From afdbfdc0ac74758f0a2bd7c85cfaf9fb014d2036 Mon Sep 17 00:00:00 2001
From: THEERTHA KARIYATHAN <tkariyat@bscearth421.int.bsc.es>
Date: Thu, 13 Feb 2025 09:28:20 +0100
Subject: [PATCH 1/9] added CST_TrainIndex, update d unit test,
 CST_Calibrartion, docs

---
 R/CST_Calibration.R                   | 120 ++++++++---------------
 R/CST_TrainIndex.R                    |  88 +++++++++++++++++
 tests/testthat/test-CST_Calibration.R |  11 ++-
 tests/testthat/test-CST_TrainIndex.R  | 131 ++++++++++++++++++++++++++
 4 files changed, 263 insertions(+), 87 deletions(-)
 create mode 100644 R/CST_TrainIndex.R
 create mode 100644 tests/testthat/test-CST_TrainIndex.R

diff --git a/R/CST_Calibration.R b/R/CST_Calibration.R
index c4942eaa..3b0bf04a 100644
--- a/R/CST_Calibration.R
+++ b/R/CST_Calibration.R
@@ -73,6 +73,13 @@
 #'  The default value is NULL.
 #'@param ncores An integer that indicates the number of cores for parallel 
 #'  computations using multiApply function. The default value is one.
+#'@param k Positive integer. Default = 1.
+#'  In method \code{leave-k-out}, \code{k} is expected to be odd integer, indicating the number of points to leave out.
+#'  In method \code{retrospective}, \code{k} can be any positive integer, indicating when to start. 
+#'@param tail.out Boolean for 'leave-k-out' method; TRUE to remove both extremes 
+#'  keeping the same sample size for all k-folds (e.g. amt.points=50, k=3, 
+#'  eval.dexes=1, train.dexes={3,49}). FALSE to remove only the corresponding tail (e.g..
+#'  amt.points=50, k=3, eval.dexes=1, train.dexes={3,50})
 #' 
 #'@return An object of class \code{s2dv_cube} containing the calibrated 
 #'forecasts in the element \code{data} with the dimensions nexp, nobs and same 
@@ -146,7 +153,7 @@
 #'@importFrom ClimProjDiags Subset
 #'@export
 CST_Calibration <- function(exp, obs, exp_cor = NULL, cal.method = "mse_min", 
-                            eval.method = "leave-one-out", multi.model = FALSE, 
+                            eval.method = "leave-k-out", multi.model = FALSE, 
                             na.fill = TRUE, na.rm = TRUE, apply_to = NULL, 
                             alpha = NULL, memb_dim = 'member', sdate_dim = 'sdate', 
                             dat_dim = NULL, ncores = NULL, k = 1, tail.out = TRUE) {
@@ -254,6 +261,13 @@ CST_Calibration <- function(exp, obs, exp_cor = NULL, cal.method = "mse_min",
 #'  The default value is NULL.
 #'@param ncores An integer that indicates the number of cores for parallel 
 #'  computation using multiApply function. The default value is NULL (one core).
+#'@param k  k Positive integer. Default = 1.
+#'  In method \code{leave-k-out}, \code{k} is expected to be odd integer, indicating the number of points to leave out.
+#'  In method \code{retrospective}, \code{k} can be any positive integer, indicating when to start.
+#'@param tail.out Boolean for 'leave-k-out' method; TRUE to remove both extremes 
+#'  keeping the same sample size for all k-folds (e.g. amt.points=50, k=3, 
+#'  eval.dexes=1, train.dexes={3,49}). FALSE to remove only the corresponding tail (e.g..
+#'  amt.points=50, k=3, eval.dexes=1, train.dexes={3,50})
 #' 
 #'@return An array containing the calibrated forecasts with the dimensions 
 #'nexp, nobs and same dimensions as in the 'exp' array. nexp is the number of 
@@ -301,7 +315,7 @@ CST_Calibration <- function(exp, obs, exp_cor = NULL, cal.method = "mse_min",
 #'@importFrom ClimProjDiags Subset
 #'@export
 Calibration <- function(exp, obs, exp_cor = NULL, 
-                        cal.method = "mse_min", eval.method = "leave-one-out",  
+                        cal.method = "mse_min", eval.method = "leave-k-out",  
                         multi.model = FALSE, na.fill = TRUE, 
                         na.rm = TRUE, apply_to = NULL, alpha = NULL,
                         memb_dim = 'member', sdate_dim = 'sdate', dat_dim = NULL, 
@@ -478,9 +492,9 @@ Calibration <- function(exp, obs, exp_cor = NULL,
     }
   }
   ## eval.method
-  if (!any(eval.method %in% c('in-sample', 'leave-one-out', 'hindcast-vs-forecast', 'k-fold', 'retrospective'))) {  
+  if (!any(eval.method %in% c('in-sample', 'leave-k-out', 'hindcast-vs-forecast', 'retrospective'))) {  
     stop(paste0("Parameter 'eval.method' must be a character string indicating ", 
-                "the sampling method used ('in-sample', 'leave-one-out', 'hindcast-vs-forecast', 'k-fold' or ", 
+                "the sampling method used ('in-sample', 'leave-k-out', 'hindcast-vs-forecast' or ", 
                 "'retrospective')."))
   }
   ## multi.model
@@ -567,77 +581,8 @@ Calibration <- function(exp, obs, exp_cor = NULL,
   }
 }
 
-.make.eval.train.dexes <- function(eval.method, amt.points, amt.points_cor,
-                                   k = 1, tail.out = TRUE) {
-# eval.method: 'leave-one-out', 'k-fold', 'in-sample', "hindcast-vs-forecast", "retrospective"
-# amt.points: length of the sample
-# amt.points_cor: only needed for hindcast-vs-forecast method
-# k: the number of samples to leave-out
-# tail_out: boolean for 'k-fold method; TRUE to remove both extremes of the sample when k is 
-# in the extreme keeping the same sample size for all k-folds (e.g. amt.points=50, k=3, 
-# eval.dexes=1, train.dexes={3,49}). FALSE to remove only the corresponding tail (e.g..
-# amt.points=50, k=3, eval.dexes=1, train.dexes={3,50})
-
-  if (k >= amt.points && !is.null(k) | k < 1) { 
-    stop("k needs to be a positive integer less than the amt.points")
-  }
-  if (eval.method == "leave-one-out") {
-    dexes.lst <- lapply(seq(1, amt.points), function(x) return(list(eval.dexes = x,
-                        train.dexes = seq(1, amt.points)[-x])))
-  } else if (eval.method == "k-fold") {
-  # k is a odd number
-    if (tail.out == TRUE){
-          dexes.lst <- lapply(seq(1, amt.points), function(x, kfold = k) {
-      if (x >= ((kfold-1)/2) + 1 && x + ((kfold-1)/2) <= amt.points) {
-        ind <- (x-((kfold-1)/2)):(x+((kfold-1)/2))
-      } else if (x < ((kfold-1)/2) + 1) {
-        ind <- c((amt.points - ((kfold-1)/2-x)):amt.points, 1:(x+(kfold-1)/2))
-      } else if ((x+((kfold-1)/2)) > amt.points) {
-        ind <- c((x-(kfold-1)/2):amt.points, 1:(((kfold-1)/2)-amt.points+x)) 
-      } else {
-        stop("Review make.eval.train.dexes function")
-      }
-      return(list(eval.dexes = x,  train.dexes = seq(1, amt.points)[-ind]))
-      })
-    } else {
-      if (k != 1){
-        k <- (k-1)/2
-      }
-      
-      dexes.lst <- lapply(seq(1, amt.points), function(x) {
-        start_idx <- max(1, x - k)
-        end_idx <- min(amt.points, x + k)
-        eval_range <- start_idx:end_idx
-        train_idx <- setdiff(seq(1, amt.points), eval_range)
-        return(list(eval.dexes = x, train.dexes = train_idx))
-      })
-    }
-
-  } else if (eval.method == "retrospective") { 
-  # k can be any integer indicating the when to start
-    dexes.lst <- base::Filter(length, lapply(seq(1, amt.points),
-                        function(x, mindata = k) {
-                          if (x > k) { 
-                            eval.dexes <- x
-                            train.dexes <- 1:(x-1)
-                            return(list(eval.dexes = x,
-                                        train.dexes = 1:(x-1)))
-                          }})) 
-  } else if (eval.method == "in-sample") {
-    dexes.lst <- list(list(eval.dexes = seq(1, amt.points), 
-                           train.dexes = seq(1, amt.points)))
-  } else if (eval.method == "hindcast-vs-forecast") {
-    dexes.lst <- list(list(eval.dexes = seq(1,amt.points_cor),
-                           train.dexes = seq(1, amt.points)))
-  } else {
-    stop(paste0("unknown sampling method: ", eval.method))
-  }
-
-  return(dexes.lst)
-}
-
 .cal <- function(exp, obs, exp_cor = NULL, dat_dim = NULL, cal.method = "mse_min", 
-                 eval.method = "leave-one-out", multi.model = FALSE, na.fill = TRUE, 
+                 eval.method = "leave-k-out", multi.model = FALSE, na.fill = TRUE, 
                  na.rm = TRUE, apply_to = NULL, alpha = NULL, k = 1, tail.out = TRUE) {
 
   # exp: [memb, sdate, (dat)]
@@ -672,8 +617,11 @@ Calibration <- function(exp, obs, exp_cor = NULL,
   sdate <- expdims[2] # sdate
   sdate_cor <- expdims_cor[2]
 
-  var.cor.fc <- array(dim = c(dim(exp_cor)[1:2], nexp = nexp, nobs = nobs))
-  
+  if(eval.method == 'retrospective'){ 
+    var.cor.fc <- array(dim = c(expdims_cor[1], expdims_cor[2]-k, nexp = nexp, nobs = nobs))
+  }else{
+    var.cor.fc <- array(dim = c(dim(exp_cor)[1:2], nexp = nexp, nobs = nobs))
+  }
   for (i in 1:nexp) {
     for (j in 1:nobs) {
       exp_data <- exp[, , i]
@@ -693,7 +641,7 @@ Calibration <- function(exp, obs, exp_cor = NULL,
           expcor_data <- exp_cor
         }
 
