diff --git a/R/SelectPeriodOnData.R b/R/SelectPeriodOnData.R index d0dbb6023debe423403cd54a314ac0f347b3a486..8cec416124582c8304609f18b730694a8f5dce6f 100644 --- a/R/SelectPeriodOnData.R +++ b/R/SelectPeriodOnData.R @@ -1,4 +1,65 @@ -#' Select a period on Dates +#' Select a period on Data on 's2dv_cube' objects +#' +#' Auxiliary function to subset data for a specific period. +#' +#'@param data an 's2dv_cube' object as provided function \code{CST_Load} in package CSTools. +#'@param start a parameter to defined the initial date of the period to select from the data by providing a list of two elements: the initial date of the period and the initial month of the period. +#'@param end a parameter to defined the final date of the period to select from the data by providing a list of two elements: the final day of the period and the final month of the period. +#'@param time_dim a character string indicating the name of the dimension to compute select the dates. By default, it is set to 'ftime'. More than one dimension name matching the dimensions provided in the object \code{data$data} can be specified. +#'@param ncores an integer indicating the number of cores to use in parallel computation. +#' +#'@return A 's2dv_cube' object containing the subset of the object \code{data$data} during the period requested from \code{start} to \code{end}. +#' +#'@import multiApply +#' +#'@examples +#'exp <- CSTools::lonlat_prec +#'exp$data <- array(rnorm(5 * 3 * 214 * 2), +#' c(memb = 5, sdate = 3, ftime = 214, lon = 2)) +#'exp$Dates[[1]] <- c(seq(as.Date("01-05-2000", format = "%d-%m-%Y"), +#' as.Date("30-11-2000", format = "%d-%m-%Y"), by = 'day'), +#' seq(as.Date("01-05-2001", format = "%d-%m-%Y"), +#' as.Date("30-11-2001", format = "%d-%m-%Y"), by = 'day'), +#' seq(as.Date("01-05-2002", format = "%d-%m-%Y"), +#' as.Date("30-11-2002", format = "%d-%m-%Y"), by = 'day')) +#'Period <- CST_SelectPeriodOnData(exp, start = list(21, 6), end = list(21, 9)) +#'all.equal(exp$data[1,1,52:144,1], Period$data[,1,1,1]) +#'all.equal(exp$data[1,2,52:144,1], Period$data[,1,2,1]) +#'@export +CST_SelectPeriodOnData <- function(data, start, end, time_dim = 'ftime', ncores = NULL) { + if (!inherits(data, 's2dv_cube')) { + stop("Parameter 'data' must be of the class 's2dv_cube', ", + "as output by CSTools::CST_Load.") + } + # when subsetting is needed, dimensions are also needed: + if (!is.null(start) && !is.null(end)) { + if (is.null(dim(data$Dates$start))) { + if (length(data$Dates$start) != dim(data$data)[time_dim]) { + if (length(data$Dates$start) == + prod(dim(data$data)[time_dim] * dim(data$data)['sdate'])) { + dim(data$Dates$start) <- c(dim(data$data)[time_dim], + dim(data$data)['sdate']) + } + } else { + warning("Dimensions in 'data' element 'Dates$start' are missed and", + "all data would be used.") + } + } + } + res <- SelectPeriodOnData(data$data, data$Dates[[1]], + start = start, end = end, + time_dim = time_dim, ncores = ncores) + data$data <- res + if (!is.null(start) && !is.null(end)) { + data$Dates <- SelectPeriodOnDates(dates = data$Dates[[1]], + start = start, end = end, + time_dim = time_dim, ncores = ncores) + } + return(data) +} + + +#' Select a period on Data on multidimensional array objects #' #' Auxiliary function to subset data for a specific period. #' @@ -22,7 +83,11 @@ #' as.Date("30-11-2001", format = "%d-%m-%Y"), by = 'day'), #' seq(as.Date("01-05-2002", format = "%d-%m-%Y"), #' as.Date("30-11-2002", format = "%d-%m-%Y"), by = 'day')) -#'Period <- SelectPeriodOnDates(Dates, start = list(21, 6), end = list(21, 9)) +#'dim(Dates) <- c(ftime = 214, sdate = 3) +#'Period <- SelectPeriodOnData(data, Dates, start = list(21, 6), end = list(21, 9)) +#'all.equal(data[1,1,52:144,1], res[,1,1,1]) +#'all.equal(data[1,2,52:144,1], res[,1,2,1]) +#' #'@export SelectPeriodOnData <- function(data, dates, start, end, time_dim = 'ftime', ncores = NULL) { diff --git a/R/TotalTimeExceedingThreshold.R b/R/TotalTimeExceedingThreshold.R new file mode 100644 index 0000000000000000000000000000000000000000..2e41273d1212395ef6fc17421cd1f4d15336e239 --- /dev/null +++ b/R/TotalTimeExceedingThreshold.R @@ -0,0 +1,11 @@ +#' Total Time Exceeding Threshold on 's2dv_cube' objects +#' +#'TotalTimeExceedingThreshold computes the total time (e.g. days) above/below a given threshold for a given period. +#'The threshold can be a fixed value (e.g. 35°C) or a percentile corresponding to a fixed value. +#'Providing daily temperature maximum data, the following indicators can be obtained by using this function: +#'\itemize{ +#' \item\code{SU35}{Number of Heat Stress Days - 35°C in summer: The total count of days when daily maximum temperatures exceed 35°C in the seven months into the future.} +#' \item\code{SU36}{Number of Heat Stress Days - 36°C in summer: The total count of days when daily maximum temperatures exceed 36°C from June 21st to September 21st.} + + + diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 0000000000000000000000000000000000000000..79cf4a7bcd6331048eb88561a58357cf6bda2e75 --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,4 @@ +library(testthat) +library(CSIndicators) + +test_check("CSIndicators") diff --git a/tests/testthat/test-SelectPeriod.R b/tests/testthat/test-SelectPeriod.R new file mode 100644 index 0000000000000000000000000000000000000000..5716b1a23f87e970126dc0846b18d268cfb7305b --- /dev/null +++ b/tests/testthat/test-SelectPeriod.R @@ -0,0 +1,178 @@ +context("Generic tests") + #source("R/zzz.R") + #source("R/SelectPeriodOnDates.R") + #source("R/SelectPeriodOnData.R") + library(s2dv) +test_that("Decadal", { + # -------- DECADAL ----------# + # decadal: 1 sdate several consequtive years: + dates <- seq(as.Date("01-01-2000", "%d-%m-%Y", tz = 'UTC'), + as.Date("31-12-2005","%d-%m-%Y", tz = 'UTC'), "day") + # No dims -> test .position + output <- c( + seq(as.Date("2000-02-01", "%Y-%m-%d"), as.Date("2000-02-10", "%Y-%m-%d"), 'day'), + seq(as.Date("2001-02-01", "%Y-%m-%d"), as.Date("2001-02-10", "%Y-%m-%d"), 'day'), + seq(as.Date("2002-02-01", "%Y-%m-%d"), as.Date("2002-02-10", "%Y-%m-%d"), 'day'), + seq(as.Date("2003-02-01", "%Y-%m-%d"), as.Date("2003-02-10", "%Y-%m-%d"), 'day'), + seq(as.Date("2004-02-01", "%Y-%m-%d"), as.Date("2004-02-10", "%Y-%m-%d"), 'day'), + seq(as.Date("2005-02-01", "%Y-%m-%d"), as.Date("2005-02-10", "%Y-%m-%d"), 'day')) + dim(output) <- c(ftime = 60) + expect_equal( + SelectPeriodOnDates(dates, start = list(1, 2), end = list(10, 2)), + output) + data <- array(1:(length(dates)*3), + c(memb = 1, ftime = length(dates), lon = 3)) + + expect_equal( + SelectPeriodOnData(data, dates, start = list(1, 2), end = list(10, 