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sits (version 1.5.1)

Satellite Image Time Series Analysis for Earth Observation Data Cubes

Description

An end-to-end toolkit for land use and land cover classification using big Earth observation data, based on machine learning methods applied to satellite image data cubes, as described in Simoes et al (2021) . Builds regular data cubes from collections in AWS, Microsoft Planetary Computer, Brazil Data Cube, Copernicus Data Space Environment (CDSE), Digital Earth Africa, Digital Earth Australia, NASA HLS using the Spatio-temporal Asset Catalog (STAC) protocol () and the 'gdalcubes' R package developed by Appel and Pebesma (2019) . Supports visualization methods for images and time series and smoothing filters for dealing with noisy time series. Includes functions for quality assessment of training samples using self-organized maps as presented by Santos et al (2021) . Provides machine learning methods including support vector machines, random forests, extreme gradient boosting, multi-layer perceptrons, temporal convolutional neural networks proposed by Pelletier et al (2019) , and temporal attention encoders by Garnot and Landrieu (2020) . Supports GPU processing of deep learning models using torch . Performs efficient classification of big Earth observation data cubes and includes functions for post-classification smoothing based on Bayesian inference, and methods for active learning and uncertainty assessment. Supports object-based time series analysis using package supercells . Enables best practices for estimating area and assessing accuracy of land change as recommended by Olofsson et al (2014) . Minimum recommended requirements: 16 GB RAM and 4 CPU dual-core.

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Install

install.packages('sits')

Monthly Downloads

526

Version

1.5.1

License

GPL-2

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Maintainer

Gilberto Camara

Last Published

August 19th, 2024

Functions in sits (1.5.1)

plot.probs_cube

Plot probability cubes
.check_date_parameter

Check is date is valid
plot.sar_cube

Plot SAR data cubes
plot.sits_accuracy

Plot confusion matrix
point_mt_6bands

A time series sample with data from 2000 to 2016
plot.xgb_model

Plot XGB model
plot.predicted

Plot time series predictions
plot.variance_cube

Plot variance cubes
plot.dem_cube

Plot DEM cubes
plot.probs_vector_cube

Plot probability vector cubes
plot.uncertainty_cube

Plot uncertainty cubes
plot.raster_cube

Plot RGB data cubes
hist.sits

Histogram
plot.uncertainty_vector_cube

Plot uncertainty vector cubes
plot.rfor_model

Plot Random Forest model
plot.sits_cluster

Plot a dendrogram cluster
plot.torch_model

Plot Torch (deep learning) model
sits_cluster_clean

Removes labels that are minority in each cluster.
plot.som_map

Plot a SOM map
samples_l8_rondonia_2bands

Samples of Amazon tropical forest biome for deforestation analysis
hist.uncertainty_cube

