R/lucC_allen_relations_extra.r
In e-sensing/lucCalculus: Land Use Change Calculus
#################################################################
## ##
## (c) Adeline Marinho <adelsud6@gmail.com> ##
## ##
## Image Processing Division ##
## National Institute for Space Research (INPE), Brazil ##
## ##
## ##
## R script with extra Allen's relationships ##
## ##
## 2018-08-28 ##
## ##
## J. F. Allen. Towards a general theory of action and ##
## time. Artificial Intelligence, 23(2): 123--154, 1984. ##
## ##
#################################################################
# ALLEN'S INTERVAL ALGEBRA
# Thirteen basic relation
#
# before (end_I < start_J) -> precedes
# after (start_I > end_J) -> preceded by
# meets (end_I == start_J)
# met by (end_J == start_I)
# overlaps (start_I < start_J) & (end_I > start_J) & (end_I < end_J)
# overlapped by (end_I > start_J) & (start_I < end_J) & (end_I > end_J)
# starts (start_I == start_J) & (end_I < end_J)
# started by (start_I == start_J) & (end_I > end_J)
# during (start_I > start_J) & (end_I < end_J))
# contains (start_I < start_J) & (end_I > end_J)
# finishes (start_I > start_J) & (end_I == end_J)
# finished by (start_I < start_J) & (end_I == end_J)
# equals (start_I == start_J) & (end_I == end_J)
# Derivates relations
# in (during(first_interval, second_interval) | starts(first_interval, second_interval)
# | finishes(first_interval, second_interval))
# follows (meets(first_interval, second_interval) | before(first_interval, second_interval))
# precedes (met_by(first_interval, second_interval) | after(first_interval, second_interval))
#' @title Allen Relation In
#' @name lucC_relation_in
#' @aliases lucC_relation_in
#' @author Adeline M. Maciel
#' @docType data
#'
#' @description Provide an Allen's interval relation IN which aggregates the relations DURING,
#' STARTS and FINISHES. See more at (ALLEN, J. F. "Maintaining knowledge about temporal
#' intervals". Communications of the ACM, v(26), 11, 1983, 832-843.
#' DOI: \url{http://dx.doi.org/10.1145/182.358434})
#'
#' @usage lucC_relation_in(first_raster = NULL, second_raster = NULL)
#'
#' @param first_raster Matrix. An interval between two dates.
#' @param second_raster Matrix. An interval between two dates.
#'
#' @keywords datasets
#' @return Data set with merge of two data sets
#' @importFrom dplyr bind_rows
#' @export
#'
#' @examples \dontrun{
#' library(lucCalculus)
#'
#' file <- c(system.file("extdata/raster/rasterSample.tif", package = "lucCalculus"))
#' rb_class <- raster::brick(file)
#' my_label <- c("Degradation", "Fallow_Cotton", "Forest", "Pasture", "Soy_Corn", "Soy_Cotton",
#' "Soy_Fallow", "Soy_Millet", "Soy_Sunflower", "Sugarcane", "Urban_Area", "Water")
#' my_timeline <- c("2001-09-01", "2002-09-01", "2003-09-01", "2004-09-01", "2005-09-01",
#' "2006-09-01", "2007-09-01", "2008-09-01", "2009-09-01", "2010-09-01",
#' "2011-09-01", "2012-09-01", "2013-09-01", "2014-09-01", "2015-09-01",
#' "2016-09-01")
#'
#' lucC_plot_raster(raster_obj = rb_class, timeline = my_timeline, label = my_label,
#' custom_palette = FALSE, plot_ncol = 4)
#'
#' a <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Pasture",
#' time_interval = c("2005-09-01","2009-09-01"),
#' relation_interval = "equals", label = my_label,
#' timeline = my_timeline)
#'
#' b <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Degradation",
#' time_interval = c("2005-09-01","2011-09-01"),
#' relation_interval = "equals", label = my_label,
#' timeline = my_timeline)
#'
#' # in
#' c <- lucC_relation_in(first_raster = a, second_raster = b)
#'
#' lucC_plot_raster_result(raster_obj = rb_class, data_mtx = c, timeline = my_timeline,
#' label = my_label, custom_palette = FALSE, plot_ncol = 4)
#'
#'}
#'
# 14. The 'lucC_relation_in' relation = lucC_relation_during | lucC_relation_starts | lucC_relation_finishes
lucC_relation_in <- function (first_raster = NULL, second_raster = NULL) {
# check is data set are empty
# remove rows with last and first column NA because MEETS
if (!is.null(first_raster) & !is.null(second_raster)) {
first_raster <- first_raster
second_raster <- second_raster
} else {
message("\nData with raster cannot be empty!\n")
return(result <- NULL)
}
# build intervals for each raster data set
rasters_intervals <- .lucC_build_intervals(first_ras = first_raster, second_ras = second_raster)
out1 <- lucC_relation_during(first_raster, second_raster)
out2 <- lucC_relation_starts(first_raster, second_raster)
out3 <- lucC_relation_finishes(first_raster, second_raster)
# interval = rasters_intervals[[1]] (first interval), rasters_intervals[[2]] (second_interval)
if( isTRUE(nrow(out1) > 0) & isTRUE(nrow(out2) > 0) & isTRUE(nrow(out3) > 0)) {
result <- dplyr::bind_rows(out1, out2, out3) # merge(out1, out2, out3, by = c("x","y"), all = TRUE)
if (nrow(result) > 0)
return(result)
else
return(result <- NULL)
} else if( isTRUE(nrow(out1) > 0) | isTRUE(nrow(out2) > 0) | isTRUE(nrow(out3) > 0)) {
result <- dplyr::bind_rows(out1, out2, out3)
if (nrow(result) > 0)
return(result)
else
return(result <- NULL)
} else {
message("\nRelation IN cannot be applied!\n")
return(result <- NULL)
}
}
#' @title Allen Relation Follows
#' @name lucC_relation_follows
#' @aliases lucC_relation_follows
#' @author Adeline M. Maciel
#' @docType data
#'
#' @description Provide an Allen's interval relation FOLLOWS which aggregates the relations
#' MEETS and BEFORE. See more at (ALLEN, J. F. "Maintaining knowledge about temporal
#' intervals". Communications of the ACM, v(26), 11, 1983, 832-843.
