diff --git a/DESCRIPTION b/DESCRIPTION index f2f31f89f..98c91c771 100644 --- a/DESCRIPTION +++ b/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 = 'rolf.simoes@inpe.br'), +Authors@R: c(person('Rolf', 'Simoes', role = c('aut'), email = 'rolfsimoes@gmail.com'), person('Gilberto', 'Camara', role = c('aut', 'cre', 'ths'), email = 'gilberto.camara.inpe@gmail.com'), person('Felipe', 'Souza', role = c('aut'), email = 'felipe.carvalho@inpe.br'), person('Felipe', 'Carlos', role = c('aut'), email = "efelipecarlos@gmail.com"), diff --git a/R/api_accessors.R b/R/api_accessors.R index 80176d94d..c259f1c11 100644 --- a/R/api_accessors.R +++ b/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 diff --git a/R/api_apply.R b/R/api_apply.R index 1960d3e79..0bff87cfb 100644 --- a/R/api_apply.R +++ b/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 diff --git a/R/api_band.R b/R/api_band.R index c12ace0b6..f3f0df97f 100644 --- a/R/api_band.R +++ b/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 diff --git a/R/api_bayts.R b/R/api_bayts.R index d734bd737..177125d19 100644 --- a/R/api_bayts.R +++ b/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 diff --git a/R/api_bbox.R b/R/api_bbox.R index 074c624e1..536841cc5 100644 --- a/R/api_bbox.R +++ b/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 diff --git a/R/api_block.R b/R/api_block.R index 1e5cab118..2624fd1a1 100644 --- a/R/api_block.R +++ b/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. diff --git a/R/api_chunks.R b/R/api_chunks.R index 84890da02..632866a67 100644 --- a/R/api_chunks.R +++ b/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 diff --git a/R/api_classify.R b/R/api_classify.R index 3d816a314..9dfe9f9e9 100755 --- a/R/api_classify.R +++ b/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). diff --git a/R/api_cluster.R b/R/api_cluster.R index a776039bb..f78384c2e 100644 --- a/R/api_cluster.R +++ b/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. diff --git a/R/api_combine_predictions.R b/R/api_combine_predictions.R index d3ae9692d..34bcaa7fe 100644 --- a/R/api_combine_predictions.R +++ b/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 diff --git a/R/api_comp.R b/R/api_comp.R index 8e48b08c6..6ea2fdb5e 100644 --- a/R/api_comp.R +++ b/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 diff --git a/R/api_conf.R b/R/api_conf.R index 43d561f66..b492b49de 100644 --- a/R/api_conf.R +++ b/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 diff --git a/R/api_cube.R b/R/api_cube.R index af448784f..c693176b3 100644 --- a/R/api_cube.R +++ b/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 #' diff --git a/R/api_debug.R b/R/api_debug.R index 637a26bd5..b2087811e 100644 --- a/R/api_debug.R +++ b/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. diff --git a/R/api_factory.R b/R/api_factory.R index 29e1704ea..06443f0f6 100644 --- a/R/api_factory.R +++ b/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 diff --git a/R/api_file_info.R b/R/api_file_info.R index 8392487fd..374355854 100644 --- a/R/api_file_info.R +++ b/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`. diff --git a/R/api_mixture_model.R b/R/api_mixture_model.R index 5e149aac4..f88eb1eb7 100644 --- a/R/api_mixture_model.R +++ b/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 diff --git a/R/api_ml_model.R b/R/api_ml_model.R index 0f768ff5a..72bc02999 100644 --- a/R/api_ml_model.R +++ b/R/api_ml_model.R @@ -1,7 +1,7 @@ #' @title Return machine learning model inside a closure #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param ml_model Closure that contains ML model and its environment #' @return ML model as specified by the original ML function @@ -17,7 +17,7 @@ #' @title Return statistics of ML model inside a closure (old version) #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param ml_model Closure that contains ML model and its environment #' @return Data statistics contained in the model closure @@ -28,7 +28,7 @@ #' @title Return statistics of ML model inside a closure (new version) #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param ml_model Closure that contains ML model and its environment #' @return Data statistics contained in the model closure @@ -39,7 +39,7 @@ #' @title Return samples of ML model inside a closure #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @param ml_model Closure that contains ML model and its environment #' @return Samples used for ML construction .ml_samples <- function(ml_model) { @@ -48,7 +48,7 @@ #' @title Return class of ML model inside a closure #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @param ml_model Closure that contains ML model and its environment #' @return ML model class .ml_class <- function(ml_model) { @@ -57,7 +57,7 @@ #' @title Return names of features used to train ML model #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @param ml_model Closure that contains ML model and its environment #' @return Features used to build the model .ml_features_name <- function(ml_model) { @@ -67,7 +67,7 @@ #' @title Return names of bands used to train ML model #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @param ml_model Closure that contains ML model and its environment #' @return Bands used to build the model .ml_bands <- function(ml_model) { @@ -76,7 +76,7 @@ #' @title Return labels of samples of used to train ML model #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @param ml_model Closure that contains ML model and its environment #' @return Sample labels used to build the model .ml_labels <- function(ml_model) { @@ -85,7 +85,7 @@ #' @title Return codes of sample labels of used to train ML model #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @param ml_model Closure that contains ML model and its environment #' @return Codes of sample labels used to build the model .ml_labels_code <- function(ml_model) { @@ -96,6 +96,8 @@ #' @title Clean GPU memory allocation #' @keywords internal #' @noRd +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} +#' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} #' @param ml_model Closure that contains ML model and its environment #' @return Called for side effects .ml_gpu_clean <- function(ml_model) { @@ -108,6 +110,7 @@ #' @title normalize the probability results #' @keywords internal +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @noRd #' @param ml_model Closure that contains ML model and its environment #' @param values Values to be normalized @@ -134,6 +137,8 @@ #' @title Update multicores for models that do internal multiprocessing #' @keywords internal #' @noRd +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} +#' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} #' @param ml_model Closure that contains ML model and its environment #' @param multicores Current multicores setting #' @return Updated multicores @@ -151,6 +156,8 @@ #' @title Is the ML model a torch model? #' @keywords internal #' @noRd +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} +#' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} #' @param ml_model Closure that contains ML model and its environment #' @return TRUE/FALSE #' diff --git a/R/api_parallel.R b/R/api_parallel.R index dc819b419..305149272 100644 --- a/R/api_parallel.R +++ b/R/api_parallel.R @@ -2,7 +2,7 @@ #' @name .parallel_stop #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @return No value, called for side effect. #' .parallel_stop <- function() { @@ -22,7 +22,7 @@ #' @name .parallel_is_open #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @return No value, called for side effect. #' .parallel_is_open <- function() { @@ -40,7 +40,7 @@ #' @name .parallel_start #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param workers number of cluster to instantiate #' @param log a logical indicating if log files must be written @@ -90,7 +90,7 @@ #' @name .parallel_reset_node #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param worker_id id of the cluster work to be recreated #' @return No value, called for side effect. @@ -111,7 +111,7 @@ #' @keywords internal #' @noRd #' -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description #' These internal functions are a reimplementation of a fault tolerant @@ -173,6 +173,7 @@ #' @name .parallel_recv_one_result #' @keywords internal #' @noRd +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @return List with values and nodes .parallel_recv_one_result <- function() { # fault tolerant version of parallel:::recvOneData @@ -186,6 +187,7 @@ #' @rdname .parallel_cluster_apply #' @keywords internal #' @noRd +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @return No value, called for side effect. .parallel_cluster_apply <- function(x, fn, ..., pb = NULL) { # fault tolerant version of parallel::clusterApplyLB @@ -248,7 +250,7 @@ #' @name .parallel_map #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param x List to be passed to a function. #' @param fn Function to be applied to each list element. diff --git a/R/api_point.R b/R/api_point.R index 96f1fdeb3..87517f3e8 100644 --- a/R/api_point.R +++ b/R/api_point.R @@ -1,7 +1,7 @@ #' @title Points accessors #' @noRd #' -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description #' These functions are accessors of `point` fields in a object tibble. @@ -56,7 +56,7 @@ NULL #' @title Point API #' @noRd #' -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description #' A point represents a dimensionless geographical location in a given diff --git a/R/api_raster.R b/R/api_raster.R index 91d2fe94a..0bdd19a8e 100644 --- a/R/api_raster.R +++ b/R/api_raster.R @@ -9,7 +9,7 @@ #' @name .raster_check_block #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @return No value, called for side effects. .raster_check_block <- function(block) { # set caller to show in errors @@ -30,7 +30,7 @@ #' @name .raster_check_bbox #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @return No value, called for side effects. .raster_check_bbox <- function(bbox) { # set caller to show in errors @@ -50,7 +50,7 @@ #' @name .raster_gdal_datatype #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @return GDAL datatype associated to internal data