Read STICS observation files (*.obs)

Read STICS observation files from a JavaSTICS workspace and store data into a list per usm

get_obs(
  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 observation files to read (*.obs file) or path of a single directory containing one sub-folder per USM (named as the USM names), each of them containing the corresponding files 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.

Value

A list, where each element is a data.frame of observations 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.

Details

The .obs files names must match USMs names, e.g. for a usm called "banana", the .obs file should be named banana.obs. For intercrops, the name should be suffixed by "p" for the principal and "a" for the associated plant.

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).

Examples

path <- file.path(get_examples_path(file_type = "obs"), "mixed")

# Get observations for all usms, but only banana has observations:
Meas <- get_obs(path)
#> sorghum.obs
#> IC_banana_sorghump.obsIC_banana_sorghuma.obs
#> banana.obs

# Get observations only for banana:
Meas_banana <- get_obs(path, "banana")
#> banana.obs

if (FALSE) { # \dontrun{
# Get observations with real plant names when plant
# folder is not in the workspace:
get_obs(path, "banana", javastics = "/path/to/JavaSTICS/folder")
} # }