#' DOI: \url{http://dx.doi.org/10.1145/182.358434})
#'
#' @usage lucC_relation_follows(first_raster = NULL, second_raster = NULL)
#'
#' @param first_raster Matrix. An interval between two dates.
#' @param second_raster Matrix. An interval between two dates.
#'
#' @keywords datasets
#' @return Data set with merge of two data sets
#' @importFrom dplyr bind_rows
#' @export
#'
#' @examples \dontrun{
#' library(lucCalculus)
#'
#' file <- c(system.file("extdata/raster/rasterSample.tif", package = "lucCalculus"))
#' rb_class <- raster::brick(file)
#' my_label <- c("Degradation", "Fallow_Cotton", "Forest", "Pasture", "Soy_Corn", "Soy_Cotton",
#' "Soy_Fallow", "Soy_Millet", "Soy_Sunflower", "Sugarcane", "Urban_Area", "Water")
#' my_timeline <- c("2001-09-01", "2002-09-01", "2003-09-01", "2004-09-01", "2005-09-01",
#' "2006-09-01", "2007-09-01", "2008-09-01", "2009-09-01", "2010-09-01",
#' "2011-09-01", "2012-09-01", "2013-09-01", "2014-09-01", "2015-09-01",
#' "2016-09-01")
#'
#' lucC_plot_raster(raster_obj = rb_class, timeline = my_timeline, label = my_label,
#' custom_palette = FALSE, plot_ncol = 4)
#'
#' a <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Forest",
#' time_interval = c("2001-09-01","2004-09-01"),
#' relation_interval = "equals", label = my_label,
#' timeline = my_timeline)
#'
#' b <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Degradation",
#' time_interval = c("2005-09-01","2009-09-01"),
#' relation_interval = "contains", label = my_label,
#' timeline = my_timeline)
#'
#' # follows
#' c <- lucC_relation_follows(first_raster = a, second_raster = b)
#'
#' lucC_plot_raster_result(raster_obj = rb_class, data_mtx = c, timeline = my_timeline,
#' label = my_label, custom_palette = FALSE, plot_ncol = 4)
#'
#'}
#'
# 15. The 'lucC_relation_follows' relation = lucC_relation_meets v lucC_relation_before
lucC_relation_follows <- function (first_raster = NULL, second_raster = NULL) {
# check is data set are empty
# remove rows with last and first column NA because MEETS
if (!is.null(first_raster) & !is.null(second_raster)) {
first_raster <- first_raster
second_raster <- second_raster
} else {
message("\nData with raster cannot be empty!\n")
return(result <- NULL)
}
# build intervals for each raster data set
rasters_intervals <- .lucC_build_intervals(first_ras = first_raster, second_ras = second_raster)
out1 <- lucC_relation_before(first_raster, second_raster)
out2 <- lucC_relation_meets(first_raster, second_raster)
# interval = rasters_intervals[[1]] (first interval), rasters_intervals[[2]] (second_interval)
if( isTRUE(nrow(out1) > 0) & isTRUE(nrow(out2) > 0)) {
result <- lucC_merge(out1, out2) # merge(out1, out2, by = c("x","y"), all = TRUE)
if (nrow(result) > 0)
return(result)
else
return(result <- NULL)
} else if( isTRUE(nrow(out1) > 0) | isTRUE(nrow(out2) > 0)) {
result <- dplyr::bind_rows(out1, out2)
return(result)
} else {
message("\nRelation FOLLOWS cannot be applied!\n")
return(result <- NULL)
}
}
#' @title Allen Relation Precedes
#' @name lucC_relation_precedes
#' @aliases lucC_relation_precedes
#' @author Adeline M. Maciel
#' @docType data
#'
#' @description Provide an Allen's interval relation PRECEDES which aggregates the relations
#' MET_BY and AFTER. See more at (ALLEN, J. F. "Maintaining knowledge about temporal
#' intervals". Communications of the ACM, v(26), 11, 1983, 832-843.
#' DOI: \url{http://dx.doi.org/10.1145/182.358434})
#'
#' @usage lucC_relation_precedes(first_raster = NULL, second_raster = NULL)
#'
#' @param first_raster Matrix. An interval between two dates.
#' @param second_raster Matrix. An interval between two dates.
