From 262d689578d41d2bf8c1956d32791c0345785592 Mon Sep 17 00:00:00 2001 From: THEERTHA KARIYATHAN Date: Mon, 7 Oct 2024 12:52:34 +0200 Subject: [PATCH 1/9] update 'standardized'along longname --- R/PeriodStandardization.R | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/R/PeriodStandardization.R b/R/PeriodStandardization.R index b71270f..24e46c9 100644 --- a/R/PeriodStandardization.R +++ b/R/PeriodStandardization.R @@ -125,7 +125,10 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', if (is.null(data_cor)) { data$data <- std - data$attrs$Variable$varName <- paste0(data$attrs$Variable$varName, ' standardized') + data_longname <- data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname + if(!is.null(data_longname)){ + data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname <- paste0(data_longname, ' standardized ') + } if (return_params) { return(list(spei = data, params = params)) } else { @@ -133,7 +136,10 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', } } else { data_cor$data <- std - data_cor$attrs$Variable$varName <- paste0(data_cor$attrs$Variable$varName, ' standardized') + data_cor_longname <- data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname + if(!is.null(data_cor_longname)){ + data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname <- paste0(data_cor_longname, ' standardized ') + } data_cor$attrs$Datasets <- c(data_cor$attrs$Datasets, data$attrs$Datasets) data_cor$attrs$source_files <- c(data_cor$attrs$source_files, data$attrs$source_files) return(data_cor) @@ -644,4 +650,4 @@ PeriodStandardization <- function(data, data_cor = NULL, dates = NULL, } else { return(NA) } -} \ No newline at end of file +} -- GitLab From 79bee404d1ffb600750d2d587746645b4e89e1ff Mon Sep 17 00:00:00 2001 From: THEERTHA KARIYATHAN Date: Mon, 7 Oct 2024 14:54:49 +0200 Subject: [PATCH 2/9] fixed pipeline error --- R/PeriodStandardization.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/R/PeriodStandardization.R b/R/PeriodStandardization.R index 24e46c9..32d557c 100644 --- a/R/PeriodStandardization.R +++ b/R/PeriodStandardization.R @@ -125,6 +125,7 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', if (is.null(data_cor)) { data$data <- std + data$attrs$Variable$varName <- paste0(data$attrs$Variable$varName, '') data_longname <- data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname if(!is.null(data_longname)){ data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname <- paste0(data_longname, ' standardized ') @@ -136,6 +137,7 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', } } else { data_cor$data <- std + data_cor$attrs$Variable$varName <- paste0(data_cor$attrs$Variable$varName, '') data_cor_longname <- data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname if(!is.null(data_cor_longname)){ data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname <- paste0(data_cor_longname, ' standardized ') -- GitLab From 81000b020c7338015c486ebd4905e8c58988a6a1 Mon Sep 17 00:00:00 2001 From: THEERTHA KARIYATHAN Date: Wed, 16 Oct 2024 10:42:35 +0200 Subject: [PATCH 3/9] style formatting PeriodStandardization --- R/PeriodStandardization.R | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/R/PeriodStandardization.R b/R/PeriodStandardization.R index 32d557c..3a96f2b 100644 --- a/R/PeriodStandardization.R +++ b/R/PeriodStandardization.R @@ -125,10 +125,9 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', if (is.null(data_cor)) { data$data <- std - data$attrs$Variable$varName <- paste0(data$attrs$Variable$varName, '') data_longname <- data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname - if(!is.null(data_longname)){ - data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname <- paste0(data_longname, ' standardized ') + if (!is.null(data_longname)) { + data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname <- paste(data_longname, 'standardized') } if (return_params) { return(list(spei = data, params = params)) @@ -137,10 +136,9 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', } } else { data_cor$data <- std - data_cor$attrs$Variable$varName <- paste0(data_cor$attrs$Variable$varName, '') data_cor_longname <- data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname - if(!is.null(data_cor_longname)){ - data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname <- paste0(data_cor_longname, ' standardized ') + if (!is.null(data_cor_longname)) { + data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname <- paste(data_cor_longname, 'standardized') } data_cor$attrs$Datasets <- c(data_cor$attrs$Datasets, data$attrs$Datasets) data_cor$attrs$source_files <- c(data_cor$attrs$source_files, data$attrs$source_files) -- GitLab From 5cad36114b6a60f306fafe27b82011e6f42653f2 Mon Sep 17 00:00:00 2001 From: THEERTHA KARIYATHAN Date: Wed, 16 Oct 2024 11:16:57 +0200 Subject: [PATCH 4/9] fixed pipeline error 17415 --- R/PeriodStandardization.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/R/PeriodStandardization.R b/R/PeriodStandardization.R index 3a96f2b..5564019 100644 --- a/R/PeriodStandardization.R +++ b/R/PeriodStandardization.R @@ -87,7 +87,7 @@ #'class(data) <- 's2dv_cube' #'SPEI <- CST_PeriodStandardization(data = data) #'@export -CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', +ST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', leadtime_dim = 'time', memb_dim = 'ensemble', ref_period = NULL, handle_infinity = FALSE, @@ -125,6 +125,7 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', if (is.null(data_cor)) { data$data <- std + data$attrs$Variable$varName <- paste0(data$attrs$Variable$varName, '') data_longname <- data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname if (!is.null(data_longname)) { data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname <- paste(data_longname, 'standardized') @@ -136,6 +137,7 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', } } else { data_cor$data <- std + data_cor$attrs$Variable$varName <- paste0(data$attrs$Variable$varName, '') data_cor_longname <- data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname if (!is.null(data_cor_longname)) { data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname <- paste(data_cor_longname, 'standardized') -- GitLab From b108b6476139ff1a06c651f54780e0e6a793f6ad Mon Sep 17 00:00:00 2001 From: THEERTHA KARIYATHAN Date: Wed, 16 Oct 2024 11:21:08 +0200 Subject: [PATCH 5/9] fixed pipeline error 17417 --- R/PeriodStandardization.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/PeriodStandardization.R b/R/PeriodStandardization.R index 5564019..99b7c03 100644 --- a/R/PeriodStandardization.R +++ b/R/PeriodStandardization.R @@ -87,7 +87,7 @@ #'class(data) <- 's2dv_cube' #'SPEI <- CST_PeriodStandardization(data = data) #'@export -ST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', +CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', leadtime_dim = 'time', memb_dim = 'ensemble', ref_period = NULL, handle_infinity = FALSE, -- GitLab From be6c7bed2118ec16917ac1dc4ce8931625eb6833 Mon Sep 17 00:00:00 2001 From: THEERTHA KARIYATHAN Date: Thu, 17 Oct 2024 12:42:18 +0200 Subject: [PATCH 6/9] fixed indentation --- R/PeriodStandardization.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/PeriodStandardization.R b/R/PeriodStandardization.R index 99b7c03..7d3824d 100644 --- a/R/PeriodStandardization.R +++ b/R/PeriodStandardization.R @@ -128,7 +128,7 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', data$attrs$Variable$varName <- paste0(data$attrs$Variable$varName, '') data_longname <- data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname if (!is.null(data_longname)) { - data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname <- paste(data_longname, 'standardized') + data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname <- paste(data_longname, 'standardized') } if (return_params) { return(list(spei = data, params = params)) @@ -140,7 +140,7 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', data_cor$attrs$Variable$varName <- paste0(data$attrs$Variable$varName, '') data_cor_longname <- data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname if (!is.null(data_cor_longname)) { - data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname <- paste(data_cor_longname, 'standardized') + data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname <- paste(data_cor_longname, 'standardized') } data_cor$attrs$Datasets <- c(data_cor$attrs$Datasets, data$attrs$Datasets) data_cor$attrs$source_files <- c(data_cor$attrs$source_files, data$attrs$source_files) -- GitLab From 393bc991725dd6e077db283e6226a9e8cd999681 Mon Sep 17 00:00:00 2001 From: THEERTHA KARIYATHAN Date: Thu, 24 Oct 2024 16:32:31 +0200 Subject: [PATCH 7/9] modify unit test --- R/PeriodStandardization.