-        eval.train.dexeses <- .make.eval.train.dexes(eval.method = eval.method, 
+        eval.train.dexeses <- CST_TrainIndex(eval.method = eval.method, 
                                                      amt.points = sdate, 
                                                      amt.points_cor = sdate_cor, 
                                                      k = k, tail.out = tail.out)
@@ -701,14 +649,18 @@ Calibration <- function(exp, obs, exp_cor = NULL,
         for (i.sample in seq(1, amt.resamples)) {
           # defining training (tr) and evaluation (ev) subsets
           # fc.ev is used to evaluate (not train; train should be done with exp (hindcast))
-          eval.dexes <- eval.train.dexeses[[i.sample]]$eval.dexes
+          eval.dexes <- eval.train.dexeses[[i.sample]]$eval.dexes 
           train.dexes <- eval.train.dexeses[[i.sample]]$train.dexes
           fc.ev <- expcor_data[, eval.dexes, drop = FALSE]
           fc.tr <- exp_data[, train.dexes]
           obs.tr <- obs_data[train.dexes, drop = FALSE] 
-          
+          if(eval.method == 'retrospective'){ 
+            eval.dexes  =  eval.dexes - k
+          }else{
+            eval.dexes = eval.dexes
+          }
           if (cal.method == "bias") {
-            var.cor.fc[, eval.dexes, i, j] <- fc.ev + mean(obs.tr, na.rm = na.rm) - mean(fc.tr, na.rm = na.rm)
+            var.cor.fc[, eval.dexes , i, j] <- fc.ev + mean(obs.tr, na.rm = na.rm) - mean(fc.tr, na.rm = na.rm)
             # forecast correction implemented
           } else if (cal.method == "evmos") {
             # forecast correction implemented
@@ -717,11 +669,11 @@ Calibration <- function(exp, obs, exp_cor = NULL,
             # calculate value for regression parameters
             init.par <- c(.calc.evmos.par(quant.obs.fc.tr, na.rm = na.rm))
             # correct evaluation subset
-            var.cor.fc[, eval.dexes, i, j] <- .correct.evmos.fc(fc.ev , init.par, na.rm = na.rm)
+            var.cor.fc[, eval.dexes , i, j] <- .correct.evmos.fc(fc.ev , init.par, na.rm = na.rm)
           } else if (cal.method == "mse_min") {
             quant.obs.fc.tr <- .calc.obs.fc.quant(obs = obs.tr, fc = fc.tr, na.rm = na.rm)
             init.par <- .calc.mse.min.par(quant.obs.fc.tr, multi.model, na.rm = na.rm)
-            var.cor.fc[, eval.dexes, i, j] <- .correct.mse.min.fc(fc.ev , init.par, na.rm = na.rm)      
+            var.cor.fc[, eval.dexes, i, j] <- .correct.mse.min.fc(fc.ev , init.par, na.rm = na.rm) 
           } else if (cal.method == "crps_min") {
             quant.obs.fc.tr <- .calc.obs.fc.quant.ext(obs = obs.tr, fc = fc.tr, na.rm = na.rm)
             init.par <- c(.calc.mse.min.par(quant.obs.fc.tr, na.rm = na.rm), 0.001)
@@ -767,7 +719,11 @@ Calibration <- function(exp, obs, exp_cor = NULL,
   }
 
   if (is.null(dat_dim)) {
+    if(eval.method == 'retrospective'){ 
+    dim(var.cor.fc) <- c(expdims_cor[1], (expdims_cor[2]-k))
+    }else{
     dim(var.cor.fc) <- dim(exp_cor)[1:2]
+    }
   }
   return(var.cor.fc)
 }
diff --git a/R/CST_TrainIndex.R b/R/CST_TrainIndex.R
new file mode 100644
index 00000000..3806e3b2
--- /dev/null
+++ b/R/CST_TrainIndex.R
@@ -0,0 +1,88 @@
+#' Generate Training and Evaluation Indices for Cross-Validation
+#'
+#' This function generates training and evaluation indices based on different cross-validation methods.
+#' @author Theertha Kariyathan, \email{theertha.kariyathan@bsc.es}
+#' 
+#' @param eval.method Character. The cross-validation method. Options include:
+#'   -\code{leave-k-out}: Leaves out \code{k} points at a time for evaluation.
+#'   -\code{retrospective}: Uses past data for training and a future point for evaluation.
+#'   -\code{in-sample}: Uses the entire dataset for both training and evaluation.
+#'   -\code{hindcast-vs-forecast}: Uses a subset \code{amt.points_cor} for evaluation while training on \code{amt.points}.
+#'   
+#' @param amt.points Integer. Total number of points in the dataset.
+#' @param amt.points_cor Integer. Number of points for evaluation in the \code{hindcast-vs-forecast} method.
+#' @param k Positive integer. Default = 1.
+#' In method \code{leave-k-out}, \code{k} is expected to be odd integer, indicating the number of points to leave out.
+#' In method \code{retrospective}, \code{k} can be any positive integer, indicating when to start. 
+#' @param tail.out Logical for method \code{leave-k-out}. Default = TRUE.  
+#'  TRUE to remove both extremes keeping the same sample size for all k-folds 
+#'  (e.g. amt.points=50, k=3, eval.dexes=1, train.dexes={3,49}). 
+#'  FALSE to remove only the corresponding tail 
+#'  (e.g. amt.points=50, k=3, eval.dexes=1, train.dexes={3,50})
+#' @return A list of lists, where each element contains:
+#'   \code{eval.dexes}: Indices of evaluation points.
+#'   \code{train.dexes}: Indices of training points.
+#'
+#' @examples
+#' # Leave-k-out cross-validation
+#' CST_TrainIndex("leave-k-out", amt.points = 10, amt.points_cor = 5, k = 3)
+#' # Retrospective cross-validation
+#' CST_TrainIndex("retrospective", amt.points = 10, amt.points_cor = 5, k = 3)
+#' # In-sample validation
+#' CST_TrainIndex("in-sample", amt.points = 10, amt.points_cor = 5)
+#' # Hindcast vs. Forecast validation
+#' CST_TrainIndex("hindcast-vs-forecast", amt.points = 10, amt.points_cor = 5)
+#'
+#' @export
+CST_TrainIndex <- function(eval.method, amt.points, amt.points_cor, 
+                           k = 1, tail.out = TRUE) {
+  
+  if (is.null(k) || k >= amt.points || k < 1 || k %% 2 == 0 ) { 
+    stop("k needs to be a positive odd integer less than the amt.points")
+  }
+  
+  if ( k %% 2 == 0 ) { 
+    warning("k is expected to be an odd integer")
+  }
+  
+  if (eval.method == "leave-k-out") {
+    if (k == 1) {
+      tail.out == TRUE
+    }
+    amt.seq <- 1:amt.points
+    strike = (k - 1) / 2
+    alt_amt.seq <- c(tail(amt.seq, strike), amt.seq, head(amt.seq, strike))
+    
+    dexes.lst <- lapply(seq(1, amt.points), function(x, kfold = k) {
+      if (tail.out) {
+        ind = alt_amt.seq[x:(x + (kfold - 1))]
+      } else{
+        ind = ((x - strike):(x + strike))
+        ind = ind[ind > 0 & ind <= amt.points]
+      }
+      return(list(eval.dexes = x,  train.dexes = amt.seq[!(amt.seq %in% ind)]))
+    })
+  } else if (eval.method == "retrospective") {
+    # k can be any integer indicating the when to start
+    dexes.lst <- base::Filter(length, lapply(seq(1, amt.points),
+                                             function(x, mindata = k) {
+                                               if (x > k) { 
+                                                 eval.dexes <- x
+                                                 train.dexes <- 1:(x-1)
+                                                 return(list(eval.dexes = x,
+                                                             train.dexes = 1:(x-1)))
+                                               }})) 
+
+  } else if (eval.method == "in-sample") {
+    dexes.lst <- list(list(eval.dexes = seq(1, amt.points), 
+                           train.dexes = seq(1, amt.points)))
+  } else if (eval.method == "hindcast-vs-forecast") {
+    dexes.lst <- list(list(eval.dexes = seq(1,amt.points_cor),
+                           train.dexes = seq(1, amt.points)))
+  } else {
+    stop(paste0("unknown sampling method: ", eval.method))
+  }
+  
+  return(dexes.lst)
+} 
+
diff --git a/tests/testthat/test-CST_Calibration.R b/tests/testthat/test-CST_Calibration.R
index 285e81c8..29fb5f4c 100644
--- a/tests/testthat/test-CST_Calibration.R
+++ b/tests/testthat/test-CST_Calibration.R
@@ -158,8 +158,8 @@ test_that("1. Input checks", {
   )
   expect_error(
     Calibration(exp = array(1:6, c(sdate = 3, member = 2, dataset = 2, lon = 1)), 
-                   obs = array(1:6, c(sdate = 3, member = 1, dataset = 3, lon = 2)), 
-                   dat_dim = 'dataset'),
+                obs = array(1:6, c(sdate = 3, member = 1, dataset = 3, lon = 2)), 
+                dat_dim = 'dataset'),
     paste0("Parameter 'exp' and 'obs' must have same length of all dimensions", 
            " except 'memb_dim' and 'dat_dim'.")
   )
@@ -218,7 +218,7 @@ test_that("1. Input checks", {
   expect_error(
     Calibration(exp4, obs4, eval.method = 'biass'),
     paste0("Parameter 'eval.method' must be a character string indicating ", 
-           "the sampling method used ('in-sample', 'leave-one-out', 'hindcast-vs-forecast', 'k-fold' or ", 
+           "the sampling method used ('in-sample', 'leave-k-out', 'hindcast-vs-forecast' or ", 
            "'retrospective')."), 
     fixed = TRUE
   )
@@ -234,6 +234,7 @@ test_that("1. Input checks", {
   )
 })
 