#'
#' @keywords datasets
#' @return Data set with merge of two data sets
#' @importFrom dplyr bind_rows
#' @export
#'
#' @examples \dontrun{
#' library(lucCalculus)
#'
#' file <- c(system.file("extdata/raster/rasterSample.tif", package = "lucCalculus"))
#' rb_class <- raster::brick(file)
#' my_label <- c("Degradation", "Fallow_Cotton", "Forest", "Pasture", "Soy_Corn", "Soy_Cotton",
#' "Soy_Fallow", "Soy_Millet", "Soy_Sunflower", "Sugarcane", "Urban_Area", "Water")
#' my_timeline <- c("2001-09-01", "2002-09-01", "2003-09-01", "2004-09-01", "2005-09-01",
#' "2006-09-01", "2007-09-01", "2008-09-01", "2009-09-01", "2010-09-01",
#' "2011-09-01", "2012-09-01", "2013-09-01", "2014-09-01", "2015-09-01",
#' "2016-09-01")
#'
#' lucC_plot_raster(raster_obj = rb_class, timeline = my_timeline, label = my_label,
#' custom_palette = FALSE, plot_ncol = 4)
#'
#' a <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Degradation",
#' time_interval = c("2005-09-01","2007-09-01"),
#' relation_interval = "equals", label = my_label,
#' timeline = my_timeline)
#'
#' b <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Forest",
#' time_interval = c("2001-09-01","2004-09-01"),
#' relation_interval = "contains", label = my_label,
#' timeline = my_timeline)
#'
#' # precedes
#' c <- lucC_relation_precedes(first_raster = a, second_raster = b)
#'
#' lucC_plot_raster_result(raster_obj = rb_class, data_mtx = c, timeline = my_timeline,
#' label = my_label, custom_palette = FALSE, plot_ncol = 4)
#'
#'}
#'
# Antonyms of follows
# 16. The 'lucC_relation_precedes' relation = lucC_relation_met_by || lucC_relation_after
lucC_relation_precedes <- function (first_raster = NULL, second_raster = NULL) {
# check is data set are empty
# remove rows with last and first column NA because MEETS
if (!is.null(first_raster) & !is.null(second_raster)) {
first_raster <- first_raster
second_raster <- second_raster
} else {
message("\nData with raster cannot be empty!\n")
return(result <- NULL)
}
# build intervals for each raster data set
rasters_intervals <- .lucC_build_intervals(first_ras = first_raster, second_ras = second_raster)
out1 <- lucC_relation_after(first_raster, second_raster)
out2 <- lucC_relation_met_by(first_raster, second_raster)
# interval = rasters_intervals[[1]] (first interval), rasters_intervals[[2]] (second_interval)
if( isTRUE(nrow(out1) > 0) & isTRUE(nrow(out2) > 0)) {
result <- lucC_merge(out1, out2) # merge(out1, out2, by = c("x","y"), all = TRUE)
if (nrow(result) > 0)
return(result)
else
return(result <- NULL)
} else if( isTRUE(nrow(out1) > 0) | isTRUE(nrow(out2) > 0)) {
result <- dplyr::bind_rows(out1, out2)
return(result)
} else {
message("\nRelation PRECEDES cannot be applied!\n")
return(result <- NULL)
}
}
#' @title Allen Occurs
#' @name lucC_occurs
#' @aliases lucC_occurs
#' @author Adeline M. Maciel
#' @docType data
#'
#' @description Provide an interval relation OCCURS which asserts that classes
#' of two distinct data set occurs in the same interval, is an intersection
#'
#' @usage lucC_occurs(first_raster = NULL, second_raster = NULL)
#'
#' @param first_raster Matrix. An interval between two dates.
#' @param second_raster Matrix. An interval between two dates.
#'
#' @keywords datasets
#' @return Data set with merge of two data sets that values are in the same interval
#' @importFrom tidyr gather spread
#' @importFrom stats na.omit
#' @export
#'
#' @examples \dontrun{
#' library(lucCalculus)
#'
#' file <- c(system.file("extdata/raster/rasterSample.tif", package = "lucCalculus"))
#' rb_class <- raster::brick(file)
#' my_label <- c("Degradation", "Fallow_Cotton", "Forest", "Pasture", "Soy_Corn", "Soy_Cotton",
#' "Soy_Fallow", "Soy_Millet", "Soy_Sunflower", "Sugarcane", "Urban_Area", "Water")
#' my_timeline <- c("2001-09-01", "2002-09-01", "2003-09-01", "2004-09-01", "2005-09-01",
#' "2006-09-01", "2007-09-01", "2008-09-01", "2009-09-01", "2010-09-01",
#' "2011-09-01", "2012-09-01", "2013-09-01", "2014-09-01", "2015-09-01",
#' "2016-09-01")
#'
#' lucC_plot_raster(raster_obj = rb_class, timeline = my_timeline, label = my_label,
#' custom_palette = FALSE, plot_ncol = 4)
#'
#' a <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Degradation",
#' time_interval = c("2001-09-01","2007-09-01"),
#' relation_interval = "contains", label = my_label,
#' timeline = my_timeline)
#'
#' b <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Forest",
#' time_interval = c("2001-09-01","2007-09-01"),
#' relation_interval = "contains", label = my_label,
#' timeline = my_timeline)
#'
#' # occurs
#' c <- lucC_occurs(first_raster = a, second_raster = b)
#'
#' lucC_plot_raster_result(raster_obj = rb_class, data_mtx = c, timeline = my_timeline,
#' label = my_label, custom_palette = FALSE, plot_ncol = 4)
#'
#'}
#'
#
# The 'lucC_occurs'
lucC_occurs <- function (first_raster = NULL, second_raster = NULL) {
# check is data set are empty
# remove rows with last and first column NA because MEETS
if (!is.null(first_raster) & !is.null(second_raster)) {
first_raster <- as.data.frame(first_raster)
second_raster <- as.data.frame(second_raster)
} else {
message("\nData with raster cannot be empty!\n")
return(result <- NULL)
}
# interval = rasters_intervals[[1]] (first interval), rasters_intervals[[2]] (second_interval)
if( isTRUE(nrow(first_raster) > 0) & isTRUE(nrow(second_raster) > 0)) {
## preserve only the last column
# result <- first_raster %>%
# dplyr::mutate(check = ifelse(is.na(match(paste0(.$x, .$y),
# paste0(second_raster$x, second_raster$y))),"No", "Yes")) %>%
# base::subset(check == 'Yes') %>%
# dplyr::select(-check) %>%
# as.matrix()
# result <- first_raster %>%
# dplyr::left_join(second_raster %>% dplyr::transmute(x, y, check = 'yes')) %>%
# tidyr::replace_na(list(check = 'no')) %>%
# subset(check == 'yes') %>%
# dplyr::select(-check)
# # other solution
points_same_coord <- merge(first_raster, second_raster, by = c("x","y"))
if (isTRUE(nrow(points_same_coord) > 0)){
#point_df <- reshape2::melt(as.data.frame(points_same_coord), id.vars = c("x","y")) %>%
# stats::na.omit()
point_df <- as.data.frame(points_same_coord) %>%
tidyr::gather(variable, value, -x, -y) %>%
stats::na.omit()
# remove .x and .y
point_df$variable <- gsub("[$.xy\\.,]", "", point_df$variable)
# remove duplicated lines
point_df <- point_df[!duplicated(point_df), ]
# return matrix format
#result <- reshape2::dcast(point_df, x+y ~ variable, value.var= "value")
result <- point_df %>%
tidyr::spread(variable, value)
return(result)
} else {
message("\nRelation OCCURS cannot be applied!\n
raster 1 and raster 2 has no relation!")
