R: Satellite Image Time Series Analysis for Earth Observation Data Cubes

# Satellite Image Time Series Analysis for Earth Observation Data Cubes

## Documentation for package ‘sits’ version 1.5.4

- DESCRIPTION file
- Code demos. Use demo() to run them.
- Package NEWS

## Help Pages

C H I P S

sits-package | sits

## -- C --

cerrado_2classes | Samples of classes Cerrado and Pasture

## -- H --

hist.probs_cube | histogram of prob cubes
hist.raster_cube | histogram of data cubes
hist.sits | Histogram
hist.uncertainty_cube | Histogram uncertainty cubes

## -- I --

impute_linear | Replace NA values by linear interpolation
impute_mean | Remove NA using mean
impute_mean_window | Remove NA using weighted moving average
impute_median | Remove NA using median

## -- P --

plot | Plot time series and data cubes
plot.class_cube | Plot classified images
plot.class_vector_cube | Plot Segments
plot.dem_cube | Plot DEM cubes
plot.geo_distances | Make a kernel density plot of samples distances.
plot.patterns | Plot patterns that describe classes
plot.predicted | Plot time series predictions
plot.probs_cube | Plot probability cubes
plot.probs_vector_cube | Plot probability vector cubes
plot.raster_cube | Plot RGB data cubes
plot.rfor_model | Plot Random Forest model
plot.sar_cube | Plot SAR data cubes
plot.sits | Plot time series and data cubes
plot.sits_accuracy | Plot confusion matrix
plot.sits_cluster | Plot a dendrogram cluster
plot.sits_model | Message for models whose plots are not available
plot.som_clean_samples | Plot SOM samples evaluated
plot.som_evaluate_cluster | Plot confusion between clusters
plot.som_map | Plot a SOM map
plot.torch_model | Plot Torch (deep learning) model
plot.uncertainty_cube | Plot uncertainty cubes
plot.uncertainty_vector_cube | Plot uncertainty vector cubes
plot.variance_cube | Plot variance cubes
plot.vector_cube | Plot RGB vector data cubes
plot.xgb_model | Plot XGB model
point_mt_6bands | A time series sample with data from 2000 to 2016