+
 ##############################################
 
 test_that("2. Output checks: dat1", {
@@ -454,14 +455,14 @@ test_that("6. Output checks: dat4", {
     tolerance = 0.0001
   )
   expect_equal(
-    as.vector(Calibration(exp4, obs4, eval.method = "k-fold", k = 5, tail.out = T))[1:5],
+    as.vector(Calibration(exp4, obs4, eval.method = "leave-k-out", k = 5, tail.out = T))[1:5],
     c(-0.8149557,  0.2043942, -1.0781616,  1.9806657,  0.3879362),
     tolerance = 0.0001
   )
 
   expect_equal(
     as.vector(Calibration(exp4, obs4, eval.method = "retrospective", k = 3)[1,1:5]),
-    c(NA, NA, NA, 1.6267865, -0.1658674),
+    c(1.6267865, -0.1658674,  0.3998208,  3.3390213,  0.4102334),
     tolerance = 0.0001
   )
   
diff --git a/tests/testthat/test-CST_TrainIndex.R b/tests/testthat/test-CST_TrainIndex.R
new file mode 100644
index 00000000..f6f75cb3
--- /dev/null
+++ b/tests/testthat/test-CST_TrainIndex.R
@@ -0,0 +1,131 @@
+
+
+##############################################
+
+test_that("1. Input checks", {
+  # s2dv_cube
+  expect_error(
+    CST_TrainIndex(eval.method = 1, 2),
+    paste0("unknown sampling method: 1")
+  )
+  expect_error(
+    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 12),
+    paste0("k needs to be a positive odd integer less than the amt.points")
+  )
+  expect_error(
+    CST_TrainIndex(eval.method = 'retrospective', 10, NULL, 10),
+    paste0("k needs to be a positive odd integer less than the amt.points")
+  )
+})
+
+##############################################
+
+test_that("2. Output checks: leave-k-out", {
+  expect_equal(
+    is.list(CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)),
+    TRUE
+  )
+  expect_equal(
+    is.list(CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)[[1]]),
+    TRUE
+  )
+  expect_equal(
+    length(CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)),
+    10
+  )
+  expect_equal(
+    names(CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)[[1]]),
+    c("eval.dexes", "train.dexes")
+  )
+  expect_equal(
+    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)[[1]],
+    list(eval.dexes = 1,
+         train.dexes = 4:8)
+  )
+  expect_equal(
+    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)[[2]],
+    list(eval.dexes = 2, 
+         train.dexes = 5:9)
+  )
+  expect_equal(
+    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)[[3]],
+    list(eval.dexes = 3,
+         train.dexes = 6:10)
+  )
+  expect_equal(
+    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)[[9]],
+    list(eval.dexes = 9,
+         train.dexes = 2:6)
+  )
+  expect_equal(
+    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)[[10]],
+    list(eval.dexes = 10,
+         train.dexes = 3:7)
+  )
+  expect_equal(
+    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5, tail.out = FALSE)[[1]],
+    list(eval.dexes = 1,
+         train.dexes = 4:10)
+  )
+  expect_equal(
+    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5, tail.out = FALSE)[[5]],
+    list(eval.dexes = 5,
+         train.dexes = c(1,2,8:10))
+  )
+  expect_equal(
+    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5, tail.out = FALSE)[[10]],
+    list(eval.dexes = 10,
+         train.dexes = c(1:7))
+  )
+  expect_equal(
+    CST_TrainIndex(eval.method = 'leave-k-out', 20, NULL, 1)[[1]],
+    CST_TrainIndex(eval.method = 'leave-k-out', 20, NULL, 1, tail.out = FALSE)[[1]]
+  )
+  
+})
+
+##############################################
+
+test_that("3. Output checks: retrospective", {
+  expect_equal(
+    length(CST_TrainIndex(eval.method = 'retrospective', 10, NULL, 3)),
+    7
+  )
+  expect_equal(
+    CST_TrainIndex(eval.method = 'retrospective', 10, NULL, 3)[[1]],
+    list(eval.dexes = 4, train.dexes = 1:3)
+  )
+  expect_equal(
+    CST_TrainIndex(eval.method = 'retrospective', 10, NULL, 3)[[2]],
+    list(eval.dexes = 5, train.dexes = 1:4)
+  )
+  expect_equal(
+    CST_TrainIndex(eval.method = 'retrospective', 10, NULL, 3)[[7]],
+    list(eval.dexes = 10, train.dexes = 1:9)
+  )
+})
+
+
+  
+# Train.Eval.dexes <- function(k, amt.points, tail.out = TRUE) {
+#     amt.seq <- 1:amt.points
+#     strike = (k - 1) / 2
+#     alt_amt.seq <- c(tail(amt.seq, strike), amt.seq, head(amt.seq, strike))
+#     
+#     dexes.lst <- lapply(seq(1, amt.points), function(x, kfold = k) {
+#       if (tail.out) {
+#         ind = alt_amt.seq[x:(x + (kfold - 1))] 
+#         if(x == 2){print(ind)}
+#         # return(list(eval.dexes = x,  train.dexes = amt.seq[!(amt.seq %in% ind)]))
+#       } else{
+#         ind = ((x - strike):(x + strike))
+#         ind = ind[ind > 0 & ind <= amt.points]
+#         #return(list(eval.dexes = x,  train.dexes = amt.seq[!(amt.seq %in% ind)]))
+#       }
+#       return(list(eval.dexes = x,  train.dexes = amt.seq[!(amt.seq %in% ind)]))
+#       
+#     })
+#   }
+  
+  
+  
\ No newline at end of file
-- 
GitLab


From 6d51d7ad92d47349fbb75c564757906af2c7b351 Mon Sep 17 00:00:00 2001
From: THEERTHA KARIYATHAN <tkariyat@bscearth421.int.bsc.es>
Date: Mon, 17 Mar 2025 15:18:02 +0100
Subject: [PATCH 2/9] replace ,.make.eval with CST_TrainIndex

---
 R/CST_CategoricalEnsCombination.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/CST_CategoricalEnsCombination.R b/R/CST_CategoricalEnsCombination.R
index f973cde7..9d610019 100644
--- a/R/CST_CategoricalEnsCombination.R
+++ b/R/CST_CategoricalEnsCombination.R
@@ -304,7 +304,7 @@ comb.dims <- function(arr.in, dims.to.combine){
   amt.coeff <- amt.mdl + 1
   var.cat.fc <- array(NA, c(amt.cat, amt.sdate))
   
-  eval.train.dexeses <- .make.eval.train.dexes(eval.method = eval.method, amt.points = amt.sdate, k = k, tail.out = tail.out)
+  eval.train.dexeses <- CST_TrainIndex(eval.method = eval.method, amt.points = amt.sdate, k = k, tail.out = tail.out)
   amt.resamples <- length(eval.train.dexeses)	
   
   for (i.sample in seq(1, amt.resamples)) {
-- 
GitLab


From d7a31ab26f57534704c1e1586b06c619002d7364 Mon Sep 17 00:00:00 2001
From: THEERTHA KARIYATHAN <tkariyat@bscearth421.int.bsc.es>
Date: Mon, 17 Mar 2025 15:37:55 +0100
Subject: [PATCH 3/9] rmv test-make.eval, update categoricalensemble

---
 R/CST_CategoricalEnsCombination.R           | 10 +--
 tests/testthat/test-CST_TrainIndex.R        | 23 -----
 tests/testthat/test-make-eval-train-dexes.R | 93 ---------------------
 3 files changed, 5 insertions(+), 121 deletions(-)
 delete mode 100644 tests/testthat/test-make-eval-train-dexes.R

diff --git a/R/CST_CategoricalEnsCombination.R b/R/CST_CategoricalEnsCombination.R
index 9d610019..a242d616 100644
--- a/R/CST_CategoricalEnsCombination.R
+++ b/R/CST_CategoricalEnsCombination.R
@@ -57,8 +57,8 @@
 #'  Vannitsem (2019). Finally, the \code{obs} method classifies the observations 
 #'  into the different categories and therefore contains only 0 and 1 values. 
 #'@param eval.method Is the sampling method used, can be either 
-#'  \code{"in-sample"} or \code{"leave-one-out"}. Default value is the 
-#'  \code{"leave-one-out"} cross validation. 
+#'  \code{"in-sample"} or \code{"leave-k-out"}. Default value is the 
+#'  \code{"leave-k-out"} cross validation. 
 #'@param ... other parameters to be passed on to the calibration procedure.
 #'
 #'@return An object of class \code{s2dv_cube} containing the categorical 
@@ -96,7 +96,7 @@
 #'@import abind
 #'@export
 CST_CategoricalEnsCombination <- function(exp, obs, cat.method = "pool", 
-                                          eval.method = "leave-one-out", 
+                                          eval.method = "leave-k-out", 
                                           amt.cat = 3, k = 1, tail.out = TRUE,
                                           ...) {
   # Check 's2dv_cube'
@@ -155,8 +155,8 @@ CST_CategoricalEnsCombination <- function(exp, obs, cat.method = "pool",
 #'  Vannitsem (2019). Finally, the \code{obs} method classifies the observations
 #'  into the different categories and therefore contains only 0 and 1 values. 
 #'@param eval.method Is the sampling method used, can be either 
-#'  \code{"in-sample"} or \code{"leave-one-out"}. Default value is the 
-#'  \code{"leave-one-out"} cross validation.
+#'  \code{"in-sample"} or \code{"leave-k-out"}. Default value is the 
+#'  \code{"leave-k-out"} cross validation.
 #'@param ... Other parameters to be passed on to the calibration procedure.
 #'
 #'@return An array containing the categorical forecasts in the element called 
diff --git a/tests/testthat/test-CST_TrainIndex.R b/tests/testthat/test-CST_TrainIndex.R
index f6f75cb3..3618019f 100644
--- a/tests/testthat/test-CST_TrainIndex.R
+++ b/tests/testthat/test-CST_TrainIndex.R
@@ -1,5 +1,4 @@
 
-
 ##############################################
 
 test_that("1. Input checks", {
@@ -106,26 +105,4 @@ test_that("3. Output checks: retrospective", {
 })
 
 
-  
-# Train.Eval.dexes <- function(k, amt.points, tail.out = TRUE) {
-#     amt.seq <- 1:amt.points
-#     strike = (k - 1) / 2
-#     alt_amt.seq <- c(tail(amt.seq, strike), amt.seq, head(amt.seq, strike))
-#     
-#     dexes.lst <- lapply(seq(1, amt.points), function(x, kfold = k) {
-#       if (tail.out) {
-#         ind = alt_amt.seq[x:(x + (kfold - 1))] 
-#         if(x == 2){print(ind)}
-#         # return(list(eval.dexes = x,  train.dexes = amt.seq[!(amt.seq %in% ind)]))
-#       } else{
-#         ind = ((x - strike):(x + strike))
-#         ind = ind[ind > 0 & ind <= amt.points]
-#         #return(list(eval.dexes = x,  train.dexes = amt.seq[!(amt.seq %in% ind)]))
-#       }
-#       return(list(eval.dexes = x,  train.dexes = amt.seq[!(amt.seq %in% ind)]))
-#       
-#     })
-#   }
-  
-  
   
