Package 'PEcAn.ED2'

Description

Check if value is between (inclusive) a range

Usage

between(x, lower, upper)

Arguments

Description

Check internal file formatting, and optionally check for compatibility against related files.

Usage

check_css(css, pss = NULL)

check_pss(pss, site = NULL)

check_site(site)

Arguments

Value

NULL (invisibly)

Description

Check individual ED metfile

Usage

check_ed_metfile(metfile, variables)

Arguments

Value

NULL, invisibly, if successful or throw an error

Description

Check that the object has all components, and throw an error if anything is wrong. Optionally, do some basic checks of actualy meteorology files as well.

Usage

check_ed_metheader(ed_metheader, check_files = TRUE)

check_ed_metheader_format(ed_metheader_format, check_files = TRUE)

Arguments

Details

check_ed_metheader_format checks an individual format (one item in the ed_metheader list). check_ed_metheader applies these checks to each item in the format list.

Description

Check the basic structure of ed2in object, as well as consistency among arguments (e.g. run dates and coordinates are within the range of vegetation and meteorology data).

Usage

check_ed2in(ed2in)

Arguments

Description

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

Usage

convert.samples.ED(trait.samples)

Arguments

Value

matrix or dataframe with values transformed

Author(s)

Shawn Serbin, David LeBauer, Carl Davidson, Ryan Kelly

Description

Create css, pss, and site files from examples

Usage

create_css(input, check = TRUE)

create_pss(input, check = TRUE)

create_site(input, check = TRUE)

Arguments

Value

css, pss, or site object (data.frame, possibly with attributes)

Description

Create full ED vegetation input object

Usage

create_ed_veg(css, pss, site, latitude, longitude, check = TRUE, ...)

Arguments

Description

For a given date, figure out its month and return all of the dates for that month.

Usage

dates_in_month(date)

Arguments

Value

Sequence of dates from the first to the last day of the month.

Description

Download and unzip common ED inputs from a public Open Science Framework (OSF) repository (https://osf.io/b6umf). Inputs include the Olson Global Ecosystems (OGE) database (oge2OLD) and the chd and dgd databases.

Usage

download_edi(directory)

Arguments

Details

The total download size around 28 MB.

Value

TRUE, invisibly

Description

Lookup function for translating commonly used ED variables returns out list, readvar variables to read from file, expr if any derivation is needed

Usage

ed.var(varname)

Arguments

Description

Convert ED2IN ITIMEA/Z string to hour and minute

Usage

ed2in2time(itimea)

Arguments

Value

List containing numeric values of hour and minute

Description

Example css, pss, and site objects

Usage

example_css

example_pss

example_site

Format

An object of class tbl_df (inherits from tbl, data.frame) with 1 rows and 10 columns.

An object of class tbl_df (inherits from tbl, data.frame) with 1 rows and 14 columns.

An object of class tbl_df (inherits from tbl, data.frame) with 1 rows and 7 columns.

Description

A helper function to extract a named vector of pft numbers from settings$pfts. Will use pft numbers in settings if they exist, otherwise it'll match using the pftmapping dataset

Usage

extract_pfts(pfts)

Arguments

Value

named numeric vector

Description

Get ED2 config.xml file

Usage

get_configxml.ED2(rundir, runid)

Arguments

Author(s)

Alexey Shiklomanov

Description

Extract sequence of dates from ED2IN file

Usage

get_ed2in_dates(ed2in)

Arguments

Value

Vector of dates from start date to end date by 1 day

Description

Automatically determine latitude or longitude from an ED input filepath. If the latitude/longitude regular expression isn't matched, this will throw an error.

Usage

get_latlon(filepath, latlon)

Arguments

Value

Numeric value of latitude or longitude

Description

Figure out the dates for which a given meteorology is available by parsing the matching file names.

Usage

get_met_dates(ed_metheader)

Arguments

Value

Vector of dates for a run

Description

Get ED history restart file path

Usage

get_restartfile.ED2(mod_outdir, runid, file.time)

Arguments

Author(s)

Alexey Shiklomanov

Description

Simple test if object inheirts from class "ed2in".

