From cb0a3a3a1a0a4402a9d0a765695c0c9e5a39c13a Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Fri, 17 Jan 2020 18:10:02 +0100
Subject: [PATCH 1/5] Modify Corr.R with Apply feature

---
 DESCRIPTION                |   3 +-
 NAMESPACE                  |   1 -
 R/Corr.R                   | 460 +++++++++++++++++++------------------
 man/Corr.Rd                | 141 +++++-------
 tests/testthat/test-Corr.R | 165 +++++++++++++
 5 files changed, 456 insertions(+), 314 deletions(-)
 create mode 100644 tests/testthat/test-Corr.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 0045265c..6780c83d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -50,7 +50,8 @@ Imports:
     ncdf4,
     parallel,
     plyr,
-    SpecsVerification (>= 0.5.0)
+    SpecsVerification (>= 0.5.0),
+    multiApply (>= 2.0.0)
 Suggests:
     easyVerification,
     testthat
diff --git a/NAMESPACE b/NAMESPACE
index 4e855789..67268b6f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,7 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
 export(.BrierScore)
-export(.Corr)
 export(.RMS)
 export(.RMSSS)
 export(.RatioRMS)
diff --git a/R/Corr.R b/R/Corr.R
index 41900230..a675ce32 100644
--- a/R/Corr.R
+++ b/R/Corr.R
@@ -1,72 +1,66 @@
-#'Computes the correlation coefficient between an array of forecasts and their corresponding observations
+#'Compute the correlation coefficient between an array of forecast and their corresponding observation
 #'
-#'Calculates the correlation coefficient (Pearson, Kendall or Spearman) for 
-#'an array of forecasts and observations. The input should be an array with 
-#'dimensions c(no. of datasets, no. of start dates, no. of forecast times, 
-#'no. of lons, no. of lats.), where the longitude and latitude dimensions are 
-#'optional. The correlations are computed along the poscor dimension which 
-#'should correspond to the startdate dimension. If compROW is given, the 
-#'correlations are computed only if rows along the compROW dimension are 
-#'complete between limits[1] and limits[2], i.e. there are no NAs between 
-#'limits[1] and limits[2]. This option can be activated if the user wishes to 
-#'account only for the forecasts for which observations are available at all 
+#'Calculate the correlation coefficient (Pearson, Kendall or Spearman) for 
+#'an array of forecast and an array of observation.  
+#'The correlations are computed along sdate_dim, the dimension corresponding 
+#'to the startdate dimension. If comp_dim is given, the correlations are 
+#'computed only if data along the comp_dim dimension are complete between  
+#'limits[1] and limits[2], i.e., there is no NA between limits[1] and 
+#'limits[2]. This option can be activated if the user wishes to account only 
+#'for the forecasts which the corresponding observations are available at all 
 #'leadtimes. \cr 
-#'Default: limits[1] = 1 and limits[2] = length(compROW dimension).\cr 
-#'The confidence interval is computed by a Fisher transformation.\cr 
-#'The significance level relies on a one-sided student-T distribution.\cr 
-#'We can modifiy the treshold of the test modifying siglev (default value=0.95).\cr\cr 
-#'.Corr calculates the correlation between the ensemble mean and the 
-#'observations, using an N by M matrix (exp) of forecasts and a vector of 
-#'observations (obs) as input.
+#'The confidence interval is computed by the Fisher transformation.\cr 
+#'The significance level relies on an one-sided student-T distribution.\cr 
 #'
-#'@param var_exp Array of experimental data.
-#'@param var_obs Array of observational data, same dimensions as var_exp 
-#'  except along posloop dimension, where the length can be nobs instead of nexp.
-#'@param posloop Dimension nobs and nexp.
-#'@param poscor Dimension along which correlation are to be computed (the 
-#'  dimension of the start dates).
-#'@param compROW Data taken into account only if (compROW)th row is complete.
-#'  Default = NULL.
-#'@param limits Complete between limits[1] & limits[2]. Default = NULL.
-#'@param siglev Significance level. Default = 0.95.
-#'@param method Type of correlation: 'pearson', 'spearman' or 'kendall'. 
-#'  Default='pearson'
-#'@param conf Whether to compute confidence intervals (default = 'TRUE') or 
-#'  not (FALSE).
-#'@param pval Whether to compute statistical significance p-value (default = 'TRUE') 
-#'  or not (FALSE).
-#'@param exp N by M matrix of N forecasts from M ensemble members.
-#'@param obs Vector of the corresponding observations of length N.
+#'@param exp A named numeric array of experimental data, with at least two 
+#'  dimensions 'sdate_dim' and 'memb_dim'.
+#'@param obs A named numeric array of observational data, same dimensions as  
+#'  parameter 'exp' except along memb_dim.
+#'@param memb_dim A character string indicating the name of member (nobs/nexp) 
+#'  dimension. The default value is 'member'.
+#'@param sdate_dim A character string indicating the name of dimension along  
+#'  which the correlations are computed. The default value is 'sdate'.
+#'@param comp_dim A character string indicating the name of dimension along which
+#'  the data is taken into account only if it is complete. The default value
+#'  is NULL.
+#'@param limits A vector of two integers indicating the range along comp_dim to 
+#'  be completed. The default is c(1, length(comp_dim dimension)).
+#'@param siglev A numeric indicating the confidence level for the 
+#'  regression computation. The default value is 0.95.
+#'@param method A character string indicating the type of correlation: 
+#'  'pearson', 'spearman', or 'kendall'. The default value is 'pearson'.
+#'@param conf A logical value indicating whether to retrieve the confidence 
+#'  intervals or not. The default value is TRUE.
+#'@param pval A logical value indicating whether to compute or not the p-value 
+#'  of the test Ho: Corr = 0. The default value is TRUE.
+#'@param ncores An integer indicating the number of cores to use for parallel 
+#'  computation. The default value is 1.
 #'
 #'@return 
-#'Corr: Array with dimensions :\cr 
-#'c(# of datasets along posloop in var_exp, # of datasets along posloop in 
-#'var_obs, 4, all other dimensions of var_exp & var_obs except poscor).\cr 
-#'The third dimension, of length 4 maximum, contains to the lower limit of 
-#'the 95\% confidence interval, the correlation, the upper limit of the 95\% 
-#'confidence interval and the 95\% significance level given by a one-sided 
-#'T-test. If the p-value is disabled via \code{pval = FALSE}, this dimension 
-#'will be of length 3. If the confidence intervals are disabled via 
-#'\code{conf = FALSE}, this dimension will be of length 2. If both are 
-#'disabled, this will be of length 2. \cr\cr
-#'.Corr:
-#'  \itemize{
-#'    \item{$corr}{The correlation statistic.}
-#'    \item{$p_val}{Corresponds to the p values for the \code{siglev}\% 
-#'    (only present if \code{pval = TRUE}) for the correlation.} 
-#'    \item{$conf_low}{Corresponds to the upper limit of the \code{siglev}\% 
-#'    (only present if \code{conf = TRUE}) for the correlation.} 
-#'    \item{$conf_high}{Corresponds to the lower limit of the \code{siglev}\% 
-#'    (only present if \code{conf = TRUE}) for the correlation.}
-#'  }
+#'A list containing the numeric arrays with dimension:\cr 
+#'(# of datasets along memb_dim in exp, # of datasets along memb_dim in obs, 
+#'all other dimensions of exp & obs except sdate_dim).\cr 
+#'\item{$corr}{
+#'  The correlation coefficient. 
+#'}
+#'\item{$p_val}{
+#'  The p-value. Only present if \code{pval = TRUE}.
+#'}
+#'\item{$conf.lower}{
+#'  The lower confidence interval. Only present if \code{conf = TRUE}.
+#'}
+#'\item{$conf.upper}{
+#'  The upper confidence interval. Only present if \code{conf = TRUE}.
+#'}
 #'
 #'@keywords datagen
 #'@author History:\cr
-#'  0.1  -  2011-04  (V. Guemas, \email{vguemas@@bsc.es})  -  Original code\cr
-#'1.0  -  2013-09  (N. Manubens, \email{nicolau.manubens@@bsc.es})  -  Formatting to R CRAN\cr
-#'1.1  -  2014-10  (M. Menegoz, \email{martin.menegoz@@bsc.es})  -  Adding siglev argument\cr
+#'0.1  -  2011-04  (V. Guemas, \email{vguemas@bsc.es})  -  Original code\cr
+#'1.0  -  2013-09  (N. Manubens, \email{nicolau.manubens@bsc.es})  -  Formatting to R CRAN\cr
+#'1.1  -  2014-10  (M. Menegoz, \email{martin.menegoz@bsc.es})  -  Adding siglev argument\cr
 #'1.2  -  2015-03  (L.P. Caron, \email{louis-philippe.caron@@bsc.es})  - Adding method argument\cr
-#'1.3  -  2017-02  (A. Hunter, \email{alasdair.hunter@@bsc.es})  -  Adapted to veriApply()
+#'1.3  -  2017-02  (A. Hunter, \email{alasdair.hunter@bsc.es})  -  Adapted to veriApply()
+#'3.0  -  2020-01  (A. Ho, \email{an.ho@bsc.es})  -  Adapt to multiApply
 #'@examples
 #'# Load sample data as in Load() example: 
 #'example(Load) 
@@ -78,200 +72,212 @@
 #'# Smooth along lead-times   
 #'smooth_ano_exp <- Smoothing(ano_exp, runmean_months, dim_to_smooth) 
 #'smooth_ano_obs <- Smoothing(ano_obs, runmean_months, dim_to_smooth) 
-#'dim_to_mean <- 2  # Mean along members 
-#'required_complete_row <- 3  # Discard start dates which contain any NA lead-times 
 #'leadtimes_per_startdate <- 60 
-#'corr <- Corr(Mean1Dim(smooth_ano_exp, dim_to_mean),              
-#'             Mean1Dim(smooth_ano_obs, dim_to_mean),              
-#'             compROW = required_complete_row,              
+#'corr <- Corr(smooth_ano_exp, 
+#'             smooth_ano_obs,
+#'             comp_dim = 'ftime', #Discard start dates which contain any NA ftime             
 #'             limits = c(ceiling((runmean_months + 1) / 2),                         
 #'             leadtimes_per_startdate - floor(runmean_months / 2))) 
-#'  \donttest{
-#'PlotVsLTime(corr, toptitle = "correlations", ytitle = "correlation",             
-#'            monini = 11, limits = c(-1, 2), listexp = c('CMIP5 IC3'),