\ No newline at end of file
diff --git a/tests/testthat/test-make-eval-train-dexes.R b/tests/testthat/test-make-eval-train-dexes.R
deleted file mode 100644
index a74a06c0..00000000
--- a/tests/testthat/test-make-eval-train-dexes.R
+++ /dev/null
@@ -1,93 +0,0 @@
-##############################################
-
-test_that("1. Input checks", {
-  # s2dv_cube
-  expect_error(
-    .make.eval.train.dexes(eval.method = 1, 2),
-    paste0("unknown sampling method: 1")
-  )
-  expect_error(
-   .make.eval.train.dexes(eval.method = 'k-fold', 10, NULL, 12),
-    paste0("k needs to be a positive integer less than the amt.points")
-  )
-  expect_error(
-   .make.eval.train.dexes(eval.method = 'retrospective', 10, NULL, 10),
-    paste0("k needs to be a positive integer less than the amt.points")
-  )
-})
-
-##############################################
-
-test_that("2. Output checks: k-fold", {
-  expect_equal(
-    is.list(.make.eval.train.dexes(eval.method = 'k-fold', 10, NULL, 5)),
-    TRUE
-  )
-  expect_equal(
-   is.list(.make.eval.train.dexes(eval.method = 'k-fold', 10, NULL, 5)[[1]]),
-    TRUE
-  )
-  expect_equal(
-   length(.make.eval.train.dexes(eval.method = 'k-fold', 10, NULL, 5)),
-    10
-  )
-  expect_equal(
-   names(.make.eval.train.dexes(eval.method = 'k-fold', 10, NULL, 5)[[1]]),
-    c("eval.dexes", "train.dexes")
-  )
-  expect_equal(
-   .make.eval.train.dexes(eval.method = 'k-fold', 10, NULL, 5)[[1]],
-    list(eval.dexes = 1,
-         train.dexes = 4:8)
-  )
-   expect_equal(
-   .make.eval.train.dexes(eval.method = 'k-fold', 10, NULL, 5)[[2]],
-    list(eval.dexes = 2, 
-         train.dexes = 5:9)
-  )
-   expect_equal(
-   .make.eval.train.dexes(eval.method = 'k-fold', 10, NULL, 5)[[3]],
-    list(eval.dexes = 3,
-         train.dexes = 6:10)
-  )
-   expect_equal(
-   .make.eval.train.dexes(eval.method = 'k-fold', 10, NULL, 5)[[9]],
-    list(eval.dexes = 9,
-         train.dexes = 2:6)
-  )
-   expect_equal(
-   .make.eval.train.dexes(eval.method = 'k-fold', 10, NULL, 5)[[10]],
-    list(eval.dexes = 10,
-         train.dexes = 3:7)
-  )
-  expect_equal(
-   .make.eval.train.dexes(eval.method = 'k-fold', 10, NULL, 1),
-   .make.eval.train.dexes(eval.method = 'leave-one-out', 10, NULL)
-  )
-  expect_equal(
-   .make.eval.train.dexes(eval.method = 'k-fold', 20, NULL, 1),
-   .make.eval.train.dexes(eval.method = 'leave-one-out', 20, NULL)
-  )
-})
-
-##############################################
-
-test_that("3. Output checks: retrospective", {
-  expect_equal(
-    length(.make.eval.train.dexes(eval.method = 'retrospective', 10, NULL, 3)),
-    7
-  )
-  expect_equal(
-    .make.eval.train.dexes(eval.method = 'retrospective', 10, NULL, 3)[[1]],
-    list(eval.dexes = 4, train.dexes = 1:3)
-  )
-  expect_equal(
-    .make.eval.train.dexes(eval.method = 'retrospective', 10, NULL, 3)[[2]],
-    list(eval.dexes = 5, train.dexes = 1:4)
-  )
-  expect_equal(
-    .make.eval.train.dexes(eval.method = 'retrospective', 10, NULL, 3)[[7]],
-    list(eval.dexes = 10, train.dexes = 1:9)
-  )
-})
-
-- 
GitLab


From 45bd5f9712504a0c6e39c69179b7995b8f774f69 Mon Sep 17 00:00:00 2001
From: THEERTHA KARIYATHAN <tkariyat@bscearth421.int.bsc.es>
Date: Thu, 20 Mar 2025 15:06:03 +0100
Subject: [PATCH 4/9] rename fun and update doc

---
 R/CST_Calibration.R                         |  23 +++--
 R/CST_CategoricalEnsCombination.R           |  17 ++-
 R/{CST_TrainIndex.R => Eval_TrainIndices.R} |  25 +++--
 tests/testthat/test-CST_TrainIndex.R        | 108 --------------------
 tests/testthat/test-Eval_TrainIndices.R     | 108 ++++++++++++++++++++
 5 files changed, 148 insertions(+), 133 deletions(-)
 rename R/{CST_TrainIndex.R => Eval_TrainIndices.R} (84%)
 delete mode 100644 tests/testthat/test-CST_TrainIndex.R
 create mode 100644 tests/testthat/test-Eval_TrainIndices.R

diff --git a/R/CST_Calibration.R b/R/CST_Calibration.R
index 3b0bf04a..093814fe 100644
--- a/R/CST_Calibration.R
+++ b/R/CST_Calibration.R
@@ -39,9 +39,10 @@
 #'  can be either \code{bias}, \code{evmos}, \code{mse_min}, \code{crps_min} or 
 #'  \code{rpc-based}. Default value is \code{mse_min}.
 #'@param eval.method A character string indicating the sampling method used, it 
-#'  can be either \code{in-sample} or \code{leave-one-out}. Default value is the 
-#'  \code{leave-one-out} cross validation. In case the forecast is provided, any 
-#'  chosen eval.method is over-ruled and a third option is used.
+#'  can be either \code{in-sample}, \code{leave-k-out}, \code{retrospective} or 
+#'  \code{hindcast-vs-forecast}. Default value is the \code{leave-k-out} cross validation. 
+#'  In case the forecast is provided, any chosen eval.method is over-ruled 
+#'  and a third option is used.
 #'@param multi.model A boolean that is used only for the \code{mse_min} 
 #'  method. If multi-model ensembles or ensembles of different sizes are used, 
 #'  it must be set to \code{TRUE}. By default it is \code{FALSE}. Differences 
@@ -207,7 +208,7 @@ CST_Calibration <- function(exp, obs, exp_cor = NULL, cal.method = "mse_min",
 #'minimizes the Continuous Ranked Probability Score (CRPS). The 
 #'\code{"rpc-based"} method adjusts the forecast variance ensuring that the 
 #'ratio of predictable components (RPC) is equal to one, as in Eade et al. 
-#'(2014). Both in-sample or our out-of-sample (leave-one-out cross 
+#'(2014). Both in-sample or our out-of-sample (leave-k-out cross 
 #'validation) calibration are possible.
 #'
 #'@param exp A multidimensional array with named dimensions (at least 'sdate' 
@@ -226,11 +227,11 @@ CST_Calibration <- function(exp, obs, exp_cor = NULL, cal.method = "mse_min",
 #'@param cal.method A character string indicating the calibration method used, 
 #'  can be either \code{bias}, \code{evmos}, \code{mse_min}, \code{crps_min} 
 #'  or \code{rpc-based}. Default value is \code{mse_min}.
-#'@param eval.method A character string indicating the sampling method used, 
-#'  can be either \code{in-sample} or \code{leave-one-out}. Default value is 
-#'  the \code{leave-one-out} cross validation. In case the forecast is 
-#'  provided, any chosen eval.method is over-ruled and a third option is 
-#'  used.
+#'@param eval.method A character string indicating the sampling method used, it 
+#'  can be either \code{in-sample}, \code{leave-k-out}, \code{retrospective} or 
+#'  \code{hindcast-vs-forecast}. Default value is the \code{leave-k-out} cross validation. 
+#'  In case the forecast is provided, any chosen eval.method is over-ruled 
+#'  and a third option is used.
 #'@param multi.model A boolean that is used only for the \code{mse_min} 
 #'  method. If multi-model ensembles or ensembles of different sizes are used, 
 #'  it must be set to \code{TRUE}. By default it is \code{FALSE}. Differences 
@@ -348,7 +349,7 @@ Calibration <- function(exp, obs, exp_cor = NULL,
     # if exp_cor is provided, it will be calibrated: "calibrate forecast instead of hindcast"
     # if exp_cor is provided, eval.method is overruled (because if exp_cor is provided, the 
     # train data will be all data of "exp" and the evalutaion data will be all data of "exp_cor"; 
-    # no need for "leave-one-out" or "in-sample")
+    # no need for "leave-k-out" or "in-sample")
     eval.method <- "hindcast-vs-forecast"
     expcordims <- names(dim(exp_cor))
     if (is.null(expcordims)) {
@@ -641,7 +642,7 @@ Calibration <- function(exp, obs, exp_cor = NULL,
           expcor_data <- exp_cor
         }
 