return(result <- NULL)
}
} else {
message("\nRelation OCCURS cannot be applied!\n")
return(result <- NULL)
}
}
#' @title LucC Merge
#' @name lucC_merge
#' @aliases lucC_merge
#' @author Adeline M. Maciel
#' @docType data
#'
#' @description Merge two data sets by different columns and rows. Because base::merge replace values in initial years
#'
#' @usage lucC_merge(first_raster = NULL, second_raster = NULL)
#'
#' @param first_raster Matrix. An interval between two dates.
#' @param second_raster Matrix. An interval between two dates.
#'
#' @keywords datasets
#' @return Data set merged with two data sets that values are in the same interval
#' @importFrom tidyr gather spread
#' @importFrom dplyr bind_rows anti_join
#' @importFrom stats na.omit
#' @importFrom plyr rbind.fill.matrix
#' @export
#'
#' @examples \dontrun{
#' library(lucCalculus)
#
# file <- c(system.file("extdata/raster/rasterSample.tif", package = "lucCalculus"))
# rb_class <- raster::brick(file)
# my_label <- c("Degradation", "Fallow_Cotton", "Forest", "Pasture", "Soy_Corn", "Soy_Cotton",
# "Soy_Fallow", "Soy_Millet", "Soy_Sunflower", "Sugarcane", "Urban_Area", "Water")
# my_timeline <- c("2001-09-01", "2002-09-01", "2003-09-01", "2004-09-01", "2005-09-01",
# "2006-09-01", "2007-09-01", "2008-09-01", "2009-09-01", "2010-09-01",
# "2011-09-01", "2012-09-01", "2013-09-01", "2014-09-01", "2015-09-01",
# "2016-09-01")
#
# lucC_plot_raster(raster_obj = rb_class, timeline = my_timeline, label = my_label,
# custom_palette = FALSE, plot_ncol = 4)
#
# a <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Degradation",
# time_interval = c("2001-09-01","2007-09-01"),
# relation_interval = "contains", label = my_label,
# timeline = my_timeline)
#
# b <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Pasture",
# time_interval = c("2001-09-01","2007-09-01"),
# relation_interval = "contains", label = my_label,
# timeline = my_timeline)
#
# # merge
# c <- lucC_merge(first_raster = a, second_raster = b)
#
# lucC_plot_raster_result(raster_obj = rb_class, data_mtx = c, timeline = my_timeline,
# label = my_label, custom_palette = FALSE, plot_ncol = 4)
#'
#'}
#'
# The 'lucC_merge'
lucC_merge <- function (first_raster = NULL, second_raster = NULL) {
# check is data set are empty
# first_raster <- data.table::as.data.table(first_raster)
# second_raster <- data.table::as.data.table(second_raster)
first_raster <- as.data.frame(first_raster)
second_raster <- as.data.frame(second_raster)
if( isTRUE(nrow(first_raster) > 0) & isTRUE(nrow(second_raster) > 0)) {
# first raster
# first_raster <- reshape2::melt(as.data.frame(first_raster), id.vars = c("x","y"), na.rm = TRUE)
# remove factors
first_raster[,] <- lapply(first_raster, function(x) {as.character(x)})
first_raster$x = as.numeric(as.character(first_raster$x))
first_raster$y = as.numeric(as.character(first_raster$y))
# remove factors
second_raster[,] <- lapply(second_raster, function(x) {as.character(x)})
second_raster$x = as.numeric(as.character(second_raster$x))
second_raster$y = as.numeric(as.character(second_raster$y))
# separate only row in both data sets
row_both <- base::merge(first_raster, second_raster, by = c("x", "y"))
# if exists location equals, serpate them of the other data set and after merge then
if (isTRUE(nrow(row_both) > 0)){
# long format
temp <- tidyr::gather(row_both, variable, value, -x, -y, na.rm = TRUE)
# remove .x and .y
temp$variable <- gsub("[$.xy\\.,]", "", temp$variable)
#remove duplicates
temp <- temp[!duplicated(temp), ]
# result
new_row_both <- tidyr::spread(temp, variable, value)
# remove them of the original data set
first_raster <- first_raster %>% dplyr::anti_join(new_row_both, by = c("x", "y")) # keep rows without matching ID
second_raster <- second_raster %>% dplyr::anti_join(new_row_both, by = c("x", "y")) # keep rows without matching ID
# all to matrix format
first_raster <- as.matrix(first_raster)
second_raster <- as.matrix(second_raster)
new_row_both <- as.matrix(new_row_both)
# merge all data set
result <- plyr::rbind.fill.matrix(first_raster, second_raster) %>%
plyr::rbind.fill.matrix(., new_row_both) %>%
as.data.frame()
if (nrow(result) > 0){
return(result)
} else {
message("\nRelation MERGE cannot be applied!\n
raster 1 and raster 2 has no relation!")
return(result <- NULL)
}
# if no exists locations in both data sets, merge only two data sets
} else {
# all to matrix format
first_raster <- as.matrix(first_raster)
second_raster <- as.matrix(second_raster)
result <- plyr::rbind.fill.matrix(first_raster, second_raster) %>%
as.data.frame()
if (nrow(result) > 0){
return(result)
} else {
message("\nRelation MERGE cannot be applied!\n
raster 1 and raster 2 has no relation!")