## -- S --

samples_l8_rondonia_2bands | Samples of Amazon tropical forest biome for deforestation analysis
samples_modis_ndvi | Samples of nine classes for the state of Mato Grosso
sits | sits
sits_accuracy | Assess classification accuracy
sits_accuracy.class_cube | Assess classification accuracy
sits_accuracy.class_vector_cube | Assess classification accuracy
sits_accuracy.default | Assess classification accuracy
sits_accuracy.derived_cube | Assess classification accuracy
sits_accuracy.raster_cube | Assess classification accuracy
sits_accuracy.sits | Assess classification accuracy
sits_accuracy.tbl_df | Assess classification accuracy
sits_add_base_cube | Add base maps to a time series data cube
sits_apply | Apply a function on a set of time series
sits_apply.default | Apply a function on a set of time series
sits_apply.derived_cube | Apply a function on a set of time series
sits_apply.raster_cube | Apply a function on a set of time series
sits_apply.sits | Apply a function on a set of time series
sits_as_sf | Return a sits_tibble or raster_cube as an sf object.
sits_as_sf.default | Return a sits_tibble or raster_cube as an sf object.
sits_as_sf.raster_cube | Return a sits_tibble or raster_cube as an sf object.
sits_as_sf.sits | Return a sits_tibble or raster_cube as an sf object.
sits_as_sf.vector_cube | Return a sits_tibble or raster_cube as an sf object.
sits_as_stars | Convert a data cube into a stars object
sits_as_terra | Convert a data cube into a Spatial Raster object from terra
sits_as_terra.class_cube | Convert a data cube into a Spatial Raster object from terra
sits_as_terra.probs_cube | Convert a data cube into a Spatial Raster object from terra
sits_as_terra.raster_cube | Convert a data cube into a Spatial Raster object from terra
sits_as_terra.uncertainty_cube | Convert a data cube into a Spatial Raster object from terra
sits_as_terra.variance_cube | Convert a data cube into a Spatial Raster object from terra
sits_bands | Get the names of the bands
sits_bands.default | Get the names of the bands
sits_bands.patterns | Get the names of the bands
sits_bands.raster_cube | Get the names of the bands
sits_bands.sits | Get the names of the bands
sits_bands.sits_model | Get the names of the bands
sits_bands<- | Get the names of the bands
sits_bands<-.default | Get the names of the bands
sits_bands<-.raster_cube | Get the names of the bands
sits_bands<-.sits | Get the names of the bands
sits_bbox | Get the bounding box of the data
sits_bbox.default | Get the bounding box of the data
sits_bbox.raster_cube | Get the bounding box of the data
sits_bbox.sits | Get the bounding box of the data
sits_bbox.tbl_df | Get the bounding box of the data
sits_classify | Classify time series or data cubes
sits_classify.default | Classify time series or data cubes
sits_classify.derived_cube | Classify time series or data cubes
sits_classify.raster_cube | Classify a regular raster cube
sits_classify.sits | Classify a set of time series
sits_classify.tbl_df | Classify time series or data cubes
sits_classify.vector_cube | Classify a segmented data cube
sits_clean | Cleans a classified map using a local window
sits_clean.class_cube | Cleans a classified map using a local window
sits_clean.default | Cleans a classified map using a local window
sits_clean.derived_cube | Cleans a classified map using a local window
sits_clean.raster_cube | Cleans a classified map using a local window
sits_cluster_clean | Removes labels that are minority in each cluster.
sits_cluster_dendro | Find clusters in time series samples
sits_cluster_frequency | Show label frequency in each cluster produced by dendrogram analysis
sits_colors | Function to retrieve sits color table
sits_colors_qgis | Function to save color table as QML style for data cube
sits_colors_qgis.class_cube | Function to save color table as QML style for data cube
sits_colors_qgis.class_vector_cube | Function to save color table as QML style for data cube
sits_colors_reset | Function to reset sits color table
sits_colors_set | Function to set sits color table
sits_colors_show | Function to show colors in SITS
sits_combine_predictions | Estimate ensemble prediction based on list of probs cubes
sits_combine_predictions.average | Estimate ensemble prediction based on list of probs cubes
sits_combine_predictions.default | Estimate ensemble prediction based on list of probs cubes
sits_combine_predictions.uncertainty | Estimate ensemble prediction based on list of probs cubes
sits_confidence_sampling | Suggest high confidence samples to increase the training set.
sits_config | Configure parameters for sits package
sits_config_show | Show current sits configuration
sits_config_user_file | Create a user configuration file.
sits_cube | Create data cubes from image collections
sits_cube.local_cube | Create sits cubes from cubes in flat files in a local
sits_cube.results_cube | Create a results cube from local files
sits_cube.stac_cube | Create data cubes from image collections accessible by STAC
sits_cube.vector_cube | Create a vector cube from local files
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_filter | Filter time series with smoothing filter
sits_formula_linear | Define a linear formula for classification models
sits_formula_logref | Define a loglinear formula for classification models
sits_geo_dist | Compute the minimum distances among samples and prediction points.
sits_get_class | Get values from classified maps
sits_get_class.csv | Get values from classified maps