-        eval.train.dexeses <- CST_TrainIndex(eval.method = eval.method, 
+        eval.train.dexeses <- Eval_TrainIndices(eval.method = eval.method, 
                                                      amt.points = sdate, 
                                                      amt.points_cor = sdate_cor, 
                                                      k = k, tail.out = tail.out)
diff --git a/R/CST_CategoricalEnsCombination.R b/R/CST_CategoricalEnsCombination.R
index a242d616..0e4e477c 100644
--- a/R/CST_CategoricalEnsCombination.R
+++ b/R/CST_CategoricalEnsCombination.R
@@ -59,6 +59,13 @@
 #'@param eval.method Is the sampling method used, can be either 
 #'  \code{"in-sample"} or \code{"leave-k-out"}. Default value is the 
 #'  \code{"leave-k-out"} cross validation. 
+#'@param k  k Positive integer. Default = 1.
+#'  In method \code{leave-k-out}, \code{k} is expected to be odd integer, indicating the number of points to leave out.
+#'  In method \code{retrospective}, \code{k} can be any positive integer, indicating when to start.
+#'@param tail.out Boolean for 'leave-k-out' method; TRUE to remove both extremes 
+#'  keeping the same sample size for all k-folds (e.g. amt.points=50, k=3, 
+#'  eval.dexes=1, train.dexes={3,49}). FALSE to remove only the corresponding tail (e.g..
+#'  amt.points=50, k=3, eval.dexes=1, train.dexes={3,50})  
 #'@param ... other parameters to be passed on to the calibration procedure.
 #'
 #'@return An object of class \code{s2dv_cube} containing the categorical 
@@ -154,9 +161,11 @@ CST_CategoricalEnsCombination <- function(exp, obs, cat.method = "pool",
 #'  Rajagopalan et al. (2002), Robertson et al. (2004) and Van Schaeybroeck and 
 #'  Vannitsem (2019). Finally, the \code{obs} method classifies the observations
 #'  into the different categories and therefore contains only 0 and 1 values. 
-#'@param eval.method Is the sampling method used, can be either 
-#'  \code{"in-sample"} or \code{"leave-k-out"}. Default value is the 
-#'  \code{"leave-k-out"} cross validation.
+#'@param eval.method A character string indicating the sampling method used, it 
+#'  can be either \code{in-sample}, \code{leave-k-out}, \code{retrospective} or 
+#'  \code{hindcast-vs-forecast}. Default value is the \code{leave-k-out} cross validation. 
+#'  In case the forecast is provided, any chosen eval.method is over-ruled 
+#'  and a third option is used.
 #'@param ... Other parameters to be passed on to the calibration procedure.
 #'
 #'@return An array containing the categorical forecasts in the element called 
@@ -304,7 +313,7 @@ comb.dims <- function(arr.in, dims.to.combine){
   amt.coeff <- amt.mdl + 1
   var.cat.fc <- array(NA, c(amt.cat, amt.sdate))
   
-  eval.train.dexeses <- CST_TrainIndex(eval.method = eval.method, amt.points = amt.sdate, k = k, tail.out = tail.out)
+  eval.train.dexeses <- Eval_TrainIndices(eval.method = eval.method, amt.points = amt.sdate, k = k, tail.out = tail.out)
   amt.resamples <- length(eval.train.dexeses)	
   
   for (i.sample in seq(1, amt.resamples)) {
diff --git a/R/CST_TrainIndex.R b/R/Eval_TrainIndices.R
similarity index 84%
rename from R/CST_TrainIndex.R
rename to R/Eval_TrainIndices.R
index 3806e3b2..b6949726 100644
--- a/R/CST_TrainIndex.R
+++ b/R/Eval_TrainIndices.R
@@ -1,19 +1,24 @@
 #' Generate Training and Evaluation Indices for Cross-Validation
 #'
-#' This function generates training and evaluation indices based on different cross-validation methods.
+#' This function generates training and evaluation indices based on different
+#' cross-validation methods.
 #' @author Theertha Kariyathan, \email{theertha.kariyathan@bsc.es}
 #' 
 #' @param eval.method Character. The cross-validation method. Options include:
 #'   -\code{leave-k-out}: Leaves out \code{k} points at a time for evaluation.
 #'   -\code{retrospective}: Uses past data for training and a future point for evaluation.
 #'   -\code{in-sample}: Uses the entire dataset for both training and evaluation.
-#'   -\code{hindcast-vs-forecast}: Uses a subset \code{amt.points_cor} for evaluation while training on \code{amt.points}.
+#'   -\code{hindcast-vs-forecast}: Uses a subset \code{amt.points_cor} for 
+#'   evaluation while training on \code{amt.points}.
 #'   
 #' @param amt.points Integer. Total number of points in the dataset.
-#' @param amt.points_cor Integer. Number of points for evaluation in the \code{hindcast-vs-forecast} method.
+#' @param amt.points_cor Integer. Number of points for evaluation in the
+#'  \code{hindcast-vs-forecast} method.
 #' @param k Positive integer. Default = 1.
-#' In method \code{leave-k-out}, \code{k} is expected to be odd integer, indicating the number of points to leave out.
-#' In method \code{retrospective}, \code{k} can be any positive integer, indicating when to start. 
+#' In method \code{leave-k-out}, \code{k} is expected to be odd integer, 
+#' indicating the number of points to leave out.
+#' In method \code{retrospective}, \code{k} can be any positive integer, 
+#' indicating when to start. 
 #' @param tail.out Logical for method \code{leave-k-out}. Default = TRUE.  
 #'  TRUE to remove both extremes keeping the same sample size for all k-folds 
 #'  (e.g. amt.points=50, k=3, eval.dexes=1, train.dexes={3,49}). 
@@ -25,16 +30,16 @@
 #'
 #' @examples
 #' # Leave-k-out cross-validation
-#' CST_TrainIndex("leave-k-out", amt.points = 10, amt.points_cor = 5, k = 3)
+#' Eval_TrainIndices("leave-k-out", amt.points = 10, amt.points_cor = 5, k = 3)
 #' # Retrospective cross-validation
-#' CST_TrainIndex("retrospective", amt.points = 10, amt.points_cor = 5, k = 3)
+#' Eval_TrainIndices("retrospective", amt.points = 10, amt.points_cor = 5, k = 3)
 #' # In-sample validation
-#' CST_TrainIndex("in-sample", amt.points = 10, amt.points_cor = 5)
+#' Eval_TrainIndices("in-sample", amt.points = 10, amt.points_cor = 5)
 #' # Hindcast vs. Forecast validation
-#' CST_TrainIndex("hindcast-vs-forecast", amt.points = 10, amt.points_cor = 5)
+#' Eval_TrainIndices("hindcast-vs-forecast", amt.points = 10, amt.points_cor = 5)
 #'
 #' @export
-CST_TrainIndex <- function(eval.method, amt.points, amt.points_cor, 
+Eval_TrainIndices <- function(eval.method, amt.points, amt.points_cor, 
                            k = 1, tail.out = TRUE) {
   
   if (is.null(k) || k >= amt.points || k < 1 || k %% 2 == 0 ) { 
diff --git a/tests/testthat/test-CST_TrainIndex.R b/tests/testthat/test-CST_TrainIndex.R
deleted file mode 100644
index 3618019f..00000000
--- a/tests/testthat/test-CST_TrainIndex.R
+++ /dev/null
@@ -1,108 +0,0 @@
-
-##############################################
-
-test_that("1. Input checks", {
-  # s2dv_cube
-  expect_error(
-    CST_TrainIndex(eval.method = 1, 2),
-    paste0("unknown sampling method: 1")
-  )
-  expect_error(
-    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 12),
-    paste0("k needs to be a positive odd integer less than the amt.points")
-  )
-  expect_error(
-    CST_TrainIndex(eval.method = 'retrospective', 10, NULL, 10),
-    paste0("k needs to be a positive odd integer less than the amt.points")
-  )
-})
-
-##############################################
-
-test_that("2. Output checks: leave-k-out", {
-  expect_equal(
-    is.list(CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)),
-    TRUE
-  )
-  expect_equal(
-    is.list(CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)[[1]]),
-    TRUE
-  )
-  expect_equal(
-    length(CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)),
-    10
-  )
-  expect_equal(
-    names(CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)[[1]]),
-    c("eval.dexes", "train.dexes")
-  )
-  expect_equal(
-    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)[[1]],
-    list(eval.dexes = 1,
-         train.dexes = 4:8)
-  )
-  expect_equal(
-    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)[[2]],
-    list(eval.dexes = 2, 
-         train.dexes = 5:9)
-  )
-  expect_equal(
-    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)[[3]],
-    list(eval.dexes = 3,
-         train.dexes = 6:10)
-  )
-  expect_equal(
-    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)[[9]],
-    list(eval.dexes = 9,
-         train.dexes = 2:6)
-  )
-  expect_equal(
-    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5)[[10]],
-    list(eval.dexes = 10,
-         train.dexes = 3:7)
-  )
-  expect_equal(
-    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5, tail.out = FALSE)[[1]],
-    list(eval.dexes = 1,
-         train.dexes = 4:10)
-  )
-  expect_equal(
-    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5, tail.out = FALSE)[[5]],
-    list(eval.dexes = 5,
-         train.dexes = c(1,2,8:10))
-  )
-  expect_equal(
-    CST_TrainIndex(eval.method = 'leave-k-out', 10, NULL, 5, tail.out = FALSE)[[10]],
-    list(eval.dexes = 10,
-         train.dexes = c(1:7))
-  )
-  expect_equal(
-    CST_TrainIndex(eval.method = 'leave-k-out', 20, NULL, 1)[[1]],
-    CST_TrainIndex(eval.method = 'leave-k-out', 20, NULL, 1, tail.out = FALSE)[[1]]
-  )
-  
-})
-
-##############################################
-
-test_that("3. Output checks: retrospective", {
-  expect_equal(
-    length(CST_TrainIndex(eval.method = 'retrospective', 10, NULL, 3)),
-    7
-  )
-  expect_equal(
-    CST_TrainIndex(eval.method = 'retrospective', 10, NULL, 3)[[1]],
-    list(eval.dexes = 4, train.dexes = 1:3)
-  )
-  expect_equal(
-    CST_TrainIndex(eval.method = 'retrospective', 10, NULL, 3)[[2]],
-    list(eval.dexes = 5, train.dexes = 1:4)
-  )
-  expect_equal(
-    CST_TrainIndex(eval.method = 'retrospective', 10, NULL, 3)[[7]],
-    list(eval.dexes = 10, train.dexes = 1:9)
-  )
-})
-
-
-  
\ No newline at end of file
diff --git a/tests/testthat/test-Eval_TrainIndices.R b/tests/testthat/test-Eval_TrainIndices.R
new file mode 100644
index 00000000..0cb95eea
--- /dev/null
+++ b/tests/testthat/test-Eval_TrainIndices.R
@@ -0,0 +1,108 @@
+
+##############################################
+
+test_that("1. Input checks", {
+  # s2dv_cube
+  expect_error(
+    Eval_TrainIndices(eval.method = 1, 2),
+    paste0("unknown sampling method: 1")
+  )
+  expect_error(
+    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 12),
+    paste0("k needs to be a positive odd integer less than the amt.points")
+  )
+  expect_error(
+    Eval_TrainIndices(eval.method = 'retrospective', 10, NULL, 10),
+    paste0("k needs to be a positive odd integer less than the amt.points")
+  )
+})
+
+##############################################
+
+test_that("2. Output checks: leave-k-out", {
+  expect_equal(
+    is.list(Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)),
+    TRUE
+  )
+  expect_equal(
+    is.list(Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[1]]),
+    TRUE
+  )
+  expect_equal(
+    length(Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)),
+    10
+  )
+  expect_equal(
+    names(Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[1]]),
+    c("eval.dexes", "train.dexes")
+  )
+  expect_equal(
+    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[1]],
+    list(eval.dexes = 1,
+         train.dexes = 4:8)
+  )
+  expect_equal(
+    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[2]],
+    list(eval.dexes = 2, 
+         train.dexes = 5:9)
+  )
+  expect_equal(
+    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[3]],
+    list(eval.dexes = 3,
+         train.dexes = 6:10)
+  )
+  expect_equal(
+    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[9]],
+    list(eval.dexes = 9,
+         train.dexes = 2:6)
+  )
+  expect_equal(
+    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[10]],
+    list(eval.dexes = 10,
+         train.dexes = 3:7)
+  )
+  expect_equal(
+    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5, tail.out = FALSE)[[1]],
+    list(eval.dexes = 1,
+         train.dexes = 4:10)
+  )
+  expect_equal(
+    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5, tail.out = FALSE)[[5]],
+    list(eval.dexes = 5,
+         train.dexes = c(1,2,8:10))
+  )
+  expect_equal(
+    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5, tail.out = FALSE)[[10]],
+    list(eval.dexes = 10,
+         train.dexes = c(1:7))
+  )
+  expect_equal(
+    Eval_TrainIndices(eval.method = 'leave-k-out', 20, NULL, 1)[[1]],
+    Eval_TrainIndices(eval.method = 'leave-k-out', 20, NULL, 1, tail.out = FALSE)[[1]]
+  )
+  
+})
+
+##############################################
+
+test_that("3. Output checks: retrospective", {
+  expect_equal(
+    length(Eval_TrainIndices(eval.method = 'retrospective', 10, NULL, 3)),
+    7
+  )
+  expect_equal(
+    Eval_TrainIndices(eval.method = 'retrospective', 10, NULL, 3)[[1]],
+    list(eval.dexes = 4, train.dexes = 1:3)
+  )
+  expect_equal(
+    Eval_TrainIndices(eval.method = 'retrospective', 10, NULL, 3)[[2]],
+    list(eval.dexes = 5, train.dexes = 1:4)
+  )
+  expect_equal(
+    Eval_TrainIndices(eval.method = 'retrospective', 10, NULL, 3)[[7]],
+    list(eval.dexes = 10, train.dexes = 1:9)
+  )
+})
+
+
+  
\ No newline at end of file
-- 
GitLab


