update documentation

DESCRIPTION

@@ -2,7 +2,7 @@ Package: sits
 Type: Package
 Version: 1.5.3
 Title: Satellite Image Time Series Analysis for Earth Observation Data Cubes
-Authors@R: c(person('Rolf', 'Simoes', role = c('aut'), email = '[email protected]'),
+Authors@R: c(person('Rolf', 'Simoes', role = c('aut'), email = '[email protected]'),
              person('Gilberto', 'Camara', role = c('aut', 'cre', 'ths'), email = '[email protected]'),
              person('Felipe', 'Souza', role = c('aut'), email = '[email protected]'),
              person('Felipe', 'Carlos', role = c('aut'), email = "[email protected]"),

R/api_accessors.R

@@ -1,7 +1,7 @@
 #' @title Bouding box accessors
 #' @noRd
 #'
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @description
 #' These functions are accessors of raster data and bbox structures.
@@ -153,7 +153,7 @@
 #' @title Resolution accessors
 #' @noRd
 #'
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @description
 #' These functions are read-only accessors of chunk fields

R/api_apply.R

@@ -2,7 +2,7 @@
 #' @name .apply
 #' @keywords internal
 #' @noRd
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @param  data      Tibble.
 #' @param  col       Column where function should be applied
@@ -38,7 +38,7 @@
 #' @name .apply_feature
 #' @keywords internal
 #' @noRd
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @param  feature         Subset of a data cube containing the input bands
 #'                         used in the expression

R/api_band.R

@@ -1,5 +1,6 @@
 #' @title Rename bands (S3 Generic function)
 #' @name .band_rename
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #' @noRd
 #' @param x sits object (time series or cube)
 #' @param bands new bands for the object

R/api_bayts.R

@@ -1,6 +1,7 @@
 #' @title Create statistics for BAYTS algorithm
 #' @name .bayts_create_stats
 #' @keywords internal
+#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br}
 #' @noRd
 #' @param samples     Samples
 #' @param stats       Tibble with statistics

R/api_bbox.R

@@ -17,7 +17,7 @@
 #' @title Bounding box API
 #' @noRd
 #'
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @description
 #' A bounding box represents a rectangular geographical region in a certain

R/api_block.R

@@ -1,7 +1,7 @@
 #' @title Block API
 #' @noRd
 #'
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @param x  Any object to extract a block.
 #'
@@ -42,7 +42,7 @@ NULL
 #' @title Block accessors
 #' @noRd
 #'
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @description
 #' These functions are accessors of block fields in a vector.

R/api_chunks.R

@@ -1,7 +1,7 @@
 #' @title Chunks API
 #' @noRd
 #'
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @description
 #' A chunk is a tibble of rectangular regions defining a matrix and

R/api_classify.R

@@ -2,7 +2,7 @@
 #' @name .classify_tile
 #' @keywords internal
 #' @noRd
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br}
 #'
 #' @description Classifies a block of data using multicores. It breaks
@@ -251,7 +251,7 @@
 #' @name .classify_tile
 #' @keywords internal
 #' @noRd
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br}
 #'
 #' @description Classifies a block of data using multicores. It breaks
@@ -427,7 +427,7 @@
 #' @keywords internal
 #' @noRd
 #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br}
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes,     \email{rolfsimoes@@gmail.com}
 #'
 #' @param  tile            Input tile to read data.
 #' @param  block           Bounding box in (col, row, ncols, nrows).

R/api_cluster.R

@@ -2,7 +2,7 @@
 #' @name .cluster_validity
 #' @keywords internal
 #' @noRd
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @description Compute different cluster validity indices. This function needs
 #' as input a sits tibble with `cluster` column.
@@ -38,7 +38,7 @@
 #' @name .cluster_dendrogram
 #' @keywords internal
 #' @noRd
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br}
 #'
 #' @description Cluster time series in hierarchical mode.
@@ -95,7 +95,7 @@
 #' @name .cluster_dendro_bestcut
 #' @keywords internal
 #' @noRd
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @description Reads a dendrogram object and its corresponding sits tibble and
 #' computes the best number of clusters that maximizes the adjusted Rand index.