Usage

is.ed2in(x)

Arguments

Description

Mostly useful when recursive and full.names are both FALSE: The current implementation sets full.names internally, and for recursive listings list.files(..., include.dirs = FALSE) is equivalent and faster.

Usage

list.files.nodir(path, ...)

Arguments

Author(s)

Alexey Shiklomanov

Description

Descriptions of ED met header variable flags.

Usage

met_flag_description

Format

An object of class tbl_df (inherits from tbl, data.frame) with 5 rows and 2 columns.

Details

data.frame with the following columns:

• flag – Numeric flag (in header file)

• flag_description – Description of flag

Description

Helpful information about ED_MET_DRIVER files.

Usage

met_variable_description

Format

An object of class tbl_df (inherits from tbl, data.frame) with 15 rows and 3 columns.

Details

data.frame with the following columns:

• variable – Variable name

• description – Variable description

• unit – Variable unit (character, parse-able by udunints2)

Description

If files already exist in 'Outfolder', the default function is NOT to overwrite them and only gives user the notice that file already exists. If user wants to overwrite the existing files, just change overwrite statement below to TRUE.

Usage

met2model.ED2(
  in.path,
  in.prefix,
  outfolder,
  start_date,
  end_date,
  lst = 0,
  lat = NA,
  lon = NA,
  overwrite = FALSE,
  verbose = FALSE,
  leap_year = TRUE,
  ...
)

Arguments

Description

Modified from code to convert ED2's HDF5 output into the NACP Intercomparison format (ALMA using netCDF)

Usage

model2netcdf.ED2(
  outdir,
  sitelat,
  sitelon,
  start_date,
  end_date,
  pfts,
  settings = NULL,
  process_partial = FALSE
)

Arguments

Details

if settings is provided, then values for missing arguments sitelat, sitelon, start_date, end_date, and pfts will be taken from it

Author(s)

Michael Dietze, Shawn Serbin, Rob Kooper, Toni Viskari, Istem Fer

Description

Wrapper around modifyList to allow expanding a data.frame by modifying only a single column.

Usage

modify_df(input, base)

Arguments

Value

Modified data.frame

Description

This is a convenience function for modifying an ed2in list object. Arguments passed in all caps are assumed to be ED2IN namelist parameters and are inserted directly into the ed2in list objects. Lowercase arguments are defined explicitly (see "Parameters"), and those that do not match explicit arguments will be ignored with a warning. Because the lowercase arguments come with additional validity checks, they are recommended over modifying the ED2IN file directly via uppercase arguments. For all lowercase arguments, the default (NULL) means to use whatever is currently in the input ed2in.

Usage

modify_ed2in(
  ed2in,
  ...,
  veg_prefix = NULL,
  latitude = NULL,
  longitude = NULL,
  met_driver = NULL,
  start_date = NULL,
  end_date = NULL,
  EDI_path = NULL,
  output_types = NULL,
  output_dir = NULL,
  run_dir = NULL,
  runtype = NULL,
  run_name = NULL,
  include_these_pft = NULL,
  pecan_defaults = FALSE,
  add_if_missing = FALSE,
  check_paths = TRUE,
  .dots = list()
)

Arguments

Details

Namelist arguments are applied last, and will silently overwrite any arguments set by special case arguments.

Namelist arguments can be stored in a list and passed in via the .dots argument (e.g. .dots = list(SFILIN = "/path/prefix_", ...)), or using the ⁠rlang::!!!⁠ splicing operator. If both are provided, they will be spliced together, with the ... taking precedence.

For output_types, select one or more of the following:

• "fast" – Fast analysis; mostly polygon-level averages (IFOUTPUT)

• "daily – Daily means (one file per day) (IDOUTPUT)

• "monthly" – Monthly means (one file per month) (IMOUTPUT)

• "monthly_diurnal" – Monthly means of the diurnal cycle (one file per month) (IQOUTPUT)

• "annual" – Annual (one file per year) (IYOUTPUT)

• "instant" – Instantaneous fluxes, mostly polygon-level variables, one file per year (ITOUTPUT)

• "restart" – Restart file for HISTORY runs. (ISOUTPUT)

• "all" – All output types

Value

Modified ed2in list object. See read_ed2in.