sits_get_class.data.frame | Get values from classified maps
sits_get_class.default | Get values from classified maps
sits_get_class.sf | Get values from classified maps
sits_get_class.shp | Get values from classified maps
sits_get_class.sits | Get values from classified maps
sits_get_data | Get time series from data cubes and cloud services
sits_get_data.csv | Get time series using CSV files
sits_get_data.data.frame | Get time series using sits objects
sits_get_data.default | Get time series from data cubes and cloud services
sits_get_data.sf | Get time series using sf objects
sits_get_data.shp | Get time series using shapefiles
sits_get_data.sits | Get time series using sits objects
sits_get_probs | Get values from probability maps
sits_get_probs.csv | Get values from probability maps
sits_get_probs.data.frame | Get values from probability maps
sits_get_probs.default | Get values from probability maps
sits_get_probs.sf | Get values from probability maps
sits_get_probs.shp | Get values from probability maps
sits_get_probs.sits | Get values from probability maps
sits_impute | Replace NA values in time series with imputation function
sits_kfold_validate | Cross-validate time series samples
sits_labels | Get labels associated to a data set
sits_labels.default | Get labels associated to a data set
sits_labels.derived_cube | Get labels associated to a data set
sits_labels.derived_vector_cube | Get labels associated to a data set
sits_labels.patterns | Get labels associated to a data set
sits_labels.raster_cube | Get labels associated to a data set
sits_labels.sits | Get labels associated to a data set
sits_labels.sits_model | Get labels associated to a data set
sits_labels<- | Change the labels of a set of time series
sits_labels<-.class_cube | Change the labels of a classified raster cube
sits_labels<-.class_vector_cube | Change the labels of a class vector data cube
sits_labels<-.default | Change the labels of other data structures
sits_labels<-.probs_cube | Change the labels of a probs raster cube
sits_labels<-.probs_vector_cube | Change the labels of a probs vector data cube
sits_labels<-.sits | Change the labels of a set of time series
sits_labels_summary | Inform label distribution of a set of time series
sits_labels_summary.sits | Inform label distribution of a set of time series
sits_label_classification | Build a labelled image from a probability cube
sits_label_classification.default | Build a labelled image from a probability cube
sits_label_classification.derived_cube | Build a labelled image from a probability cube
sits_label_classification.probs_cube | Build a labelled image from a probability cube
sits_label_classification.probs_vector_cube | Build a labelled image from a probability cube
sits_label_classification.raster_cube | Build a labelled image from a probability cube
sits_lightgbm | Train light gradient boosting model
sits_lighttae | Train a model using Lightweight Temporal Self-Attention Encoder
sits_list_collections | List the cloud collections supported by sits
sits_lstm_fcn | Train a Long Short Term Memory Fully Convolutional Network
sits_merge | Merge two data sets (time series or cubes)
sits_merge.default | Merge two data sets (time series or cubes)
sits_merge.raster_cube | Merge two data sets (time series or cubes)
sits_merge.sits | Merge two data sets (time series or cubes)
sits_mgrs_to_roi | Convert MGRS tile information to ROI in WGS84
sits_mixture_model | Multiple endmember spectral mixture analysis
sits_mixture_model.default | Multiple endmember spectral mixture analysis
sits_mixture_model.derived_cube | Multiple endmember spectral mixture analysis
sits_mixture_model.raster_cube | Multiple endmember spectral mixture analysis
sits_mixture_model.sits | Multiple endmember spectral mixture analysis
sits_mixture_model.tbl_df | Multiple endmember spectral mixture analysis
sits_mlp | Train multi-layer perceptron models using torch
sits_model_export | Export classification models
sits_model_export.sits_model | Export classification models
sits_mosaic | Mosaic classified cubes
sits_patterns | Find temporal patterns associated to a set of time series
sits_predictors | Obtain predictors for time series samples
sits_pred_features | Obtain numerical values of predictors for time series samples
sits_pred_normalize | Normalize predictor values
sits_pred_references | Obtain categorical id and predictor labels for time series samples
sits_pred_sample | Obtain a fraction of the predictors data frame
sits_reclassify | Reclassify a classified cube
sits_reclassify.class_cube | Reclassify a classified cube
sits_reclassify.default | Reclassify a classified cube
sits_reduce | Reduces a cube or samples from a summarization function
sits_reduce.raster_cube | Reduces a cube or samples from a summarization function
sits_reduce.sits | Reduces a cube or samples from a summarization function
sits_reduce_imbalance | Reduce imbalance in a set of samples
sits_regularize | Build a regular data cube from an irregular one
sits_regularize.combined_cube | Build a regular data cube from an irregular one
sits_regularize.default | Build a regular data cube from an irregular one
sits_regularize.dem_cube | Build a regular data cube from an irregular one
sits_regularize.derived_cube | Build a regular data cube from an irregular one
sits_regularize.ogh_cube | Build a regular data cube from an irregular one
sits_regularize.rainfall_cube | Build a regular data cube from an irregular one
sits_regularize.raster_cube | Build a regular data cube from an irregular one