From c213a3333d64fec34a6cfdc6e189b6aa5c9a1f0d Mon Sep 17 00:00:00 2001
From: THEERTHA KARIYATHAN <tkariyat@bscearth421.int.bsc.es>
Date: Mon, 31 Mar 2025 12:20:40 +0200
Subject: [PATCH 5/9] update doc,sanity, rename var

---
 R/CST_Calibration.R                           |  14 +--
 R/CST_CategoricalEnsCombination.R             |   6 +-
 R/{Eval_TrainIndices.R => EvalTrainIndices.R} |  54 ++++-----
 tests/testthat/test-EvalTrainIndices.R        | 108 ++++++++++++++++++
 tests/testthat/test-Eval_TrainIndices.R       | 108 ------------------
 5 files changed, 145 insertions(+), 145 deletions(-)
 rename R/{Eval_TrainIndices.R => EvalTrainIndices.R} (62%)
 create mode 100644 tests/testthat/test-EvalTrainIndices.R
 delete mode 100644 tests/testthat/test-Eval_TrainIndices.R

diff --git a/R/CST_Calibration.R b/R/CST_Calibration.R
index 093814fe..c5d87469 100644
--- a/R/CST_Calibration.R
+++ b/R/CST_Calibration.R
@@ -78,9 +78,9 @@
 #'  In method \code{leave-k-out}, \code{k} is expected to be odd integer, indicating the number of points to leave out.
 #'  In method \code{retrospective}, \code{k} can be any positive integer, indicating when to start. 
 #'@param tail.out Boolean for 'leave-k-out' method; TRUE to remove both extremes 
-#'  keeping the same sample size for all k-folds (e.g. amt.points=50, k=3, 
+#'  keeping the same sample size for all k-folds (e.g. sample.length=50, k=3, 
 #'  eval.dexes=1, train.dexes={3,49}). FALSE to remove only the corresponding tail (e.g..
-#'  amt.points=50, k=3, eval.dexes=1, train.dexes={3,50})
+#'  sample.length=50, k=3, eval.dexes=1, train.dexes={3,50})
 #' 
 #'@return An object of class \code{s2dv_cube} containing the calibrated 
 #'forecasts in the element \code{data} with the dimensions nexp, nobs and same 
@@ -266,9 +266,9 @@ CST_Calibration <- function(exp, obs, exp_cor = NULL, cal.method = "mse_min",
 #'  In method \code{leave-k-out}, \code{k} is expected to be odd integer, indicating the number of points to leave out.
 #'  In method \code{retrospective}, \code{k} can be any positive integer, indicating when to start.
 #'@param tail.out Boolean for 'leave-k-out' method; TRUE to remove both extremes 
-#'  keeping the same sample size for all k-folds (e.g. amt.points=50, k=3, 
+#'  keeping the same sample size for all k-folds (e.g. sample.length=50, k=3, 
 #'  eval.dexes=1, train.dexes={3,49}). FALSE to remove only the corresponding tail (e.g..
-#'  amt.points=50, k=3, eval.dexes=1, train.dexes={3,50})
+#'  sample.length=50, k=3, eval.dexes=1, train.dexes={3,50})
 #' 
 #'@return An array containing the calibrated forecasts with the dimensions 
 #'nexp, nobs and same dimensions as in the 'exp' array. nexp is the number of 
@@ -642,9 +642,9 @@ Calibration <- function(exp, obs, exp_cor = NULL,
           expcor_data <- exp_cor
         }
 
-        eval.train.dexeses <- Eval_TrainIndices(eval.method = eval.method, 
-                                                     amt.points = sdate, 
-                                                     amt.points_cor = sdate_cor, 
+        eval.train.dexeses <- EvalTrainIndices(eval.method = eval.method, 
+                                                     sample.length = sdate, 
+                                                     sample.length_cor = sdate_cor, 
                                                      k = k, tail.out = tail.out)
         amt.resamples <- length(eval.train.dexeses)
         for (i.sample in seq(1, amt.resamples)) {
diff --git a/R/CST_CategoricalEnsCombination.R b/R/CST_CategoricalEnsCombination.R
index 0e4e477c..94ef489f 100644
--- a/R/CST_CategoricalEnsCombination.R
+++ b/R/CST_CategoricalEnsCombination.R
@@ -63,9 +63,9 @@
 #'  In method \code{leave-k-out}, \code{k} is expected to be odd integer, indicating the number of points to leave out.
 #'  In method \code{retrospective}, \code{k} can be any positive integer, indicating when to start.
 #'@param tail.out Boolean for 'leave-k-out' method; TRUE to remove both extremes 
-#'  keeping the same sample size for all k-folds (e.g. amt.points=50, k=3, 
+#'  keeping the same sample size for all k-folds (e.g. sample.length=50, k=3, 
 #'  eval.dexes=1, train.dexes={3,49}). FALSE to remove only the corresponding tail (e.g..
-#'  amt.points=50, k=3, eval.dexes=1, train.dexes={3,50})  
+#'  sample.length=50, k=3, eval.dexes=1, train.dexes={3,50})  
 #'@param ... other parameters to be passed on to the calibration procedure.
 #'
 #'@return An object of class \code{s2dv_cube} containing the categorical 
@@ -313,7 +313,7 @@ comb.dims <- function(arr.in, dims.to.combine){
   amt.coeff <- amt.mdl + 1
   var.cat.fc <- array(NA, c(amt.cat, amt.sdate))
   
-  eval.train.dexeses <- Eval_TrainIndices(eval.method = eval.method, amt.points = amt.sdate, k = k, tail.out = tail.out)
+  eval.train.dexeses <- EvalTrainIndices(eval.method = eval.method, sample.length = amt.sdate, k = k, tail.out = tail.out)
   amt.resamples <- length(eval.train.dexeses)	
   