-#'            listobs = c('ERSST'), biglab = FALSE, hlines = c(-1, 0, 1),
-#'            fileout = 'tos_cor.eps')
-#'  }
 #'
-#'# The following example uses veriApply combined with .Corr instead of Corr
-#'  \dontrun{
-#'require(easyVerification)  
-#'Corr2 <- s2dverification:::.Corr
-#'corr2 <- veriApply("Corr2", 
-#'                   smooth_ano_exp, 
-#'                   # see ?veriApply for how to use the 'parallel' option
-#'                   Mean1Dim(smooth_ano_obs, dim_to_mean), 
-#'                   tdim = 3, ensdim = 2)
-#'  }
 #'@rdname Corr
 #'@importFrom stats cor pt qnorm 
 #'@export
-Corr <- function(var_exp, var_obs, posloop = 1, poscor = 2, compROW = NULL, 
-                 limits = NULL, siglev = 0.95, method = 'pearson', 
-                 conf = TRUE, pval = TRUE) {
-  #
-  #  Remove data along compROW dim if there is at least one NA between limits
-  # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-  #
-  if (!is.null(compROW)) {
-    if (is.null(limits)) {
-      limits <- c(1, dim(var_obs)[compROW])
+Corr <- function(exp, obs, memb_dim = 'member', sdate_dim = 'sdate', 
+                 comp_dim = NULL, limits = NULL,
+                 siglev = 0.95, method = 'pearson', 
+                 conf = TRUE, pval = TRUE, ncores = 1) {
+
+  # Check inputs 
+  ## exp and obs (1)
+  if (is.null(exp) | is.null(obs)) {
+    stop("Parameter 'exp' and 'obs' cannot be NULL.")
+  }
+  if (!is.numeric(exp) | !is.numeric(obs)) {
+    stop("Parameter 'exp' and 'obs' must be a numeric array.")
+  }
+  if (is.null(dim(exp)) | is.null(dim(obs))) {
+    stop(paste0("Parameter 'exp' and 'obs' must be at least two dimensions ",
+                "containing sdate_dim and memb_dim."))
+  }
+  if(any(is.null(names(dim(exp))))| any(nchar(names(dim(exp))) == 0) |
+     any(is.null(names(dim(obs))))| any(nchar(names(dim(obs))) == 0)) {
+    stop("Parameter 'exp' and 'obs' must have dimension names.")
+  }
+  if(!all(names(dim(exp)) %in% names(dim(obs))) | 
+     !all(names(dim(obs)) %in% names(dim(exp)))) {
+    stop("Parameter 'exp' and 'obs' must have same dimension name")
+  }
+  ## memb_dim
+  if (!is.character(memb_dim) | length(memb_dim) > 1) {
+    stop("Parameter 'memb_dim' must be a character string.")
+  }
+  if (!memb_dim %in% names(dim(exp)) | !memb_dim %in% names(dim(obs))) {
+    stop("Parameter 'memb_dim' is not found in 'exp' or 'obs' dimension.")
+  }
+  ## sdate_dim
+  if (!is.character(sdate_dim) | length(sdate_dim) > 1) {
+    stop("Parameter 'sdate_dim' must be a character string.")
+  }
+  if (!sdate_dim %in% names(dim(exp)) | !sdate_dim %in% names(dim(obs))) {
+    stop("Parameter 'sdate_dim' is not found in 'exp' or 'obs' dimension.")
+  }
+  ##comp_dim
+  if (!is.null(comp_dim)) {
+    if (!is.character(comp_dim) | length(comp_dim) > 1) {
+      stop("Parameter 'comp_dim' must be a character string.")
+    }
+    if (!comp_dim %in% names(dim(exp)) | !comp_dim %in% names(dim(obs))) {
+      stop("Parameter 'comp_dim' is not found in 'exp' or 'obs' dimension.")
     }
-    outrows <- (is.na(Mean1Dim(var_obs, compROW, narm = FALSE, limits))) 
-    outrows <- InsertDim(outrows, compROW, dim(var_obs)[compROW])
-    var_obs[which(outrows)] <- NA
   }
-  #
-  #  Enlarge var_exp & var_obs to 10 dim + move posloop & poscor to 1st & 2nd 
-  #  pos 
-  # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-  # 
-  dimsvar <- dim(var_exp)
-  for (iind in 1:length(dimsvar)) {
-    if (iind != posloop & dim(var_obs)[iind] != dimsvar[iind]) { 
-      stop("var_exp & var_obs must have same dimensions except along posloop")
+  ##limits
+  if (!is.null(limits)) {
+    if (is.null(comp_dim)) {
+      stop("Paramter 'com_dim' cannot be NULL if 'limits' is assigned.")
+    }
+    if (!is.numeric(limits) | any(limits %% 1 != 0) | any(limits < 0) | 
+        length(limits) != 2 | any(limits > dim(exp)[comp_dim])) {
+      stop(paste0("Parameter 'limits' must be a vector of two positive ",
+                  "integers smaller than the length of paramter 'comp_dim'."))
     }
   }
-  if (dimsvar[poscor] < 3 ) {
-    stop("At least 3 values required to compute correlation")
+  ## siglev
+  if (!is.numeric(siglev) | siglev < 0 | siglev > 1 | length(siglev) > 1) {
+    stop("Parameter 'siglev' must be a numeric number between 0 and 1.")
   }
-  if (method != "kendall" && method != "spearman" && method != "pearson") {
-    stop("Wrong correlation method")
+  ## method
+  if (!(method %in% c("kendall", "spearman", "pearson"))) {
+    stop("Parameter 'method' must be one of 'kendall', 'spearman' or 'pearson'.")}
+  ## conf
+  if (!is.logical(conf) | length(conf) > 1) {
+    stop("Parameter 'conf' must be one logical value.")
   }
-  nexp <- dimsvar[posloop]
-  nobs <- dim(var_obs)[posloop]
-  var_exp <- Enlarge(var_exp, 10)
-  var_obs <- Enlarge(var_obs, 10)
-  posaperm <- numeric(10)
-  posaperm[1] <- posloop
-  posaperm[2] <- poscor
-  posaperm[3:10] <- seq(1, 10)[-c(posloop, poscor)]
-  var_exp <- aperm(var_exp, posaperm)
-  var_obs <- aperm(var_obs, posaperm)
-  dimsaperm <- dim(var_exp)
-  #
-  
-  # Check the siglev arguments:
-  # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-  if (siglev > 1 || siglev < 0) {
-    stop("siglev need to be higher than O and lower than 1")
+  ## pval
+  if (!is.logical(pval) | length(pval) > 1) {
+    stop("Parameter 'pval' must be one logical value.")
   }
-  #
-  #  Loop to compute correlation for each grid point
-  # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-  #
-  dim_val <- 2
-  dim_pval <- 4
-  nvals <- 1 + 2*conf + pval
-  if (!conf) {
-    dim_val <- 1
-    dim_pval <- 2
-  } else {
-    conf_low <- (1 - siglev) / 2
-    conf_high <- 1 - conf_low
+  ## ncores
+  if (!is.null(ncores)) {
+    if (!is.numeric(ncores) | ncores %% 1 != 0 | ncores < 0 |
+      length(ncores) > 1) {
+      stop("Parameter 'ncores' must be a positive integer.")
+    }
+  } 
+  ## exp and obs (2)
+  name_exp <- sort(names(dim(exp)))
+  name_obs <- sort(names(dim(obs)))
+  name_exp <- name_exp[-which(name_exp == memb_dim)]
+  name_obs <- name_obs[-which(name_obs == memb_dim)]
+  if(!all(dim(exp)[name_exp] == dim(obs)[name_obs])) {
+    stop(paste0("Parameter 'exp' and 'obs' must have same length of ",
+                "all dimension expect 'memb_dim'."))
   }
-  CORR <- array(dim = c(nexp, nobs, nvals, dimsaperm[3:10]))
-  for (jexp in 1:nexp) {
-    for (jobs in 1:nobs) {
-      for (j3 in 1:dimsaperm[3]) {
-        for (j4 in 1:dimsaperm[4]) {
-          for (j5 in 1:dimsaperm[5]) {
-            for (j6 in 1:dimsaperm[6]) {
-              for (j7 in 1:dimsaperm[7]) {
-                for (j8 in 1:dimsaperm[8]) {
-                  for (j9 in 1:dimsaperm[9]) {
-                    for (j10 in 1:dimsaperm[10]) {
-                      tmp1 <- var_exp[jexp, , j3, j4, j5, j6, j7, j8, j9, 
-                                      j10]
-                      tmp2 <- var_obs[jobs, , j3, j4, j5, j6, j7, j8, j9,
-                                      j10]
-                      if (any(!is.na(tmp1)) && sum(!is.na(tmp2)) > 2) {
-                        toto <- cor(tmp1, tmp2, use = "pairwise.complete.obs", method = method)
-                        CORR[jexp, jobs, dim_val, j3, j4, j5, j6, j7, j8, j9, j10] <- toto
-                        #eno <- min(Eno(tmp2, 1), Eno(tmp1, 1))
-                        if (pval || conf) {
-                          if (method == "kendall" | method == "spearman") {
-                            eno <- Eno(rank(tmp2), 1)                          
-                          } else if (method == "pearson") {
-                            eno <- Eno(tmp2, 1)                          
-                          }
-                        }
-                        if (pval) {
-                          #t <- qt(0.95, eno - 2)
-                          t <- qt(siglev, eno - 2)
-                          CORR[jexp, jobs, dim_pval, j3, j4, j5, j6, j7, j8, j9, 
-                               j10] <- sqrt((t * t) / ((t * t) + eno - 2))
-                        }
-                        if (conf) {
-                          CORR[jexp, jobs, 1, j3, j4, j5, j6, j7, j8, j9, 
-                               j10] <- tanh(atanh(toto) + qnorm(conf_high) / sqrt(
-                                 #j10] <- tanh(atanh(toto) + qnorm(0.975) / sqrt(
-                                 eno - 3))
-                          CORR[jexp, jobs, 3, j3, j4, j5, j6, j7, j8, j9, 
-                               j10] <- tanh(atanh(toto) + qnorm(conf_low) / sqrt(
-                                 #j10] <- tanh(atanh(toto) + qnorm(0.025) / sqrt(
-                                 eno - 3))
-                        }
-                      }
-                    }
-                  }
-                }
-              }
-            }
-          }
-        }
-      }
+  if (dim(exp)[sdate_dim] < 3) {
+    stop("The length of sdate_dim must be at least 3 to compute correlation.")
+  }
+
+  ###############################
+  # Calculate Corr
+
+  # Remove data along comp_dim dim if there is at least one NA between limits
+  if (!is.null(comp_dim)) {
+    if (is.null(limits)) {
+      limits <- c(1, dim(obs)[comp_dim])
     }
+    pos <- which(names(dim(obs)) == comp_dim)
+    outrows <- is.na(Mean1Dim(obs, pos, narm = FALSE, limits))
+    outrows <- InsertDim(outrows, pos, dim(obs)[comp_dim])
+    obs[which(outrows)] <- NA
   }
-  #
-  dim(CORR) <- c(nexp, nobs, nvals, dimsvar[-c(posloop, poscor)])
-  #  
-  #  Output
-  # ~~~~~~~~
-  #
-  CORR
+
+ res <- Apply(list(exp, obs), 
+              target_dims = list(c(sdate_dim, memb_dim), 
+                                 c(sdate_dim, memb_dim)),
+              fun = .Corr, 
+              siglev = siglev, method = method, 
+              conf = conf, pval = pval, ncores = ncores)
+ return(res)
 }
 