return(result <- NULL)
}
}
} else if ( isTRUE(nrow(first_raster) > 0) | isTRUE(nrow(second_raster) > 0)) {
result <- dplyr::bind_rows(first_raster, second_raster)
return(result)
} else {
return(result <- NULL)
}
}
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#################################################################
## ##
## (c) Adeline Marinho <adelsud6@gmail.com> ##
## ##
## Image Processing Division ##
## National Institute for Space Research (INPE), Brazil ##
## ##
## ##
## R script with extra Allen's relationships ##
## ##
## 2018-08-28 ##
## ##
## J. F. Allen. Towards a general theory of action and ##
## time. Artificial Intelligence, 23(2): 123--154, 1984. ##
## ##
#################################################################
# ALLEN'S INTERVAL ALGEBRA
# Thirteen basic relation
#
# before (end_I < start_J) -> precedes
# after (start_I > end_J) -> preceded by
# meets (end_I == start_J)
# met by (end_J == start_I)
# overlaps (start_I < start_J) & (end_I > start_J) & (end_I < end_J)
# overlapped by (end_I > start_J) & (start_I < end_J) & (end_I > end_J)
# starts (start_I == start_J) & (end_I < end_J)
# started by (start_I == start_J) & (end_I > end_J)
# during (start_I > start_J) & (end_I < end_J))
# contains (start_I < start_J) & (end_I > end_J)
# finishes (start_I > start_J) & (end_I == end_J)
# finished by (start_I < start_J) & (end_I == end_J)
# equals (start_I == start_J) & (end_I == end_J)
# Derivates relations
# in (during(first_interval, second_interval) | starts(first_interval, second_interval)
# | finishes(first_interval, second_interval))
# follows (meets(first_interval, second_interval) | before(first_interval, second_interval))
# precedes (met_by(first_interval, second_interval) | after(first_interval, second_interval))
#' @title Allen Relation In
#' @name lucC_relation_in
#' @aliases lucC_relation_in
#' @author Adeline M. Maciel
#' @docType data
#'
#' @description Provide an Allen's interval relation IN which aggregates the relations DURING,
#' STARTS and FINISHES. See more at (ALLEN, J. F. "Maintaining knowledge about temporal
#' intervals". Communications of the ACM, v(26), 11, 1983, 832-843.
#' DOI: \url{http://dx.doi.org/10.1145/182.358434})
#'
#' @usage lucC_relation_in(first_raster = NULL, second_raster = NULL)
#'
#' @param first_raster Matrix. An interval between two dates.
#' @param second_raster Matrix. An interval between two dates.
#'
#' @keywords datasets
#' @return Data set with merge of two data sets
#' @importFrom dplyr bind_rows
#' @export
#'
#' @examples \dontrun{
#' library(lucCalculus)
#'
#' file <- c(system.file("extdata/raster/rasterSample.tif", package = "lucCalculus"))
#' rb_class <- raster::brick(file)
#' my_label <- c("Degradation", "Fallow_Cotton", "Forest", "Pasture", "Soy_Corn", "Soy_Cotton",
#' "Soy_Fallow", "Soy_Millet", "Soy_Sunflower", "Sugarcane", "Urban_Area", "Water")
#' my_timeline <- c("2001-09-01", "2002-09-01", "2003-09-01", "2004-09-01", "2005-09-01",
#' "2006-09-01", "2007-09-01", "2008-09-01", "2009-09-01", "2010-09-01",
#' "2011-09-01", "2012-09-01", "2013-09-01", "2014-09-01", "2015-09-01",
#' "2016-09-01")
#'
#' lucC_plot_raster(raster_obj = rb_class, timeline = my_timeline, label = my_label,
#' custom_palette = FALSE, plot_ncol = 4)
#'
#' a <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Pasture",
#' time_interval = c("2005-09-01","2009-09-01"),
#' relation_interval = "equals", label = my_label,
#' timeline = my_timeline)
#'
#' b <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Degradation",
#' time_interval = c("2005-09-01","2011-09-01"),
#' relation_interval = "equals", label = my_label,
#' timeline = my_timeline)
#'
#' # in
#' c <- lucC_relation_in(first_raster = a, second_raster = b)
#'
#' lucC_plot_raster_result(raster_obj = rb_class, data_mtx = c, timeline = my_timeline,
#' label = my_label, custom_palette = FALSE, plot_ncol = 4)
#'
#'}
#'
# 14. The 'lucC_relation_in' relation = lucC_relation_during | lucC_relation_starts | lucC_relation_finishes
lucC_relation_in <- function (first_raster = NULL, second_raster = NULL) {
# check is data set are empty
# remove rows with last and first column NA because MEETS
if (!is.null(first_raster) & !is.null(second_raster)) {
first_raster <- first_raster
second_raster <- second_raster
} else {
message("\nData with raster cannot be empty!\n")
return(result <- NULL)
}
# build intervals for each raster data set
rasters_intervals <- .lucC_build_intervals(first_ras = first_raster, second_ras = second_raster)
out1 <- lucC_relation_during(first_raster, second_raster)
out2 <- lucC_relation_starts(first_raster, second_raster)
out3 <- lucC_relation_finishes(first_raster, second_raster)
# interval = rasters_intervals[[1]] (first interval), rasters_intervals[[2]] (second_interval)
if( isTRUE(nrow(out1) > 0) & isTRUE(nrow(out2) > 0) & isTRUE(nrow(out3) > 0)) {
result <- dplyr::bind_rows(out1, out2, out3) # merge(out1, out2, out3, by = c("x","y"), all = TRUE)
if (nrow(result) > 0)
return(result)
else
return(result <- NULL)
} else if( isTRUE(nrow(out1) > 0) | isTRUE(nrow(out2) > 0) | isTRUE(nrow(out3) > 0)) {
result <- dplyr::bind_rows(out1, out2, out3)
if (nrow(result) > 0)
return(result)
else
return(result <- NULL)
} else {
message("\nRelation IN cannot be applied!\n")
return(result <- NULL)
}
}
#' @title Allen Relation Follows
#' @name lucC_relation_follows
#' @aliases lucC_relation_follows
#' @author Adeline M. Maciel
#' @docType data
#'
#' @description Provide an Allen's interval relation FOLLOWS which aggregates the relations
#' MEETS and BEFORE. See more at (ALLEN, J. F. "Maintaining knowledge about temporal
#' intervals". Communications of the ACM, v(26), 11, 1983, 832-843.
