Package 'geeLite'

Fetch ISO 3166 Country and Subdivision Codes

Description

Returns a data frame containing ISO 3166-1 country codes and ISO 3166-2 subdivision codes for the specified administrative level.

Usage

fetch_regions(admin_lvl = 0)

Arguments

admin_lvl

[optional] (integer) Administrative level to retrieve: 0 for country-level (ISO 3166-1), 1 for first-level subdivisions (ISO 3166-2), or NULL to include both (default: 0).

Value

A data frame containing region names, ISO 3166-2 codes, and the corresponding administrative levels.

Examples

# Example: Fetch ISO 3166-1 country codes
## Not run: 
  fetch_regions()

## End(Not run)

---

Fetch Variable Information from an SQLite Database

Description

Displays information on the available variables in the SQLite database (data/geelite.db).

Usage

fetch_vars(
  path,
  format = c("data.frame", "markdown", "latex", "html", "pipe", "simple", "rst")
)

Arguments

path	[mandatory] (character) Path to the root directory of the generated database.
format	[optional] (character) A character string. Possible values are "data.frame" (default) to return a data.frame object, or one of "markdown", "latex", "html", "pipe" (Pandoc's pipe tables), "simple" (Pandoc's simple tables), and "rst" to be passed on to knitr for formatting.

Value

Returns the variable information in the selected format. If format = "data.frame", a data.frame is returned. For other formats, the output is printed in the specified format and NULL is returned invisibly.

Examples

# Example: Printing the available variables
## Not run: 
  fetch_vars(path = "path/to/db")

## End(Not run)

---

Install and Configure a Conda Environment for 'rgee'

Description

Sets up a Conda environment with all required Python and R dependencies for using the rgee package, including a specific version of the earthengine-api. If Conda is not available, the user will be prompted to install Miniconda. The created environment is automatically registered for use with rgee.

Usage

gee_install(conda = "rgee", python_version = "3.11", force_recreate = FALSE)

Arguments

conda	[optional] (character) Name of the Conda environment to create or use. Defaults to "rgee".
python_version	[optional] (character) Python version to use when creating the Conda environment. Defaults to "3.11".
force_recreate	[optional] (logical) If TRUE, deletes and recreates the Conda environment even if it already exists. Defaults to FALSE.

Value

Invisibly returns the name of the Conda environment used or created.

Note

Even after installation, users must manually accept the Conda Terms of Service (ToS) using the 'conda tos accept' command before package installation can proceed. Clear instructions will be provided if ToS acceptance is needed.

Examples

# Example: Creating a Conda environment with 'rgee' dependencies
## Not run: 
  gee_install()

## End(Not run)

---

Print the Configuration File

Description

Reads and prints the configuration file from the database's root directory in a human-readable format.

Usage

get_config(path)

Arguments

path	[mandatory] (character) The path to the root directory of the generated database.

Value

A character string representing the formatted JSON content of the configuration file.

Examples

# Example: Printing the configuration file
## Not run: 
  get_config(path = "path/to/db")

## End(Not run)

---

Print the State File

Description

Reads and prints the state file from the database's root directory in a human-readable format.

Usage

get_state(path)

Arguments

path	[mandatory] (character) The path to the root directory of the generated database.

Value

A character string representing the formatted JSON content of the state file.

Examples

# Example: Printing the state file
## Not run: 
  get_state(path = "path/to/db")

## End(Not run)

---

Initialize Post-Processing Folder and Files

Description

Creates a postp folder at path and adds two files: structure.json and functions.R.

Usage

init_postp(path, verbose = TRUE)

Arguments

path	[mandatory] character The path to the root directory where the postp folder should be created.
verbose	[optional] (logical) Display messages (default: TRUE).

Details

The structure.json file is initialized with "default": null. The functions.R file contains simple example functions that match the default "do nothing" behavior plus a z-score example.

Value

No return value, called for side effects.

Examples

# Example: Initialize post-processing files in the database directory
## Not run: 
  init_postp("path/to/db")

## End(Not run)

---

Modify Configuration File

Description

Modifies the configuration file located in the specified root directory of the generated database (config/config.json) by updating values corresponding to the specified keys.

Usage

modify_config(path, keys, new_values, verbose = TRUE)

Arguments

path	[mandatory] (character) The path to the root directory of the generated database.
keys	[mandatory] (list) A list specifying the path to the values in the configuration file that need updating. Each path should correspond to a specific element in the configuration.
new_values	[mandatory] (list) A list of new values to replace the original values at the locations specified by 'keys'. The length of new_values must match the length of keys.
verbose	[optional] (logical) If TRUE, displays messages about the updates made (default: TRUE).

Value

No return value, called for side effects.

Examples

# Example: Modifying the configuration file
## Not run: 
  modify_config(
    path = "path/to/db",
    keys = list("limit", c("source", "MODIS/061/MOD13A2", "NDVI")),
    new_values = list(1000, "mean")
  )

## End(Not run)

---

Reading, Aggregating, and Processing the SQLite Database

Description

Reads, aggregates, and processes the SQLite database (data/geelite.db).