R/api_combine_predictions.R

@@ -3,7 +3,7 @@
 #' @name  .comb
 #' @noRd
 #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br}
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @param  probs_cubes   List of probability data cubes.
 #' @param  uncert_cubes  List of uncertainty cubes to be used as local weights.
@@ -77,7 +77,7 @@
 #' @name  .comb_tiles
 #' @noRd
 #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br}
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @param  probs_tiles   List of probability tiles.
 #' @param  uncert_cubes  List of uncertainty tiles.
@@ -210,7 +210,7 @@
 #' @name  .comb_fn_average
 #' @noRd
 #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br}
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @param  cubes         List of probability cubes.
 #' @param  weights       Weights for weigthed average
@@ -236,7 +236,7 @@
 #' @name  .comb_fn_uncertainty
 #' @noRd
 #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br}
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @param  cubes         List of probability cubes.
 #' @return A combined tile-band-block raster object

R/api_comp.R

@@ -1,7 +1,7 @@
 #' @title  Comparison functions
 #' @noRd
 #'
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br}
 #'
 #' @description

R/api_conf.R

@@ -1,7 +1,7 @@
 #' @title Set configuration parameters
 #' @name .conf_set_options
 #' @noRd
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @param processing_bloat       Estimated growth size of R memory relative
 #'                               to block size.
@@ -963,7 +963,7 @@
 #' @title Basic access config functions
 #' @noRd
 #'
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @description
 #' These are basic functions to access config options.
@@ -1005,7 +1005,7 @@ NULL
 #' @title Config functions eo_cube
 #' @noRd
 #'
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @description
 #' These are syntactic sugar functions to easily access config options for
@@ -1076,7 +1076,7 @@ NULL
 #' @title Config functions for derived_cube
 #' @noRd
 #'
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @description
 #' These are syntactic sugar functions to easily access config options for
@@ -1143,7 +1143,7 @@ NULL
 #' @title Band configuration accessors
 #' @noRd
 #'
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @description
 #' These functions are read-only accessors of band_conf objects. A

R/api_cube.R

@@ -596,7 +596,7 @@ NULL
 #' @name .cube_s3class
 #' @keywords internal
 #' @noRd
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @param  cube         input data cube
 #' @return class of the cube
@@ -654,7 +654,7 @@ NULL
 #' @name .cube_ncols
 #' @keywords internal
 #' @noRd
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @param  cube  input data cube
 #' @return integer
@@ -676,7 +676,7 @@ NULL
 #' @name .cube_nrows
 #' @keywords internal
 #' @noRd
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @param  cube  input data cube
 #' @return integer
@@ -698,7 +698,7 @@ NULL
 #' @name .cube_source
 #' @keywords internal
 #' @noRd
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #'@param  cube input data cube
 #'

R/api_debug.R

@@ -1,7 +1,7 @@
 #' @title Log functions
 #' @noRd
 #'
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @description
 #' logs to a CSV file the following values:
@@ -81,7 +81,7 @@
 #' @title Log functions
 #' @noRd
 #'
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @description
 #' When called without parameters retrieves the current debug flag value.

R/api_factory.R

@@ -1,6 +1,6 @@
 #' @title Create a closure for calling functions with and without data
 #' @name .factory_function
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br}
 #' @keywords internal
 #' @noRd

R/api_file_info.R

@@ -1,6 +1,6 @@
 #' @title File info API
 #' @noRd
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @description
 #' Set of functions for handling `file_info`.

R/api_mixture_model.R

@@ -2,7 +2,8 @@
 #' @title Apply a mixture model to a set of time series
 #' @keywords internal
 #' @noRd
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @param  samples      Time series
 #' @param  em           Endmembers bands
@@ -25,7 +26,8 @@
 #' @title Apply a mixture model to a raster feature
 #' @keywords internal
 #' @noRd
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @param  feature      Raster feature where mixture is to be applied
 #' @param  block        Image block
@@ -120,7 +122,8 @@
 #' @title Read data to compute a mixture model
 #' @keywords internal
 #' @noRd
-#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
+#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br}
+#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com}
 #'
 #' @param  tile         Raster tile
 #' @param  block        Image block