Description

This will generate the CSV file needed by write configs to write the config.xml. This is a hack right now, all this information should be in the PEcAn DB.

Usage

parse.history(historyfile, outfile = "")

Arguments

Author(s)

Rob Kooper

Description

Generate a vector of integer indices for mapping ED state cohort vectors onto patches, for instance for use with tapply.

Usage

patch_cohort_index(nc)

Arguments

Author(s)

Alexey Shiklomanov

Description

A dataset matching PEcAn PFT names to ED PFT numbers.

Usage

pftmapping

Format

A data frame with 73 rows and 2 variables:

PEcAn

PEcAn PFT names

ED

ED2 PFT numbers

...

Source

https://github.com/EDmodel/ED2/wiki/Plant-functional-types

Description

Adds the latitude and longitude, or checks if they are formatted correctly. Then, splits the prefix into the directory and base name, appends the suffix to the base name (adding a starting dot, if necessary), and returns the filename as a character.

Usage

prepare_ed_veg_filename(path_prefix, suffix, latitude = NULL, longitude = NULL)

Arguments

Value

Character string of full formatted file path

Description

Sets attributes to NULL before printing, so the output isn't as messy.

Usage

## S3 method for class 'ed2in'
print(x, ...)

Arguments

Description

Puts a select number of variables from the monthly -E- files into a nc_var list to be written to a .nc file.

Usage

put_E_values(
  yr,
  nc_var,
  var_list,
  lat,
  lon,
  start_date,
  end_date,
  begins,
  ends,
  out
)

Arguments

Value

a list of ncdim4 objects

Description

Function for put -T- values to nc_var list

Usage

put_T_values(
  yr,
  nc_var,
  var_list,
  lat,
  lon,
  start_date,
  end_date,
  begins,
  ends,
  out
)

Arguments

Description

Read files into objects usable by other PEcAn.ED2 utilities, and optionally check for errors.

Usage

read_css(filepath, check = TRUE, ...)

read_pss(filepath, check = TRUE)

read_site(filepath, check = TRUE, ...)

Arguments

Value

data.frame containing

Description

This function reads in monthly output (-E- .h5 files) from ED2, does unit conversions, and returns a list to be passed to put_E_values(). Cohort level variables (i.e. those ending in "_CO") are often (always?) in per-plant units rather than per area. This function converts them to per area using the plant density and patch area before converting units to PEcAn standards.

Usage

read_E_files(
  yr,
  yfiles,
  h5_files,
  outdir,
  start_date,
  end_date,
  pfts,
  settings = NULL
)

Arguments

Details

if settings is provided, then values for missing arguments for start_date, end_date, and pfts will be taken from it

Value

a list

Description

Read a ED_MET_DRIVER_HEADER file into a list-like object that can be manipulated within R. Returns a list of file formats.

Usage

read_ed_metheader(filename, check = TRUE, check_files = TRUE)

Arguments

Details

The output is an unnamed list with each element corresponding to a single file format. Each file format contains the following elements:

• path_prefix – Path and prefix of files

• nlon – Number of longitude grid cells

• nlat – Number of latitude grid cells

• dx – Size of longitude grid cell

• dy – Size of latitude grid cell

• xmin – Minimum longitude

• ymin – Minimum latitude

• variables – Data frame of variables, with the columns described below. Starred columns are required for writing. This table is left joined with met_variable_description and met_flag_description.

  • variable – Variable name

  • description – Variable description

  • unit – Variable unit

  • update_frequency – Update frequency (seconds) or scalar values if flag=4

  • flag – Variable flags.

  • flag_description – Description of variable flag

The formatting of a meteorology header file is as follows (from the ED GitHub Wiki):

<number of file formats>    # Repeat lines below this number of times
<path and prefix of files>
<nlon>, <nlat>, <dx>, <dy>, <xmin>, <ymin>
<number of variables>
<list of variable names>
<list of update frequencies (seconds) or scalar values if flag=4>
<list of variable flags>

The variables in the third row are defined as follows:

Value

List of ED met input parameters. See Details.

Description

Read ED2 css, pss, and site files into a single ED input object.