sits_regularize.sar_cube | Build a regular data cube from an irregular one
sits_resnet | Train ResNet classification models
sits_rfor | Train random forest models
sits_roi_to_mgrs | Given a ROI, find MGRS tiles intersecting it.
sits_roi_to_tiles | Find tiles of a given ROI and Grid System
sits_run_examples | Informs if sits examples should run
sits_run_tests | Informs if sits tests should run
sits_sample | Sample a percentage of a time series
sits_sampling_design | Allocation of sample size to strata
sits_segment | Segment an image
sits_select | Filter a data set (tibble or cube) for bands, tiles, and dates
sits_select.default | Filter a data set (tibble or cube) for bands, tiles, and dates
sits_select.raster_cube | Filter a data set (tibble or cube) for bands, tiles, and dates
sits_select.sits | Filter a data set (tibble or cube) for bands, tiles, and dates
sits_sgolay | Filter time series with Savitzky-Golay filter
sits_slic | Segment an image using SLIC
sits_smooth | Smooth probability cubes with spatial predictors
sits_smooth.default | Smooth probability cubes with spatial predictors
sits_smooth.derived_cube | Smooth probability cubes with spatial predictors
sits_smooth.probs_cube | Smooth probability cubes with spatial predictors
sits_smooth.probs_vector_cube | Smooth probability cubes with spatial predictors
sits_smooth.raster_cube | Smooth probability cubes with spatial predictors
sits_snic | Segment an image using SNIC
sits_som_clean_samples | Cleans the samples based on SOM map information
sits_som_evaluate_cluster | Evaluate cluster
sits_som_map | Build a SOM for quality analysis of time series samples
sits_som_remove_samples | Evaluate cluster
sits_stats | Obtain statistics for all sample bands
sits_stratified_sampling | Allocation of sample size to strata
sits_svm | Train support vector machine models
sits_tae | Train a model using Temporal Self-Attention Encoder
sits_tempcnn | Train temporal convolutional neural network models
sits_texture | Apply a set of texture measures on a data cube.
sits_texture.default | Apply a set of texture measures on a data cube.
sits_texture.derived_cube | Apply a set of texture measures on a data cube.
sits_texture.raster_cube | Apply a set of texture measures on a data cube.
sits_tiles_to_roi | Convert MGRS tile information to ROI in WGS84
sits_timeline | Get timeline of a cube or a set of time series
sits_timeline.default | Get timeline of a cube or a set of time series
sits_timeline.derived_cube | Get timeline of a cube or a set of time series
sits_timeline.raster_cube | Get timeline of a cube or a set of time series
sits_timeline.sits | Get timeline of a cube or a set of time series
sits_timeline.sits_model | Get timeline of a cube or a set of time series
sits_timeline.tbl_df | Get timeline of a cube or a set of time series
sits_timeseries_to_csv | Export a a full sits tibble to the CSV format
sits_to_csv | Export a sits tibble metadata to the CSV format
sits_to_csv.default | Export a sits tibble metadata to the CSV format
sits_to_csv.sits | Export a sits tibble metadata to the CSV format
sits_to_csv.tbl_df | Export a sits tibble metadata to the CSV format
sits_to_xlsx | Save accuracy assessments as Excel files
sits_to_xlsx.list | Save accuracy assessments as Excel files
sits_to_xlsx.sits_accuracy | Save accuracy assessments as Excel files
sits_train | Train classification models
sits_tuning | Tuning machine learning models hyper-parameters
sits_tuning_hparams | Tuning machine learning models hyper-parameters
sits_uncertainty | Estimate classification uncertainty based on probs cube
sits_uncertainty.default | Estimate classification uncertainty based on probs cube
sits_uncertainty.probs_cube | Estimate classification uncertainty based on probs cube
sits_uncertainty.probs_vector_cube | Estimate classification uncertainty based on probs cube
sits_uncertainty.raster_cube | Estimate classification uncertainty based on probs cube
sits_uncertainty_sampling | Suggest samples for enhancing classification accuracy
sits_validate | Validate time series samples
sits_variance | Calculate the variance of a probability cube
sits_variance.default | Calculate the variance of a probability cube
sits_variance.derived_cube | Calculate the variance of a probability cube
sits_variance.probs_cube | Calculate the variance of a probability cube
sits_variance.raster_cube | Calculate the variance of a probability cube
sits_view | View data cubes and samples in leaflet
sits_view.class_cube | View data cubes and samples in leaflet
sits_view.class_vector_cube | View data cubes and samples in leaflet
sits_view.data.frame | View data cubes and samples in leaflet
sits_view.default | View data cubes and samples in leaflet
sits_view.probs_cube | View data cubes and samples in leaflet
sits_view.raster_cube | View data cubes and samples in leaflet
sits_view.sits | View data cubes and samples in leaflet
sits_view.som_map | View data cubes and samples in leaflet
sits_view.uncertainty_cube | View data cubes and samples in leaflet
sits_view.vector_cube | View data cubes and samples in leaflet
sits_whittaker | Filter time series with whittaker filter
sits_xgboost | Train extreme gradient boosting models
summary.class_cube | Summarize data cubes
summary.raster_cube | Summarize data cubes
summary.sits | Summarize sits
summary.sits_accuracy | Summarize accuracy matrix for training data
summary.sits_area_accuracy | Summarize accuracy matrix for area data
summary.variance_cube | Summarize variance cubes