Merge pull request #431 from e-sensing/dev

Pre-release v0.15.0

.drone.yml

@@ -4,7 +4,7 @@ name: default
 steps:
 - name: test
   pull: always
-  image: brazildatacube/sits-base:0.12.0
+  image: brazildatacube/sits:0.14
   commands:
   - R -e 'pacman::p_load(desc::desc_get_deps()[desc::desc_get_deps()[["type"]] != "Depends",][["package"]], install = T, update = F, character.only = T)'
   - R -e 'v<-gsub("(>) |(>=) ", "", desc::desc_get_deps()[desc::desc_get_deps()[["type"]] != "Depends" & desc::desc_get_deps()[["version"]] != "*", ][["version"]]); pacman::p_install_version(package = desc::desc_get_deps()[desc::desc_get_deps()[["type"]] != "Depends" & desc::desc_get_deps()[["version"]] != "*", ][["package"]], version = v)'
@@ -16,7 +16,7 @@ steps:
 
 - name: coverage
   pull: always
-  image: brazildatacube/sits-base:0.12.0
+  image: brazildatacube/sits:0.14
   environment:
     CODECOV_TOKEN:
       from_secret: codecov_token

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: sits
 Type: Package
-Version: 0.14.1-1
+Version: 0.15.0
 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'),
@@ -38,58 +38,47 @@ Imports:
     grDevices,
     ggplot2,
     graphics,
-    httr,
+    knitr,
     lubridate (>= 1.7.0),
     parallel,
     purrr (>= 0.3.0),
     raster (>= 3.4),
-    reshape2,
     rstac (>= 0.9.1-4),
-    scales,
     sf (>= 0.9),
     slider (>= 0.1.5),
     stats,
-    terra (>= 1.3),
+    terra (>= 1.4-11),
     tibble (>= 3.0),
     utils
 Suggests:
-    aws.s3 (>= 0.3.21),
     caret,
     dendextend,
-    devtools,
     dtwclust,
     dtwSat,
     e1071,
-    flexclust,
     gdalcubes,
-    imputeTS, 
+    httr,
     keras (>= 2.6.0),
     kohonen,
-    knitr,
-    MASS,
-    mapview,
+    leafem,
+    leaflet,
     methods,
     mgcv,
     nnet,
     openxlsx,
-    ptw,
-    reticulate (>= 1.18),
     randomForest,
     Rcpp,
     RcppArmadillo,
     Rwtss (>= 0.9.1),
-    signal,
+    scales,
     stars,
-    stringr,
     testthat (>= 3.0.2),
     tidyr,
     xgboost,
-    withr,
     zoo
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 Config/testthat/start-first: cube, wtss, raster, bdc, ml
-VignetteBuilder: knitr
 LinkingTo:
     Rcpp,
     RcppArmadillo
@@ -100,7 +89,6 @@ Collate:
     'sits-package.R'
     'sits_accuracy.R'
     'sits_bands.R'
-    'sits_bands_set.R'
     'sits_bbox.R'
     'sits_brewer.R'
     'sits_classification.R'
@@ -146,6 +134,7 @@ Collate:
     'sits_roi.R'
     'sits_satveg.R'
     'sits_select.R'
+    'sits_signal.R'
     'sits_shp.R'
     'sits_smooth.R'
     'sits_smooth_aux_functions.R'
@@ -155,8 +144,6 @@ Collate:
     'sits_source_api_bdc.R'
     'sits_source_api_deafrica.R'
     'sits_source_api_local.R'
-    'sits_source_api_probs.R'
-    'sits_source_api_opendata.R'
     'sits_source_api_satveg.R'
     'sits_source_api_stac.R'
     'sits_source_api_usgs.R'

