get_sim: Load and format STICS daily output file(s)

In SticsRFiles: Read and Modify 'STICS' Input/Output Files

Load and format STICS daily output file(s)

Description

Reads and format daily output file(s) (mod_s*.sti) for usm(s) with possible selection on variable names, cumulative DOY and dates

Usage

get_sim(
  workspace,
  usm = NULL,
  var = NULL,
  dates = NULL,
  usms_file = NULL,
  javastics = NULL,
  verbose = TRUE,
  usm_name = lifecycle::deprecated(),
  var_list = lifecycle::deprecated(),
  dates_list = lifecycle::deprecated(),
  usms_filepath = lifecycle::deprecated(),
  javastics_path = lifecycle::deprecated()
)

Arguments

workspace	Vector of path(s) of directory(ies) containing the STICS output files to read (mod_s*.sti file) or path of a single directory containing one sub-folder per USM (named as the USM names), each of them containing the corresponding STICS output file to read. In the second case, the argument usm must also be provided.
usm	Vector of USM names. Optional, if not provided, the function returns the results for all USMs.
var	Vector of variable names for which results have to be provided. Optional, all variables considered by default. See get_var_info() to get the list of STICS variables names.
dates	list of dates to filter (POSIX date)
usms_file	Path of a USM xml file. Optional, if provided, the plant names are added in the Plant column (see details).
javastics	Path of JavaSTICS Optional, should be provided in addition to usms_file to get the plant codes if the plant files used are not in the workspace but in the JavaSTICS distribution (see Details).
verbose	Logical value for displaying or not information while running
usm_name	usm_name is no longer supported, use usm instead.
var_list	var_list is no longer supported, use var instead.
dates_list	dates_list is no longer supported, use dates instead.
usms_filepath	usms_filepath is no longer supported, use usms_file instead.
javastics_path	javastics_path is no longer supported, use javastics instead.

Details

If usm is not specified (or equal to NULL), the function reads the files from all usms in the workspace(s).

If usms_file is provided and if the associated plant file is found, the plant names in the "Plant" column of the generated data.frame are either the plant code (as specified in the plant file) or the name of the plant file, if the plant file is not found.

If usms_file is not specified, the plants are named "plant_1" by default (+ "plant_2" for intercrops).

Value

A list, where each element is a data.frame of simulation results for the given usm. The list is named after the USM name.

Intercrops are returned in a single data.frame, and are identified using either the "Plant" or "Dominance" columns.

See Details section for more information about the "Plant" column.

Examples

path <- get_examples_path(file_type = "sti")
sim_data <- get_sim(path, "banana")

SticsRFiles documentation built on Sept. 12, 2024, 7:41 a.m.