#' DOI: \url{http://dx.doi.org/10.1145/182.358434})
#'
#' @usage lucC_relation_follows(first_raster = NULL, second_raster = NULL)
#'
#' @param first_raster Matrix. An interval between two dates.
#' @param second_raster Matrix. An interval between two dates.
#'
#' @keywords datasets
#' @return Data set with merge of two data sets
#' @importFrom dplyr bind_rows
#' @export
#'
#' @examples \dontrun{
#' library(lucCalculus)
#'
#' file <- c(system.file("extdata/raster/rasterSample.tif", package = "lucCalculus"))
#' rb_class <- raster::brick(file)
#' my_label <- c("Degradation", "Fallow_Cotton", "Forest", "Pasture", "Soy_Corn", "Soy_Cotton",
#' "Soy_Fallow", "Soy_Millet", "Soy_Sunflower", "Sugarcane", "Urban_Area", "Water")
#' my_timeline <- c("2001-09-01", "2002-09-01", "2003-09-01", "2004-09-01", "2005-09-01",
#' "2006-09-01", "2007-09-01", "2008-09-01", "2009-09-01", "2010-09-01",
#' "2011-09-01", "2012-09-01", "2013-09-01", "2014-09-01", "2015-09-01",
#' "2016-09-01")
#'
#' lucC_plot_raster(raster_obj = rb_class, timeline = my_timeline, label = my_label,
#' custom_palette = FALSE, plot_ncol = 4)
#'
#' a <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Forest",
#' time_interval = c("2001-09-01","2004-09-01"),
#' relation_interval = "equals", label = my_label,
#' timeline = my_timeline)
#'
#' b <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Degradation",
#' time_interval = c("2005-09-01","2009-09-01"),
#' relation_interval = "contains", label = my_label,
#' timeline = my_timeline)
#'
#' # follows
#' c <- lucC_relation_follows(first_raster = a, second_raster = b)
#'
#' lucC_plot_raster_result(raster_obj = rb_class, data_mtx = c, timeline = my_timeline,
#' label = my_label, custom_palette = FALSE, plot_ncol = 4)
#'
#'}
#'
# 15. The 'lucC_relation_follows' relation = lucC_relation_meets v lucC_relation_before
lucC_relation_follows <- function (first_raster = NULL, second_raster = NULL) {
# check is data set are empty
# remove rows with last and first column NA because MEETS
if (!is.null(first_raster) & !is.null(second_raster)) {
first_raster <- first_raster
second_raster <- second_raster
} else {
message("\nData with raster cannot be empty!\n")
return(result <- NULL)
}
# build intervals for each raster data set
rasters_intervals <- .lucC_build_intervals(first_ras = first_raster, second_ras = second_raster)
out1 <- lucC_relation_before(first_raster, second_raster)
out2 <- lucC_relation_meets(first_raster, second_raster)
# interval = rasters_intervals[[1]] (first interval), rasters_intervals[[2]] (second_interval)
if( isTRUE(nrow(out1) > 0) & isTRUE(nrow(out2) > 0)) {
result <- lucC_merge(out1, out2) # merge(out1, out2, by = c("x","y"), all = TRUE)
if (nrow(result) > 0)
return(result)
else
return(result <- NULL)
} else if( isTRUE(nrow(out1) > 0) | isTRUE(nrow(out2) > 0)) {
result <- dplyr::bind_rows(out1, out2)
return(result)
} else {
message("\nRelation FOLLOWS cannot be applied!\n")
return(result <- NULL)
}
}
#' @title Allen Relation Precedes
#' @name lucC_relation_precedes
#' @aliases lucC_relation_precedes
#' @author Adeline M. Maciel
#' @docType data
#'
#' @description Provide an Allen's interval relation PRECEDES which aggregates the relations
#' MET_BY and AFTER. See more at (ALLEN, J. F. "Maintaining knowledge about temporal
#' intervals". Communications of the ACM, v(26), 11, 1983, 832-843.
#' DOI: \url{http://dx.doi.org/10.1145/182.358434})
#'
#' @usage lucC_relation_precedes(first_raster = NULL, second_raster = NULL)
#'
#' @param first_raster Matrix. An interval between two dates.
#' @param second_raster Matrix. An interval between two dates.