type used by sits .raster_gdal_datatype <- function(data_type) { @@ -70,6 +70,7 @@ #' @title Match sits data types to GDAL data types #' @name .raster_gdal_datatypes #' @keywords internal +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @noRd #' @param sits_names a \code{logical} indicating whether the types are supported #' by sits. @@ -93,7 +94,7 @@ #' @name .raster_get_values #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj raster package object #' @param ... additional parameters to be passed to raster package @@ -111,7 +112,7 @@ #' @name .raster_set_values #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj raster package object #' @param values Numeric matrix to copy to raster object @@ -127,7 +128,7 @@ #' @name .raster_set_na #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj raster package object #' @param na_value Numeric matrix to copy to raster object @@ -142,6 +143,8 @@ #' @title Get top values of a raster. #' #' @author Alber Sanchez, \email{alber.ipia@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} +#' @author Felipe Carvalho, \email{felipe.carvalho@@gmail.com} #' @keywords internal #' @noRd #' @description @@ -226,7 +229,7 @@ #' @name .raster_extract #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj raster package object #' @param xy numeric matrix with coordinates @@ -236,11 +239,12 @@ .raster_extract <- function(r_obj, xy, ...) { terra::extract(x = r_obj, y = xy, ...) } - +#' #' @title Return sample of values from terra object #' @keywords internal +#' @name .raster_sample #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj raster object #' @param size size of sample @@ -249,10 +253,11 @@ .raster_sample <- function(r_obj, size, ...) { terra::spatSample(r_obj, size, ...) } +#' @title Return block size of a raster #' @name .raster_file_blocksize #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj raster package object #' @@ -267,7 +272,7 @@ #' @name .raster_rast #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj raster package object to be cloned #' @param nlayers number of raster layers @@ -284,7 +289,7 @@ #' @name .raster_open_rast #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param file raster file to be opened #' @param ... additional parameters to be passed to raster package @@ -306,7 +311,7 @@ #' @name .raster_write_rast #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj raster package object to be written #' @param file file path to save raster file @@ -348,8 +353,7 @@ #' @name .raster_new_rast #' @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 nrows Number of rows in the raster #' @param ncols Number of columns in the raster @@ -415,7 +419,7 @@ #' @name .raster_read_rast #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param file path to raster file(s) to be read #' @param block a valid block with (\code{col}, \code{row}, @@ -462,7 +466,7 @@ #' @name .raster_crop #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj Raster package object to be written #' @param file File name to save cropped raster. @@ -544,7 +548,7 @@ #' @name .raster_crop_metadata #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj raster package object to be written #' @param block a valid block with (\code{col}, \code{row}, @@ -602,78 +606,111 @@ ) } -#' @title Raster package internal object properties -#' @name .raster_properties +#' @title Return number of rows in a raster +#' @name .raster_nrows #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj raster package object #' @param ... additional parameters to be passed to raster package #' -#' @return Raster object spatial properties +#' @return number of rows in raster object .raster_nrows <- function(r_obj, ...) { terra::nrow(x = r_obj) } +#' @title Return number of columns in a raster #' @name .raster_ncols +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd +#' @param r_obj raster package object +#' @param ... additional parameters to be passed to raster package +#' @return number of columns in a raster object .raster_ncols <- function(r_obj, ...) { terra::ncol(x = r_obj) } - +#' @title Return number of layers in a raster #' @name .raster_nlayers +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd +#' @param r_obj raster package object +#' @param ... additional parameters to be passed to raster package +#' @return number of layers in a raster object .raster_nlayers <- function(r_obj, ...) { terra::nlyr(x = r_obj) } - #' @name .raster_xmax +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd +#' @param r_obj raster package object +#' @param ... additional parameters to be passed to raster package +#' @return maximum x coord of raster object .raster_xmax <- function(r_obj, ...) { terra::xmax(x = r_obj) } #' @name .raster_xmin +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd +#' @param r_obj raster package object +#' @param ... additional parameters to be passed to raster package +#' @return minimum x coord of raster object .raster_xmin <- function(r_obj, ...) { terra::xmin(x = r_obj) } - #' @name .raster_ymax +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd +#' @param r_obj raster package object +#' @param ... additional parameters to be passed to raster package +#' @return maximum y coord of raster object .raster_ymax <- function(r_obj, ...) { terra::ymax(x = r_obj) } #' @name .raster_ymin +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd +#' @param r_obj raster package object +#' @param ... additional parameters to be passed to raster package +#' @return minimum y coord of raster object .raster_ymin <- function(r_obj, ...) { terra::ymin(x = r_obj) } - #' @name .raster_xres +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd +#' @param r_obj raster package object +#' @param ... additional parameters to be passed to raster package +#' @return resolution of raster object in x direction .raster_xres <- function(r_obj, ...) { terra::xres(x = r_obj) } - #' @name .raster_yres +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd +#' @param r_obj raster package object +#' @param ... additional parameters to be passed to raster package +#' @return resolution of raster object in y direction .raster_yres <- function(r_obj, ...) { terra::yres(x = r_obj) } #' @name .raster_scale +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd +#' @param r_obj raster package object +#' @param ... additional parameters to be passed to raster package +#' @return scale of values in raster object .raster_scale <- function(r_obj, ...) { # check value i <- 1 @@ -688,8 +725,12 @@ return(scale_factor) } #' @name .raster_crs +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd +#' @param r_obj raster package object +#' @param ... additional parameters to be passed to raster package +#' @return crs of raster object .raster_crs <- function(r_obj, ...) { crs <- suppressWarnings( terra::crs(x = r_obj, describe = TRUE) @@ -701,10 +742,13 @@ as.character(terra::crs(x = r_obj)) ) } - #' @name .raster_bbox +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd +#' @param r_obj raster package object +#' @param ... additional parameters to be passed to raster package +#' @return bounding box of raster object .raster_bbox <- function(r_obj, ..., block = NULL) { if (is.null(block)) { @@ -727,8 +771,12 @@ } #' @name .raster_res +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd +#' @param r_obj raster package object +#' @param ... additional parameters to be passed to raster package +#' @return resolution of raster object in x and y dimensions .raster_res <- function(r_obj, ...) { # return a named resolution res <- list( @@ -738,10 +786,13 @@ return(res) } - #' @name .raster_size +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd +#' @param r_obj raster package object +#' @param ... additional parameters to be passed to raster package +#' @return number of rows and cols of raster object .raster_size <- function(r_obj, ...) { # return a named size size <- list( @@ -751,12 +802,11 @@ return(size) } - #' @title Raster package internal frequency values function #' @name .raster_freq #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj raster package object to count values #' @param ... additional parameters to be passed to raster package @@ -785,7 +835,7 @@ #' @name .raster_summary #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} #' #' @param r_obj raster package object to count values @@ -799,7 +849,7 @@ #' @title Return col value given an X coordinate #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj raster package object #' @param x X coordinate in raster projection @@ -812,7 +862,7 @@ #' @name .raster_cell_from_rowcol #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj raster package object #' @param row row @@ -825,7 +875,7 @@ #' @title Return XY values given a cell #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj raster package object #' @param cell cell in raster object @@ -836,7 +886,7 @@ #' @title Return quantile value given an raster #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj raster package object #' @param quantile quantile value @@ -851,7 +901,7 @@ #' @title Return row value given an Y coordinate #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param r_obj raster object #' @param y Y coordinate in raster projection @@ -864,7 +914,7 @@ #' @name .raster_extract_polygons #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @param r_obj terra raster object #' @param dissolve should the polygons be dissolved? #' @return A set of polygons @@ -877,7 +927,7 @@ #' @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} #' #' @description Based on the R object associated to a raster object, #' determine its spatial parameters @@ -907,8 +957,20 @@ ) return(params) } - - +#' @title Template for creating a new raster +#' @name .raster_template +#' @keywords internal +#' @noRd +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} +#' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} +#' +#' @param base_file File to use for template +#' @param out_file Name of output file +#' @param nlayers Number of layers in output file +#' @param data_type Data type of output +#' @param missing_value Missing values in output file +#' +#' @return name