Merge pull request #541 from rolfsimoes/feature/apply

Feature/apply
e-sensing · Jan 13, 2022 · f0879bd · f0879bd
2 parents 38ca8b0 + 802a530
commit f0879bd
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: sits
 Type: Package
-Version: 0.15.1-1
+Version: 0.16.0
 Title: Satellite Image Time Series Analysis for Remote Sensing Data Cubes
 Authors@R: c(person('Rolf', 'Simoes', role = c('aut'), email = 'rolf.simoes@inpe.br'),
              person('Gilberto', 'Camara', role = c('aut', 'cre'), email = 'gilberto.camara@inpe.br'),
@@ -35,14 +35,15 @@ Imports:
     data.table (>= 1.13),
     dplyr (>= 1.0.0),
     gdalUtilities,
+    geojsonsf,
     grDevices,
     ggplot2,
     graphics,
+    jsonlite,
     knitr,
     lubridate (>= 1.7.0),
     parallel,
     purrr (>= 0.3.0),
-    raster (>= 3.4),
     Rcpp (>= 1.0.7),
     rstac (>= 0.9.1-5),
     sf (>= 0.9),
@@ -68,6 +69,7 @@ Suggests:
     nnet,
     openxlsx,
     randomForest,
+    raster (>= 3.4),
     RcppArmadillo,
     Rwtss (>= 0.9.1),
     scales,
@@ -77,7 +79,7 @@ Suggests:
     xgboost,
     zoo
 Config/testthat/edition: 3
-Config/testthat/parallel: true
+Config/testthat/parallel: false
 Config/testthat/start-first: cube, wtss, raster, bdc, ml
 LinkingTo:
     Rcpp,
@@ -87,6 +89,7 @@ Collate:
     'RcppExports.R'
     'data.R'
     'sits-package.R'
+    'sits_apply.R'
     'sits_accuracy.R'
     'sits_bands.R'
     'sits_bbox.R'
@@ -103,24 +106,21 @@ Collate:
     'sits_distances.R'
     'sits_dt_reference.R'
     'sits_factory.R'
+    'sits_file_info.R'
     'sits_filters.R'
     'sits_gdalcubes.R'
     'sits_get_data.R'
     'sits_imputation.R'
-    'sits_keras.R'
     'sits_labels.R'
     'sits_label_classification.R'
     'sits_machine_learning.R'
     'sits_merge.R'
     'sits_mlp.R'
-    'sits_ops_bands.R'
     'sits_parallel.R'
     'sits_patterns.R'
     'sits_pipe.R'
     'sits_plot.R'
-    'sits_processing_estimate.R'
     'sits_raster_api.R'
-    'sits_raster_api_raster.R'
     'sits_raster_api_terra.R'
     'sits_raster_blocks.R'
     'sits_raster_data.R'
@@ -130,7 +130,6 @@ Collate:
     'sits_roi.R'
     'sits_satveg.R'
     'sits_select.R'
-    'sits_signal.R'
     'sits_shp.R'
     'sits_smooth.R'
     'sits_smooth_aux_functions.R'
@@ -151,6 +150,7 @@ Collate:
     'sits_tibble.R'
     'sits_timeline.R'
     'sits_twdtw.R'
+    'sits_uncertainty.R'
     'sits_validate.R'
     'sits_view.R'
     'sits_values.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -2,107 +2,71 @@
 