2)), + + array(c(c(32:41, 398:407, 763:772, 1128:1137, 1493:1502, 1859:1868), + c(32:41, 398:407, 763:772, 1128:1137, 1493:1502, 1859:1868) + 2192, + c(32:41, 398:407, 763:772, 1128:1137, 1493:1502, 1859:1868) + 2 * 2192), + c(ftime = 60, memb = 1, lon = 3))) + + output2 <- c( + seq(as.Date("2000-02-01", "%Y-%m-%d"), as.Date("2000-04-10", "%Y-%m-%d"), 'day'), + seq(as.Date("2001-02-01", "%Y-%m-%d"), as.Date("2001-04-10", "%Y-%m-%d"), 'day'), + seq(as.Date("2002-02-01", "%Y-%m-%d"), as.Date("2002-04-10", "%Y-%m-%d"), 'day'), + seq(as.Date("2003-02-01", "%Y-%m-%d"), as.Date("2003-04-10", "%Y-%m-%d"), 'day'), + seq(as.Date("2004-02-01", "%Y-%m-%d"), as.Date("2004-04-10", "%Y-%m-%d"), 'day'), + seq(as.Date("2005-02-01", "%Y-%m-%d"), as.Date("2005-04-10", "%Y-%m-%d"), 'day')) + dim(output2) <- c(ftime = 416) + expect_equal( + SelectPeriodOnDates(dates, start = list(1, 2), end = list(10, 4)), + output2) + + expect_equal( + SelectPeriodOnData(data, dates, start = list(1, 2), end = list(10, 4)), + array(c(c(32:101, 398:466, 763:831, 1128:1196, 1493:1562, 1859:1927), + c(32:101, 398:466, 763:831, 1128:1196, 1493:1562, 1859:1927) + 2192, + c(32:101, 398:466, 763:831, 1128:1196, 1493:1562, 1859:1927) + 2 * 2192), + c(ftime = 416, memb = 1, lon = 3))) + + # 1 dim -> test Apply + dim(dates) <- c(ftime = length(dates)) + expect_equal( + SelectPeriodOnDates(dates, start = list(1, 2), end = list(10, 2)), + output) # no need to check on Data, repited + expect_equal( + SelectPeriodOnDates(dates, start = list(1, 2), end = list(10, 4)), + output2) # no need to check on Data, repited + + # decadal: 5 sdates several consequtive years + dates <- rep(seq(as.Date("01-01-2000", "%d-%m-%Y", tz = 'UTC'), + as.Date("31-12-2005","%d-%m-%Y", tz = 'UTC'), "day"), 5) + dim(dates) <- c(ftime = 2192, sdate = 5) + output3 <- rep(output, 5) + dim(output3) <- c(ftime = 60, sdate = 5) + expect_equal( + SelectPeriodOnDates(dates, start = list(1, 2), end = list(10, 2)), + output3) + + data <- array(1:(length(dates)*3), + c(memb = 1, sdate = 5, ftime = length(dates)/5, lon = 3)) + expect_equal( #To be extended for all sdate dimensions: + SelectPeriodOnData(data, dates, start = list(1, 2), end = list(10, 2))[,1,1,1], + c(1:10 * 5 + 151, 1:10 * 5 + 1981, 1:10 * 5 + 3806, + 1:10 * 5 + 5631, 1:10 * 5 + 7456, 1:10 * 5 + 9286)) + output4 <- rep(output2, 5) + dim(output4) <- c(ftime = 416, sdate = 5) + expect_equal( + SelectPeriodOnDates(dates, start = list(1, 2), end = list(10, 4)), + output4) + + expect_equal( #To be extended for all ftime dimensions: + SelectPeriodOnData(data, dates, start = list(1, 2), end = list(10, 4))[1,1,,1], + 156:160) + + # Multiple dims: sdate, fyear, ftime + library(CSTools) + dates <- SplitDim(dates, indices = dates[,1], + split_dim = 'ftime', freq = 'year') + dates <- as.POSIXct(dates * 24 * 3600, origin = '1970-01-01', tz = 'UTC') + output5 <- SplitDim(output3, indices = output3[,1], split_dim = 'ftime' , freq = 'year') + output5 <- as.POSIXct(output5 * 24 * 3600, origin = '1970-01-01', tz = 'UTC') + expect_equal( + SelectPeriodOnDates(dates, start = list(1, 2), end = list(10, 2)), + output5) + data <- array(1:(366*6*5*3), + c(memb = 1, sdate = 5, year = 6, ftime = 366, lon = 3)) + expect_equal( + SelectPeriodOnData(data, dates, start = list(1, 2), end = list(10, 2)), + InsertDim(Reorder(data[,,,32:41,], c('ftime', 