-#'@rdname Corr
-#'@importFrom stats cor pt qnorm
-#'@export
-.Corr <- function(exp, obs, siglev = 0.95, method = 'pearson', 
-                  conf = TRUE, pval = TRUE) {
+.Corr <- function(exp, obs, siglev = siglev, method = method, 
+                  conf = conf, pval = pval) {
 
-  # Check 'method'
-  if (!(method %in% c("kendall", "spearman", "pearson"))) {
-    stop("Parameter 'method' must be one of 'kendall', 'spearman' or 'pearson'.")
-    #  Check 'siglev'
-    if (siglev > 1 || siglev < 0) {
-      stop("Parameter 'siglev' must be higher than O and lower than 1.")
-    }
+  # exp: [sdate, member_exp]
+  # obs: [sdate, member_obs]
+  n_exp <- as.numeric(dim(exp)[2])
+  n_obs <- as.numeric(dim(obs)[2])
+  
+  CORR <- array(dim = c(n_exp = n_exp, n_obs = n_obs))
+  eno_expand <- array(dim = c(n_exp = n_exp, n_obs = n_obs))
+  p_val <- array(dim = c(n_exp = n_exp, n_obs = n_obs))
+
+  # ens_mean
+  for (i in 1:n_obs) {
+
+    CORR[, i] <- sapply(1:n_exp, 
+                          function(x) {
+    if (any(!is.na(exp[, x])) && sum(!is.na(obs[, i])) > 2) {
+cor(exp[, x], obs[, i],
+                                       use = "pairwise.complete.obs", 
+                                       method = method)
+} else {
+    CORR[, i] <- NA
+}
+})
   }
 
-  p_val <- NULL
-  conflow <- NULL
-  confhigh <- NULL
-  ens_mean <- rowMeans(exp)
-  CORR <- cor(obs, ens_mean, use = "pairwise.complete.obs", method = method)
-  if (pval || conf) {
-    if (method == "kendall" || method == "spearman") {
-      eno <- Eno(rank(obs), 1)                          
+#  if (pval) {
+#    for (i in 1:n_obs) {
+#      p_val[, i] <- try(sapply(1:n_exp,
+#                           function(x) {(cor.test(exp[, x], obs[, i],
+#                                         use = "pairwise.complete.obs",
+#                                         method = method)$p.value)/2}), silent = TRUE)
+#      if (class(p_val[, i]) == 'character') {
+#        p_val[, i] <- NA
+#      }
+#    }
+#  }
+
+  if (pval | conf) {
+    if (method == "kendall" | method == "spearman") {
+      tmp <- apply(obs, 2, rank)
+      eno <- Eno(tmp, 1)
+#      eno <- Eno(tmp, sdate_dim)  #replace the upper line with this when using new Eno()
     } else if (method == "pearson") {
       eno <- Eno(obs, 1)                          
+#      eno <- Eno(obs, sdate_dim)  #replace the upper line with this when using new Eno()
+    }
+  
+    for (i in 1:n_exp) {
+      eno_expand[i, ] <- eno
     }
   }
-  if (pval && (method == "pearson")) {
-    t <-sqrt(CORR * CORR * (eno - 2) / (1 - (CORR ^ 2)))
-    p_val <- pt(t, eno - 2, lower.tail = FALSE)
+#############old#################
+#This doesn't return error but it's diff from cor.test() when method is spearman and kendall
+  if (pval) {
+    t <-sqrt(CORR * CORR * (eno_expand - 2) / (1 - (CORR ^ 2)))
+    p_val <- pt(t, eno_expand - 2, lower.tail = FALSE)
   } 
-  if (conf && (method == "pearson")) {
+###################################
+  if (conf) {
     conf_low <- (1 - siglev) / 2
     conf_high <- 1 - conf_low
-    conf_int <- c(tanh(atanh(CORR) + qnorm(conf_low) / sqrt(eno - 3)), 
-                  tanh(atanh(CORR) + qnorm(conf_high) / sqrt(eno - 3)))
-    conf_int <- conf_int[!is.na(CORR)]
-    conflow <- conf_int[1]
-    confhigh <- conf_int[2]
-  } 
-  #  Output
-  invisible(result <- list(corr = CORR, p_val = p_val, conf_low = conflow, conf_high = confhigh))
+    conflow <- tanh(atanh(CORR) + qnorm(conf_low) / sqrt(eno_expand - 3))
+    confhigh <- tanh(atanh(CORR) + qnorm(conf_high) / sqrt(eno_expand - 3))
+  }
+
+  if (pval & conf) {
+    res <- list(corr = CORR, p_val = p_val, 
+                conf_low = conflow, conf_high = confhigh)
+  } else if (pval & !conf) {
+    res <- list(corr = CORR, p_val = p_val)
+  } else if (!pval & conf) {
+    res <- list(corr = CORR,
+                conf_low = conflow, conf_high = confhigh)
+  } else {
+    res <- list(corr = CORR)
+  }
+
+  return(res) 
+
 }
diff --git a/man/Corr.Rd b/man/Corr.Rd
index e311813d..2bc58c28 100644
--- a/man/Corr.Rd
+++ b/man/Corr.Rd
@@ -1,89 +1,77 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/Corr.R
 \name{Corr}
-\alias{.Corr}
 \alias{Corr}
-\title{Computes the correlation coefficient between an array of forecasts and their corresponding observations}
+\title{Compute the correlation coefficient between an array of forecast and their corresponding observation}
 \usage{
-Corr(var_exp, var_obs, posloop = 1, poscor = 2, compROW = NULL,
+Corr(exp, obs, memb_dim = "member", sdate_dim = "sdate", comp_dim = NULL,
   limits = NULL, siglev = 0.95, method = "pearson", conf = TRUE,
-  pval = TRUE)
-
-.Corr(exp, obs, siglev = 0.95, method = "pearson", conf = TRUE,
-  pval = TRUE)
+  pval = TRUE, ncores = 1)
 }
 \arguments{
-\item{var_exp}{Array of experimental data.}
-
-\item{var_obs}{Array of observational data, same dimensions as var_exp 
-except along posloop dimension, where the length can be nobs instead of nexp.}
+\item{exp}{A named numeric array of experimental data, with at least two 
+dimensions 'sdate_dim' and 'memb_dim'.}
 