NAMESPACE

@@ -1,13 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method("sits_bands<-",cube)
-S3method("sits_bands<-",patterns)
-S3method("sits_bands<-",predicted)
-S3method("sits_bands<-",sits)
 S3method("sits_labels<-",pattern)
 S3method("sits_labels<-",sits)
-S3method(.gc_format_col,aws_cube)
-S3method(.gc_format_col,opendata_cube)
 S3method(.raster_check_package,default)
 S3method(.raster_check_package,raster)
 S3method(.raster_check_package,terra)
@@ -64,36 +58,18 @@ S3method(.raster_yres,terra)
 S3method(.sits_roi_bbox,ll)
 S3method(.sits_roi_bbox,sf)
 S3method(.sits_roi_bbox,xy)
-S3method(.source_access_test,local_cube)
-S3method(.source_access_test,satveg_cube)
-S3method(.source_access_test,stac_cube)
-S3method(.source_access_test,wtss_cube)
-S3method(.source_cube,local_cube)
-S3method(.source_cube,probs_cube)
+S3method(.source_collection_access_test,satveg_cube)
+S3method(.source_collection_access_test,stac_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,aws_cube)
-S3method(.source_item_get_bands,bdc_cube)
-S3method(.source_item_get_bands,deafrica_cube)
-S3method(.source_item_get_bands,opendata_cube)
-S3method(.source_item_get_bands,usgs_cube)
-S3method(.source_item_get_date,aws_cube)
-S3method(.source_item_get_date,bdc_cube)
-S3method(.source_item_get_date,deafrica_cube)
-S3method(.source_item_get_date,opendata_cube)
-S3method(.source_item_get_date,usgs_cube)
-S3method(.source_item_get_hrefs,aws_cube)
+S3method(.source_item_get_bands,stac_cube)
+S3method(.source_item_get_date,stac_cube)
 S3method(.source_item_get_hrefs,bdc_cube)
-S3method(.source_item_get_hrefs,deafrica_cube)
-S3method(.source_item_get_hrefs,opendata_cube)
+S3method(.source_item_get_hrefs,stac_cube)
 S3method(.source_item_get_hrefs,usgs_cube)
-S3method(.source_item_get_resolutions,aws_cube)
-S3method(.source_item_get_resolutions,bdc_cube)
-S3method(.source_item_get_resolutions,deafrica_cube)
-S3method(.source_item_get_resolutions,opendata_cube)
-S3method(.source_item_get_resolutions,usgs_cube)
-S3method(.source_items_bands_select,aws_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)
@@ -102,33 +78,19 @@ S3method(.source_items_fileinfo,wtss_cube)
 S3method(.source_items_new,aws_cube)
 S3method(.source_items_new,bdc_cube)
 S3method(.source_items_new,deafrica_cube)
-S3method(.source_items_new,opendata_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,bdc_cube)
-S3method(.source_items_tile_get_bbox,deafrica_cube)
-S3method(.source_items_tile_get_bbox,opendata_cube)
-S3method(.source_items_tile_get_bbox,usgs_cube)
+S3method(.source_items_tile_get_bbox,stac_cube)
 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,opendata_cube)
 S3method(.source_items_tile_get_crs,usgs_cube)
-S3method(.source_items_tile_get_name,aws_cube)
 S3method(.source_items_tile_get_name,bdc_cube)
 S3method(.source_items_tile_get_name,deafrica_cube)
-S3method(.source_items_tile_get_name,opendata_cube)
-S3method(.source_items_tile_get_name,usgs_cube)
-S3method(.source_items_tile_get_size,aws_cube)
-S3method(.source_items_tile_get_size,bdc_cube)
-S3method(.source_items_tile_get_size,deafrica_cube)
-S3method(.source_items_tile_get_size,opendata_cube)
-S3method(.source_items_tile_get_size,usgs_cube)
+S3method(.source_items_tile_get_name,stac_cube)
 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,opendata_cube)
 S3method(.source_items_tiles_group,usgs_cube)
 S3method(plot,classified_image)
 S3method(plot,keras_model)
@@ -143,22 +105,18 @@ S3method(print,sits_area_assessment)
 S3method(print,sits_assessment)
 S3method(sits_accuracy,classified_image)
 S3method(sits_accuracy,sits)
-S3method(sits_bands,cube)
 S3method(sits_bands,patterns)
 S3method(sits_bands,sits)
+S3method(sits_bands,sits_cube)
 S3method(sits_bands,sits_model)
-S3method(sits_bbox,cube)
 S3method(sits_bbox,sits)
+S3method(sits_bbox,sits_cube)
 S3method(sits_classify,raster_cube)
 S3method(sits_classify,sits)
-S3method(sits_cube,aws_cube)
-S3method(sits_cube,bdc_cube)
-S3method(sits_cube,deafrica_cube)
 S3method(sits_cube,default)
 S3method(sits_cube,local_cube)
-S3method(sits_cube,opendata_cube)
-S3method(sits_cube,probs_cube)
 S3method(sits_cube,satveg_cube)
+S3method(sits_cube,stac_cube)
 S3method(sits_cube,wtss_cube)
 S3method(sits_get_data,csv_raster_cube)
 S3method(sits_get_data,csv_satveg_cube)
@@ -169,16 +127,16 @@ S3method(sits_get_data,shp_raster_cube)
 S3method(sits_get_data,shp_satveg_cube)
 S3method(sits_get_data,shp_wtss_cube)
 S3method(sits_get_data,wtss_cube)
-S3method(sits_labels,cube)
 S3method(sits_labels,patterns)
 S3method(sits_labels,sits)
+S3method(sits_labels,sits_cube)
 S3method(sits_labels,sits_model)
 S3method(sits_labels_summary,sits)
-S3method(sits_merge,cube)
 S3method(sits_merge,sits)
-S3method(sits_select,cube)
+S3method(sits_merge,sits_cube)
 S3method(sits_select,patterns)
 S3method(sits_select,sits)
+S3method(sits_select,sits_cube)
 S3method(sits_smooth,bayes)
 S3method(sits_smooth,bilateral)
 S3method(sits_smooth,gaussian)
@@ -193,9 +151,10 @@ S3method(sits_values,bands_dates_cases)
 S3method(sits_values,cases_dates_bands)
 S3method(sits_view,classified_image)
 S3method(sits_view,raster_cube)
+S3method(sits_view,sits)
 export("%>%")
-export("sits_bands<-")
 export("sits_labels<-")
+export(.source_cube_local_cube)
 export(sits_ResNet)
 export(sits_TempCNN)
 export(sits_accuracy)
@@ -211,7 +170,6 @@ export(sits_config)
 export(sits_config_show)
 export(sits_create_folds)
 export(sits_cube)
-export(sits_cube_copy)
 export(sits_data_to_csv)
 export(sits_envelope)
 export(sits_filter)
@@ -224,10 +182,8 @@ export(sits_interp)
 export(sits_keras_diagnostics)
 export(sits_kfold_validate)
 export(sits_label_classification)
-export(sits_label_majority)
 export(sits_labels)
 export(sits_labels_summary)
-export(sits_lda)
 export(sits_linear_interp)
 export(sits_list_collections)
 export(sits_merge)
@@ -238,7 +194,6 @@ export(sits_mlr)
 export(sits_mutate_bands)
 export(sits_ndwi)
 export(sits_patterns)
-export(sits_qda)
 export(sits_regularize)
 export(sits_rfor)
 export(sits_sample)

