizadp because it depends on what you're interested in.

Note these are raw fluxes, not corrected for core dry weight. Is this what you'd like them normalized by?

Pore plates not working

Pore plates not pulling water from soil cores.

1-Nov:
Spoke to SoilMoisture technician. Our plate saturation/storage technique may be the problem. Immersing the plates entirely in water creates an "air sandwich" inside the plates, since water is pushing in from all sides.
Suggested drying the plates in the oven, and then saturating by placing in a shallow pan of water. The bottom of the plates should be in contact with the water, but the top should be exposed to air. That allows water to flow up through the plates via capillary action, and the air has a way to escape from the top.

redoing WRC

set1: soil
wt. of ring: 97.35 g
wt. of dry soil added (approx.): 66.33 g

set2: soil+sand
wt. of ring: 96.33 g
wt. of dry sample added (approx.): 75.69 g

• saturation begun: jul-21
• HYPROP started: jul-22
• HYPROP ended
• WP4C (x3)

Picarro code

@bpbond Can you copy/clone the most updated Picarro script to this repo? (Not sure where that is -- perhaps your script for Aditi?)
I'll have Picarro data soon for the hysteresis drying phase, and I'd like to work on that.
Thanks!