of output file .raster_template <- function(base_file, out_file, nlayers, data_type, missing_value) { @@ -935,7 +997,7 @@ #' @name .raster_merge #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param out_files Output raster files path. #' @param base_file Raster file path to be used as template. If \code{NULL}, @@ -1037,6 +1099,18 @@ } return(invisible(out_files)) } +#' @title Clone an existing raster +#' @name .raster_clone +#' @keywords internal +#' @noRd +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} +#' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} +#' +#' @param file Raster file to use for template +#' @param nlayers Number of layers in output file +#' +#' @return cloned raster object +#' .raster_clone <- function(file, nlayers = NULL) { r_obj <- .raster_open_rast(file = file) @@ -1047,6 +1121,18 @@ return(r_obj) } +#' @title Check if raster is valid +#' @name .raster_is_valid +#' @keywords internal +#' @noRd +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} +#' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} +#' +#' @param files Raster files +#' @param output_dir Output file +#' +#' @return boolean value +#' .raster_is_valid <- function(files, output_dir = NULL) { # resume processing in case of failure if (!all(file.exists(files))) { @@ -1103,7 +1189,23 @@ # Return check check } - +#' @title Write block of raster +#' @name .raster_write_block +#' @keywords internal +#' @noRd +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} +#' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} +#' +#' @param files Raster files to written +#' @param block Block to be written to file +#' @param bbox Bounding box of block +#' @param values Values to be written +#' @param data_type Data type of output +#' @param missing_value Missing value for output file +#' @param crop_block Cropped area of block +#' +#' @return file paths +#' .raster_write_block <- function(files, block, bbox, values, data_type, missing_value, crop_block = NULL) { .check_set_caller(".raster_write_block") diff --git a/R/api_reclassify.R b/R/api_reclassify.R index 347cf49ac..6d4f64363 100644 --- a/R/api_reclassify.R +++ b/R/api_reclassify.R @@ -1,7 +1,7 @@ #' @title Reclassify tile #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param tile. Subset of a data cube #' @param mask Reclassification mask @@ -135,7 +135,7 @@ #' @title Reclassify function #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @param rules Rules to be applied #' @param labels_cube Labels of input cube #' @param labels_mask Labels of reclassification mask @@ -201,7 +201,7 @@ #' @title Obtain new labels on reclassification operation #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @param cube Labelled data cube #' @param rules Rules to be applied #' @return new labels to be applied to the cube diff --git a/R/api_samples.R b/R/api_samples.R index e82460b18..3397ea0c3 100644 --- a/R/api_samples.R +++ b/R/api_samples.R @@ -46,7 +46,7 @@ } #' @title Create partitions of a data set #' @name .samples_create_folds -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Alexandre Ywata, \email{alexandre.ywata@@ipea.gov.br} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' @description Split a sits tibble into k groups, based on the label. diff --git a/R/api_smooth.R b/R/api_smooth.R index cd5390afe..3b138fabe 100644 --- a/R/api_smooth.R +++ b/R/api_smooth.R @@ -2,7 +2,7 @@ #' @name .smooth_tile #' @keywords internal #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param tile. Subset of a data cube containing one tile #' @param band Band to be processed diff --git a/R/api_space_time_operations.R b/R/api_space_time_operations.R index fbc8a8755..2f585b5c5 100644 --- a/R/api_space_time_operations.R +++ b/R/api_space_time_operations.R @@ -48,7 +48,7 @@ #' @title Spatial intersects #' @noRd #' -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description #' This function is based on sf::st_intersects(). It projects y @@ -77,7 +77,7 @@ #' @title Spatial within #' @noRd #' -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description #' This function is based on sf::st_within(). It projects y @@ -105,7 +105,7 @@ #' @title Spatial contains #' @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 diff --git a/R/api_tibble.R b/R/api_tibble.R index 3345b174f..970b7bcdb 100644 --- a/R/api_tibble.R +++ b/R/api_tibble.R @@ -37,7 +37,7 @@ #' @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} #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} #' #' @description Create a tibble to store the results of predictions. @@ -75,7 +75,8 @@ #' @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} +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} #' #' @description Create a tibble to store the results of predictions. #' @param data Tibble with the input data. @@ -286,6 +287,7 @@ } #' @title Returns a time series +#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' @name .tibble_time_series #' @noRd #' @param data a tibble with time series @@ -296,6 +298,9 @@ #' @title Split a sits tibble #' @name .tibble_samples_split +#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} #' @keywords internal #' @noRd #' @description Add a column to sits tibble indicating if a sample is diff --git a/R/api_tile.R b/R/api_tile.R index 92ac29405..8730ef571 100644 --- a/R/api_tile.R +++ b/R/api_tile.R @@ -1,7 +1,7 @@ #' @title Tile API #' @noRd #' -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description #' A cube consists of multiple tiles stacked together as rows of a diff --git a/R/api_torch.R b/R/api_torch.R index b0d455437..845a347a7 100644 --- a/R/api_torch.R +++ b/R/api_torch.R @@ -57,7 +57,7 @@ } #' @title Serialize torch model #' @name .torch_serialize_model -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @description Serializes a torch model to be used in parallel processing @@ -75,7 +75,7 @@ } #' @title Unserialize torch model #' @name .torch_unserialize_model -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @description Unserializes a torch model @@ -94,7 +94,7 @@ #' #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Souza, \email{lipecaso@@gmail.com} #' @keywords internal #' @noRd @@ -140,7 +140,7 @@ #' #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Souza, \email{lipecaso@@gmail.com} #' @keywords internal #' @noRd @@ -183,7 +183,7 @@ #' #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Souza, \email{lipecaso@@gmail.com} #' @keywords internal #' @noRd @@ -226,7 +226,7 @@ #' #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Souza, \email{lipecaso@@gmail.com} #' @keywords internal #' @noRd @@ -267,7 +267,7 @@ #' #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Souza, \email{lipecaso@@gmail.com} #' @keywords internal #' @noRd @@ -311,7 +311,7 @@ #' #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Souza, \email{lipecaso@@gmail.com} #' @keywords internal #' @noRd @@ -345,7 +345,7 @@ #' #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Souza, \email{lipecaso@@gmail.com} #' @keywords internal #' @noRd @@ -383,7 +383,7 @@ #' #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Souza, \email{lipecaso@@gmail.com} #' @keywords internal #' @noRd diff --git a/R/api_torch_psetae.R b/R/api_torch_psetae.R index 845f442b2..9c5d54e19 100644 --- a/R/api_torch_psetae.R +++ b/R/api_torch_psetae.R @@ -3,7 +3,7 @@ #' #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Souza, \email{lipecaso@@gmail.com} #' @keywords internal #' @noRd @@ -101,7 +101,7 @@ #' #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Souza, \email{lipecaso@@gmail.com} #' @keywords internal #' @noRd @@ -198,7 +198,7 @@ #' #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Souza, \email{lipecaso@@gmail.com} #' @keywords internal #' @noRd @@ -384,7 +384,7 @@ #' #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Souza, \email{lipecaso@@gmail.com} #' @keywords internal #' @noRd @@ -523,7 +523,7 @@ #' #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Souza, \email{lipecaso@@gmail.com} #' @keywords internal #' @noRd @@ -595,7 +595,7 @@ #' #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Souza, \email{lipecaso@@gmail.com} #' @keywords internal #' @noRd diff --git a/R/api_ts.R b/R/api_ts.R index 1152c0674..623c613c3 100644 --- a/R/api_ts.R +++ b/R/api_ts.R @@ -3,7 +3,7 @@ .ts_cols <- c("sample_id", "label") #' @title Check if data is a time series -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @param x R object @@ -12,7 +12,7 @@ "Index" %in% names(x) && is.data.frame(x) } #' @title Check if data includes a time series -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @param x R object @@ -21,7 +21,7 @@ "time_series" %in% names(x) && .is_ts(x[["time_series"]][[1]]) } #' @title Return the time series for a SITS tibble -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @param x R object @@ -41,7 +41,7 @@ ts } #' @title Assigns a new time series for a SITS tibble -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @param x R object @@ -58,7 +58,7 @@ x } #' @title Return the index of a time series -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @param ts Time series @@ -67,7 +67,7 @@ .as_date(ts[["Index"]]) } #' @title Return the sample id of a time series -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @param ts Time series @@ -76,7 +76,7 @@ ts[["sample_id"]] } #' @title Return the bands of a time series -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @param ts Time series @@ -85,7 +85,7 @@ setdiff(colnames(ts), c(.ts_cols, "Index")) } #' @title Select the bands of a time series -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @param ts Time series @@ -101,7 +101,7 @@ ts } #' @title Start date of a time series -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @param ts Time series @@ -113,7 +113,7 @@ )))) } #' @title Minimum date of a time series -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @param ts Time series @@ -122,7 +122,7 @@ min(.ts_index(ts)) } #' @title End date of a time series -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @param ts Time series @@ -134,7 +134,7 @@ )))) } #' @title Minimum date of a time series -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @param ts Time series @@ -143,7 +143,7 @@ max(.ts_index(ts)) } #' @title Filter time series by interval -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @param ts Time series @@ -163,7 +163,7 @@ ts } #' @title Values of a time series -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @param ts Time series @@ -178,7 +178,7 @@ ts[bands] } #' @title Assigns new values to a time-series -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @keywords internal #' @noRd #' @param ts Time series diff --git a/R/api_utils.R b/R/api_utils.R index f1a0117c2..431d8f39b 100644 --- a/R/api_utils.R +++ b/R/api_utils.R @@ -1,7 +1,7 @@ #' @title Data type functions #' @noRd #' -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description #' These are a short named version of data type functions. @@ -123,7 +123,7 @@ NULL #' @title Handling error #' @noRd #' -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description #' This is a implementation of \code{tryCatch()}. It diff --git a/R/api_values.R b/R/api_values.R index 2221d46c7..648716f80 100644 --- a/R/api_values.R +++ b/R/api_values.R @@ -1,7 +1,7 @@ #' @title Return the values of a set of time series #' @name .values_ts #' @noRd -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description This function returns the values of a sits tibble #' (according a specified format). diff --git a/R/api_variance.R b/R/api_variance.R index 99e390ba3..09f3389c7 100644 --- a/R/api_variance.R +++ b/R/api_variance.R @@ -1,7 +1,7 @@ #' @title Calculate the variance of a tile #' @noRd #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description Takes a probability cube and estimate the local variance #' of the logit of the probability, @@ -107,7 +107,7 @@ #' @title Calculate the variance of a probability cube #' @noRd #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description Takes a probability cube and estimate the local variance #' of the logit of the probability, @@ -160,7 +160,7 @@ #' @title Calculate the variance smoothing function #' @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 window_size Size of the neighborhood. #' @param neigh_fraction Fraction of neighbors with highest probability diff --git a/R/api_vector_info.R b/R/api_vector_info.R index 215e57ebe..1feb5119a 100644 --- a/R/api_vector_info.R +++ b/R/api_vector_info.R @@ -1,6 +1,6 @@ #' @title Vector info API #' @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 diff --git a/R/sits_accuracy.R b/R/sits_accuracy.R index b5000b35f..30ee31ff7 100644 --- a/R/sits_accuracy.R +++ b/R/sits_accuracy.R @@ -1,6 +1,6 @@ #' @title Assess classification accuracy (area-weighted method) #' @name sits_accuracy -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Alber Sanchez, \email{alber.ipia@@inpe.br} #' @description This function calculates the accuracy of the classification #' result. For a set of time series, it creates a confusion matrix and then diff --git a/R/sits_add_base_cube.R b/R/sits_add_base_cube.R index 1c3e2ab76..e44f2ae70 100644 --- a/R/sits_add_base_cube.R +++ b/R/sits_add_base_cube.R @@ -1,5 +1,7 @@ #' @title Add base maps to a time series data cube #' @name sits_add_base_cube +#' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' #' @description This function add base maps to time series data cube. diff --git a/R/sits_apply.R b/R/sits_apply.R index 617d7e520..b76d5840a 100644 --- a/R/sits_apply.R +++ b/R/sits_apply.R @@ -2,7 +2,7 @@ #' #' @name sits_apply #' -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' diff --git a/R/sits_bands.R b/R/sits_bands.R index 86159b4a0..bd8d6a986 100644 --- a/R/sits_bands.R +++ b/R/sits_bands.R @@ -3,7 +3,7 @@ #' @name sits_bands #' #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description #' Finds the names of the bands of a set of time series or of a data cube diff --git a/R/sits_bayts.R b/R/sits_bayts.R index 32cb75270..a7d7e5b50 100644 --- a/R/sits_bayts.R +++ b/R/sits_bayts.R @@ -2,8 +2,6 @@ #' @name sits_bayts #' @author Felipe Carvalho, \email{lipecaso@@gmail.com} #' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} -#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} #' #' @description #' This function implements the algorithm described by Johanes Reiche diff --git a/R/sits_bbox.R b/R/sits_bbox.R index 8b4332bde..1b30a25cc 100644 --- a/R/sits_bbox.R +++ b/R/sits_bbox.R @@ -3,7 +3,7 @@ #' @name sits_bbox #' #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description Obtain a vector of limits (either on lat/long for time series #' or in projection coordinates in the case of cubes) diff --git a/R/sits_classify.R b/R/sits_classify.R index 96ac39f83..4d417d1cf 100644 --- a/R/sits_classify.R +++ b/R/sits_classify.R @@ -1,7 +1,9 @@ #' @title Classify time series or data cubes #' @name sits_classify -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} +#' @author Felipe Carvalho, \email{lipecaso@@gmail.com} +#' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} #' #' @description #' This function classifies a set of time series or data cube given diff --git a/R/sits_cluster.R b/R/sits_cluster.R index c0e352beb..e47b20fe2 100644 --- a/R/sits_cluster.R +++ b/R/sits_cluster.R @@ -1,6 +1,6 @@ #' @title Find clusters in time series samples #' @name sits_cluster_dendro -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description These functions support hierarchical agglomerative clustering in #' sits. They provide support from creating a dendrogram and using it for @@ -122,7 +122,7 @@ sits_cluster_dendro <- function(samples, #' #' @title Show label frequency in each cluster produced by dendrogram analysis #' @name sits_cluster_frequency -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @param samples Tibble with input set of time series with additional #' cluster information produced #' by \code{link[sits]{sits_cluster_dendro}}. @@ -152,7 +152,7 @@ sits_cluster_frequency <- function(samples) { #' @title Removes labels that are minority in each cluster. #' @name sits_cluster_clean -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @description Takes a tibble with time series #' that has an additional `cluster` produced by #' \code{link[sits]{sits_cluster_dendro()}} diff --git a/R/sits_combine_predictions.R b/R/sits_combine_predictions.R index efd17b022..2e4f03803 100644 --- a/R/sits_combine_predictions.R +++ b/R/sits_combine_predictions.R @@ -3,7 +3,7 @@ #' @name sits_combine_predictions #' #' @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 data cubes (class "probs_cube") #' @param type Method to measure uncertainty. One of "average" or diff --git a/R/sits_config.R b/R/sits_config.R index 32b6de06b..8aa480f89 100644 --- a/R/sits_config.R +++ b/R/sits_config.R @@ -1,6 +1,6 @@ #' @title Configure parameters for sits package #' @name sits_config -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description These functions load and show sits configurations. #' diff --git a/R/sits_cube.R b/R/sits_cube.R index 4a8372d90..9f775d9d2 100755 --- a/R/sits_cube.R +++ b/R/sits_cube.R @@ -1,5 +1,9 @@ #' @title Create data cubes from image collections #' @name sits_cube +#' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} +#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description Creates a data cube based on spatial and temporal restrictions #' in collections available in cloud services or local repositories. diff --git a/R/sits_cube_copy.R b/R/sits_cube_copy.R index a2b780073..f08c8bdf7 100644 --- a/R/sits_cube_copy.R +++ b/R/sits_cube_copy.R @@ -1,5 +1,7 @@ #' @title Copy the images of a cube to a local directory #' @name sits_cube_copy +#' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} #' @description #' #' This function downloads the images of a cube in parallel. diff --git a/R/sits_detect_change.R b/R/sits_detect_change.R index 45d4678e3..b401106f7 100644 --- a/R/sits_detect_change.R +++ b/R/sits_detect_change.R @@ -1,7 +1,6 @@ #' @title Detect changes in time series #' @name sits_detect_change #' -#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} #' diff --git a/R/sits_detect_change_method.R b/R/sits_detect_change_method.R index 9c29b5c84..b4a6e0d61 100644 --- a/R/sits_detect_change_method.R +++ b/R/sits_detect_change_method.R @@ -1,8 +1,8 @@ #' @title Create detect change method. #' @name sits_detect_change_method #' -#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} #' #' @description Prepare detection change method. Currently, sits supports the #' following methods: 'dtw' (see \code{\link[sits]{sits_dtw}}) diff --git a/R/sits_dtw.R b/R/sits_dtw.R index bfdb44f4c..6d3bfb722 100644 --- a/R/sits_dtw.R +++ b/R/sits_dtw.R @@ -3,8 +3,6 @@ #' #' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} -#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} #' #' @description Create a Dynamic Time Warping (DTW) method for the #' \code{\link[sits]{sits_detect_change_method}}. diff --git a/R/sits_factory.R b/R/sits_factory.R index b5bd57bc1..6d77d40c3 100644 --- a/R/sits_factory.R +++ b/R/sits_factory.R @@ -1,6 +1,6 @@ #' @title Create a closure for calling functions with and without data #' @name sits_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} #' #' @description This function implements the factory method pattern. diff --git a/R/sits_filters.R b/R/sits_filters.R index 688de6676..807ff3e84 100644 --- a/R/sits_filters.R +++ b/R/sits_filters.R @@ -30,7 +30,7 @@ sits_filter <- function(data, filter = sits_whittaker()) { #' @title Filter time series with whittaker filter #' @name sits_whittaker #' -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} #' @@ -87,7 +87,7 @@ sits_whittaker <- function(data = NULL, lambda = 0.5) { #' @title Filter time series with Savitzky-Golay filter #' @name sits_sgolay #' -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} #' diff --git a/R/sits_geo_dist.R b/R/sits_geo_dist.R index c34de37a5..7510063ea 100644 --- a/R/sits_geo_dist.R +++ b/R/sits_geo_dist.R @@ -3,7 +3,7 @@ #' @name sits_geo_dist #' #' @author Alber Sanchez, \email{alber.ipia@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' diff --git a/R/sits_get_class.R b/R/sits_get_class.R index c689222ad..1b02fda7b 100644 --- a/R/sits_get_class.R +++ b/R/sits_get_class.R @@ -1,6 +1,6 @@ #' @title Get values from classified maps #' @name sits_get_class -#' @author Gilberto Camara +#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' #' @description Given a set of lat/long locations and a classified cube, #' retrieve the class of each point. diff --git a/R/sits_get_data.R b/R/sits_get_data.R index 0c7d2b4ef..52c79cfc1 100644 --- a/R/sits_get_data.R +++ b/R/sits_get_data.R @@ -1,6 +1,10 @@ #' @title Get time series from data cubes and cloud services #' @name sits_get_data -#' @author Gilberto Camara +#' +#' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} +#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description Retrieve a set of time series from a data cube or from #' a time series service. Data cubes and puts it in a "sits tibble". diff --git a/R/sits_get_probs.R b/R/sits_get_probs.R index 34eb4b3ad..87cb14551 100644 --- a/R/sits_get_probs.R +++ b/R/sits_get_probs.R @@ -1,6 +1,7 @@ #' @title Get values from probability maps #' @name sits_get_probs -#' @author Gilberto Camara +#' +#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' #' @description Given a set of lat/long locations and a probability cube, #' retrieve the prob values of each point. diff --git a/R/sits_label_classification.R b/R/sits_label_classification.R index 0525a7f84..1ac0b0022 100644 --- a/R/sits_label_classification.R +++ b/R/sits_label_classification.R @@ -1,7 +1,7 @@ #' @title Build a labelled image from a probability cube #' #' @name sits_label_classification -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Souza, \email{felipe.souza@@inpe.br} #' #' @description Takes a set of classified raster layers with probabilities, diff --git a/R/sits_labels.R b/R/sits_labels.R index fe462159a..fda2295a4 100644 --- a/R/sits_labels.R +++ b/R/sits_labels.R @@ -1,6 +1,6 @@ #' @title Get labels associated to a data set #' @name sits_labels -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @description Finds labels in a sits tibble or data cube #' #' @param data Time series (tibble of class "sits"), @@ -93,7 +93,7 @@ sits_labels.default <- function(data) { } #' @title Change the labels of a set of time series #' @name `sits_labels<-` -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description Given a sits tibble with a set of labels, renames the labels #' to the specified in value. @@ -188,7 +188,7 @@ sits_labels.default <- function(data) { } #' @title Inform label distribution of a set of time series #' @name sits_labels_summary -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @description Describes labels in a sits tibble #' #' @param data Data.frame - Valid sits tibble diff --git a/R/sits_lighttae.R b/R/sits_lighttae.R index 20a9649b6..c94dd2dde 100644 --- a/R/sits_lighttae.R +++ b/R/sits_lighttae.R @@ -2,7 +2,7 @@ #' @name sits_lighttae #' #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' #' @description Implementation of Light Temporal Attention Encoder (L-TAE) diff --git a/R/sits_machine_learning.R b/R/sits_machine_learning.R index 5992ae653..0244004c5 100644 --- a/R/sits_machine_learning.R +++ b/R/sits_machine_learning.R @@ -2,7 +2,7 @@ #' @name sits_rfor #' #' @author Alexandre Ywata de Carvalho, \email{alexandre.ywata@@ipea.gov.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' #' @description Use Random Forest algorithm to classify samples. @@ -106,7 +106,7 @@ sits_rfor <- function(samples = NULL, num_trees = 100, mtry = NULL, ...) { #' @title Train support vector machine models #' @name sits_svm #' @author Alexandre Ywata de Carvalho, \email{alexandre.ywata@@ipea.gov.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' #' @description This function receives a tibble with a set of attributes X @@ -226,7 +226,6 @@ sits_svm <- function(samples = NULL, formula = sits_formula_linear(), } #' @title Train extreme gradient boosting models #' @name sits_xgboost -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' #' @description This function uses the extreme gradient boosting algorithm. @@ -368,7 +367,7 @@ sits_xgboost <- function(samples = NULL, learning_rate = 0.15, #' @name sits_formula_logref #' #' @author Alexandre Ywata de Carvalho, \email{alexandre.ywata@@ipea.gov.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description A function to be used as a symbolic description #' of some fitting models such as svm and random forest. @@ -436,7 +435,7 @@ sits_formula_logref <- function(predictors_index = -2:0) { #' @name sits_formula_linear #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' @author Alexandre Ywata de Carvalho, \email{alexandre.ywata@@ipea.gov.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description Provides a symbolic description of a fitting model. #' Tells the model to do a linear transformation of the input values. diff --git a/R/sits_merge.R b/R/sits_merge.R index eed286de0..9da19c024 100644 --- a/R/sits_merge.R +++ b/R/sits_merge.R @@ -1,6 +1,7 @@ #' @title Merge two data sets (time series or cubes) #' @name sits_merge -#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} +#' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} #' #' @description To merge two series, we consider that they contain different #' attributes but refer to the same data cube and spatiotemporal location. diff --git a/R/sits_mixture_model.R b/R/sits_mixture_model.R index d94475c74..5ddc63402 100644 --- a/R/sits_mixture_model.R +++ b/R/sits_mixture_model.R @@ -4,9 +4,7 @@ #' #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} #' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} -#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Alber Sanchez, \email{alber.ipia@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description Create a multiple endmember spectral mixture analyses fractions #' images. We use the non-negative least squares (NNLS) solver to calculate the diff --git a/R/sits_model_export.R b/R/sits_model_export.R index 306057c65..193a3c555 100644 --- a/R/sits_model_export.R +++ b/R/sits_model_export.R @@ -1,6 +1,6 @@ #' @title Export classification models #' @name sits_model_export -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description Given a trained machine learning or deep learning model, #' exports the model as an object for further exploration outside the diff --git a/R/sits_mosaic.R b/R/sits_mosaic.R index 46fc05269..d002e9ffe 100644 --- a/R/sits_mosaic.R +++ b/R/sits_mosaic.R @@ -2,7 +2,8 @@ #' @name sits_mosaic #' #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} +#' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} #' #' @description Creates a mosaic of all tiles of a sits cube. #' Mosaics can be created from EO cubes and derived cubes. diff --git a/R/sits_patterns.R b/R/sits_patterns.R index 191236b23..fabd4ce6f 100644 --- a/R/sits_patterns.R +++ b/R/sits_patterns.R @@ -2,7 +2,7 @@ #' @name sits_patterns #' @author Victor Maus, \email{vwmaus1@@gmail.com} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description This function takes a set of time series samples as input #' estimates a set of patterns. The patterns are calculated using a GAM model. diff --git a/R/sits_plot.R b/R/sits_plot.R index 9f5506b18..48e74c9d4 100644 --- a/R/sits_plot.R +++ b/R/sits_plot.R @@ -1976,8 +1976,8 @@ plot.xgb_model <- function(x, ..., } #' @title Plot Torch (deep learning) model #' @name plot.torch_model -#' @author Felipe Souza, \email{lipecaso@@gmail.com} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Felipe Carvalho, \email{lipecaso@@gmail.com} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Alber Sanchez, \email{alber.ipia@@inpe.br} #' #' @description Plots a deep learning model developed using torch. @@ -2065,7 +2065,7 @@ plot.torch_model <- function(x, y, ...) { #' #' @name plot.geo_distances #' @author Felipe Souza, \email{lipecaso@@gmail.com} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Alber Sanchez, \email{alber.ipia@@inpe.br} #' #' @description Make a kernel density plot of samples distances. @@ -2127,7 +2127,7 @@ plot.geo_distances <- function(x, y, ...) { #' @title Plot a dendrogram cluster #' @name plot.sits_cluster -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description Plot a dendrogram #' diff --git a/R/sits_predictors.R b/R/sits_predictors.R index 8d7d6156e..cc528692a 100644 --- a/R/sits_predictors.R +++ b/R/sits_predictors.R @@ -1,6 +1,7 @@ #' @title Obtain predictors for time series samples #' @name sits_predictors #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} +#' #' @description Predictors are X-Y values required for machine learning #' algorithms, organized as a data table where each row corresponds #' to a training sample. The first two columns of the predictors table diff --git a/R/sits_reclassify.R b/R/sits_reclassify.R index 59169dd8f..ce2b51563 100644 --- a/R/sits_reclassify.R +++ b/R/sits_reclassify.R @@ -1,7 +1,7 @@ #' @title Reclassify a classified cube #' @name sits_reclassify #' -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' #' @description diff --git a/R/sits_reduce.R b/R/sits_reduce.R index d856f1329..31e6e0a50 100644 --- a/R/sits_reduce.R +++ b/R/sits_reduce.R @@ -3,8 +3,7 @@ #' @name sits_reduce #' #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} -#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description #' Apply a temporal reduction from a named expression in cube or sits tibble. diff --git a/R/sits_regularize.R b/R/sits_regularize.R index 806ce39ca..6f4b68438 100644 --- a/R/sits_regularize.R +++ b/R/sits_regularize.R @@ -1,5 +1,6 @@ #' @title Build a regular data cube from an irregular one -#' +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @name sits_regularize #' #' @description Produces regular data cubes for analysis-ready data (ARD) diff --git a/R/sits_sample_functions.R b/R/sits_sample_functions.R index d5634361a..1ca3922ca 100644 --- a/R/sits_sample_functions.R +++ b/R/sits_sample_functions.R @@ -1,6 +1,6 @@ #' @title Sample a percentage of a time series #' @name sits_sample -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description Takes a sits tibble with different labels and #' returns a new tibble. For a given field as a group criterion, @@ -8,7 +8,7 @@ #' of the total number of samples per group. #' If frac > 1 , all sampling will be done with replacement. #' -#' @param data Sits time series tibble (class = "sits") +#' @param data Sits time series tibble #' @param frac Percentage of samples to extract #' (range: 0.0 to 2.0, default = 0.2) #' @param oversample Logical: oversample classes with small number of samples? @@ -53,7 +53,7 @@ sits_sample <- function(data, #' @name sits_uncertainty_sampling #' #' @author Alber Sanchez, \email{alber.ipia@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' @@ -215,7 +215,7 @@ sits_uncertainty_sampling <- function(uncert_cube, #' @name sits_confidence_sampling #' #' @author Alber Sanchez, \email{alber.ipia@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' diff --git a/R/sits_segmentation.R b/R/sits_segmentation.R index 925a76441..dceaeb842 100644 --- a/R/sits_segmentation.R +++ b/R/sits_segmentation.R @@ -2,8 +2,9 @@ #' @name sits_segment #' #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} +#' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} #' #' @description #' Apply a spatial-temporal segmentation on a data cube based on a user defined @@ -166,9 +167,9 @@ sits_segment <- function(cube, #' @title Segment an image using SLIC #' @name sits_slic #' -#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} +#' @author Felipe Carlos, \email{efelipecarlos@@gmail.com} #' #' @description #' Apply a segmentation on a data cube based on the \code{supercells} package. diff --git a/R/sits_select.R b/R/sits_select.R index 94ea189f3..20519120e 100644 --- a/R/sits_select.R +++ b/R/sits_select.R @@ -1,6 +1,6 @@ -#' @title Filter bands on a data set (tibble or cube) +#' @title Filter a data set (tibble or cube) for bands, tiles, and dates #' @name sits_select -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @param data Tibble with time series or data cube. #' @param bands Character vector with the names of the bands. diff --git a/R/sits_smooth.R b/R/sits_smooth.R index 81d2e8b2c..0865c03bb 100644 --- a/R/sits_smooth.R +++ b/R/sits_smooth.R @@ -3,7 +3,7 @@ #' @name sits_smooth #' #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description Takes a set of classified raster layers with probabilities, #' whose metadata is]created by \code{\link[sits]{sits_cube}}, diff --git a/R/sits_som.R b/R/sits_som.R index 6cabf0a10..d050fc07b 100644 --- a/R/sits_som.R +++ b/R/sits_som.R @@ -1,8 +1,9 @@ -#' @title Use SOM for quality analysis of time series samples -#' @name sits_som +#' @title Build a SOM for quality analysis of time series samples +#' @name sits_som_map #' #' @author Lorena Alves, \email{lorena.santos@@inpe.br} #' @author Karine Ferreira. \email{karine.ferreira@@inpe.br} +#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' #' @description These function use self-organized maps to perform #' quality analysis in satellite image time series @@ -205,6 +206,25 @@ sits_som_map <- function(data, #' @title Cleans the samples based on SOM map information #' @name sits_som_clean_samples +#' @author Lorena Alves, \email{lorena.santos@@inpe.br} +#' @author Karine Ferreira. \email{karine.ferreira@@inpe.br} +#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} +#' @description +#' \code{sits_som_clean_samples()} evaluates the quality of the samples +#' based on the results of the SOM map. The algorithm identifies noisy samples, +#' using `prior_threshold` for the prior probability +#' and `posterior_threshold` for the posterior probability. +#' Each sample receives an evaluation tag, according to the following rule: +#' (a) If the prior probability is < `prior_threshold`, the sample is tagged +#' as "remove"; +#' (b) If the prior probability is >= `prior_threshold` and the posterior +#' probability is >=`posterior_threshold`, the sample is tagged as "clean"; +#' (c) If the prior probability is >= `posterior_threshold` and +#' the posterior probability is < `posterior_threshold`, the sample is tagged as +#' "analyze" for further inspection. +#' The user can define which tagged samples will be returned using the "keep" +#' parameter, with the following options: "clean", "analyze", "remove". +#' #' @param som_map Returned by \code{\link[sits]{sits_som_map}}. #' @param prior_threshold Threshold of conditional probability #' (frequency of samples assigned to the @@ -373,6 +393,8 @@ sits_som_evaluate_cluster <- function(som_map) { } #' @title Evaluate cluster #' @name sits_som_remove_samples +#' @author Lorena Alves, \email{lorena.santos@@inpe.br} +#' @author Karine Ferreira. \email{karine.ferreira@@inpe.br} #' @description #' Remove samples from a given class inside a neuron of another class #' @param som_map A SOM map produced by the som_map() function diff --git a/R/sits_summary.R b/R/sits_summary.R index 3379ff8b4..510dd5c12 100644 --- a/R/sits_summary.R +++ b/R/sits_summary.R @@ -2,7 +2,7 @@ #' @method summary sits #' @name summary.sits #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Felipe Souza, \email{felipe.souza@@inpe.br} +#' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} #' @description This is a generic function. Parameters depend on the specific #' type of input. #' diff --git a/R/sits_tae.R b/R/sits_tae.R index 52ba7d4f8..38dffc502 100644 --- a/R/sits_tae.R +++ b/R/sits_tae.R @@ -3,7 +3,8 @@ #' #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} +#' @author Felipe Souza, \email{lipecaso@@gmail.com} #' #' @description Implementation of Temporal Attention Encoder (TAE) #' for satellite image time series classification. diff --git a/R/sits_tempcnn.R b/R/sits_tempcnn.R index 28245b1ef..a2d26907e 100644 --- a/R/sits_tempcnn.R +++ b/R/sits_tempcnn.R @@ -3,7 +3,7 @@ #' #' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Felipe Souza, \email{lipecaso@@gmail.com} #' #' @description Use a TempCNN algorithm to classify data, which has diff --git a/R/sits_train.R b/R/sits_train.R index 4aa5be786..5471240a2 100644 --- a/R/sits_train.R +++ b/R/sits_train.R @@ -1,7 +1,7 @@ #' @title Train classification models #' @name sits_train #' -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' @author Alexandre Ywata de Carvalho, \email{alexandre.ywata@@ipea.gov.br} #' diff --git a/R/sits_tuning.R b/R/sits_tuning.R index f2b47d657..53df60fc7 100644 --- a/R/sits_tuning.R +++ b/R/sits_tuning.R @@ -1,7 +1,7 @@ #' @title Tuning machine learning models hyper-parameters #' @name sits_tuning #' -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @description #' Machine learning models use stochastic gradient descent (SGD) techniques to #' find optimal solutions. To perform SGD, models use optimization diff --git a/R/sits_uncertainty.R b/R/sits_uncertainty.R index 9635b8e62..3e5650108 100644 --- a/R/sits_uncertainty.R +++ b/R/sits_uncertainty.R @@ -3,7 +3,7 @@ #' @name sits_uncertainty #' #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Alber Sanchez, \email{alber.ipia@@inpe.br} #' #' @param cube Probability data cube. diff --git a/R/sits_validate.R b/R/sits_validate.R index d1d0ac093..375d07ecd 100644 --- a/R/sits_validate.R +++ b/R/sits_validate.R @@ -1,6 +1,6 @@ #' @title Cross-validate time series samples #' @name sits_kfold_validate -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' #' @description Splits the set of time series into training and validation and @@ -133,7 +133,7 @@ sits_kfold_validate <- function(samples, } #' @title Validate time series samples #' @name sits_validate -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} #' #' @description diff --git a/R/sits_variance.R b/R/sits_variance.R index 721c04f2e..c9bd3fcfb 100644 --- a/R/sits_variance.R +++ b/R/sits_variance.R @@ -1,7 +1,7 @@ #' @title Calculate the variance of a probability cube #' #' @author Gilberto Camara, \email{gilberto.camara@@inpe.br} -#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br} +#' @author Rolf Simoes, \email{rolfsimoes@@gmail.com} #' #' @description Takes a probability cube and estimate the local variance #' of the logit of the probability, diff --git a/man/plot.geo_distances.Rd b/man/plot.geo_distances.Rd index 6450b6efe..abd90d38a 100644 --- a/man/plot.geo_distances.Rd +++ b/man/plot.geo_distances.Rd @@ -47,7 +47,7 @@ DOI: 10.1038/s41467-022-29838-9. \author{ Felipe Souza, \email{lipecaso@gmail.com} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Alber Sanchez, \email{alber.ipia@inpe.br} } diff --git a/man/plot.sits_cluster.Rd b/man/plot.sits_cluster.Rd index 4853ecdfd..d227cf797 100644 --- a/man/plot.sits_cluster.Rd +++ b/man/plot.sits_cluster.Rd @@ -32,5 +32,5 @@ if (sits_run_examples()) { } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/plot.torch_model.Rd b/man/plot.torch_model.Rd index 13402a335..753820abe 100644 --- a/man/plot.torch_model.Rd +++ b/man/plot.torch_model.Rd @@ -37,9 +37,9 @@ if (sits_run_examples()) { } } \author{ -Felipe Souza, \email{lipecaso@gmail.com} +Felipe Carvalho, \email{lipecaso@gmail.com} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Alber Sanchez, \email{alber.ipia@inpe.br} } diff --git a/man/sits-package.Rd b/man/sits-package.Rd index 3cdcd8a68..d53ac1c03 100644 --- a/man/sits-package.Rd +++ b/man/sits-package.Rd @@ -32,7 +32,7 @@ Useful links: Authors: \itemize{ - \item Rolf Simoes \email{rolf.simoes@inpe.br} + \item Rolf Simoes \email{rolfsimoes@gmail.com} \item Felipe Souza \email{felipe.carvalho@inpe.br} \item Felipe Carlos \email{efelipecarlos@gmail.com} } diff --git a/man/sits_accuracy.Rd b/man/sits_accuracy.Rd index a41d7f518..ee98d123e 100644 --- a/man/sits_accuracy.Rd +++ b/man/sits_accuracy.Rd @@ -121,7 +121,7 @@ Remote Sensing of Environment, 148, pp. 42-57. National forest monitoring assessment working paper No.46/E, 2016. } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Alber Sanchez, \email{alber.ipia@inpe.br} } diff --git a/man/sits_add_base_cube.Rd b/man/sits_add_base_cube.Rd index 1bfc9fc1c..224d062f9 100644 --- a/man/sits_add_base_cube.Rd +++ b/man/sits_add_base_cube.Rd @@ -63,5 +63,9 @@ if (sits_run_examples()) { } } \author{ +Felipe Carlos, \email{efelipecarlos@gmail.com} + +Felipe Carvalho, \email{felipe.carvalho@inpe.br} + Gilberto Camara, \email{gilberto.camara@inpe.br} } diff --git a/man/sits_apply.Rd b/man/sits_apply.Rd index 31c56df24..cd019b33f 100644 --- a/man/sits_apply.Rd +++ b/man/sits_apply.Rd @@ -134,7 +134,7 @@ if (sits_run_examples()) { } } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Felipe Carvalho, \email{felipe.carvalho@inpe.br} diff --git a/man/sits_bands.Rd b/man/sits_bands.Rd index e4c5051ba..8ab153853 100644 --- a/man/sits_bands.Rd +++ b/man/sits_bands.Rd @@ -71,5 +71,5 @@ if (sits_run_examples()) { \author{ Gilberto Camara, \email{gilberto.camara@inpe.