 S3method("sits_labels<-",probs_cube)
 S3method("sits_labels<-",sits)
-S3method(.raster_check_package,default)
-S3method(.raster_check_package,raster)
+S3method(.gc_arrange_images,default)
+S3method(.gc_arrange_images,first)
 S3method(.raster_check_package,terra)
-S3method(.raster_crop,raster)
 S3method(.raster_crop,terra)
-S3method(.raster_crs,raster)
 S3method(.raster_crs,terra)
-S3method(.raster_data_type,raster)
 S3method(.raster_data_type,terra)
-S3method(.raster_extent,raster)
-S3method(.raster_extent,terra)
-S3method(.raster_extract,raster)
 S3method(.raster_extract,terra)
-S3method(.raster_focal,raster)
-S3method(.raster_focal,terra)
-S3method(.raster_freq,raster)
 S3method(.raster_freq,terra)
-S3method(.raster_get_values,raster)
 S3method(.raster_get_values,terra)
-S3method(.raster_ncols,raster)
 S3method(.raster_ncols,terra)
-S3method(.raster_new_rast,raster)
 S3method(.raster_new_rast,terra)
-S3method(.raster_nlayers,raster)
 S3method(.raster_nlayers,terra)
-S3method(.raster_nrows,raster)
 S3method(.raster_nrows,terra)
-S3method(.raster_open_rast,raster)
 S3method(.raster_open_rast,terra)
-S3method(.raster_open_stack,raster)
 S3method(.raster_open_stack,terra)
-S3method(.raster_rast,raster)
 S3method(.raster_rast,terra)
-S3method(.raster_read_rast,raster)
-S3method(.raster_read_rast,terra)
-S3method(.raster_read_stack,raster)
 S3method(.raster_read_stack,terra)
-S3method(.raster_resample_methods,raster)
-S3method(.raster_resample_methods,terra)
-S3method(.raster_set_values,raster)
 S3method(.raster_set_values,terra)
-S3method(.raster_write_rast,raster)
 S3method(.raster_write_rast,terra)
-S3method(.raster_xmax,raster)
 S3method(.raster_xmax,terra)
-S3method(.raster_xmin,raster)
 S3method(.raster_xmin,terra)
-S3method(.raster_xres,raster)
 S3method(.raster_xres,terra)
-S3method(.raster_ymax,raster)
 S3method(.raster_ymax,terra)
-S3method(.raster_ymin,raster)
 S3method(.raster_ymin,terra)
-S3method(.raster_yres,raster)
 S3method(.raster_yres,terra)
+S3method(.sits_parse_roi_cube,ll)
+S3method(.sits_parse_roi_cube,sf)
+S3method(.sits_parse_roi_cube,xy)
+S3method(.sits_rename_bands,raster_cube)
+S3method(.sits_rename_bands,sits)
 S3method(.sits_roi_bbox,ll)
 S3method(.sits_roi_bbox,sf)
 S3method(.sits_roi_bbox,xy)
 S3method(.source_collection_access_test,mspc_cube)
 S3method(.source_collection_access_test,satveg_cube)
 S3method(.source_collection_access_test,stac_cube)
+S3method(.source_collection_access_test,usgs_cube)
 S3method(.source_collection_access_test,wtss_cube)
 S3method(.source_cube,satveg_cube)
 S3method(.source_cube,stac_cube)
 S3method(.source_cube,wtss_cube)
 S3method(.source_item_get_bands,stac_cube)
+S3method(.source_item_get_cloud_cover,stac_cube)
 S3method(.source_item_get_date,stac_cube)
 S3method(.source_item_get_hrefs,bdc_cube)
 S3method(.source_item_get_hrefs,stac_cube)
 S3method(.source_item_get_hrefs,usgs_cube)
-S3method(.source_item_get_resolution,stac_cube)
 S3method(.source_items_bands_select,stac_cube)
 S3method(.source_items_cube,stac_cube)
 S3method(.source_items_cube,wtss_cube)
-S3method(.source_items_fileinfo,stac_cube)
-S3method(.source_items_fileinfo,wtss_cube)
+S3method(.source_items_fid,stac_cube)
+S3method(.source_items_file_info,wtss_cube)
 S3method(.source_items_new,"mspc_cube_landsat-8-c2-l2")
 S3method(.source_items_new,"mspc_cube_sentinel-2-l2a")
 S3method(.source_items_new,aws_cube)
 S3method(.source_items_new,bdc_cube)
 S3method(.source_items_new,deafrica_cube)
 S3method(.source_items_new,usgs_cube)
 S3method(.source_items_new,wtss_cube)
-S3method(.source_items_tile_get_bbox,aws_cube)
-S3method(.source_items_tile_get_bbox,stac_cube)
-S3method(.source_items_tile_get_crs,"mspc_cube_landsat-8-c2-l2")
-S3method(.source_items_tile_get_crs,"mspc_cube_sentinel-2-l2a")
-S3method(.source_items_tile_get_crs,aws_cube)
-S3method(.source_items_tile_get_crs,bdc_cube)
-S3method(.source_items_tile_get_crs,deafrica_cube)
-S3method(.source_items_tile_get_crs,usgs_cube)
-S3method(.source_items_tile_get_name,"mspc_cube_sentinel-2-l2a")
-S3method(.source_items_tile_get_name,bdc_cube)
-S3method(.source_items_tile_get_name,deafrica_cube)
-S3method(.source_items_tile_get_name,stac_cube)
-S3method(.source_items_tiles_group,"mspc_cube_landsat-8-c2-l2")
-S3method(.source_items_tiles_group,"mspc_cube_sentinel-2-l2a")
-S3method(.source_items_tiles_group,aws_cube)
-S3method(.source_items_tiles_group,bdc_cube)
-S3method(.source_items_tiles_group,deafrica_cube)
-S3method(.source_items_tiles_group,usgs_cube)
+S3method(.source_items_tile,"mspc_cube_landsat-8-c2-l2")
+S3method(.source_items_tile,"mspc_cube_sentinel-2-l2a")
+S3method(.source_items_tile,aws_cube)
+S3method(.source_items_tile,bdc_cube)
+S3method(.source_items_tile,deafrica_cube)
+S3method(.source_items_tile,usgs_cube)
 S3method(plot,classified_image)
 S3method(plot,keras_model)
 S3method(plot,patterns)
@@ -112,10 +76,13 @@ S3method(plot,raster_cube)
 S3method(plot,sits)
 S3method(plot,som_evaluate_cluster)
 S3method(plot,som_map)
+S3method(plot,uncertainty_cube)
 S3method(print,sits_area_assessment)
 S3method(print,sits_assessment)
 S3method(sits_accuracy,classified_image)
 S3method(sits_accuracy,sits)
+S3method(sits_apply,raster_cube)
+S3method(sits_apply,sits)
 S3method(sits_bands,patterns)
 S3method(sits_bands,sits)
 S3method(sits_bands,sits_cube)
@@ -143,8 +110,8 @@ S3method(sits_labels,sits)
 S3method(sits_labels,sits_cube)
 S3method(sits_labels,sits_model)
 S3method(sits_labels_summary,sits)
+S3method(sits_merge,raster_cube)
 S3method(sits_merge,sits)
-S3method(sits_merge,sits_cube)
 S3method(sits_select,patterns)
 S3method(sits_select,sits)
 S3method(sits_select,sits_cube)
@@ -157,7 +124,9 @@ S3method(sits_timeline,raster_cube)
 S3method(sits_timeline,satveg_cube)
 S3method(sits_timeline,sits)
 S3method(sits_timeline,sits_model)
+S3method(sits_timeline,uncertainty_cube)
 S3method(sits_timeline,wtss_cube)
+S3method(sits_uncertainty,entropy)
 S3method(sits_values,bands_cases_dates)
 S3method(sits_values,bands_dates_cases)
 S3method(sits_values,cases_dates_bands)
@@ -166,7 +135,8 @@ S3method(sits_view,raster_cube)
 S3method(sits_view,sits)
 export("%>%")
 export("sits_labels<-")
-export(.source_cube_local_cube)
+export(.sits_parse_roi_cube)
+export(.sits_roi_sf_to_geojson)
 export(sits_ResNet)
 export(sits_TempCNN)
 export(sits_accuracy)
@@ -186,7 +156,6 @@ export(sits_formula_linear)
 export(sits_formula_logref)
 export(sits_get_data)
 export(sits_impute_linear)
-export(sits_interp)
 export(sits_kfold_validate)
 export(sits_label_classification)
 export(sits_labels)
@@ -196,7 +165,6 @@ export(sits_merge)
 export(sits_metadata_to_csv)
 export(sits_mlp)
 export(sits_mlr)
-export(sits_mutate_bands)
 export(sits_patterns)
 export(sits_regularize)
 export(sits_rfor)
@@ -215,12 +183,14 @@ export(sits_to_xlsx)
 export(sits_to_zoo)
 export(sits_train)
 export(sits_twdtw_classify)
+export(sits_uncertainty)
 export(sits_values)
 export(sits_view)
 export(sits_whittaker)
 export(sits_xgboost)
 importFrom(Rcpp,sourceCpp)
 importFrom(data.table,":=")
+importFrom(dplyr,.data)
 importFrom(lubridate,"%m+%")
 importFrom(lubridate,"%within%")
 importFrom(magrittr,"%>%")