-\item{posloop}{Dimension nobs and nexp.}
+\item{obs}{A named numeric array of observational data, same dimensions as
+parameter 'exp' except along memb_dim.}
 
-\item{poscor}{Dimension along which correlation are to be computed (the 
-dimension of the start dates).}
+\item{memb_dim}{A character string indicating the name of member (nobs/nexp) 
+dimension. The default value is 'member'.}
 
-\item{compROW}{Data taken into account only if (compROW)th row is complete.
-Default = NULL.}
+\item{sdate_dim}{A character string indicating the name of dimension along
+which the correlations are computed. The default value is 'sdate'.}
 
-\item{limits}{Complete between limits[1] & limits[2]. Default = NULL.}
+\item{comp_dim}{A character string indicating the name of dimension along which
+the data is taken into account only if it is complete. The default value
+is NULL.}
 
-\item{siglev}{Significance level. Default = 0.95.}
+\item{limits}{A vector of two integers indicating the range along comp_dim to 
+be completed. The default is c(1, length(comp_dim dimension)).}
 
-\item{method}{Type of correlation: 'pearson', 'spearman' or 'kendall'. 
-Default='pearson'}
+\item{siglev}{A numeric indicating the confidence level for the 
+regression computation. The default value is 0.95.}
 
-\item{conf}{Whether to compute confidence intervals (default = 'TRUE') or 
-not (FALSE).}
+\item{method}{A character string indicating the type of correlation: 
+'pearson', 'spearman', or 'kendall'. The default value is 'pearson'.}
 
-\item{pval}{Whether to compute statistical significance p-value (default = 'TRUE') 
-or not (FALSE).}
+\item{conf}{A logical value indicating whether to retrieve the confidence 
+intervals or not. The default value is TRUE.}
 
-\item{exp}{N by M matrix of N forecasts from M ensemble members.}
+\item{pval}{A logical value indicating whether to compute or not the p-value 
+of the test Ho: Corr = 0. The default value is TRUE.}
 
-\item{obs}{Vector of the corresponding observations of length N.}
+\item{ncores}{An integer indicating the number of cores to use for parallel 
+computation. The default value is 1.}
 }
 \value{
-Corr: Array with dimensions :\cr 
-c(# of datasets along posloop in var_exp, # of datasets along posloop in 
-var_obs, 4, all other dimensions of var_exp & var_obs except poscor).\cr 
-The third dimension, of length 4 maximum, contains to the lower limit of 
-the 95\% confidence interval, the correlation, the upper limit of the 95\% 
-confidence interval and the 95\% significance level given by a one-sided 
-T-test. If the p-value is disabled via \code{pval = FALSE}, this dimension 
-will be of length 3. If the confidence intervals are disabled via 
-\code{conf = FALSE}, this dimension will be of length 2. If both are 
-disabled, this will be of length 2. \cr\cr
-.Corr:
- \itemize{
-   \item{$corr}{The correlation statistic.}
-   \item{$p_val}{Corresponds to the p values for the \code{siglev}\% 
-   (only present if \code{pval = TRUE}) for the correlation.} 
-   \item{$conf_low}{Corresponds to the upper limit of the \code{siglev}\% 
-   (only present if \code{conf = TRUE}) for the correlation.} 
-   \item{$conf_high}{Corresponds to the lower limit of the \code{siglev}\% 
-   (only present if \code{conf = TRUE}) for the correlation.}
- }
+A list containing the numeric arrays with dimension:\cr 
+(# of datasets along memb_dim in exp, # of datasets along memb_dim in obs, 
+all other dimensions of exp & obs except sdate_dim).\cr 
+\item{$corr}{
+ The correlation coefficient. 
+}
+\item{$p_val}{
+ The p-value. Only present if \code{pval = TRUE}.
+}
+\item{$conf.lower}{
+ The lower confidence interval. Only present if \code{conf = TRUE}.
+}
+\item{$conf.upper}{
+ The upper confidence interval. Only present if \code{conf = TRUE}.
+}
 }
 \description{
-Calculates the correlation coefficient (Pearson, Kendall or Spearman) for 
-an array of forecasts and observations. The input should be an array with 
-dimensions c(no. of datasets, no. of start dates, no. of forecast times, 
-no. of lons, no. of lats.), where the longitude and latitude dimensions are 
-optional. The correlations are computed along the poscor dimension which 
-should correspond to the startdate dimension. If compROW is given, the 
-correlations are computed only if rows along the compROW dimension are 
-complete between limits[1] and limits[2], i.e. there are no NAs between 
-limits[1] and limits[2]. This option can be activated if the user wishes to 
-account only for the forecasts for which observations are available at all 
+Calculate the correlation coefficient (Pearson, Kendall or Spearman) for 
+an array of forecast and an array of observation.  
+The correlations are computed along sdate_dim, the dimension corresponding 
+to the startdate dimension. If comp_dim is given, the correlations are 
+computed only if data along the comp_dim dimension are complete between  
+limits[1] and limits[2], i.e., there is no NA between limits[1] and 
+limits[2]. This option can be activated if the user wishes to account only 
+for the forecasts which the corresponding observations are available at all 
 leadtimes. \cr 
-Default: limits[1] = 1 and limits[2] = length(compROW dimension).\cr 
-The confidence interval is computed by a Fisher transformation.\cr 
-The significance level relies on a one-sided student-T distribution.\cr 
-We can modifiy the treshold of the test modifying siglev (default value=0.95).\cr\cr 
-.Corr calculates the correlation between the ensemble mean and the 
-observations, using an N by M matrix (exp) of forecasts and a vector of 
-observations (obs) as input.
+The confidence interval is computed by the Fisher transformation.\cr 
+The significance level relies on an one-sided student-T distribution.\cr
 }
 \examples{
 # Load sample data as in Load() example: 
@@ -96,39 +84,22 @@ dim_to_smooth <- 4
 # Smooth along lead-times   
 smooth_ano_exp <- Smoothing(ano_exp, runmean_months, dim_to_smooth) 
 smooth_ano_obs <- Smoothing(ano_obs, runmean_months, dim_to_smooth) 
-dim_to_mean <- 2  # Mean along members 
-required_complete_row <- 3  # Discard start dates which contain any NA lead-times 
 leadtimes_per_startdate <- 60 
-corr <- Corr(Mean1Dim(smooth_ano_exp, dim_to_mean),              
-            Mean1Dim(smooth_ano_obs, dim_to_mean),              
-            compROW = required_complete_row,              
+corr <- Corr(smooth_ano_exp, 
+            smooth_ano_obs,
+            comp_dim = 'ftime', #Discard start dates which contain any NA ftime             
             limits = c(ceiling((runmean_months + 1) / 2),                         
             leadtimes_per_startdate - floor(runmean_months / 2))) 
- \donttest{
-PlotVsLTime(corr, toptitle = "correlations", ytitle = "correlation",             
-           monini = 11, limits = c(-1, 2), listexp = c('CMIP5 IC3'),
-           listobs = c('ERSST'), biglab = FALSE, hlines = c(-1, 0, 1),
-           fileout = 'tos_cor.eps')
- }
 
