Input files

Every tool reads CSV files with one header row, .xlsx workbooks (first sheet), LI-6800 native logs, and standard input (-). Columns are found by name, so files from different sources work without renaming. Each tool reports the columns it used, and any conversion it made, in warnings.

Photosynthesis

Input	Column names tried, in order	Notes
A	A	µmol m⁻² s⁻¹
Ci	Ci	µmol mol⁻¹
Light	Qabs, Q	Absorbed PPFD; Qabs wins when both are present
Temperature	Tleaf, T	Values below 200 are read as °C and converted to Kelvin
Curve	CurveID, curve	Optional; groups rows into curves for per-curve constraints

Names are matched ignoring case. Rows missing any of A, Ci, light or temperature are dropped and counted in warnings.

LI-6800 files are recognized automatically:

• .xlsx exports: PhytKit reads the Measurements sheet and finds the row holding both A and Ci.
• Native logs: it reads the [Data] block.

In both, it skips the category and units rows and keeps the data rows.

Stomatal conductance

Input	Column names tried	Notes
Conductance	gsw_corrected, gsw, gs, gtw, g_sw, gvw, stomatal_conductance, conductance, cond, gs_w	mol m⁻² s⁻¹; values above 10 are read as mmol and divided by 1000
Light (BTA)	Qin, Qabs, Q, PARi, PPFD, PAR, Qamb, PFD, light, Qi, PARin
VPD	VPDleaf, VPDl, VpdL, VPD, VpdA, SVPleaf, leaf_vpd, vpd_leaf, VPDL, D, Dleaf	kPa
Ds	Ds, D_s	mmol mol⁻¹; used directly by BTA
Pressure	Pa, Patm, P_atm, pressure, atm_pressure, press, Patm_kPa	kPa; 101.325 if absent
A (Medlyn)	A, A_solved, Anet, A_net, Photo, assimilation, An
CO₂ (Medlyn)	Cs, C_s, CO2_s, Ca, CO2_a, CO2, Ca_s	420 µmol mol⁻¹ if absent

BTA converts VPD to Ds with \(D_s = 1000\,\mathrm{VPD}/P_{atm}\); Medlyn converts Ds to kPa the other way. Files from the LI-600 and LI-6800 are read directly: PhytKit finds the column-name row and skips the units row.

Plant hydraulics

Input	Column names tried	Notes
Water potential	P, Psi (MPa), Psi(MPa), WP (MPa), WP(MPa), Psi_MPa, Psi, psi, WP, water_potential, potential, MPa, Pressure, P_MPa, Pa, then Psi (bar), Psi(bar), WP (bar), Psi_bar	MPa. Columns named in bar are converted. Positive tension is made negative.
PLC	PLC, plc, loss, percent_loss, PLC_pct, PLCpercent, pld	Percent, or a 0–1 fraction
Conductance	K, k, Kleaf, Kstem, Kroot, Kplant, Kmax, ... with a space, _ or - separator; conductance, conductivity	Used when there's no PLC column
Relative water content	RWC, rwc, RWC (%), relative_water_content, water_content, RWC_pct, w	Fraction, or a percentage (above 1.5)

Names are matched loosely, ignoring case, spaces, underscores and unit punctuation. So water potential, water_potential and WaterPotential are the same.

Soil water retention

Input	Column names tried	Notes
Matric potential	the water-potential names above, plus matric_potential, matric, suction, tension, pressure_head, head, h, kPa, hPa, cm, psi_MPa	MPa unless --units says otherwise. Positive suction is accepted.
Water content	theta, θ, VWC, vwc, theta_v, SWC, swc, volumetric_water_content, water_content, moisture, VMC, WC	Fraction, or a percentage (above 1.5)

LI-600 files

pk li600 correct needs gsw, Tref, Tleaf, rh_r, rh_s, flow, P_atm and E_apparent. pk li600 estimate needs gsw (or gsw_corrected), Qamb and Tleaf, and keeps ETR if present. Both find the column-name row within the first five rows and skip a units row below it.