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/PeriodStandardization.R b/R/PeriodStandardization.R index 7d3824d..cdf385e 100644 --- a/R/PeriodStandardization.R +++ b/R/PeriodStandardization.R @@ -125,7 +125,7 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', if (is.null(data_cor)) { data$data <- std - data$attrs$Variable$varName <- paste0(data$attrs$Variable$varName, '') + #data$attrs$Variable$varName <- paste0(data$attrs$Variable$varName, '') data_longname <- data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname if (!is.null(data_longname)) { data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname <- paste(data_longname, 'standardized') @@ -137,7 +137,7 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', } } else { data_cor$data <- std - data_cor$attrs$Variable$varName <- paste0(data$attrs$Variable$varName, '') + #data_cor$attrs$Variable$varName <- paste0(data$attrs$Variable$varName, '') data_cor_longname <- data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname if (!is.null(data_cor_longname)) { data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname <- paste(data_cor_longname, 'standardized') -- GitLab From bfeaa5fedfb731f24d90ce0ad096da48a89348d0 Mon Sep 17 00:00:00 2001 From: THEERTHA KARIYATHAN Date: Mon, 28 Oct 2024 12:32:34 +0100 Subject: [PATCH 8/9] unit test check metadata --- tests/testthat/test-PeriodStandardization.R | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/tests/testthat/test-PeriodStandardization.R b/tests/testthat/test-PeriodStandardization.R index 1e816c0..4def61d 100644 --- a/tests/testthat/test-PeriodStandardization.R +++ b/tests/testthat/test-PeriodStandardization.R @@ -38,7 +38,15 @@ dims3 <- c(syear = 6, time = 2, lat = 2, ensemble = 25) set.seed(1) dat3 <- array(abs(rnorm(600, 21.19, 25.64)), dim = dims) - +# dat4 +test <- NULL +test$data <- array(rnorm(600, -204.1, 78.1), dim = dims) +test$dims <- dims +test$coords <- setNames(as.list(as.numeric(test$dims)), names(test$dims)) +test$attrs <- list(Variable = list(varName = 'prlr', + metadata = list(units = "m s-1", + longname = "Total precipitation"))) +class(test) <- 's2dv_cube' ############################################## test_that("1. Initial checks CST_PeriodStandardization", { @@ -152,11 +160,18 @@ test_that("1. Initial checks PeriodStandardization", { test_that("2. Output checks", { # CST_PeriodStandardization + prlr <- CST_PeriodStandardization(data = test) + expect_equal( + names(prlr), + c("data", "dims", "coords", "attrs") + ) + SPEI_s2dv_cube <- CST_PeriodStandardization(data = cube1) expect_equal( names(SPEI_s2dv_cube), - c('data', 'attrs') + c('data') ) + # PeriodStandardization SPEI <- PeriodStandardization(data = dat1) expect_equal( -- GitLab From 37ffdf0e89b0585eb16a60b90ac3a64e0df505d0 Mon Sep 17 00:00:00 2001 From: THEERTHA KARIYATHAN Date: Thu, 31 Oct 2024 11:55:31 +0100 Subject: [PATCH 9/9] removed empty argument data --- R/PeriodStandardization.R | 2 -- 1 file changed, 2 deletions(-) diff --git a/R/PeriodStandardization.R b/R/PeriodStandardization.R index cdf385e..00ebc71 100644 --- a/R/PeriodStandardization.R +++ b/R/PeriodStandardization.R @@ -125,7 +125,6 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', if (is.null(data_cor)) { data$data <- std - #data$attrs$Variable$varName <- paste0(data$attrs$Variable$varName, '') data_longname <- data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname if (!is.null(data_longname)) { data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname <- paste(data_longname, 'standardized') @@ -137,7 +136,6 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', } } else { data_cor$data <- std - #data_cor$attrs$Variable$varName <- paste0(data$attrs$Variable$varName, '') data_cor_longname <- data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname if (!is.null(data_cor_longname)) { data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname <- paste(data_cor_longname, 'standardized') -- GitLab