-# The following example uses veriApply combined with .Corr instead of Corr
- \dontrun{
-require(easyVerification)  
-Corr2 <- s2dverification:::.Corr
-corr2 <- veriApply("Corr2", 
-                  smooth_ano_exp, 
-                  # see ?veriApply for how to use the 'parallel' option
-                  Mean1Dim(smooth_ano_obs, dim_to_mean), 
-                  tdim = 3, ensdim = 2)
- }
 }
 \author{
 History:\cr
- 0.1  -  2011-04  (V. Guemas, \email{vguemas@bsc.es})  -  Original code\cr
+0.1  -  2011-04  (V. Guemas, \email{vguemas@bsc.es})  -  Original code\cr
 1.0  -  2013-09  (N. Manubens, \email{nicolau.manubens@bsc.es})  -  Formatting to R CRAN\cr
 1.1  -  2014-10  (M. Menegoz, \email{martin.menegoz@bsc.es})  -  Adding siglev argument\cr
 1.2  -  2015-03  (L.P. Caron, \email{louis-philippe.caron@bsc.es})  - Adding method argument\cr
 1.3  -  2017-02  (A. Hunter, \email{alasdair.hunter@bsc.es})  -  Adapted to veriApply()
+3.0  -  2020-01  (A. Ho, \email{an.ho@bsc.es})  -  Adapt to multiApply
 }
 \keyword{datagen}
 
diff --git a/tests/testthat/test-Corr.R b/tests/testthat/test-Corr.R
new file mode 100644
index 00000000..ab487afa
--- /dev/null
+++ b/tests/testthat/test-Corr.R
@@ -0,0 +1,165 @@
+context("s2dverification::Corr tests")
+
+##############################################
+  # dat1
+  set.seed(1)
+  exp1 <- array(rnorm(240), dim = c(dataset = 1, member = 2, sdate = 5,
+                                   ftime = 3, lat = 2, lon = 4))
+
+  set.seed(2)
+  obs1 <- array(rnorm(120), dim = c(dataset = 1, member = 1, sdate = 5,
+                                   ftime = 3, lat = 2, lon = 4))
+  set.seed(2)
+  na <- floor(runif(10, min = 1, max = 120))
+  obs1[na] <- NA
+
+##############################################
+test_that("1. Input checks", {
+
+  expect_error(
+  Corr(c(), c()),
+  "Parameter 'exp' and 'obs' cannot be NULL."
+  )
+  expect_error(
+  Corr(c('b'), c('a')),
+  "Parameter 'exp' and 'obs' must be a numeric array."
+  )
+  expect_error(
+  Corr(c(1:10), c(2:4)),
+  paste0("Parameter 'exp' and 'obs' must be at least two dimensions ",
+         "containing sdate_dim and memb_dim.")
+  )
+  expect_error(
+  Corr(array(1:10, dim = c(2, 5)), array(1:4, dim = c(2, 2))),
+  "Parameter 'exp' and 'obs' must have dimension names."
+  )
+  expect_error(
+  Corr(array(1:10, dim = c(a = 2, c = 5)), array(1:4, dim = c(a = 2, b = 2))),
+  "Parameter 'exp' and 'obs' must have same dimension name"
+  )
+  expect_error(
+  Corr(exp1, obs1, memb_dim = 1),
+  "Parameter 'memb_dim' must be a character string."
+  )
+  expect_error(
+  Corr(exp1, obs1, memb_dim = 'a'),
+  "Parameter 'memb_dim' is not found in 'exp' or 'obs' dimension."
+  )
+  expect_error(
+  Corr(exp1, obs1, sdate_dim = c('sdate', 'a')),
+  "Parameter 'sdate_dim' must be a character string."
+  )
+  expect_error(
+  Corr(exp1, obs1, sdate_dim = 'a'),
+  "Parameter 'sdate_dim' is not found in 'exp' or 'obs' dimension."
+  )
+  expect_error(
+  Corr(exp1, obs1, comp_dim = c('sdate', 'ftime')),
+  "Parameter 'comp_dim' must be a character string."
+  )
+  expect_error(
+  Corr(exp1, obs1, comp_dim = 'a'),
+  "Parameter 'comp_dim' is not found in 'exp' or 'obs' dimension."
+  )
+  expect_error(
+  Corr(exp1, obs1, limits = c(1,3)),
+  "Paramter 'com_dim' cannot be NULL if 'limits' is assigned."
+  )
+  expect_error(
+  Corr(exp1, obs1, comp_dim = 'ftime', limits = c(1)),
+  paste0("Parameter 'limits' must be a vector of two positive ",
+                  "integers smaller than the length of paramter 'comp_dim'.")
+  )
+  expect_error(
+  Corr(exp1, obs1, siglev = -1),
+  "Parameter 'siglev' must be a numeric number between 0 and 1."
+  )
+  expect_error(
+  Corr(exp1, obs1, method = 1),
+  "Parameter 'method' must be one of 'kendall', 'spearman' or 'pearson'."
+  )
+  expect_error(
+  Corr(exp1, obs1, conf = 1),
+  "Parameter 'conf' must be one logical value."
+  )
+  expect_error(
+  Corr(exp1, obs1, pval = 'TRUE'),
+  "Parameter 'pval' must be one logical value."
+  )
+  expect_error(
+  Corr(exp1, obs1, ncores = 1.5),
+  "Parameter 'ncores' must be a positive integer."
+  )
+  expect_error(
+  Corr(exp = array(1:10, dim = c(sdate = 1, member = 5, a = 1)),
+       obs = array(1:4, dim = c(a = 1, sdate = 2, member = 2))),
+  "Parameter 'exp' and 'obs' must have same length of all dimension expect 'memb_dim'."
+  )
+  expect_error(
+  Corr(exp = array(1:10, dim = c(sdate = 2, member = 5, a = 1)),
+       obs = array(1:4, dim = c(a = 1, sdate = 2, member = 2))),
+  "The length of sdate_dim must be at least 3 to compute correlation."
+  )
+
+})
+
+##############################################
+test_that("2. Output checks: dat1", {
+
+  expect_equal(
+    dim(Corr(exp1, obs1)$corr),
+    c(n_exp = 2, n_obs = 1, dataset = 1, ftime = 3, lat = 2, lon = 4)
+  )
+  expect_equal(
+    head(Corr(exp1, obs1)$corr),
+    c(0.11503859, -0.46959987, -0.64113021, 0.09776572, -0.32393603, 0.27565829), 
+    tolerance = 0.001
+  )
+  expect_equal(
+    length(which(is.na(Corr(exp1, obs1)$p_val))),
+    2
+  )
+  expect_equal(
+    max(Corr(exp1, obs1)$conf_low, na.rm = T),
+    0.6332941,
+    tolerance = 0.001
+  )
+  expect_equal(
+    length(which(is.na(Corr(exp1, obs1, comp_dim = 'ftime')$corr))),
+    6
+  )
+  expect_equal(
+    length(which(is.na(Corr(exp1, obs1, comp_dim = 'ftime', limits = c(2, 3))$corr))),
+    2
+  )
+  expect_equal(
+    summary(Corr(exp1, obs1, siglev = 0.99)$conf_high)[1],
+    c(Min. = 0.2748),
+    tolerance = 0.0001
+  )
+  expect_equal(
+    length(Corr(exp1, obs1, conf = FALSE, pval = FALSE)),
+    1
+  )
+  expect_equal(
+    length(Corr(exp1, obs1, conf = FALSE)),
+    2
+  )
+  expect_equal(
+    length(Corr(exp1, obs1, pval = FALSE)),
+    3
+  )
+  expect_equal(
+    head(Corr(exp1, obs1, method = 'spearman')$corr),
+    c(-0.3, -0.4, -0.6, 0.3, -0.3, 0.2)
+  )
+  expect_equal(
+    range(Corr(exp1, obs1, method = 'spearman', comp_dim = 'ftime')$p_val, na.rm = T),
+    c(0.0, 0.5),
+    tolerance = 0.001
+  )
+
+})
+
+##############################################
+
-- 
GitLab


From ce18173fdf37fba32ccabc7b54785b4798938870 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Fri, 17 Jan 2020 18:22:58 +0100
Subject: [PATCH 2/5] Add @import multiApply

---
 NAMESPACE | 1 +
 R/Corr.R  | 1 +
 2 files changed, 2 insertions(+)

diff --git a/NAMESPACE b/NAMESPACE
index 67268b6f..24746631 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -89,6 +89,7 @@ import(graphics)
 import(mapproj)
 import(maps)
 import(methods)
+import(multiApply)
 import(ncdf4)
 import(parallel)
 import(plyr)
diff --git a/R/Corr.R b/R/Corr.R
index a675ce32..00ac7eab 100644
--- a/R/Corr.R
+++ b/R/Corr.R
@@ -80,6 +80,7 @@
 #'             leadtimes_per_startdate - floor(runmean_months / 2))) 
 #'
 #'@rdname Corr
+#'@import multiApply
 #'@importFrom stats cor pt qnorm 
 #'@export
 Corr <- function(exp, obs, memb_dim = 'member', sdate_dim = 'sdate', 
-- 
GitLab


From e35986638a167e1fb5085ce5babfb8af3277a822 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Mon, 20 Jan 2020 18:57:30 +0100
Subject: [PATCH 3/5] Small fix

---
 R/Corr.R    | 8 ++++----
 man/Corr.Rd | 6 +++---
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/R/Corr.R b/R/Corr.R
index 00ac7eab..55d9ec25 100644
--- a/R/Corr.R
+++ b/R/Corr.R
@@ -46,10 +46,10 @@
 #'\item{$p_val}{
 #'  The p-value. Only present if \code{pval = TRUE}.
 #'}
-#'\item{$conf.lower}{
+#'\item{$conf:low}{
 #'  The lower confidence interval. Only present if \code{conf = TRUE}.
 #'}
-#'\item{$conf.upper}{
+#'\item{$conf_high}{
 #'  The upper confidence interval. Only present if \code{conf = TRUE}.
 #'}
 #'
@@ -86,7 +86,7 @@
 Corr <- function(exp, obs, memb_dim = 'member', sdate_dim = 'sdate', 
                  comp_dim = NULL, limits = NULL,
                  siglev = 0.95, method = 'pearson', 
-                 conf = TRUE, pval = TRUE, ncores = 1) {
+                 conf = TRUE, pval = TRUE, ncores = NULL) {
 
