Commands

All commands print one JSON object to standard output, unless noted. On failure they print an error object and exit with code 1 (see Errors). Add --help to any command, or run pk help <command>, for its arguments and options.

Options take a value as --name value or --name=value. Yes/no options are given alone (--rows), and --no-rows or --rows=false turns one off. Options marked repeatable can be given several times, and list options accept comma-separated values. Unknown options, values of the wrong type or out of range, extra arguments, and an option given twice with different values are all errors.

pk describe

pk describe            # every tool, model and the li600 options
pk describe <model>    # one model: inputs, parameters, bounds, constraints, equation

pk fit

pk fit <tool> <file...> [options]

<tool> is photosynthesis, stomatal, hydraulics or soil. With several files, or with --group-by, each file or group is fitted separately (see Output).

Option	Value	Meaning
--model	model name	Model to fit. Defaults: fvcb, bta, vulnerability, vanGenuchten. If you leave it out for stomatal, hydraulics or soil, the first model whose parser reads the file is used.
--fit	names, repeatable	Fit only these parameters
--fix	names, repeatable	Hold these parameters fixed
--set	name=value, repeatable	Starting value, or the value a fixed parameter is held at
--max-iter	whole number ≥ 1	Iteration limit (default 200)
--no-constraint	key, repeatable	Turn off one soft constraint
--constraints	none	Turn off every soft constraint
--weight	key=value, repeatable	Weight for one soft constraint
--units	MPa, kPa, bar, m, cm	Units of ψ (soil only; default MPa)
--group-by	column	Split one file into a fit per value of the column
--survey	file, repeatable	Rescale mode: survey points to rescale A to (photosynthesis only)
--stat	mean, median, max	Statistic for rescaling (default mean)
--ref-ci	number	Reference Ci for rescaling (default: the highest Ci in the curve)
--predicted	—	Include predicted and observed values in the output
--format	json, csv	csv prints one row per fit

pk li600 correct

pk li600 correct <file|-> [options]

Option	Value	Meaning
--sidedness	number	1 (default) for stomata on one side, 2 for both
--thermal-conductance	number	Instrument heat exchange, W °C⁻¹ (default 0.007)
--rows	—	Include every reading in the JSON
--out	file	Also write the original file with the corrected columns added
--format	json, csv	csv prints only the corrected columns

pk li600 estimate

pk li600 estimate <file|-> [options]

Option	Value	Meaning
--model	fvcb, fvcbC4, empiricalA	Photosynthesis model (default fvcb)
--params	file	Parameter file: pk fit JSON, a CSV of fitted parameters, a Parameter/Value table, or name = value lines
--set	name=value, repeatable	Override one parameter
--ca	number	Ambient CO₂, µmol mol⁻¹ (default 420)
--absorptance	number	Leaf absorptance applied to Qamb (default 0.85)
--min-gsw	number	Conductance floor (default 0.001); 0 leaves lower readings unsolved
--rows	—	Include every reading in the JSON
--out	file	Also write the original file with the solved columns added
--format	json, csv	csv prints only the solved columns

pk concat

pk concat <file...> [options]

Option	Value	Meaning
--out	file	Write the merged CSV to a file, and print a JSON summary
--format	json, csv	Default csv (the merged file) without --out, json with it

Errors

{
  "ok": false,
  "command": "fit",
  "error": {
    "code": "unknown_parameter",
    "message": "--fix Vcmax: fvcb has no parameter \"Vcmax\".",
    "usage": true,
    "hint": "Did you mean Vcmax25? Parameters: Vcmax25, Jmax25, ...",
    "help": "pk fit <tool> <file...> [options]"
  }
}

hint is present when there's a specific fix to suggest, and help is present on usage errors. usage is true when the command line was wrong and false when a file or its data was. pk describe lists these codes too, under errors.

Code	usage	Meaning
unknown_command	true	No such command
unknown_option	true	The command has no such option
missing_argument	true	A required argument, such as the input file, is missing
too_many_arguments	true	More arguments than the command takes
missing_value	true	An option that needs a value was given without one
invalid_value	true	An option's value is the wrong type or out of range
duplicate_option	true	An option that takes one value was given twice with different values
invalid_combination	true	Options or arguments that can't be used together
not_applicable	true	An option that doesn't apply to this tool or model
unknown_tool	true	pk fit was given a tool it doesn't have
unknown_model	true	No such model, or not one for this tool
unknown_parameter	true	The model has no parameter by that name
unknown_constraint	true	The model has no soft constraint by that name
nothing_to_fit	true	Every parameter is fixed
missing_input	true	Data passed from Python lacks one of the model's input columns
file_not_found	false	An input file doesn't exist
not_a_file	false	An input path is a folder
permission_denied	false	An input file can't be read
read_failed	false	An input file couldn't be read for another reason
write_failed	false	An --out file couldn't be written
invalid_data	false	A file was read but doesn't hold the data the command needs
rescale_failed	false	Rescale mode couldn't compute a factor from the survey and curve data

Input from standard input

Give - as the file to read from standard input, for example cat readings.csv | pk li600 correct -.