Usage

read_ed_veg(path_prefix, latitude = NULL, longitude = NULL, check = TRUE)

Arguments

Value

List containing css, pss, and site objects, latitude and longitude, and orig_paths, a list of paths to the original css, pss, and site files.

Description

Parse an ED2IN file to a named list.

Usage

read_ed2in(filename)

Arguments

Value

Named list of tag = value

Description

State data assimilation read-restart for ED2

Usage

read_restart.ED2(outdir, runid, stop.time, settings, var.names, params)

Arguments

Author(s)

Alexey Shiklomanov, Istem Fer

Examples

## Not run: 
  outdir <- "~/sda-hackathon/outputs"
  runid <- "99000000020"
  settings_file <- "outputs/pecan.CONFIGS.xml"
  settings <- PEcAn.settings::read.settings(settings_file)
  forecast <- read_restart.ED2(...)

## End(Not run)

Description

S-file contents are not written to standard netcdfs but are used by read_restart from SDA's perspective it doesn't make sense to write and read to ncdfs because ED restarts from history files

Usage

read_S_files(sfile, outdir, pfts, pecan_names = NULL, settings = NULL, ...)

Arguments

Description

Function for reading -T- files

Usage

read_T_files(
  yr,
  yfiles,
  h5_files,
  outdir,
  start_date,
  end_date,
  pfts = NULL,
  settings = NULL
)

Arguments

Details

e.g. yr = 1999 yfiles = 1999 2000 h5_files = "analysis-T-1999-00-00-000000-g01.h5" "analysis-T-2000-00-00-000000-g01.h5"

Description

Clear out old config and ED model run files.

Usage

remove.config.ED2(main.outdir = settings$outdir, settings)

Arguments

Value

nothing, removes config files as side effect

Author(s)

Shawn Serbin, David LeBauer, Alexey Shikomanov

Description

Uses base::system2 to run ED or EDR via a Singularity container.

Usage

run_ed_singularity(
  img_path,
  ed2in_path,
  app = "ED",
  singularity_args = NULL,
  ...
)

Arguments

Details

On some systems, to run Singularity properly, you will need to bind additional paths. To do this, pass the arguments as a character vector to singularity_args. For instance:

bindpaths <- c("/scratch", "/data")
run_ed_singularity(..., singularity_args = paste("--bind", bindpaths))

By default, base::system2 prints the output to the console. To store standard ED output in a variable as a character vector, set stdout = TRUE. To redirect all output to the variable, including GCC exceptions, use stderr = TRUE (this will automatically set stdout = TRUE as well). Output can also be redirected to a file via stderr = "/path/to/file.log".

Description

This functions approximates landscape equilibrium steady state for vegetation and soil pools using the successional trajectory of a single patch modeled with disturbance off and the prescribed disturbance rates for runs (Xia et al. 2012 GMD 5:1259-1271).

Usage

SAS.ED2(
  dir.analy,
  dir.histo,
  outdir,
  lat,
  lon,
  blckyr,
  prefix,
  treefall,
  param.args = SAS.ED2.param.Args(),
  sufx = "g01.h5"
)

Arguments

Author(s)

Christine Rollinson, modified from original by Jaclyn Hatala-Matthes (2/18/14) 2014 Feb: Original ED SAS solution Script at PalEON modeling HIPS sites (Matthes) 2015 Aug: Modifications for greater site flexibility & updated ED 2016 Jan: Adaptation for regional-scale runs (single-cells run independently, but executed in batches) 2018 Jul: Conversion to function, Christine Rollinson July 2018

Description

sets parameters and defaults for the ED2 semi-analytical spin-up

Usage

SAS.ED2.param.Args(
  decomp_scheme = 2,
  kh_active_depth = -0.2,
  decay_rate_fsc = 11,
  decay_rate_stsc = 4.5,
  decay_rate_ssc = 0.2,
  Lc = 0.049787,
  c2n_slow = 10,
  c2n_structural = 150,
  r_stsc = 0.3,
  rh_decay_low = 0.24,
  rh_decay_high = 0.6,
  rh_low_temp = 18 + 273.15,
  rh_high_temp = 45 + 273.15,
  rh_decay_dry = 12,
  rh_decay_wet = 36,
  rh_dry_smoist = 0.48,
  rh_wet_smoist = 0.98,
  resp_opt_water = 0.8938,
  resp_water_below_opt = 5.0786,
  resp_water_above_opt = 4.5139,
  resp_temperature_increase = 0.0757,
  rh_lloyd_1 = 308.56,
  rh_lloyd_2 = 1/56.02,
  rh_lloyd_3 = 227.15,
  yrs.met = 30,
  sm_fire = 0,
  fire_intensity = 0,
  slxsand = 0.33,
  slxclay = 0.33
)