   # Check inputs 
   ## exp and obs (1)
@@ -134,7 +134,7 @@ Corr <- function(exp, obs, memb_dim = 'member', sdate_dim = 'sdate',
   ##limits
   if (!is.null(limits)) {
     if (is.null(comp_dim)) {
-      stop("Paramter 'com_dim' cannot be NULL if 'limits' is assigned.")
+      stop("Paramter 'comp_dim' cannot be NULL if 'limits' is assigned.")
     }
     if (!is.numeric(limits) | any(limits %% 1 != 0) | any(limits < 0) | 
         length(limits) != 2 | any(limits > dim(exp)[comp_dim])) {
diff --git a/man/Corr.Rd b/man/Corr.Rd
index 2bc58c28..e63742f2 100644
--- a/man/Corr.Rd
+++ b/man/Corr.Rd
@@ -6,7 +6,7 @@
 \usage{
 Corr(exp, obs, memb_dim = "member", sdate_dim = "sdate", comp_dim = NULL,
   limits = NULL, siglev = 0.95, method = "pearson", conf = TRUE,
-  pval = TRUE, ncores = 1)
+  pval = TRUE, ncores = NULL)
 }
 \arguments{
 \item{exp}{A named numeric array of experimental data, with at least two 
@@ -53,10 +53,10 @@ all other dimensions of exp & obs except sdate_dim).\cr
 \item{$p_val}{
  The p-value. Only present if \code{pval = TRUE}.
 }
-\item{$conf.lower}{
+\item{$conf:low}{
  The lower confidence interval. Only present if \code{conf = TRUE}.
 }
-\item{$conf.upper}{
+\item{$conf_high}{
  The upper confidence interval. Only present if \code{conf = TRUE}.
 }
 }
-- 
GitLab


From 334db984abd2a25c3ac9fcceb2634450d5e8f281 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Mon, 20 Jan 2020 19:02:06 +0100
Subject: [PATCH 4/5] Small fix

---
 R/Corr.R                   | 2 +-
 man/Corr.Rd                | 2 +-
 tests/testthat/test-Corr.R | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/Corr.R b/R/Corr.R
index 55d9ec25..dd914dbb 100644
--- a/R/Corr.R
+++ b/R/Corr.R
@@ -34,7 +34,7 @@
 #'@param pval A logical value indicating whether to compute or not the p-value 
 #'  of the test Ho: Corr = 0. The default value is TRUE.
 #'@param ncores An integer indicating the number of cores to use for parallel 
-#'  computation. The default value is 1.
+#'  computation. The default value is NULL.
 #'
 #'@return 
 #'A list containing the numeric arrays with dimension:\cr 
diff --git a/man/Corr.Rd b/man/Corr.Rd
index e63742f2..a6d79b9f 100644
--- a/man/Corr.Rd
+++ b/man/Corr.Rd
@@ -41,7 +41,7 @@ intervals or not. The default value is TRUE.}
 of the test Ho: Corr = 0. The default value is TRUE.}
 
 \item{ncores}{An integer indicating the number of cores to use for parallel 
-computation. The default value is 1.}
+computation. The default value is NULL.}
 }
 \value{
 A list containing the numeric arrays with dimension:\cr 
diff --git a/tests/testthat/test-Corr.R b/tests/testthat/test-Corr.R
index ab487afa..557e5f0e 100644
--- a/tests/testthat/test-Corr.R
+++ b/tests/testthat/test-Corr.R
@@ -63,7 +63,7 @@ test_that("1. Input checks", {
   )
   expect_error(
   Corr(exp1, obs1, limits = c(1,3)),
-  "Paramter 'com_dim' cannot be NULL if 'limits' is assigned."
+  "Paramter 'comp_dim' cannot be NULL if 'limits' is assigned."
   )
   expect_error(
   Corr(exp1, obs1, comp_dim = 'ftime', limits = c(1)),
-- 
GitLab


From 781cf6730025871976eaec8e353cce16d1d13fd5 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Wed, 29 Jan 2020 19:55:45 +0100
Subject: [PATCH 5/5] Use new Eno() in Corr()

---
 R/Corr.R                   | 151 ++++++++++++++++++++-----------------
 man/Corr.Rd                |  58 +++++++-------
 tests/testthat/test-Corr.R |  24 +++---
 3 files changed, 121 insertions(+), 112 deletions(-)

diff --git a/R/Corr.R b/R/Corr.R
index dd914dbb..59bd1ec9 100644
--- a/R/Corr.R
+++ b/R/Corr.R
@@ -1,55 +1,55 @@
 #'Compute the correlation coefficient between an array of forecast and their corresponding observation
 #'
 #'Calculate the correlation coefficient (Pearson, Kendall or Spearman) for 
-#'an array of forecast and an array of observation.  
-#'The correlations are computed along sdate_dim, the dimension corresponding 
-#'to the startdate dimension. If comp_dim is given, the correlations are 
-#'computed only if data along the comp_dim dimension are complete between  
-#'limits[1] and limits[2], i.e., there is no NA between limits[1] and 
-#'limits[2]. This option can be activated if the user wishes to account only 
-#'for the forecasts which the corresponding observations are available at all 
-#'leadtimes. \cr 
-#'The confidence interval is computed by the Fisher transformation.\cr 
-#'The significance level relies on an one-sided student-T distribution.\cr 
+#'an array of forecast and an array of observation. The correlations are 
+#'computed along time_dim, the startdate dimension. If comp_dim is given, 
+#'the correlations are computed only if data along the comp_dim dimension are 
+#'complete between limits[1] and limits[2], i.e., there is no NA between 
+#'limits[1] and limits[2]. This option can be activated if the user wants to 
+#'account only for the forecasts which the corresponding observations are 
+#'available at all leadtimes.\cr 
+#'The confidence interval is computed by the Fisher transformation and the 
+#'significance level relies on an one-sided student-T distribution.\cr 
 #'
 #'@param exp A named numeric array of experimental data, with at least two 
-#'  dimensions 'sdate_dim' and 'memb_dim'.
+#'  dimensions 'time_dim' and 'memb_dim'.
 #'@param obs A named numeric array of observational data, same dimensions as  
 #'  parameter 'exp' except along memb_dim.
+#'@param time_dim A character string indicating the name of dimension along  
+#'  which the correlations are computed. The default value is 'sdate'.
 #'@param memb_dim A character string indicating the name of member (nobs/nexp) 
 #'  dimension. The default value is 'member'.
-#'@param sdate_dim A character string indicating the name of dimension along  
-#'  which the correlations are computed. The default value is 'sdate'.
 #'@param comp_dim A character string indicating the name of dimension along which
 #'  the data is taken into account only if it is complete. The default value
 #'  is NULL.
 #'@param limits A vector of two integers indicating the range along comp_dim to 
 #'  be completed. The default is c(1, length(comp_dim dimension)).
-#'@param siglev A numeric indicating the confidence level for the 
-#'  regression computation. The default value is 0.95.
 #'@param method A character string indicating the type of correlation: 
 #'  'pearson', 'spearman', or 'kendall'. The default value is 'pearson'.
-#'@param conf A logical value indicating whether to retrieve the confidence 
-#'  intervals or not. The default value is TRUE.
 #'@param pval A logical value indicating whether to compute or not the p-value 
 #'  of the test Ho: Corr = 0. The default value is TRUE.
+#'@param conf A logical value indicating whether to retrieve the confidence 
+#'  intervals or not. The default value is TRUE.
+#'@param conf.lev A numeric indicating the confidence level for the 
+#'  regression computation. The default value is 0.95.
 #'@param ncores An integer indicating the number of cores to use for parallel 
 #'  computation. The default value is NULL.
 #'
 #'@return 
 #'A list containing the numeric arrays with dimension:\cr 
-#'(# of datasets along memb_dim in exp, # of datasets along memb_dim in obs, 
-#'all other dimensions of exp & obs except sdate_dim).\cr 
+#'  c(nexp, nobs, all other dimensions of exp except time_dim).\cr
+#'nexp is the number of experiment (i.e., memb_dim in exp), and nobs is the 
+#'number of observation (i.e., memb_dim in obs).\cr
 #'\item{$corr}{
 #'  The correlation coefficient. 
 #'}
-#'\item{$p_val}{
+#'\item{$p.val}{
 #'  The p-value. Only present if \code{pval = TRUE}.
 #'}
-#'\item{$conf:low}{
+#'\item{$conf.lower}{
 #'  The lower confidence interval. Only present if \code{conf = TRUE}.
 #'}
-#'\item{$conf_high}{
+#'\item{$conf.upper}{
 #'  The upper confidence interval. Only present if \code{conf = TRUE}.
 #'}
 #'
@@ -57,10 +57,10 @@
 #'@author History:\cr
 #'0.1  -  2011-04  (V. Guemas, \email{vguemas@bsc.es})  -  Original code\cr
 #'1.0  -  2013-09  (N. Manubens, \email{nicolau.manubens@bsc.es})  -  Formatting to R CRAN\cr
-#'1.1  -  2014-10  (M. Menegoz, \email{martin.menegoz@bsc.es})  -  Adding siglev argument\cr
+#'1.1  -  2014-10  (M. Menegoz, \email{martin.menegoz@bsc.es})  -  Adding conf.lev argument\cr
 #'1.2  -  2015-03  (L.P. Caron, \email{louis-philippe.caron@@bsc.es})  - Adding method argument\cr
 #'1.3  -  2017-02  (A. Hunter, \email{alasdair.hunter@bsc.es})  -  Adapted to veriApply()
-#'3.0  -  2020-01  (A. Ho, \email{an.ho@bsc.es})  -  Adapt to multiApply
+#'3.0  -  2020-01  (A. Ho, \email{an.ho@bsc.es})  -  Adapt multiApply feature
 #'@examples
 #'# Load sample data as in Load() example: 
 #'example(Load) 
@@ -83,10 +83,10 @@
 #'@import multiApply
 #'@importFrom stats cor pt qnorm 
 #'@export
-Corr <- function(exp, obs, memb_dim = 'member', sdate_dim = 'sdate', 
+Corr <- function(exp, obs, time_dim = 'sdate', memb_dim = 'member', 
                  comp_dim = NULL, limits = NULL,
-                 siglev = 0.95, method = 'pearson', 
-                 conf = TRUE, pval = TRUE, ncores = NULL) {
+                 method = 'pearson', pval = TRUE, conf = TRUE,
+                 conf.lev = 0.95, ncores = NULL) {
 