NEWS.md

@@ -2,10 +2,40 @@
 
 We are preparing to release the package on CRAN and are making relevant changes in the development version.
 
+# What's new in SITS version 0.15.0 
+
+### New features in SITS version 0.15.0
+
+* Support for regularization of collections in DEAFRICA and USGS improvement
+* Collection `S2_10_16D_STK-1` removed from BDC source in config file
+* Add a color for `NoClass` label improvement
+* Change `mapview` to `leaflet` package
+* Standardize cube creation parameters
+* Remove `CLASSIFIED` and `PROBS` sources from config file
+* Change minimal version requirement of `terra` package to 1.4-11
+* Update `sits_list_collections()` to indicate open data collection
+* Geographical visualization of samples
+* Remove dependencies on packages `ptw`, `signal` and `MASS`
+* Add support to `open_data` collections in config file
+* Change default `output_dir` parameter
+* Remove `sits_cube_clone()` function
+* Plot RGB images from raster cubes
+* Fixed error in `sits_select()` for bands in raster cube
+* Update examples in demo
+* Support open data collections of DEAFRICA and AWS
+* Support USGS STAC Landsat 8 catalog
+* User can provide resampling method to `sits_regularize()` function
+* Add support to open data collections on 'AWS' source
+* Remove `OPENDATA` source
+* Update documentation
+* Resolve ambiguity in "bands" parameter for data cubes
+* Remove "sits_bands" assignment function
+* Include "labels" information only on probs and labelled data cubes
+* Remove `S2_10-1` BDC collection from config
+* Other bug fixes
 
 # What's new in SITS version 0.14.1
 
-
 ### New features in SITS version 0.14.1-1
 
 * Bug in cube generated by sits_regularize() cannot have "CLOUD" band

R/RcppExports.R

@@ -29,3 +29,7 @@ normalize_data <- function(data, min, max) {
     .Call(`_sits_normalize_data`, data, min, max)
 }
 
+smooth_whit <- function(data, lambda, length) {
+    .Call(`_sits_smooth_whit`, data, lambda, length)
+}
+

R/sits_ResNet.R

@@ -93,8 +93,7 @@ sits_ResNet <- function(samples = NULL,
     result_fun <- function(data) {
         # verifies if keras package is installed
         if (!requireNamespace("keras", quietly = TRUE)) {
-            stop(paste("keras required for this function to work.",
-                       "Please install it."), call. = FALSE)
+            stop("Please install package keras", call. = FALSE)
         }
 
         valid_activations <- c("relu", "elu", "selu", "sigmoid")
@@ -270,8 +269,7 @@ sits_ResNet <- function(samples = NULL,
 
             # verifies if keras package is installed
             if (!requireNamespace("keras", quietly = TRUE)) {
-                stop(paste("keras required for this function to work.",
-                           "Please install it."), call. = FALSE)
+                stop("Please install package keras", call. = FALSE)
             }
 
             # restore model keras

R/sits_TempCNN.R

@@ -92,8 +92,7 @@ sits_TempCNN <- function(samples = NULL,
 
         # verifies if keras package is installed
         if (!requireNamespace("keras", quietly = TRUE)) {
-            stop(paste("keras required for this function to work.",
-                       "Please install it."), call. = FALSE)
+            stop("Please install package keras", call. = FALSE)
         }
 
         # pre-conditions
@@ -281,8 +280,7 @@ sits_TempCNN <- function(samples = NULL,
 
             # verifies if keras package is installed
             if (!requireNamespace("keras", quietly = TRUE)) {
-                stop(paste("keras required for this function to work.",
-                           "Please install it."), call. = FALSE)
+                stop("Please install package keras", call. = FALSE)
             }
 
             # restore model keras