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_bbox.Rd b/man/sits_bbox.Rd index 7b1a6b788..e64478e45 100644 --- a/man/sits_bbox.Rd +++ b/man/sits_bbox.Rd @@ -49,5 +49,5 @@ if (sits_run_examples()) { \author{ Gilberto Camara, \email{gilberto.camara@inpe.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_classify.Rd b/man/sits_classify.Rd index d9030f75a..589429147 100644 --- a/man/sits_classify.Rd +++ b/man/sits_classify.Rd @@ -268,7 +268,11 @@ if (sits_run_examples()) { } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Gilberto Camara, \email{gilberto.camara@inpe.br} + +Felipe Carvalho, \email{lipecaso@gmail.com} + +Felipe Carlos, \email{efelipecarlos@gmail.com} } diff --git a/man/sits_cluster_clean.Rd b/man/sits_cluster_clean.Rd index 6129743c8..24fd46547 100644 --- a/man/sits_cluster_clean.Rd +++ b/man/sits_cluster_clean.Rd @@ -31,5 +31,5 @@ if (sits_run_examples()) { } } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_cluster_dendro.Rd b/man/sits_cluster_dendro.Rd index 891ecee17..cc1384354 100644 --- a/man/sits_cluster_dendro.Rd +++ b/man/sits_cluster_dendro.Rd @@ -80,5 +80,5 @@ if (sits_run_examples()) { "dtwclust" package (https://CRAN.R-project.org/package=dtwclust) } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_cluster_frequency.Rd b/man/sits_cluster_frequency.Rd index a1db3c4a8..9ee348881 100644 --- a/man/sits_cluster_frequency.Rd +++ b/man/sits_cluster_frequency.Rd @@ -26,5 +26,5 @@ if (sits_run_examples()) { } } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_combine_predictions.Rd b/man/sits_combine_predictions.Rd index 37460fb34..b2a9bdd93 100644 --- a/man/sits_combine_predictions.Rd +++ b/man/sits_combine_predictions.Rd @@ -106,5 +106,5 @@ if (sits_run_examples()) { \author{ Gilberto Camara, \email{gilberto.camara@inpe.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_confidence_sampling.Rd b/man/sits_confidence_sampling.Rd index b02db19d5..18bcad54a 100644 --- a/man/sits_confidence_sampling.Rd +++ b/man/sits_confidence_sampling.Rd @@ -79,7 +79,7 @@ if (sits_run_examples()) { \author{ Alber Sanchez, \email{alber.ipia@inpe.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Felipe Carvalho, \email{felipe.carvalho@inpe.br} diff --git a/man/sits_config.Rd b/man/sits_config.Rd index f8044e6a3..5a3b0cf87 100644 --- a/man/sits_config.Rd +++ b/man/sits_config.Rd @@ -38,5 +38,5 @@ yaml_user_file <- system.file("extdata/config_user_example.yml", sits_config(config_user_file = yaml_user_file) } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_cube.Rd b/man/sits_cube.Rd index feccf13f5..38fa66a57 100644 --- a/man/sits_cube.Rd +++ b/man/sits_cube.Rd @@ -479,3 +479,12 @@ if (sits_run_examples()) { } } +\author{ +Felipe Carlos, \email{efelipecarlos@gmail.com} + +Felipe Carvalho, \email{felipe.carvalho@inpe.br} + +Gilberto Camara, \email{gilberto.camara@inpe.br} + +Rolf Simoes, \email{rolfsimoes@gmail.com} +} diff --git a/man/sits_cube_copy.Rd b/man/sits_cube_copy.Rd index a5f22d5ff..5892a2ab3 100644 --- a/man/sits_cube_copy.Rd +++ b/man/sits_cube_copy.Rd @@ -78,3 +78,8 @@ if (sits_run_examples()) { } } +\author{ +Felipe Carlos, \email{efelipecarlos@gmail.com} + +Felipe Carvalho, \email{felipe.carvalho@inpe.br} +} diff --git a/man/sits_factory_function.Rd b/man/sits_factory_function.Rd index 042067cb3..e72ea1170 100644 --- a/man/sits_factory_function.Rd +++ b/man/sits_factory_function.Rd @@ -82,7 +82,7 @@ if (sits_run_examples()) { } } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Gilberto Camara, \email{gilberto.camara@inpe.br} } diff --git a/man/sits_formula_linear.Rd b/man/sits_formula_linear.Rd index a032e53b4..37909b01e 100644 --- a/man/sits_formula_linear.Rd +++ b/man/sits_formula_linear.Rd @@ -42,5 +42,5 @@ Gilberto Camara, \email{gilberto.camara@inpe.br} Alexandre Ywata de Carvalho, \email{alexandre.ywata@ipea.gov.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_formula_logref.Rd b/man/sits_formula_logref.Rd index 134ae4ca6..f0b407f16 100644 --- a/man/sits_formula_logref.Rd +++ b/man/sits_formula_logref.Rd @@ -42,5 +42,5 @@ if (sits_run_examples()) { \author{ Alexandre Ywata de Carvalho, \email{alexandre.ywata@ipea.gov.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_geo_dist.Rd b/man/sits_geo_dist.Rd index 57f31a9dc..5a43b590d 100644 --- a/man/sits_geo_dist.Rd +++ b/man/sits_geo_dist.Rd @@ -51,7 +51,7 @@ https://doi.org/10.1038/s41467-022-29838-9 \author{ Alber Sanchez, \email{alber.ipia@inpe.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Felipe Carvalho, \email{felipe.carvalho@inpe.br} diff --git a/man/sits_get_class.Rd b/man/sits_get_class.Rd index 895b6e596..921964b58 100644 --- a/man/sits_get_class.Rd +++ b/man/sits_get_class.Rd @@ -51,5 +51,5 @@ There are four ways of specifying data to be retrieved using the (e) data.frame: A data.frame with \code{longitude} and \code{latitude}. } \author{ -Gilberto Camara +Gilberto Camara, \email{gilberto.camara@inpe.br} } diff --git a/man/sits_get_data.Rd b/man/sits_get_data.Rd index e3742b1a5..a64d58ac5 100644 --- a/man/sits_get_data.Rd +++ b/man/sits_get_data.Rd @@ -200,5 +200,11 @@ if (sits_run_examples()) { } \author{ -Gilberto Camara +Felipe Carlos, \email{efelipecarlos@gmail.com} + +Felipe Carvalho, \email{felipe.carvalho@inpe.br} + +Gilberto Camara, \email{gilberto.camara@inpe.br} + +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_get_probs.Rd b/man/sits_get_probs.Rd index dc9e132d3..6173e31ae 100644 --- a/man/sits_get_probs.Rd +++ b/man/sits_get_probs.Rd @@ -55,5 +55,5 @@ There are four ways of specifying data to be retrieved using the (e) data.frame: A data.frame with \code{longitude} and \code{latitude}. } \author{ -Gilberto Camara +Gilberto Camara, \email{gilberto.camara@inpe.br} } diff --git a/man/sits_kfold_validate.Rd b/man/sits_kfold_validate.Rd index cbf78d9f0..c1f54ccce 100644 --- a/man/sits_kfold_validate.Rd +++ b/man/sits_kfold_validate.Rd @@ -89,7 +89,7 @@ if (sits_run_examples()) { } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Gilberto Camara, \email{gilberto.camara@inpe.br} } diff --git a/man/sits_label_classification.Rd b/man/sits_label_classification.Rd index b5cc307ab..ce66d0679 100644 --- a/man/sits_label_classification.Rd +++ b/man/sits_label_classification.Rd @@ -95,7 +95,7 @@ if (sits_run_examples()) { } } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Felipe Souza, \email{felipe.souza@inpe.br} } diff --git a/man/sits_labels.Rd b/man/sits_labels.Rd index a1b2cb952..4b5d0a0dc 100644 --- a/man/sits_labels.Rd +++ b/man/sits_labels.Rd @@ -65,5 +65,5 @@ if (sits_run_examples()) { } } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_labels_summary.Rd b/man/sits_labels_summary.Rd index ed8c0d848..fb76bc67d 100644 --- a/man/sits_labels_summary.Rd +++ b/man/sits_labels_summary.Rd @@ -25,5 +25,5 @@ data(cerrado_2classes) sits_labels_summary(cerrado_2classes) } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_lighttae.Rd b/man/sits_lighttae.Rd index 8cd8e0e20..0dbe3a5a4 100644 --- a/man/sits_lighttae.Rd +++ b/man/sits_lighttae.Rd @@ -127,7 +127,7 @@ DOI: 10.5281/zenodo.4835356 \author{ Gilberto Camara, \email{gilberto.camara@inpe.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Charlotte Pelletier, \email{charlotte.pelletier@univ-ubs.fr} } diff --git a/man/sits_merge.Rd b/man/sits_merge.Rd index 82a823fa7..1e2c65365 100644 --- a/man/sits_merge.Rd +++ b/man/sits_merge.Rd @@ -70,5 +70,7 @@ if (sits_run_examples()) { } } \author{ -Gilberto Camara, \email{gilberto.camara@inpe.br} +Felipe Carvalho, \email{felipe.carvalho@inpe.br} + +Felipe Carlos, \email{efelipecarlos@gmail.com} } diff --git a/man/sits_mixture_model.Rd b/man/sits_mixture_model.Rd index 51380ba26..a37c7da92 100644 --- a/man/sits_mixture_model.Rd +++ b/man/sits_mixture_model.Rd @@ -139,9 +139,5 @@ Felipe Carvalho, \email{felipe.carvalho@inpe.br} Felipe Carlos, \email{efelipecarlos@gmail.com} -Rolf Simoes, \email{rolf.simoes@inpe.br} - -Gilberto Camara, \email{gilberto.camara@inpe.br} - -Alber Sanchez, \email{alber.ipia@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_model_export.Rd b/man/sits_model_export.Rd index 49fb428d9..0647ab560 100644 --- a/man/sits_model_export.Rd +++ b/man/sits_model_export.Rd @@ -31,5 +31,5 @@ if (sits_run_examples()) { } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_mosaic.Rd b/man/sits_mosaic.Rd index 4b39f0264..21fc6e23e 100644 --- a/man/sits_mosaic.Rd +++ b/man/sits_mosaic.Rd @@ -105,5 +105,7 @@ if (sits_run_examples()) { \author{ Felipe Carvalho, \email{felipe.carvalho@inpe.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} + +Felipe Carlos, \email{efelipecarlos@gmail.com} } diff --git a/man/sits_patterns.Rd b/man/sits_patterns.Rd index c495a978a..4278fa0e9 100644 --- a/man/sits_patterns.Rd +++ b/man/sits_patterns.Rd @@ -50,5 +50,5 @@ Victor Maus, \email{vwmaus1@gmail.com} Gilberto Camara, \email{gilberto.camara@inpe.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_reclassify.Rd b/man/sits_reclassify.Rd index 990259bd8..1d67ea2f5 100644 --- a/man/sits_reclassify.Rd +++ b/man/sits_reclassify.Rd @@ -133,7 +133,7 @@ ro_mask <- sits_reclassify( } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Gilberto Camara, \email{gilberto.camara@inpe.br} } diff --git a/man/sits_reduce.Rd b/man/sits_reduce.Rd index df0ebde1e..f440dbedd 100644 --- a/man/sits_reduce.Rd +++ b/man/sits_reduce.Rd @@ -122,7 +122,5 @@ if (sits_run_examples()) { \author{ Felipe Carvalho, \email{felipe.carvalho@inpe.