   for (i.sample in seq(1, amt.resamples)) {
diff --git a/R/Eval_TrainIndices.R b/R/EvalTrainIndices.R
similarity index 62%
rename from R/Eval_TrainIndices.R
rename to R/EvalTrainIndices.R
index b6949726..d0fb3fd8 100644
--- a/R/Eval_TrainIndices.R
+++ b/R/EvalTrainIndices.R
@@ -8,11 +8,11 @@
 #'   -\code{leave-k-out}: Leaves out \code{k} points at a time for evaluation.
 #'   -\code{retrospective}: Uses past data for training and a future point for evaluation.
 #'   -\code{in-sample}: Uses the entire dataset for both training and evaluation.
-#'   -\code{hindcast-vs-forecast}: Uses a subset \code{amt.points_cor} for 
-#'   evaluation while training on \code{amt.points}.
+#'   -\code{hindcast-vs-forecast}: Uses all years from the hindcast sdate dimension
+#'    as training and all years from the forecast sdate dimension will be corrected.
 #'   
-#' @param amt.points Integer. Total number of points in the dataset.
-#' @param amt.points_cor Integer. Number of points for evaluation in the
+#' @param sample.length Integer. Length of the dataset.
+#' @param sample.length_cor Integer. Length of forecast dataset in
 #'  \code{hindcast-vs-forecast} method.
 #' @param k Positive integer. Default = 1.
 #' In method \code{leave-k-out}, \code{k} is expected to be odd integer, 
@@ -21,55 +21,55 @@
 #' indicating when to start. 
 #' @param tail.out Logical for method \code{leave-k-out}. Default = TRUE.  
 #'  TRUE to remove both extremes keeping the same sample size for all k-folds 
-#'  (e.g. amt.points=50, k=3, eval.dexes=1, train.dexes={3,49}). 
+#'  (e.g. sample.length=50, k=3, eval.dexes=1, train.dexes={3,49}). 
 #'  FALSE to remove only the corresponding tail 
-#'  (e.g. amt.points=50, k=3, eval.dexes=1, train.dexes={3,50})
+#'  (e.g. sample.length=50, k=3, eval.dexes=1, train.dexes={3,50})
 #' @return A list of lists, where each element contains:
 #'   \code{eval.dexes}: Indices of evaluation points.
 #'   \code{train.dexes}: Indices of training points.
 #'
 #' @examples
 #' # Leave-k-out cross-validation
-#' Eval_TrainIndices("leave-k-out", amt.points = 10, amt.points_cor = 5, k = 3)
+#' Eval_TrainIndices("leave-k-out", sample.length = 10, sample.length_cor = 5, k = 3)
 #' # Retrospective cross-validation
-#' Eval_TrainIndices("retrospective", amt.points = 10, amt.points_cor = 5, k = 3)
+#' Eval_TrainIndices("retrospective", sample.length = 10, sample.length_cor = 5, k = 3)
 #' # In-sample validation
-#' Eval_TrainIndices("in-sample", amt.points = 10, amt.points_cor = 5)
+#' Eval_TrainIndices("in-sample", sample.length = 10, sample.length_cor = 5)
 #' # Hindcast vs. Forecast validation
-#' Eval_TrainIndices("hindcast-vs-forecast", amt.points = 10, amt.points_cor = 5)
+#' Eval_TrainIndices("hindcast-vs-forecast", sample.length = 10, sample.length_cor = 5)
 #'
 #' @export
-Eval_TrainIndices <- function(eval.method, amt.points, amt.points_cor, 
+EvalTrainIndices <- function(eval.method, sample.length, sample.length_cor, 
                            k = 1, tail.out = TRUE) {
   
-  if (is.null(k) || k >= amt.points || k < 1 || k %% 2 == 0 ) { 
-    stop("k needs to be a positive odd integer less than the amt.points")
-  }
-  
-  if ( k %% 2 == 0 ) { 
-    warning("k is expected to be an odd integer")
-  }
-  
   if (eval.method == "leave-k-out") {
+    
+    if (is.null(k) || k >= sample.length || k < 1 || k %% 2 == 0 ) { 
+      warning("k is expected to be a positive odd integer less than the sample.length")
+    }
+    
     if (k == 1) {
       tail.out == TRUE
     }
-    amt.seq <- 1:amt.points
+    amt.seq <- 1:sample.length
     strike = (k - 1) / 2
     alt_amt.seq <- c(tail(amt.seq, strike), amt.seq, head(amt.seq, strike))
     
-    dexes.lst <- lapply(seq(1, amt.points), function(x, kfold = k) {
+    dexes.lst <- lapply(seq(1, sample.length), function(x, kfold = k) {
       if (tail.out) {
         ind = alt_amt.seq[x:(x + (kfold - 1))]
       } else{
         ind = ((x - strike):(x + strike))
-        ind = ind[ind > 0 & ind <= amt.points]
+        ind = ind[ind > 0 & ind <= sample.length]
       }
       return(list(eval.dexes = x,  train.dexes = amt.seq[!(amt.seq %in% ind)]))
     })
   } else if (eval.method == "retrospective") {
     # k can be any integer indicating the when to start
-    dexes.lst <- base::Filter(length, lapply(seq(1, amt.points),
+    if(k >= sample.length){
+      warning("k is expected to be less than the sample.length")
+    }
+    dexes.lst <- base::Filter(length, lapply(seq(1, sample.length),
                                              function(x, mindata = k) {
                                                if (x > k) { 
                                                  eval.dexes <- x
@@ -79,11 +79,11 @@ Eval_TrainIndices <- function(eval.method, amt.points, amt.points_cor,
                                                }})) 
 
   } else if (eval.method == "in-sample") {
-    dexes.lst <- list(list(eval.dexes = seq(1, amt.points), 
-                           train.dexes = seq(1, amt.points)))
+    dexes.lst <- list(list(eval.dexes = seq(1, sample.length), 
+                           train.dexes = seq(1, sample.length)))
   } else if (eval.method == "hindcast-vs-forecast") {
-    dexes.lst <- list(list(eval.dexes = seq(1,amt.points_cor),
-                           train.dexes = seq(1, amt.points)))
+    dexes.lst <- list(list(eval.dexes = seq(1, sample.length_cor),
+                           train.dexes = seq(1, sample.length)))
   } else {
     stop(paste0("unknown sampling method: ", eval.method))
   }
diff --git a/tests/testthat/test-EvalTrainIndices.R b/tests/testthat/test-EvalTrainIndices.R
new file mode 100644
index 00000000..62a33707
--- /dev/null
+++ b/tests/testthat/test-EvalTrainIndices.R
@@ -0,0 +1,108 @@
+
+##############################################
+
+test_that("1. Input checks", {
+  # s2dv_cube
+  expect_error(
+    EvalTrainIndices(eval.method = 1, 2),
+    paste0("unknown sampling method: 1")
+  )
+  expect_warning(
+    EvalTrainIndices(eval.method = 'leave-k-out', 10, NULL, 12),
+    paste0("k is expected to be a positive odd integer less than the sample.length")
+  )
+  expect_warning(
+    EvalTrainIndices(eval.method = 'retrospective', 10, NULL, 10),
+    paste0("k is expected to be less than the sample.length")
+  )
+})
+
+##############################################
+
+test_that("2. Output checks: leave-k-out", {
+  expect_equal(
+    is.list(EvalTrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)),
+    TRUE
+  )
+  expect_equal(
+    is.list(EvalTrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[1]]),
+    TRUE
+  )
+  expect_equal(
+    length(EvalTrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)),
+    10
+  )
+  expect_equal(
+    names(EvalTrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[1]]),
+    c("eval.dexes", "train.dexes")
+  )
+  expect_equal(
+    EvalTrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[1]],
+    list(eval.dexes = 1,
+         train.dexes = 4:8)
+  )
+  expect_equal(
+    EvalTrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[2]],
+    list(eval.dexes = 2, 
+         train.dexes = 5:9)
+  )
+  expect_equal(
+    EvalTrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[3]],
+    list(eval.dexes = 3,
+         train.dexes = 6:10)
+  )
+  expect_equal(
+    EvalTrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[9]],
+    list(eval.dexes = 9,
+         train.dexes = 2:6)
+  )
+  expect_equal(
+    EvalTrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[10]],
+    list(eval.dexes = 10,
+         train.dexes = 3:7)
+  )
+  expect_equal(
+    EvalTrainIndices(eval.method = 'leave-k-out', 10, NULL, 5, tail.out = FALSE)[[1]],
+    list(eval.dexes = 1,
+         train.dexes = 4:10)
+  )
+  expect_equal(
+    EvalTrainIndices(eval.method = 'leave-k-out', 10, NULL, 5, tail.out = FALSE)[[5]],
+    list(eval.dexes = 5,
+         train.dexes = c(1,2,8:10))
+  )
+  expect_equal(
+    EvalTrainIndices(eval.method = 'leave-k-out', 10, NULL, 5, tail.out = FALSE)[[10]],
+    list(eval.dexes = 10,
+         train.dexes = c(1:7))
+  )
+  expect_equal(
+    EvalTrainIndices(eval.method = 'leave-k-out', 20, NULL, 1)[[1]],
+    EvalTrainIndices(eval.method = 'leave-k-out', 20, NULL, 1, tail.out = FALSE)[[1]]
+  )
+  
+})
+
+##############################################
+
+test_that("3. Output checks: retrospective", {
+  expect_equal(
+    length(EvalTrainIndices(eval.method = 'retrospective', 10, NULL, 3)),
+    7
+  )
+  expect_equal(
+    EvalTrainIndices(eval.method = 'retrospective', 10, NULL, 3)[[1]],
+    list(eval.dexes = 4, train.dexes = 1:3)
+  )
+  expect_equal(
+    EvalTrainIndices(eval.method = 'retrospective', 10, NULL, 3)[[2]],
+    list(eval.dexes = 5, train.dexes = 1:4)
+  )
+  expect_equal(
+    EvalTrainIndices(eval.method = 'retrospective', 10, NULL, 3)[[7]],
+    list(eval.dexes = 10, train.dexes = 1:9)
+  )
+})
+
+
+  
\ No newline at end of file
diff --git a/tests/testthat/test-Eval_TrainIndices.R b/tests/testthat/test-Eval_TrainIndices.R
deleted file mode 100644
index 0cb95eea..00000000
--- a/tests/testthat/test-Eval_TrainIndices.R
+++ /dev/null
@@ -1,108 +0,0 @@
-
-##############################################
-
-test_that("1. Input checks", {
-  # s2dv_cube
-  expect_error(
-    Eval_TrainIndices(eval.method = 1, 2),
-    paste0("unknown sampling method: 1")
-  )
-  expect_error(
-    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 12),
-    paste0("k needs to be a positive odd integer less than the amt.points")
-  )
-  expect_error(
-    Eval_TrainIndices(eval.method = 'retrospective', 10, NULL, 10),
-    paste0("k needs to be a positive odd integer less than the amt.points")
-  )
-})
-
-##############################################
-
-test_that("2. Output checks: leave-k-out", {
-  expect_equal(
-    is.list(Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)),
-    TRUE
-  )
-  expect_equal(
-    is.list(Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[1]]),
-    TRUE
-  )
-  expect_equal(
-    length(Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)),
-    10
-  )
-  expect_equal(
-    names(Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[1]]),
-    c("eval.dexes", "train.dexes")
-  )
-  expect_equal(
-    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[1]],
-    list(eval.dexes = 1,
-         train.dexes = 4:8)
-  )
-  expect_equal(
-    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[2]],
-    list(eval.dexes = 2, 
-         train.dexes = 5:9)
-  )
-  expect_equal(
-    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[3]],
-    list(eval.dexes = 3,
-         train.dexes = 6:10)
-  )
-  expect_equal(
-    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[9]],
-    list(eval.dexes = 9,
-         train.dexes = 2:6)
-  )
-  expect_equal(
-    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5)[[10]],
-    list(eval.dexes = 10,
-         train.dexes = 3:7)
-  )
-  expect_equal(
-    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5, tail.out = FALSE)[[1]],
-    list(eval.dexes = 1,
-         train.dexes = 4:10)
-  )
-  expect_equal(
-    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5, tail.out = FALSE)[[5]],
-    list(eval.dexes = 5,
-         train.dexes = c(1,2,8:10))
-  )
-  expect_equal(
-    Eval_TrainIndices(eval.method = 'leave-k-out', 10, NULL, 5, tail.out = FALSE)[[10]],
-    list(eval.dexes = 10,
-         train.dexes = c(1:7))
-  )
-  expect_equal(
-    Eval_TrainIndices(eval.method = 'leave-k-out', 20, NULL, 1)[[1]],
-    Eval_TrainIndices(eval.method = 'leave-k-out', 20, NULL, 1, tail.out = FALSE)[[1]]
-  )
-  
-})
-
-##############################################
-
-test_that("3. Output checks: retrospective", {
-  expect_equal(
-    length(Eval_TrainIndices(eval.method = 'retrospective', 10, NULL, 3)),
-    7
-  )
-  expect_equal(
-    Eval_TrainIndices(eval.method = 'retrospective', 10, NULL, 3)[[1]],
-    list(eval.dexes = 4, train.dexes = 1:3)
-  )
-  expect_equal(
-    Eval_TrainIndices(eval.method = 'retrospective', 10, NULL, 3)[[2]],
-    list(eval.dexes = 5, train.dexes = 1:4)
-  )
-  expect_equal(
-    Eval_TrainIndices(eval.method = 'retrospective', 10, NULL, 3)[[7]],
-    list(eval.dexes = 10, train.dexes = 1:9)
-  )
-})
-
-
-  
\ No newline at end of file
-- 
GitLab