   # Check inputs 
   ## exp and obs (1)
@@ -98,7 +98,7 @@ Corr <- function(exp, obs, memb_dim = 'member', sdate_dim = 'sdate',
   }
   if (is.null(dim(exp)) | is.null(dim(obs))) {
     stop(paste0("Parameter 'exp' and 'obs' must be at least two dimensions ",
-                "containing sdate_dim and memb_dim."))
+                "containing time_dim and memb_dim."))
   }
   if(any(is.null(names(dim(exp))))| any(nchar(names(dim(exp))) == 0) |
      any(is.null(names(dim(obs))))| any(nchar(names(dim(obs))) == 0)) {
@@ -108,6 +108,13 @@ Corr <- function(exp, obs, memb_dim = 'member', sdate_dim = 'sdate',
      !all(names(dim(obs)) %in% names(dim(exp)))) {
     stop("Parameter 'exp' and 'obs' must have same dimension name")
   }
+  ## time_dim
+  if (!is.character(time_dim) | length(time_dim) > 1) {
+    stop("Parameter 'time_dim' must be a character string.")
+  }
+  if (!time_dim %in% names(dim(exp)) | !time_dim %in% names(dim(obs))) {
+    stop("Parameter 'time_dim' is not found in 'exp' or 'obs' dimension.")
+  }
   ## memb_dim
   if (!is.character(memb_dim) | length(memb_dim) > 1) {
     stop("Parameter 'memb_dim' must be a character string.")
@@ -115,14 +122,7 @@ Corr <- function(exp, obs, memb_dim = 'member', sdate_dim = 'sdate',
   if (!memb_dim %in% names(dim(exp)) | !memb_dim %in% names(dim(obs))) {
     stop("Parameter 'memb_dim' is not found in 'exp' or 'obs' dimension.")
   }
-  ## sdate_dim
-  if (!is.character(sdate_dim) | length(sdate_dim) > 1) {
-    stop("Parameter 'sdate_dim' must be a character string.")
-  }
-  if (!sdate_dim %in% names(dim(exp)) | !sdate_dim %in% names(dim(obs))) {
-    stop("Parameter 'sdate_dim' is not found in 'exp' or 'obs' dimension.")
-  }
-  ##comp_dim
+  ## comp_dim
   if (!is.null(comp_dim)) {
     if (!is.character(comp_dim) | length(comp_dim) > 1) {
       stop("Parameter 'comp_dim' must be a character string.")
@@ -131,7 +131,7 @@ Corr <- function(exp, obs, memb_dim = 'member', sdate_dim = 'sdate',
       stop("Parameter 'comp_dim' is not found in 'exp' or 'obs' dimension.")
     }
   }
-  ##limits
+  ## limits
   if (!is.null(limits)) {
     if (is.null(comp_dim)) {
       stop("Paramter 'comp_dim' cannot be NULL if 'limits' is assigned.")
@@ -142,21 +142,22 @@ Corr <- function(exp, obs, memb_dim = 'member', sdate_dim = 'sdate',
                   "integers smaller than the length of paramter 'comp_dim'."))
     }
   }
-  ## siglev
-  if (!is.numeric(siglev) | siglev < 0 | siglev > 1 | length(siglev) > 1) {
-    stop("Parameter 'siglev' must be a numeric number between 0 and 1.")
-  }
   ## method
   if (!(method %in% c("kendall", "spearman", "pearson"))) {
-    stop("Parameter 'method' must be one of 'kendall', 'spearman' or 'pearson'.")}
-  ## conf
-  if (!is.logical(conf) | length(conf) > 1) {
-    stop("Parameter 'conf' must be one logical value.")
+    stop("Parameter 'method' must be one of 'kendall', 'spearman' or 'pearson'.")
   }
   ## pval
   if (!is.logical(pval) | length(pval) > 1) {
     stop("Parameter 'pval' must be one logical value.")
   }
+  ## conf
+  if (!is.logical(conf) | length(conf) > 1) {
+    stop("Parameter 'conf' must be one logical value.")
+  }
+  ## conf.lev
+  if (!is.numeric(conf.lev) | conf.lev < 0 | conf.lev > 1 | length(conf.lev) > 1) {
+    stop("Parameter 'conf.lev' must be a numeric number between 0 and 1.")
+  }
   ## ncores
   if (!is.null(ncores)) {
     if (!is.numeric(ncores) | ncores %% 1 != 0 | ncores < 0 |
@@ -173,10 +174,19 @@ Corr <- function(exp, obs, memb_dim = 'member', sdate_dim = 'sdate',
     stop(paste0("Parameter 'exp' and 'obs' must have same length of ",
                 "all dimension expect 'memb_dim'."))
   }
-  if (dim(exp)[sdate_dim] < 3) {
-    stop("The length of sdate_dim must be at least 3 to compute correlation.")
+  if (dim(exp)[time_dim] < 3) {
+    stop("The length of time_dim must be at least 3 to compute correlation.")
   }
 
+
+  ###############################
+  # Sort dimension
+  name_exp <- names(dim(exp))
+  name_obs <- names(dim(obs))
+  order_obs <- match(name_exp, name_obs)
+  obs <- s2dverification:::.aperm2(obs, order_obs)
+
+
   ###############################
   # Calculate Corr
 
@@ -192,16 +202,17 @@ Corr <- function(exp, obs, memb_dim = 'member', sdate_dim = 'sdate',
   }
 
  res <- Apply(list(exp, obs), 
-              target_dims = list(c(sdate_dim, memb_dim), 
-                                 c(sdate_dim, memb_dim)),
+              target_dims = list(c(time_dim, memb_dim), 
+                                 c(time_dim, memb_dim)),
               fun = .Corr, 
-              siglev = siglev, method = method, 
-              conf = conf, pval = pval, ncores = ncores)
+              time_dim = time_dim, method = method,
+              pval = pval, conf = conf, conf.lev = conf.lev, 
+              ncores = ncores)
  return(res)
 }
 
-.Corr <- function(exp, obs, siglev = siglev, method = method, 
-                  conf = conf, pval = pval) {
+.Corr <- function(exp, obs, time_dim = 'sdate', method = 'pearson',
+                  conf = TRUE, pval = TRUE, conf.lev = 0.95) {
 
   # exp: [sdate, member_exp]
   # obs: [sdate, member_obs]
@@ -210,7 +221,7 @@ Corr <- function(exp, obs, memb_dim = 'member', sdate_dim = 'sdate',
   
   CORR <- array(dim = c(n_exp = n_exp, n_obs = n_obs))
   eno_expand <- array(dim = c(n_exp = n_exp, n_obs = n_obs))
-  p_val <- array(dim = c(n_exp = n_exp, n_obs = n_obs))
+  p.val <- array(dim = c(n_exp = n_exp, n_obs = n_obs))
 