'sdate', 'year', 'lon')), + len = 1, pos = 2, name = 'memb')) + output6 <- SplitDim(output4, indices = output4[,1], split_dim = 'ftime' , freq = 'year') + output6 <- as.POSIXct(output6 * 24 * 3600, origin = '1970-01-01', tz = 'UTC') + expect_equal( + SelectPeriodOnDates(dates, start = list(1, 2), end = list(10, 4)), + output6) + #expect_equal( # to be fixed: + # SelectPeriodOnData(data, dates, start = list(1, 2), end = list(10, 4)), + # (931:935), outer(seq(931, 3001, 30), 0:4, '+') + # InsertDim(Reorder(data[,,,32:41,], c('ftime', 'sdate', 'year', 'lon')), + # len = 1, pos = 2, name = 'memb')) +}) + + +test_that("Seasonal", { + # 1 start month, select the required 'ftime' of each 'sdate' in-between the entire timeseries + dates <- c(seq(as.Date("01-04-2000", format = "%d-%m-%Y"), + as.Date("31-10-2000", format = "%d-%m-%Y"), by = 'day'), + seq(as.Date("01-04-2001", format = "%d-%m-%Y"), + as.Date("31-10-2001", format = "%d-%m-%Y"), by = 'day'), + seq(as.Date("01-04-2002", format = "%d-%m-%Y"), + as.Date("31-10-2002", format = "%d-%m-%Y"), by = 'day'), + seq(as.Date("01-04-2003", format = "%d-%m-%Y"), + as.Date("31-10-2003", format = "%d-%m-%Y"), by = 'day')) + + output <- c(seq(as.Date("21-04-2000", format = "%d-%m-%Y"), + as.Date("21-06-2000", format = "%d-%m-%Y"), by = 'day'), + seq(as.Date("21-04-2001", format = "%d-%m-%Y"), + as.Date("21-06-2001", format = "%d-%m-%Y"), by = 'day'), + seq(as.Date("21-04-2002", format = "%d-%m-%Y"), + as.Date("21-06-2002", format = "%d-%m-%Y"), by = 'day'), + seq(as.Date("21-04-2003", format = "%d-%m-%Y"), + as.Date("21-06-2003", format = "%d-%m-%Y"), by = 'day')) + dim(output) <- c(ftime = (30 - 20 + 31 + 21) * 4) + expect_equal( + SelectPeriodOnDates(dates, start = list(21, 4), end = list(21, 6)), + output) + + # following the above case, and select the data + data <- array(1:(5 * 4 * 214 * 2), + c(memb = 5, sdate = 4, ftime = 214, lon = 2)) + dim(dates) <- c(ftime = 214, sdate = 4) + + expect_equal( + SelectPeriodOnData(data, dates, start = list(21, 4), end = list(21, 6))[,1,1,1], + data[1,1,21:82,1]) + + +# when selecting the days across two years + dates <- seq(as.Date("2000-01-01", "%Y-%m-%d"), as.Date("2003-12-31", "%Y-%m-%d"), 'day') + + output1 <- c(seq(as.Date("01-01-2000", format = "%d-%m-%Y"), + as.Date("31-01-2000", format = "%d-%m-%Y"), by = 'day'), + seq(as.Date("01-12-2000", format = "%d-%m-%Y"), + as.Date("31-01-2001", format = "%d-%m-%Y"), by = 'day'), + seq(as.Date("01-12-2001", format = "%d-%m-%Y"), + as.Date("31-01-2002", format = "%d-%m-%Y"), by = 'day'), + seq(as.Date("01-12-2002", format = "%d-%m-%Y"), + as.Date("31-01-2003", format = "%d-%m-%Y"), by = 'day'), + seq(as.Date("01-12-2003", format = "%d-%m-%Y"), + as.Date("31-12-2003", format = "%d-%m-%Y"), by = 'day')) + dim(output1) <- c(ftime = 31 * 8) + + expect_equal( + SelectPeriodOnDates(dates, start = list(1, 12), end = list(31, 1)), + output1) + # following the above case, and select the data + data1 <- array(1:(length(dates) * 2), + c(memb = 1, ftime = length(dates), lon = 2)) + expect_equal( + SelectPeriodOnData(data1, dates, start = list(1, 12), end = list(31, 1)), + array(c(c(1:31, 336:397, 701:762, 1066:1127, 1431:1461), + c(1:31, 336:397, 701:762, 1066:1127, 1431:1461) + 1461), + c(ftime = 31 * 8, memb = 1, lon = 2))) +}) +