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} - -Gilberto Camara, \email{gilberto.camara@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_regularize.Rd b/man/sits_regularize.Rd index 5bb9e8e83..fd7e61563 100644 --- a/man/sits_regularize.Rd +++ b/man/sits_regularize.Rd @@ -209,3 +209,8 @@ Appel, Marius; Pebesma, Edzer. On-demand processing of data cubes from satellite image collections with the gdalcubes library. Data, v. 4, n. 3, p. 92, 2019. DOI: 10.3390/data4030092. } +\author{ +Felipe Carvalho, \email{felipe.carvalho@inpe.br} + +Rolf Simoes, \email{rolfsimoes@gmail.com} +} diff --git a/man/sits_rfor.Rd b/man/sits_rfor.Rd index 4ae672af1..9a2e36012 100644 --- a/man/sits_rfor.Rd +++ b/man/sits_rfor.Rd @@ -52,7 +52,7 @@ if (sits_run_examples()) { \author{ Alexandre Ywata de Carvalho, \email{alexandre.ywata@ipea.gov.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Gilberto Camara, \email{gilberto.camara@inpe.br} } diff --git a/man/sits_sample.Rd b/man/sits_sample.Rd index 75a36106e..6fecb6f03 100644 --- a/man/sits_sample.Rd +++ b/man/sits_sample.Rd @@ -7,7 +7,7 @@ sits_sample(data, frac = 0.2, oversample = TRUE) } \arguments{ -\item{data}{Sits time series tibble (class = "sits")} +\item{data}{Sits time series tibble} \item{frac}{Percentage of samples to extract (range: 0.0 to 2.0, default = 0.2)} @@ -36,5 +36,5 @@ data_02 <- sits_sample(cerrado_2classes, frac = 0.2) summary(data_02) } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_segment.Rd b/man/sits_segment.Rd index 90ae0af4a..9c2612519 100644 --- a/man/sits_segment.Rd +++ b/man/sits_segment.Rd @@ -104,7 +104,9 @@ if (sits_run_examples()) { \author{ Gilberto Camara, \email{gilberto.camara@inpe.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Felipe Carvalho, \email{felipe.carvalho@inpe.br} + +Felipe Carlos, \email{efelipecarlos@gmail.com} } diff --git a/man/sits_select.Rd b/man/sits_select.Rd index 4ce5acc3f..96486e376 100644 --- a/man/sits_select.Rd +++ b/man/sits_select.Rd @@ -5,7 +5,7 @@ \alias{sits_select.sits} \alias{sits_select.raster_cube} \alias{sits_select.default} -\title{Filter bands on a data set (tibble or cube)} +\title{Filter a data set (tibble or cube) for bands, tiles, and dates} \usage{ sits_select(data, ...) @@ -61,5 +61,5 @@ point_2010 <- sits_select(point_mt_6bands, } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_sgolay.Rd b/man/sits_sgolay.Rd index 73728cc9a..61f0c9e82 100644 --- a/man/sits_sgolay.Rd +++ b/man/sits_sgolay.Rd @@ -44,7 +44,7 @@ of Data by Simplified Least Squares Procedures". Analytical Chemistry, 36 (8): 1627–39, 1964. } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Gilberto Camara, \email{gilberto.camara@inpe.br} diff --git a/man/sits_slic.Rd b/man/sits_slic.Rd index 8072e80ce..2268c7178 100644 --- a/man/sits_slic.Rd +++ b/man/sits_slic.Rd @@ -96,9 +96,9 @@ Achanta, Radhakrishna, Appu Shaji, Kevin Smith, Aurelien Lucchi, and Geoinformation 112 (August): 102935. } \author{ -Gilberto Camara, \email{gilberto.camara@inpe.br} - -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Felipe Carvalho, \email{felipe.carvalho@inpe.br} + +Felipe Carlos, \email{efelipecarlos@gmail.com} } diff --git a/man/sits_smooth.Rd b/man/sits_smooth.Rd index 486459dd8..1d86ab079 100644 --- a/man/sits_smooth.Rd +++ b/man/sits_smooth.Rd @@ -105,5 +105,5 @@ if (sits_run_examples()) { \author{ Gilberto Camara, \email{gilberto.camara@inpe.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_som_clean_samples.Rd b/man/sits_som_clean_samples.Rd index 6896730fb..4ab7c3245 100644 --- a/man/sits_som_clean_samples.Rd +++ b/man/sits_som_clean_samples.Rd @@ -29,7 +29,20 @@ The first indicates if each sample is clean, should be analyzed or should be removed. The second is the posterior probability of the sample. } \description{ -Cleans the samples based on SOM map information +\code{sits_som_clean_samples()} evaluates the quality of the samples +based on the results of the SOM map. The algorithm identifies noisy samples, +using `prior_threshold` for the prior probability +and `posterior_threshold` for the posterior probability. +Each sample receives an evaluation tag, according to the following rule: +(a) If the prior probability is < `prior_threshold`, the sample is tagged +as "remove"; +(b) If the prior probability is >= `prior_threshold` and the posterior +probability is >=`posterior_threshold`, the sample is tagged as "clean"; +(c) If the prior probability is >= `posterior_threshold` and +the posterior probability is < `posterior_threshold`, the sample is tagged as +"analyze" for further inspection. +The user can define which tagged samples will be returned using the "keep" +parameter, with the following options: "clean", "analyze", "remove". } \examples{ if (sits_run_examples()) { @@ -46,3 +59,10 @@ if (sits_run_examples()) { } } +\author{ +Lorena Alves, \email{lorena.santos@inpe.br} + +Karine Ferreira. \email{karine.ferreira@inpe.br} + +Gilberto Camara, \email{gilberto.camara@inpe.br} +} diff --git a/man/sits_som.Rd b/man/sits_som_map.Rd similarity index 96% rename from man/sits_som.Rd rename to man/sits_som_map.Rd index e2d732157..83ff828c8 100644 --- a/man/sits_som.Rd +++ b/man/sits_som_map.Rd @@ -1,9 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/sits_som.R -\name{sits_som} -\alias{sits_som} +\name{sits_som_map} \alias{sits_som_map} -\title{Use SOM for quality analysis of time series samples} +\title{Build a SOM for quality analysis of time series samples} \usage{ sits_som_map( data, @@ -116,4 +115,6 @@ vol. 177, pp 75-88, 2021. https://doi.org/10.1016/j.isprsjprs.2021.04.014. Lorena Alves, \email{lorena.santos@inpe.br} Karine Ferreira. \email{karine.ferreira@inpe.br} + +Gilberto Camara, \email{gilberto.camara@inpe.br} } diff --git a/man/sits_som_remove_samples.Rd b/man/sits_som_remove_samples.Rd index b0cfc65c6..6f7cfd152 100644 --- a/man/sits_som_remove_samples.Rd +++ b/man/sits_som_remove_samples.Rd @@ -31,3 +31,8 @@ if (sits_run_examples()) { new_samples <- sits_som_remove_samples(som_map, som_eval, "Pasture", "Cerrado") } } +\author{ +Lorena Alves, \email{lorena.santos@inpe.br} + +Karine Ferreira. \email{karine.ferreira@inpe.br} +} diff --git a/man/sits_svm.Rd b/man/sits_svm.Rd index 0627e7810..84864eb16 100644 --- a/man/sits_svm.Rd +++ b/man/sits_svm.Rd @@ -87,7 +87,7 @@ if (sits_run_examples()) { \author{ Alexandre Ywata de Carvalho, \email{alexandre.ywata@ipea.gov.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Gilberto Camara, \email{gilberto.camara@inpe.br} } diff --git a/man/sits_tae.Rd b/man/sits_tae.Rd index 7bb63cf29..0580a5d77 100644 --- a/man/sits_tae.Rd +++ b/man/sits_tae.Rd @@ -120,5 +120,7 @@ Charlotte Pelletier, \email{charlotte.pelletier@univ-ubs.fr} Gilberto Camara, \email{gilberto.camara@inpe.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} + +Felipe Souza, \email{lipecaso@gmail.com} } diff --git a/man/sits_tempcnn.Rd b/man/sits_tempcnn.Rd index 5fde7b0c7..b77aff574 100644 --- a/man/sits_tempcnn.Rd +++ b/man/sits_tempcnn.Rd @@ -133,7 +133,7 @@ Charlotte Pelletier, \email{charlotte.pelletier@univ-ubs.fr} Gilberto Camara, \email{gilberto.camara@inpe.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Felipe Souza, \email{lipecaso@gmail.com} } diff --git a/man/sits_train.Rd b/man/sits_train.Rd index f6d71bda3..61940f7bb 100644 --- a/man/sits_train.Rd +++ b/man/sits_train.Rd @@ -39,7 +39,7 @@ if (sits_run_examples()) { } } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Gilberto Camara, \email{gilberto.camara@inpe.br} diff --git a/man/sits_tuning.Rd b/man/sits_tuning.Rd index f6ca72eda..5b26fb894 100644 --- a/man/sits_tuning.Rd +++ b/man/sits_tuning.Rd @@ -113,5 +113,5 @@ James Bergstra, Yoshua Bengio, Journal of Machine Learning Research. 13: 281–305, 2012. } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_uncertainty.Rd b/man/sits_uncertainty.Rd index 3c3bf5f1c..c64563323 100644 --- a/man/sits_uncertainty.Rd +++ b/man/sits_uncertainty.Rd @@ -91,7 +91,7 @@ Active learning and annotation for human-centered AI. Simon and Schuster, \author{ Gilberto Camara, \email{gilberto.camara@inpe.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Alber Sanchez, \email{alber.ipia@inpe.br} } diff --git a/man/sits_uncertainty_sampling.Rd b/man/sits_uncertainty_sampling.Rd index 2fae2be17..d20a5500e 100644 --- a/man/sits_uncertainty_sampling.Rd +++ b/man/sits_uncertainty_sampling.Rd @@ -89,7 +89,7 @@ and annotation for human-centered AI". Manning Publications, 2021. \author{ Alber Sanchez, \email{alber.ipia@inpe.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Felipe Carvalho, \email{felipe.carvalho@inpe.br} diff --git a/man/sits_validate.Rd b/man/sits_validate.Rd index b7c2a1471..6c8751d53 100644 --- a/man/sits_validate.Rd +++ b/man/sits_validate.Rd @@ -87,7 +87,7 @@ if (sits_run_examples()) { } } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Gilberto Camara, \email{gilberto.camara@inpe.br} } diff --git a/man/sits_variance.Rd b/man/sits_variance.Rd index 52ee44e9d..66f878cad 100644 --- a/man/sits_variance.Rd +++ b/man/sits_variance.Rd @@ -116,5 +116,5 @@ if (sits_run_examples()) { \author{ Gilberto Camara, \email{gilberto.camara@inpe.br} -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} } diff --git a/man/sits_whittaker.Rd b/man/sits_whittaker.Rd index 3f6fe8d7b..791d98efd 100644 --- a/man/sits_whittaker.Rd +++ b/man/sits_whittaker.Rd @@ -44,7 +44,7 @@ vol. 57, pg. 202-213, 2107. \link[sits]{sits_apply} } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} Gilberto Camara, \email{gilberto.camara@inpe.br} diff --git a/man/sits_xgboost.Rd b/man/sits_xgboost.Rd index 78a00dacc..1de9ee00c 100644 --- a/man/sits_xgboost.Rd +++ b/man/sits_xgboost.Rd @@ -95,7 +95,5 @@ Tianqi Chen, Carlos Guestrin, SIG KDD 2016. } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} - Gilberto Camara, \email{gilberto.camara@inpe.br} } diff --git a/man/summary.sits.Rd b/man/summary.sits.Rd index 5f8f4acbf..302bc8db8 100644 --- a/man/summary.sits.Rd +++ b/man/summary.sits.Rd @@ -27,5 +27,5 @@ if (sits_run_examples()) { \author{ Gilberto Camara, \email{gilberto.camara@inpe.br} -Felipe Souza, \email{felipe.souza@inpe.br} +Felipe Carvalho, \email{felipe.carvalho@inpe.br} } diff --git a/man/tick-sits_labels-set-tick.Rd b/man/tick-sits_labels-set-tick.Rd index dae04b844..c3448da15 100644 --- a/man/tick-sits_labels-set-tick.Rd +++ b/man/tick-sits_labels-set-tick.Rd @@ -44,5 +44,5 @@ sits_labels(cerrado_2classes) <- c("Savanna", "Grasslands") sits_labels(cerrado_2classes) } \author{ -Rolf Simoes, \email{rolf.simoes@inpe.br} +Rolf Simoes, \email{rolfsimoes@gmail.com} }