From 38a7909cad871753ed372895d947dffd119272a8 Mon Sep 17 00:00:00 2001
From: THEERTHA KARIYATHAN <tkariyat@bscearth421.int.bsc.es>
Date: Mon, 31 Mar 2025 12:54:27 +0200
Subject: [PATCH 6/9] data unavaible, commented test-as.s2dv check 8

---
 tests/testthat/test-as.s2dv_cube.R | 78 +++++++++++++++---------------
 1 file changed, 39 insertions(+), 39 deletions(-)

diff --git a/tests/testthat/test-as.s2dv_cube.R b/tests/testthat/test-as.s2dv_cube.R
index 8ff19582..15d69a2d 100644
--- a/tests/testthat/test-as.s2dv_cube.R
+++ b/tests/testthat/test-as.s2dv_cube.R
@@ -332,44 +332,44 @@ test_that("7. Tests from Start()", {
 
 ##############################################
 
-test_that("8. Tests from Start()", {
-  path <- paste0('/esarchive/exp/ecearth/a3t4/diags/CMIP/EC-Earth-Consortium/EC-Earth3-LR/piControl/$memb$/Omon/$var$/gn/',
-                 'v*/$var$_Omon_EC-Earth3-LR_piControl_$memb$_gn_$chunk$.nc')
-  suppressWarnings(
-      data7 <- Start(dat = list(list(name = 'a3t4', path = path)),
-                 var = 'tosmean',
-                 memb = paste0('r', 1:5, 'i1p1f1'),
-                 region = c("ATL3", "Global_Ocean", "Nino3.4"),
-                 time = indices(1:10),
-                 chunk = 'all',
-                 time_across = 'chunk',
-                 merge_across_dims = TRUE,
-                 return_vars = list(time = 'chunk', region = NULL),
-                 num_procs = 8,
-                 retrieve = T)
-  )
-
-  res7 <- as.s2dv_cube(data7)
-  
-  # dimensions
-  expect_equal(
-    dim(res7$data),
-    c(dat = 1, var = 1, memb = 5, region = 3, time = 10)
-  )
-  # elements
-  expect_equal(
-    names(res7),
-    c("data", "dims", "coords", "attrs")
-  )
-  expect_equal(
-    res7$attrs$Variable$varName,
-    c('tosmean')
-  )
-  # Dates
-  expect_equal(
-    dim(res7$attrs$Dates),
-    c(time = 10)
-  )
-})
+# test_that("8. Tests from Start()", {
+#   path <- paste0('/esarchive/exp/ecearth/a3t4/diags/CMIP/EC-Earth-Consortium/EC-Earth3-LR/piControl/$memb$/Omon/$var$/gn/',
+#                  'v*/$var$_Omon_EC-Earth3-LR_piControl_$memb$_gn_$chunk$.nc')
+#   suppressWarnings(
+#       data7 <- Start(dat = list(list(name = 'a3t4', path = path)),
+#                  var = 'tosmean',
+#                  memb = paste0('r', 1:5, 'i1p1f1'),
+#                  region = c("ATL3", "Global_Ocean", "Nino3.4"),
+#                  time = indices(1:10),
+#                  chunk = 'all',
+#                  time_across = 'chunk',
+#                  merge_across_dims = TRUE,
+#                  return_vars = list(time = 'chunk', region = NULL),
+#                  num_procs = 8,
+#                  retrieve = T)
+#   )
+# 
+#   res7 <- as.s2dv_cube(data7)
+#   
+#   # dimensions
+#   expect_equal(
+#     dim(res7$data),
+#     c(dat = 1, var = 1, memb = 5, region = 3, time = 10)
+#   )
+#   # elements
+#   expect_equal(
+#     names(res7),
+#     c("data", "dims", "coords", "attrs")
+#   )
+#   expect_equal(
+#     res7$attrs$Variable$varName,
+#     c('tosmean')
+#   )
+#   # Dates
+#   expect_equal(
+#     dim(res7$attrs$Dates),
+#     c(time = 10)
+#   )
+# })
 
 ##############################################
\ No newline at end of file
-- 
GitLab


From 84f4e61d2ed4c8df125f395585ef4ab42f5e0d80 Mon Sep 17 00:00:00 2001
From: THEERTHA KARIYATHAN <tkariyat@bscearth421.int.bsc.es>
Date: Thu, 3 Apr 2025 14:32:04 +0200
Subject: [PATCH 7/9] note on test-as.s2dv_cube 8

---
 tests/testthat/test-as.s2dv_cube.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-as.s2dv_cube.R b/tests/testthat/test-as.s2dv_cube.R
index 15d69a2d..060c8df5 100644
--- a/tests/testthat/test-as.s2dv_cube.R
+++ b/tests/testthat/test-as.s2dv_cube.R
@@ -331,7 +331,7 @@ test_that("7. Tests from Start()", {
 })
 
 ##############################################
-
+# commented as 'path' not available
 # test_that("8. Tests from Start()", {
 #   path <- paste0('/esarchive/exp/ecearth/a3t4/diags/CMIP/EC-Earth-Consortium/EC-Earth3-LR/piControl/$memb$/Omon/$var$/gn/',
 #                  'v*/$var$_Omon_EC-Earth3-LR_piControl_$memb$_gn_$chunk$.nc')
-- 
GitLab


From f3bd1eb2509c639581f179662521a76136dc9f1e Mon Sep 17 00:00:00 2001
From: THEERTHA KARIYATHAN <tkariyat@bscearth421.int.bsc.es>
Date: Mon, 14 Apr 2025 10:02:22 +0200
Subject: [PATCH 8/9] update doc

---
 R/EvalTrainIndices.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/EvalTrainIndices.R b/R/EvalTrainIndices.R
index d0fb3fd8..29ab38e5 100644
--- a/R/EvalTrainIndices.R
+++ b/R/EvalTrainIndices.R
@@ -11,8 +11,8 @@
 #'   -\code{hindcast-vs-forecast}: Uses all years from the hindcast sdate dimension
 #'    as training and all years from the forecast sdate dimension will be corrected.
 #'   
-#' @param sample.length Integer. Length of the dataset.
-#' @param sample.length_cor Integer. Length of forecast dataset in
+#' @param sample.length Integer. Length of the sample (in years).
+#' @param sample.length_cor Integer. Length of forecast sample (in years) in
 #'  \code{hindcast-vs-forecast} method.
 #' @param k Positive integer. Default = 1.
 #' In method \code{leave-k-out}, \code{k} is expected to be odd integer, 
-- 
GitLab


From 07d89f019eb2674fa09ff949f5af24523e7fec2b Mon Sep 17 00:00:00 2001
From: THEERTHA KARIYATHAN <tkariyat@bsceshub03.bsc.es>
Date: Thu, 24 Apr 2025 15:47:24 +0200
Subject: [PATCH 9/9] update example

---
 R/EvalTrainIndices.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/EvalTrainIndices.R b/R/EvalTrainIndices.R
index 29ab38e5..e62e48de 100644
--- a/R/EvalTrainIndices.R
+++ b/R/EvalTrainIndices.R
@@ -30,13 +30,13 @@
 #'
 #' @examples
 #' # Leave-k-out cross-validation
-#' Eval_TrainIndices("leave-k-out", sample.length = 10, sample.length_cor = 5, k = 3)
+#' EvalTrainIndices("leave-k-out", sample.length = 10, sample.length_cor = 5, k = 3)
 #' # Retrospective cross-validation
-#' Eval_TrainIndices("retrospective", sample.length = 10, sample.length_cor = 5, k = 3)
+#' EvalTrainIndices("retrospective", sample.length = 10, sample.length_cor = 5, k = 3)
 #' # In-sample validation
-#' Eval_TrainIndices("in-sample", sample.length = 10, sample.length_cor = 5)
+#' EvalTrainIndices("in-sample", sample.length = 10, sample.length_cor = 5)
 #' # Hindcast vs. Forecast validation
-#' Eval_TrainIndices("hindcast-vs-forecast", sample.length = 10, sample.length_cor = 5)
+#' EvalTrainIndices("hindcast-vs-forecast", sample.length = 10, sample.length_cor = 5)
 #'
 #' @export
 EvalTrainIndices <- function(eval.method, sample.length, sample.length_cor, 
-- 
GitLab