#'
#' @keywords datasets
#' @return Data set with merge of two data sets
#' @importFrom dplyr bind_rows
#' @export
#'
#' @examples \dontrun{
#' library(lucCalculus)
#'
#' file <- c(system.file("extdata/raster/rasterSample.tif", package = "lucCalculus"))
#' rb_class <- raster::brick(file)
#' my_label <- c("Degradation", "Fallow_Cotton", "Forest", "Pasture", "Soy_Corn", "Soy_Cotton",
#' "Soy_Fallow", "Soy_Millet", "Soy_Sunflower", "Sugarcane", "Urban_Area", "Water")
#' my_timeline <- c("2001-09-01", "2002-09-01", "2003-09-01", "2004-09-01", "2005-09-01",
#' "2006-09-01", "2007-09-01", "2008-09-01", "2009-09-01", "2010-09-01",
#' "2011-09-01", "2012-09-01", "2013-09-01", "2014-09-01", "2015-09-01",
#' "2016-09-01")
#'
#' lucC_plot_raster(raster_obj = rb_class, timeline = my_timeline, label = my_label,
#' custom_palette = FALSE, plot_ncol = 4)
#'
#' a <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Degradation",
#' time_interval = c("2005-09-01","2007-09-01"),
#' relation_interval = "equals", label = my_label,
#' timeline = my_timeline)
#'
#' b <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Forest",
#' time_interval = c("2001-09-01","2004-09-01"),
#' relation_interval = "contains", label = my_label,
#' timeline = my_timeline)
#'
#' # precedes
#' c <- lucC_relation_precedes(first_raster = a, second_raster = b)
#'
#' lucC_plot_raster_result(raster_obj = rb_class, data_mtx = c, timeline = my_timeline,
#' label = my_label, custom_palette = FALSE, plot_ncol = 4)
#'
#'}
#'
# Antonyms of follows
# 16. The 'lucC_relation_precedes' relation = lucC_relation_met_by || lucC_relation_after
lucC_relation_precedes <- function (first_raster = NULL, second_raster = NULL) {
# check is data set are empty
# remove rows with last and first column NA because MEETS
if (!is.null(first_raster) & !is.null(second_raster)) {
first_raster <- first_raster
second_raster <- second_raster
} else {
message("\nData with raster cannot be empty!\n")
return(result <- NULL)
}
# build intervals for each raster data set
rasters_intervals <- .lucC_build_intervals(first_ras = first_raster, second_ras = second_raster)
out1 <- lucC_relation_after(first_raster, second_raster)
out2 <- lucC_relation_met_by(first_raster, second_raster)
# interval = rasters_intervals[[1]] (first interval), rasters_intervals[[2]] (second_interval)
if( isTRUE(nrow(out1) > 0) & isTRUE(nrow(out2) > 0)) {
result <- lucC_merge(out1, out2) # merge(out1, out2, by = c("x","y"), all = TRUE)
if (nrow(result) > 0)
return(result)
else
return(result <- NULL)
} else if( isTRUE(nrow(out1) > 0) | isTRUE(nrow(out2) > 0)) {
result <- dplyr::bind_rows(out1, out2)
return(result)
} else {
message("\nRelation PRECEDES cannot be applied!\n")
return(result <- NULL)
}
}
#' @title Allen Occurs
#' @name lucC_occurs
#' @aliases lucC_occurs
#' @author Adeline M. Maciel
#' @docType data
#'
#' @description Provide an interval relation OCCURS which asserts that classes
#' of two distinct data set occurs in the same interval, is an intersection
#'
#' @usage lucC_occurs(first_raster = NULL, second_raster = NULL)
#'
#' @param first_raster Matrix. An interval between two dates.
#' @param second_raster Matrix. An interval between two dates.
#'
#' @keywords datasets
#' @return Data set with merge of two data sets that values are in the same interval
#' @importFrom tidyr gather spread
#' @importFrom stats na.omit
#' @export
#'
#' @examples \dontrun{
#' library(lucCalculus)
#'
#' file <- c(system.file("extdata/raster/rasterSample.tif", package = "lucCalculus"))
#' rb_class <- raster::brick(file)
#' my_label <- c("Degradation", "Fallow_Cotton", "Forest", "Pasture", "Soy_Corn", "Soy_Cotton",
#' "Soy_Fallow", "Soy_Millet", "Soy_Sunflower", "Sugarcane", "Urban_Area", "Water")
#' my_timeline <- c("2001-09-01", "2002-09-01", "2003-09-01", "2004-09-01", "2005-09-01",
#' "2006-09-01", "2007-09-01", "2008-09-01", "2009-09-01", "2010-09-01",
#' "2011-09-01", "2012-09-01", "2013-09-01", "2014-09-01", "2015-09-01",
#' "2016-09-01")
#'
#' lucC_plot_raster(raster_obj = rb_class, timeline = my_timeline, label = my_label,
#' custom_palette = FALSE, plot_ncol = 4)
#'
#' a <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Degradation",
#' time_interval = c("2001-09-01","2007-09-01"),
#' relation_interval = "contains", label = my_label,
#' timeline = my_timeline)
#'
#' b <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Forest",
#' time_interval = c("2001-09-01","2007-09-01"),
#' relation_interval = "contains", label = my_label,
#' timeline = my_timeline)
#'
#' # occurs
#' c <- lucC_occurs(first_raster = a, second_raster = b)
#'
#' lucC_plot_raster_result(raster_obj = rb_class, data_mtx = c, timeline = my_timeline,
#' label = my_label, custom_palette = FALSE, plot_ncol = 4)
#'
#'}
#'
#
# The 'lucC_occurs'
lucC_occurs <- function (first_raster = NULL, second_raster = NULL) {
# check is data set are empty
# remove rows with last and first column NA because MEETS
if (!is.null(first_raster) & !is.null(second_raster)) {
first_raster <- as.data.frame(first_raster)
second_raster <- as.data.frame(second_raster)
} else {
message("\nData with raster cannot be empty!\n")
return(result <- NULL)
}
# interval = rasters_intervals[[1]] (first interval), rasters_intervals[[2]] (second_interval)
if( isTRUE(nrow(first_raster) > 0) & isTRUE(nrow(second_raster) > 0)) {
## preserve only the last column
# result <- first_raster %>%
# dplyr::mutate(check = ifelse(is.na(match(paste0(.$x, .$y),
# paste0(second_raster$x, second_raster$y))),"No", "Yes")) %>%
# base::subset(check == 'Yes') %>%
# dplyr::select(-check) %>%
# as.matrix()
# result <- first_raster %>%
# dplyr::left_join(second_raster %>% dplyr::transmute(x, y, check = 'yes')) %>%
# tidyr::replace_na(list(check = 'no')) %>%
# subset(check == 'yes') %>%
# dplyr::select(-check)
# # other solution
points_same_coord <- merge(first_raster, second_raster, by = c("x","y"))
if (isTRUE(nrow(points_same_coord) > 0)){
#point_df <- reshape2::melt(as.data.frame(points_same_coord), id.vars = c("x","y")) %>%
# stats::na.omit()
point_df <- as.data.frame(points_same_coord) %>%
tidyr::gather(variable, value, -x, -y) %>%
stats::na.omit()
# remove .x and .y
point_df$variable <- gsub("[$.xy\\.,]", "", point_df$variable)
# remove duplicated lines
point_df <- point_df[!duplicated(point_df), ]
# return matrix format
#result <- reshape2::dcast(point_df, x+y ~ variable, value.var= "value")
result <- point_df %>%
tidyr::spread(variable, value)
return(result)
} else {
message("\nRelation OCCURS cannot be applied!\n
raster 1 and raster 2 has no relation!")
return(result <- NULL)
}
} else {
message("\nRelation OCCURS cannot be applied!\n")
return(result <- NULL)
}
}
#' @title LucC Merge
#' @name lucC_merge
#' @aliases lucC_merge
#' @author Adeline M. Maciel
#' @docType data
#'
#' @description Merge two data sets by different columns and rows. Because base::merge replace values in initial years
#'
#' @usage lucC_merge(first_raster = NULL, second_raster = NULL)
#'
#' @param first_raster Matrix. An interval between two dates.