Usage

read_db(
  path,
  variables = "all",
  freq = c("month", "day", "week", "bimonth", "quarter", "season", "halfyear", "year"),
  prep_fun = NULL,
  aggr_funs = function(x) mean(x, na.rm = TRUE),
  postp_funs = NULL
)

Arguments

path	[mandatory] (character) Path to the root directory of the generated database.
variables	[optional] (character or integer) Names or IDs of the variables to be read. Use the fetch_vars function to identify available variables and IDs (default: "all").
freq	[optional] (character or NULL) The frequency for data aggregation. Options include "day", "week", "month", "bimonth", "quarter", "season", "halfyear", "year" (default: "month"). If NULL, no aggregation is performed and native dates are returned.
prep_fun	[optional] (function or NULL) A function for pre-processing time series data after expanding to daily frequency and before aggregation. This daily expansion is performed whenever freq is not NULL. If prep_fun = NULL (default), linear interpolation (via linear_interp) is applied on the daily series. If freq = NULL, no preprocessing is performed and native dates are returned.
aggr_funs	[optional] (function or list) Aggregation function(s) used when aggregating to freq. If a single function is provided, it is used for all variables. If an unnamed list of functions is provided, all functions are applied to all variables (treated as default). If a named list is provided, names must be variable names (as returned by fetch_vars) and/or "default"; named entries override the default for those variables.
postp_funs	[optional] (function or list or "external") Post- processing function(s) applied after aggregation. If a single function or NULL is provided, it is used for all variables as default. If an unnamed list of functions is provided, all are applied to all variables (treated as default). If a named list is provided, names must be variable names (as returned by fetch_vars) and/or "default"; named entries override the default for those variables. If "external", functions are loaded from postp/. Default is NULL.

Examples

# Example: Reading variables by IDs
## Not run: 
  db_list <- read_db(path = "path/to/db",
    variables = c(1, 3))

## End(Not run)

---

Build and Update the Grid Statistics Database

Description

Collects and stores grid statistics from Google Earth Engine (GEE) data in SQLite format (data/geelite.db), initializes CLI files (cli/...), and initializes or updates the state (state/state.json) and log (log/log.txt) files.

Usage

run_geelite(
  path,
  conda = "rgee",
  user = NULL,
  rebuild = FALSE,
  mode = "local",
  verbose = TRUE
)

Arguments

path	[mandatory] (character) The path to the root directory of the generated database. This must be a writable, non-temporary directory. Avoid using the home directory (~), the current working directory, or the package directory.
conda	[optional] (character) Name of the virtual Conda environment used by the rgee package (default: "rgee").
user	[optional] (character) Specifies the Google account directory within ~/.config/earthengine/. This directory stores credentials for a specific Google account (default: NULL).
rebuild	[optional] (logical) If TRUE, the database and its supplementary files are overwritten based on the configuration file (default: FALSE).
mode	[optional] (character) Mode of data extraction. Currently supports "local" or "drive" (for larger exports via Google Drive). Defaults to "local".
verbose	[optional] (logical) Display computation status and messages (default: TRUE).

Value

Invisibly returns NULL, called for side effects.

Examples

# Example: Build a Grid Statistics Database
## Not run: 
  run_geelite(path = tempdir())

## End(Not run)

---

Initialize CLI Files

Description

Creates R scripts to enable the main functions to be called through the Command Line Interface (CLI). These scripts are stored in the cli/ directory of the generated database.

Usage

set_cli(path, verbose = TRUE)

Arguments

path	[mandatory] (character) The path to the root directory of the generated database. This must be a writable, non-temporary directory. Avoid using the home directory (~), the current working directory, or the package directory.
verbose	[optional] (logical) Whether to display messages (default: TRUE).

Value

No return value, called for side effects.

Examples

## Not run: 
  set_cli(path = tempdir())

## End(Not run)

---

Initialize the Configuration File

Description

Creates a configuration file in the specified directory of the generated database (config/config.json). If the specified directory does not exist but its parent directory does, it will be created.

Usage

set_config(
  path,
  regions,
  source,
  start = "2020-01-01",
  resol,
  scale = NULL,
  limit = 10000,
  verbose = TRUE
)

Arguments

path	[mandatory] (character) The path to the root directory of the generated database. This must be a writable, non-temporary directory. Avoid using the home directory (~), the current working directory, or the package directory.
regions	[mandatory] (character) ISO 3166-1 alpha-2 country codes or ISO 3166-2 subdivision codes.
source	[mandatory] (list) Description of Google Earth Engine (GEE) datasets of interest (the complete data catalog of GEE is accessible at: https://developers.google.com/earth-engine/datasets/catalog). It is a nested list with three levels: names (list) Datasets of interest (e.g., "MODIS/061/MOD13A1"). bands (list) Bands of interest (e.g., "NDVI"). zonal_stats (character) Statistics of interest (options: "mean", "sum", "median", "min", "max", "sd").
start	[optional] (date) First date of the data collection (default: "2020-01-01").
resol	[mandatory] (integer) Resolution of the H3 bin.
scale	[optional] (integer) Specifies the nominal resolution (in meters) for image processing. If left as NULL (the default), a resolution of 1000 is used.
limit	[optional] (integer) In "local" mode, 'limit / dates' sets batch size; in "drive" mode, 'limit' is the max features per export (default: 10000).
verbose	[optional] (logical) Display messages (default: TRUE).

Value

No return value, called for side effects.

Examples

## Not run: 
  set_config(path = tempdir(),
             regions = c("SO", "YM"),
             source = list(
              "MODIS/061/MOD13A1" = list(
                "NDVI" = c("mean", "sd")
             )
            ),
            resol = 3)

## End(Not run)

---