Histogram uncertainty cubes
sits_cluster_dendro

Find clusters in time series samples
plot.som_evaluate_cluster

Plot confusion between clusters
sits_apply

Apply a function on a set of time series
print.sits_area_accuracy

Print the area-weighted accuracy
sits_colors

Function to retrieve sits color table
sits_cluster_frequency

Show label frequency in each cluster produced by dendrogram analysis
sits_as_sf

Return a sits_tibble or raster_cube as an sf object.
plot.geo_distances

Make a kernel density plot of samples distances.
samples_modis_ndvi

Samples of nine classes for the state of Mato Grosso
print.sits_accuracy

Print the values of a confusion matrix
sits_bands

Get the names of the bands
sits_config_user_file

List the cloud collections supported by sits
sits_colors_qgis

Function to save color table as QML style for data cube
sits_combine_predictions

Estimate ensemble prediction based on list of probs cubes
sits_colors_reset

Function to reset sits color table
sits_add_base_cube

Add base maps to a time series data cube
sits_accuracy_summary

Print accuracy summary
sits_confidence_sampling

Suggest high confidence samples to increase the training set.
sits_bbox

Get the bounding box of the data
sits_formula_logref

Define a loglinear formula for classification models
sits_geo_dist

Compute the minimum distances among samples and prediction points.
sits_labels

Get labels associated to a data set
sits_cube

Create data cubes from image collections
sits_cube_copy

Copy the images of a cube to a local directory
sits_factory_function

Create a closure for calling functions with and without data
sits_labels_summary

Inform label distribution of a set of time series
sits-package

sits
plot.vector_cube

Plot RGB vector data cubes
sits_colors_set

Function to set sits color table
sits_get_data

Get time series from data cubes and cloud services
sits_accuracy

Assess classification accuracy (area-weighted method)
sits_classify

Classify time series or data cubes
sits_merge

Merge two data sets (time series or cubes)
sits_mgrs_to_roi

Convert MGRS tile information to ROI in WGS84
sits_impute

Replace NA values in time series with imputation function
sits_pred_normalize

Normalize predictor values
sits_pred_sample

Obtain a fraction of the predictors data frame
sits_config_show

Show current sits configuration
sits_config

Configure parameters for sits package
sits_kfold_validate

Cross-validate time series samples
sits_label_classification

Build a labelled image from a probability cube
sits_mlp

Train multi-layer perceptron models using torch
sits_mixture_model

Multiple endmember spectral mixture analysis
sits_predictors

Obtain predictors for time series samples
sits_pred_reference

Obtain categorical id and predictor labels for time series samples
sits_smooth

Smooth probability cubes with spatial predictors
sits_som

Use SOM for quality analysis of time series samples
sits_model_export

Export classification models
sits_rfor

Train random forest models
sits_run_examples

Informs if sits examples should run
sits_reclassify

Reclassify a classified cube
sits_patterns

Find temporal patterns associated to a set of time series
sits_pred_features

Obtain numerical values of predictors for time series samples
sits_timeline

Get timeline of a cube or a set of time series
sits_select

Filter bands on a data set (tibble or cube)
sits_show_prediction

Shows the predicted labels for a classified tibble
sits_mosaic

Mosaic classified cubes
sits_segment

Segment an image
sits_to_csv

Export a sits tibble metadata to the CSV format
sits_sampling_design

Allocation of sample size to strata
sits_filter

Filter time series with smoothing filter
sits_tae

Train a model using Temporal Self-Attention Encoder
sits_som_remove_samples

Evaluate cluster
sits_sgolay

Filter time series with Savitzky-Golay filter
sits_uncertainty

Estimate classification uncertainty based on probs cube
sits_view

View data cubes and samples in leaflet
sits_reduce

Reduces a cube or samples from a summarization function
sits_slic

Segment an image using SLIC
sits_tempcnn

Train temporal convolutional neural network models
sits_uncertainty_sampling

Suggest samples for enhancing classification accuracy
sits_stats

Obtain statistics for all sample bands
sits_clean

Cleans a classified map using a local window
sits_xgboost

Train extreme gradient boosting models
sits_whittaker

Filter time series with whittaker filter
sits_lighttae

Train a model using Lightweight Temporal Self-Attention Encoder
sits_formula_linear

Define a linear formula for classification models
sits_colors_show

Function to show colors in SITS
sits_som_clean_samples

Cleans the samples based on SOM map information
summary.class_cube

Summarize data cubes
sits_run_tests

Informs if sits tests should run
sits_som_evaluate_cluster

Evaluate cluster
sits_tuning

Tuning machine learning models hyper-parameters
sits_list_collections

List the cloud collections supported by sits
sits_reduce_imbalance

Reduce imbalance in a set of samples
summary.variance_cube

Summarise variance cubes
sits_sample

Sample a percentage of a time series
sits_regularize

Build a regular data cube from an irregular one
sits_stratified_sampling

Allocation of sample size to strata
sits_svm

Train support vector machine models
`sits_labels<-`

Change the labels of a set of time series
sits_to_xlsx

Save accuracy assessments as Excel files
sits_train

Train classification models
summary.sits

Summarize sits
sits_validate

Validate time series samples
sits_variance

Calculate the variance of a probability cube
sits_tuning_hparams

Tuning machine learning models hyper-parameters
summary.sits_accuracy

Summarize accuracy matrix for training data
summary.sits_area_accuracy

Summarize accuracy matrix for area data
summary.raster_cube

Summarize data cubes
hist.raster_cube

histogram of data cubes
hist.probs_cube

histogram of prob cubes
impute_linear

Replace NA values with linear interpolation
plot.class_vector_cube

Plot Segments
plot

Plot time series
plot.class_cube

Plot classified images
cerrado_2classes

Samples of classes Cerrado and Pasture
plot.patterns

Plot patterns that describe classes