Package 'PEcAn.BIOCRO'

Convert CF-formatted met data to BioCro met

Description

Converts a CF data frame into a BioCro met input

Usage

cf2biocro(met, longitude = NULL, zulu2solarnoon = FALSE)

Arguments

met	data.table object with met for a single site; output from load.cfmet year int month int day int: day of month (1-31) doy int: day of year (1-366) hour int (0-23) date YYYY-MM-DD HH:MM:SS POSIXct wind_speed num m/s northward_wind eastward_wind ppfd optional; if missing, requires surface_downwelling_shortwave_flux_in_air surface_downwelling_shortwave_flux_in_air air_pressure (Pa) optional; if missing, requires relative_humidity specific_humidity optional; if missing, requires relative_humidity relative_humidity optional; if missing, requires air_pressure and specific_humidity precipitation_flux air_temperature
longitude	in degrees east, used for calculating solar noon
zulu2solarnoon	logical; if TRUE, convert time from GMT to local solar time.

Value

data.table / data.frame with fields

• doy day of year

• hr hour

• solar solar radiation (PPFD)

• temp temperature, degrees celsius

• rh relative humidity, as fraction (0-1)

• windspeed m/s

• precip cm/h

Author(s)

David LeBauer

---

Convert samples for biocro

Description

convert parameters from PEcAn database default units to biocro defaults

Usage

convert.samples.BIOCRO(trait.samples, biocro_version = 1)

Arguments

trait.samples	a matrix or dataframe of samples from the trait distribution
biocro_version	numeric, but currently only checks whether version is less than 1.0

Details

Performs model specific unit conversions on a list of trait values, such as those provided to write.config

Value

dataframe with values transformed

Author(s)

David LeBauer

---

Look for defaults provided as datasets in the BioCro model package

Description

When available, default parameters come in sets of three: *_initial_values, *_parameters, *_modules

Usage

get_biocro_defaults(genus)

Arguments

genus

Name of the genus (or really any string BioCro uses as a *_parameters prefix)

Value

a list in the format expected by BioCro::Gro, containing four lists named 'type', 'initial_values', 'parameters', and 'modules', or NULL if genus not found

---

Write BioCro met files

Description

Converts a met CF file to a model specific met file. The input files are called <in.path>/<in.prefix>.YYYY.cf

Usage

met2model.BIOCRO(
  in.path,
  in.prefix,
  outfolder,
  overwrite = FALSE,
  lat,
  lon,
  start_date,
  end_date,
  ...
)

Arguments

in.path	path on disk where CF file lives
in.prefix	prefix for each file
outfolder	location where model specific output is written
overwrite	logical: Write over any existing file of the same name? If FALSE, leaves the existing file untouched and skips to the next year.
lat, lon	Site latitude and longitude
start_date, end_date	Date range to convert. Each year will be written to a separate file
...	other arguments passed from PEcAn, currently ignored

Value

a dataframe of information about the written file

Author(s)

Rob Kooper, David LeBauer

---

Function to convert biocro model output to standard netCDF format

Description

Convert BioCro output to netCDF

Usage

model2netcdf.BIOCRO(result, genus = NULL, outdir, lat = -9999, lon = -9999)

Arguments

result	a dataframe of model output to be converted
genus	character: What kind of plant was being simulated? Used to correct for some genus-specific differences in model output; Eventually that will be handled inside BioCro and this argument will be removed.
outdir	Location of model output
lat	Latitude of the site
lon	Longitude of the site

Details

Converts BioCro output to netCDF. Modified from on model2netcdf.SIPNET and model2netcdf.ED2 by

Author(s)

David LeBauer, Deepak Jaiswal, Rob Kooper

---

Read BioCro Config

Description

Read BioCro config file

Usage

read.biocro.config(config.file = "config.xml")

Arguments

config.file

Path to XML file

Value

list of run configuration parameters for PEcAn

Author(s)

David LeBauer

---

Clear out previous biocro config and parameter files.

Description

Clear out previous config and parameter files.

Usage

remove.config.BIOCRO(main.outdir, settings)

Arguments

main.outdir	Primary PEcAn output directory (will be depreciated)
settings	PEcAn settings file

Value

nothing, removes config files as side effect

Author(s)

Shawn Serbin, David LeBauer

---

Run BioCro at a point

Description

Run BioCro at a point

Usage

run.biocro(
  lat,
  lon,
  metpath,
  soil.nc = NULL,
  config = config,
  coppice.interval = 1
)

Arguments

lat	latitude in decimal degrees
lon	longitude in decimal degrees
metpath	full path and name prefix of a csv file with hourly data in BioCro format, e.g. ‘/dir/met' if the files to be used are '/dir/met.2004.csv' and 'dir/met.2005.csv’
soil.nc	full path and name of a netCDF file with soil data
config	full path and name of a config.xml file containing parameter values and configuration information for BioCro
coppice.interval	numeric, number of years between cuttings for coppice plant or perennial grass. Only used with BioCro 0.9; ignored when using later versions.

Value

output from one of the BioCro::*.Gro functions (determined by config$genus), as data.table object

Author(s)

David LeBauer

---

Write configuration files for the biocro model

Description

Writes a configuration files for the biocro model

Usage

write.config.BIOCRO(defaults = NULL, trait.values, settings, run.id)

Arguments

defaults	named list with default model parameter values
trait.values	named list (or dataframe of trait values) can either be a data.frame or named list of traits, e.g. data.frame(vmax = 1, b0 = 2) or list(vmax = 1, b0 = 2)
settings	pecan settings file configured for BioCro
run.id	integer; a unique identifier for the run.

Value

nothing, writes configuration file as side effect

Author(s)

David LeBauer

---