Estimate A from porometry

Solve net assimilation A, Ci and Cc for every LI-600 reading from its conductance, light and leaf temperature and a photosynthesis parameter set. See Estimating A from conductance.

Inputs

• An LI-600 file with gsw (or gsw_corrected), Qamb and Tleaf. Correct it first (Correct LI-600 conductance), so the estimate uses the corrected conductance.
• Photosynthesis parameters for the species, usually from a pk fit of its A–Ci curves.

Steps

1. Fit the species' A–Ci curves and save the parameters:

   pk fit photosynthesis examples/aci.csv --model fvcb --set gm=1000000 --fix gm,alphaG > fvcb_fit.json
   

2. Correct the porometer file:

   pk li600 correct examples/li600.csv --sidedness 1 --out li600_corrected.csv
   

3. Estimate A, writing the solved columns into a copy of the file:

   pk li600 estimate li600_corrected.csv --params fvcb_fit.json --out li600_with_A.csv
   

   The output reports:

   • usedCorrectedGsw: whether gsw_corrected was used.
   • params: the parameter set used, after merging defaults, the file and --set.
   • ignoredParams: names in the file the model doesn't use.
   • summary: mean and maximum A, mean Ci, and mean Ci/Ca.

   li600_with_A.csv adds A_solved, Ci_solved, Cc_solved, gsw_used and Qabs.

Options

Option	Default	Meaning
--model	fvcb	fvcb, fvcbC4 or empiricalA
--params	—	Parameter file: a pk fit JSON result, a CSV of fitted parameters (last row used), a Parameter/Value table, or name = value lines
--set	—	Override one parameter, e.g. --set Vcmax25=90
--ca	420	Ambient CO₂, µmol mol⁻¹
--absorptance	0.85	Leaf absorptance applied to Qamb
--min-gsw	0.001	Floor for conductance; lower readings are raised to it and counted in clamped. 0 leaves them unsolved.

Without --params, the model's defaults are used. That's fine for trying the command, but not for real estimates:

pk li600 estimate examples/li600.csv --set Vcmax25=90 --set Jmax25=170