Arguments

Description

Converts an ed2in-like list to an ED2IN-formatted character vector.

Usage

tags2char(ed2in)

Arguments

Description

Function translating pecan vars to ED vars

Usage

translate_vars_ed(varnames)

Arguments

Examples

var.names <- c("DBH", "AGB", "AbvGrndWood")
translate_vars_ed(var.names)

Description

Writes ED specific IC files

Usage

veg2model.ED2(outfolder, veg_info, start_date, new_site, source, ens)

Arguments

Value

filenames

Author(s)

Istem Fer

Description

Functions for writing css, pss, and site files from their respective objects.

Usage

write_css(css, path_prefix, latitude = NULL, longitude = NULL)

write_pss(pss, path_prefix, latitude = NULL, longitude = NULL)

write_site(site, path_prefix, latitude = NULL, longitude = NULL)

Arguments

Details

Latitude and longitude coordinates will be converted directly to character, without any changes to their precision. If they are NULL (default), the function assumes that lat and lon are already in the path_prefix, and if they are absent, the function will throw an error.

Value

Full file path as character, invisibly

Description

Write ED met driver header from R met driver list object

Usage

write_ed_metheader(ed_metheader, filename, header_line = shQuote("header"))

Arguments

Description

Write a complete ED inputs object to disk. css, pss, and site files are automatically named and correctly formatted.

Usage

write_ed_veg(ed_veg, path_prefix)

Arguments

Value

Named list (css, pss, site) of full file paths, invisibly

Description

This writes a ED2IN file from an ed2in list. Default method writes a barebones file without comments. S3 method for ed2in objects extracts comments and their locations from the object attributes (if barebones is FALSE).

Usage

write_ed2in(ed2in, filename, custom_header = character(), barebones = FALSE)

## S3 method for class 'ed2in'
write_ed2in(ed2in, filename, custom_header = character(), barebones = FALSE)

## Default S3 method:
write_ed2in(ed2in, filename, custom_header = character(), barebones = FALSE)

Arguments

Description

Write ED2 restart file from SDA results

Usage

write_restart.ED2(
  outdir,
  runid,
  start.time,
  stop.time,
  settings,
  new.state,
  RENAME = TRUE,
  new.params,
  inputs
)

Arguments

Value

TRUE if successful

Author(s)

Alexey Shiklomanov, Istem Fer

Description

Writes an xml and ED2IN config files for use with the Ecological Demography model. Requires a pft xml object, a list of trait values for a single model run, and the name of the file to create

Usage

write.config.ED2(
  trait.values,
  settings,
  run.id,
  defaults = settings$constants,
  check = FALSE,
  ...
)

Arguments

Value

configuration file and ED2IN namelist for given run

Author(s)

David LeBauer, Shawn Serbin, Carl Davidson, Alexey Shiklomanov, Istem Fer

Description

Function for writing job.sh file for ED2 runs

Usage

write.config.jobsh.ED2(settings, run.id)

Arguments

Details

Refactored by Alexey Shiklomanov to allow use in PEcAn RTM module.

Value

Character vector containing job.sh file

Author(s)

David LeBauer, Shawn Serbin, Carl Davidson, Alexey Shiklomanov

Description

Write ED2 config.xml file

Usage

write.config.xml.ED2(settings, trait.values, defaults = settings$constants)

Arguments

Details

Refactored by Alexey Shiklomanov to allow use in PEcAn RTM module.

Value

R XML object containing full ED2 XML file

Author(s)

David LeBauer, Shawn Serbin, Carl Davidson, Alexey Shiklomanov

Description

Imports from other packages