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -1,10 +1,6 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
-apply_transition_matrix <- function(data_before, data, transition_matrix) {
-    .Call(`_sits_apply_transition_matrix`, data_before, data, transition_matrix)
-}
-
 bayes_smoother <- function(m, m_nrow, m_ncol, w, sigma, covar_sigma0) {
     .Call(`_sits_bayes_smoother`, m, m_nrow, m_ncol, w, sigma, covar_sigma0)
 }
@@ -17,6 +13,10 @@ bilateral_smoother <- function(m, m_nrow, m_ncol, w, tau) {
     .Call(`_sits_bilateral_smoother`, m, m_nrow, m_ncol, w, tau)
 }
 
+entropy_probs <- function(mtx, n) {
+    .Call(`_sits_entropy_probs`, mtx, n)
+}
+
 linear_interp <- function(mtx) {
     .Call(`_sits_linear_interp`, mtx)
 }

diff --git a/R/data.R b/R/data.R
@@ -57,3 +57,31 @@ NULL
 #'   cube (the name of the cube associated with the data),
 #'   time_series (list containing a tibble with the values of the time series).
 NULL
+
+#'@title Samples of Amazon tropical forest biome for deforestation analysis
+#'
+#'
+#' @docType data
+#' @name samples_l8_rondonia_2bands.rda
+#' @keywords datasets
+#'
+#' @description
+#' A sits tibble with time series samples from Brazilian Amazonia rain forest.
+#'
+#' The labels are: "Deforestation", "Forest", "NatNonForest" and "Pasture".
+#'
+#' The time series were extracted from the Landsat-8 BDC data cube
+#' (collection = "LC8_30_16D_STK-1", tiles = "038047").
+#' These time series comprehends a period of 12 months
+#' (25 observations) from "2018-07-12" to "2019-07-28".
+#' The extracted bands are NDVI and EVI.
+#' Cloudy values were removed and interpolated.
+#'
+#' @format
+#' A \code{sits} tibble with 160 samples.
+#'
+#'
+#' @usage data("samples_l8_rondonia_2bands")
+#'
+NULL
+