#' @param second_raster Matrix. An interval between two dates.
#'
#' @keywords datasets
#' @return Data set merged with two data sets that values are in the same interval
#' @importFrom tidyr gather spread
#' @importFrom dplyr bind_rows anti_join
#' @importFrom stats na.omit
#' @importFrom plyr rbind.fill.matrix
#' @export
#'
#' @examples \dontrun{
#' library(lucCalculus)
#
# file <- c(system.file("extdata/raster/rasterSample.tif", package = "lucCalculus"))
# rb_class <- raster::brick(file)
# my_label <- c("Degradation", "Fallow_Cotton", "Forest", "Pasture", "Soy_Corn", "Soy_Cotton",
# "Soy_Fallow", "Soy_Millet", "Soy_Sunflower", "Sugarcane", "Urban_Area", "Water")
# my_timeline <- c("2001-09-01", "2002-09-01", "2003-09-01", "2004-09-01", "2005-09-01",
# "2006-09-01", "2007-09-01", "2008-09-01", "2009-09-01", "2010-09-01",
# "2011-09-01", "2012-09-01", "2013-09-01", "2014-09-01", "2015-09-01",
# "2016-09-01")
#
# lucC_plot_raster(raster_obj = rb_class, timeline = my_timeline, label = my_label,
# custom_palette = FALSE, plot_ncol = 4)
#
# a <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Degradation",
# time_interval = c("2001-09-01","2007-09-01"),
# relation_interval = "contains", label = my_label,
# timeline = my_timeline)
#
# b <- lucC_pred_holds(raster_obj = rb_class, raster_class = "Pasture",
# time_interval = c("2001-09-01","2007-09-01"),
# relation_interval = "contains", label = my_label,
# timeline = my_timeline)
#
# # merge
# c <- lucC_merge(first_raster = a, second_raster = b)
#
# lucC_plot_raster_result(raster_obj = rb_class, data_mtx = c, timeline = my_timeline,
# label = my_label, custom_palette = FALSE, plot_ncol = 4)
#'
#'}
#'
# The 'lucC_merge'
lucC_merge <- function (first_raster = NULL, second_raster = NULL) {
# check is data set are empty
# first_raster <- data.table::as.data.table(first_raster)
# second_raster <- data.table::as.data.table(second_raster)
first_raster <- as.data.frame(first_raster)
second_raster <- as.data.frame(second_raster)
if( isTRUE(nrow(first_raster) > 0) & isTRUE(nrow(second_raster) > 0)) {
# first raster
# first_raster <- reshape2::melt(as.data.frame(first_raster), id.vars = c("x","y"), na.rm = TRUE)
# remove factors
first_raster[,] <- lapply(first_raster, function(x) {as.character(x)})
first_raster$x = as.numeric(as.character(first_raster$x))
first_raster$y = as.numeric(as.character(first_raster$y))
# remove factors
second_raster[,] <- lapply(second_raster, function(x) {as.character(x)})
second_raster$x = as.numeric(as.character(second_raster$x))
second_raster$y = as.numeric(as.character(second_raster$y))
# separate only row in both data sets
row_both <- base::merge(first_raster, second_raster, by = c("x", "y"))
# if exists location equals, serpate them of the other data set and after merge then
if (isTRUE(nrow(row_both) > 0)){
# long format
temp <- tidyr::gather(row_both, variable, value, -x, -y, na.rm = TRUE)
# remove .x and .y
temp$variable <- gsub("[$.xy\\.,]", "", temp$variable)
#remove duplicates
temp <- temp[!duplicated(temp), ]
# result
new_row_both <- tidyr::spread(temp, variable, value)
# remove them of the original data set
first_raster <- first_raster %>% dplyr::anti_join(new_row_both, by = c("x", "y")) # keep rows without matching ID
second_raster <- second_raster %>% dplyr::anti_join(new_row_both, by = c("x", "y")) # keep rows without matching ID
# all to matrix format
first_raster <- as.matrix(first_raster)
second_raster <- as.matrix(second_raster)
new_row_both <- as.matrix(new_row_both)
# merge all data set
result <- plyr::rbind.fill.matrix(first_raster, second_raster) %>%
plyr::rbind.fill.matrix(., new_row_both) %>%
as.data.frame()
if (nrow(result) > 0){
return(result)
} else {
message("\nRelation MERGE cannot be applied!\n
raster 1 and raster 2 has no relation!")
return(result <- NULL)
}
# if no exists locations in both data sets, merge only two data sets
} else {
# all to matrix format
first_raster <- as.matrix(first_raster)
second_raster <- as.matrix(second_raster)
result <- plyr::rbind.fill.matrix(first_raster, second_raster) %>%
as.data.frame()
if (nrow(result) > 0){
return(result)
} else {
message("\nRelation MERGE cannot be applied!\n
raster 1 and raster 2 has no relation!")
return(result <- NULL)
}
}
} else if ( isTRUE(nrow(first_raster) > 0) | isTRUE(nrow(second_raster) > 0)) {
result <- dplyr::bind_rows(first_raster, second_raster)
return(result)
} else {
return(result <- NULL)
}
}
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