   # ens_mean
   for (i in 1:n_obs) {
@@ -229,12 +240,12 @@ cor(exp[, x], obs[, i],
 
 #  if (pval) {
 #    for (i in 1:n_obs) {
-#      p_val[, i] <- try(sapply(1:n_exp,
+#      p.val[, i] <- try(sapply(1:n_exp,
 #                           function(x) {(cor.test(exp[, x], obs[, i],
 #                                         use = "pairwise.complete.obs",
 #                                         method = method)$p.value)/2}), silent = TRUE)
-#      if (class(p_val[, i]) == 'character') {
-#        p_val[, i] <- NA
+#      if (class(p.val[, i]) == 'character') {
+#        p.val[, i] <- NA
 #      }
 #    }
 #  }
@@ -242,13 +253,11 @@ cor(exp[, x], obs[, i],
   if (pval | conf) {
     if (method == "kendall" | method == "spearman") {
       tmp <- apply(obs, 2, rank)
-      eno <- Eno(tmp, 1)
-#      eno <- Eno(tmp, sdate_dim)  #replace the upper line with this when using new Eno()
+      names(dim(tmp))[1] <- time_dim
+      eno <- Eno(tmp, time_dim)
     } else if (method == "pearson") {
-      eno <- Eno(obs, 1)                          
-#      eno <- Eno(obs, sdate_dim)  #replace the upper line with this when using new Eno()
+      eno <- Eno(obs, time_dim)  
     }
-  
     for (i in 1:n_exp) {
       eno_expand[i, ] <- eno
     }
@@ -257,24 +266,24 @@ cor(exp[, x], obs[, i],
 #This doesn't return error but it's diff from cor.test() when method is spearman and kendall
   if (pval) {
     t <-sqrt(CORR * CORR * (eno_expand - 2) / (1 - (CORR ^ 2)))
-    p_val <- pt(t, eno_expand - 2, lower.tail = FALSE)
+    p.val <- pt(t, eno_expand - 2, lower.tail = FALSE)
   } 
 ###################################
   if (conf) {
-    conf_low <- (1 - siglev) / 2
-    conf_high <- 1 - conf_low
-    conflow <- tanh(atanh(CORR) + qnorm(conf_low) / sqrt(eno_expand - 3))
-    confhigh <- tanh(atanh(CORR) + qnorm(conf_high) / sqrt(eno_expand - 3))
+    conf.lower <- (1 - conf.lev) / 2
+    conf.upper <- 1 - conf.lower
+    conflow <- tanh(atanh(CORR) + qnorm(conf.lower) / sqrt(eno_expand - 3))
+    confhigh <- tanh(atanh(CORR) + qnorm(conf.upper) / sqrt(eno_expand - 3))
   }
 
   if (pval & conf) {
-    res <- list(corr = CORR, p_val = p_val, 
-                conf_low = conflow, conf_high = confhigh)
+    res <- list(corr = CORR, p.val = p.val, 
+                conf.lower = conflow, conf.upper = confhigh)
   } else if (pval & !conf) {
-    res <- list(corr = CORR, p_val = p_val)
+    res <- list(corr = CORR, p.val = p.val)
   } else if (!pval & conf) {
     res <- list(corr = CORR,
-                conf_low = conflow, conf_high = confhigh)
+                conf.lower = conflow, conf.upper = confhigh)
   } else {
     res <- list(corr = CORR)
   }
diff --git a/man/Corr.Rd b/man/Corr.Rd
index a6d79b9f..72edd2ca 100644
--- a/man/Corr.Rd
+++ b/man/Corr.Rd
@@ -4,23 +4,23 @@
 \alias{Corr}
 \title{Compute the correlation coefficient between an array of forecast and their corresponding observation}
 \usage{
-Corr(exp, obs, memb_dim = "member", sdate_dim = "sdate", comp_dim = NULL,
-  limits = NULL, siglev = 0.95, method = "pearson", conf = TRUE,
-  pval = TRUE, ncores = NULL)
+Corr(exp, obs, time_dim = "sdate", memb_dim = "member", comp_dim = NULL,
+  limits = NULL, method = "pearson", pval = TRUE, conf = TRUE,
+  conf.lev = 0.95, ncores = NULL)
 }
 \arguments{
 \item{exp}{A named numeric array of experimental data, with at least two 
-dimensions 'sdate_dim' and 'memb_dim'.}
+dimensions 'time_dim' and 'memb_dim'.}
 
 \item{obs}{A named numeric array of observational data, same dimensions as
 parameter 'exp' except along memb_dim.}
 
+\item{time_dim}{A character string indicating the name of dimension along
+which the correlations are computed. The default value is 'sdate'.}
+
 \item{memb_dim}{A character string indicating the name of member (nobs/nexp) 
 dimension. The default value is 'member'.}
 
-\item{sdate_dim}{A character string indicating the name of dimension along
-which the correlations are computed. The default value is 'sdate'.}
-
 \item{comp_dim}{A character string indicating the name of dimension along which
 the data is taken into account only if it is complete. The default value
 is NULL.}
@@ -28,50 +28,50 @@ is NULL.}
 \item{limits}{A vector of two integers indicating the range along comp_dim to 
 be completed. The default is c(1, length(comp_dim dimension)).}
 
-\item{siglev}{A numeric indicating the confidence level for the 
-regression computation. The default value is 0.95.}
-
 \item{method}{A character string indicating the type of correlation: 
 'pearson', 'spearman', or 'kendall'. The default value is 'pearson'.}
 
+\item{pval}{A logical value indicating whether to compute or not the p-value 
+of the test Ho: Corr = 0. The default value is TRUE.}
+
 \item{conf}{A logical value indicating whether to retrieve the confidence 
 intervals or not. The default value is TRUE.}
 
-\item{pval}{A logical value indicating whether to compute or not the p-value 
-of the test Ho: Corr = 0. The default value is TRUE.}
+\item{conf.lev}{A numeric indicating the confidence level for the 
+regression computation. The default value is 0.95.}
 
 \item{ncores}{An integer indicating the number of cores to use for parallel 
 computation. The default value is NULL.}
 }
 \value{
 A list containing the numeric arrays with dimension:\cr 
-(# of datasets along memb_dim in exp, # of datasets along memb_dim in obs, 
-all other dimensions of exp & obs except sdate_dim).\cr 
+ c(nexp, nobs, all other dimensions of exp except time_dim).\cr
+nexp is the number of experiment (i.e., memb_dim in exp), and nobs is the 
+number of observation (i.e., memb_dim in obs).\cr
 \item{$corr}{
  The correlation coefficient. 
 }
-\item{$p_val}{
+\item{$p.val}{
  The p-value. Only present if \code{pval = TRUE}.
 }
-\item{$conf:low}{
+\item{$conf.lower}{
  The lower confidence interval. Only present if \code{conf = TRUE}.
 }
-\item{$conf_high}{
+\item{$conf.upper}{
  The upper confidence interval. Only present if \code{conf = TRUE}.
 }
 }
 \description{
 Calculate the correlation coefficient (Pearson, Kendall or Spearman) for 
-an array of forecast and an array of observation.  
-The correlations are computed along sdate_dim, the dimension corresponding 
-to the startdate dimension. If comp_dim is given, the correlations are 
-computed only if data along the comp_dim dimension are complete between  
-limits[1] and limits[2], i.e., there is no NA between limits[1] and 
-limits[2]. This option can be activated if the user wishes to account only 
-for the forecasts which the corresponding observations are available at all 
-leadtimes. \cr 
-The confidence interval is computed by the Fisher transformation.\cr 
-The significance level relies on an one-sided student-T distribution.\cr
+an array of forecast and an array of observation. The correlations are 
+computed along time_dim, the startdate dimension. If comp_dim is given, 
+the correlations are computed only if data along the comp_dim dimension are 
+complete between limits[1] and limits[2], i.e., there is no NA between 
+limits[1] and limits[2]. This option can be activated if the user wants to 
+account only for the forecasts which the corresponding observations are 
+available at all leadtimes.\cr 
+The confidence interval is computed by the Fisher transformation and the 
+significance level relies on an one-sided student-T distribution.\cr
 }
 \examples{
 # Load sample data as in Load() example: 
@@ -96,10 +96,10 @@ corr <- Corr(smooth_ano_exp,
 History:\cr
 0.1  -  2011-04  (V. Guemas, \email{vguemas@bsc.es})  -  Original code\cr
 1.0  -  2013-09  (N. Manubens, \email{nicolau.manubens@bsc.es})  -  Formatting to R CRAN\cr
-1.1  -  2014-10  (M. Menegoz, \email{martin.menegoz@bsc.es})  -  Adding siglev argument\cr
+1.1  -  2014-10  (M. Menegoz, \email{martin.menegoz@bsc.es})  -  Adding conf.lev argument\cr
 1.2  -  2015-03  (L.P. Caron, \email{louis-philippe.caron@bsc.es})  - Adding method argument\cr
 1.3  -  2017-02  (A. Hunter, \email{alasdair.hunter@bsc.es})  -  Adapted to veriApply()
-3.0  -  2020-01  (A. Ho, \email{an.ho@bsc.es})  -  Adapt to multiApply
+3.0  -  2020-01  (A. Ho, \email{an.ho@bsc.es})  -  Adapt multiApply feature
 }
 \keyword{datagen}
 
diff --git a/tests/testthat/test-Corr.R b/tests/testthat/test-Corr.R
index 557e5f0e..490f5e72 100644
--- a/tests/testthat/test-Corr.R
+++ b/tests/testthat/test-Corr.R
@@ -27,7 +27,7 @@ test_that("1. Input checks", {
   expect_error(
   Corr(c(1:10), c(2:4)),
   paste0("Parameter 'exp' and 'obs' must be at least two dimensions ",
-         "containing sdate_dim and memb_dim.")
+         "containing time_dim and memb_dim.")
   )
   expect_error(
   Corr(array(1:10, dim = c(2, 5)), array(1:4, dim = c(2, 2))),
@@ -46,12 +46,12 @@ test_that("1. Input checks", {
   "Parameter 'memb_dim' is not found in 'exp' or 'obs' dimension."
   )
   expect_error(
-  Corr(exp1, obs1, sdate_dim = c('sdate', 'a')),
-  "Parameter 'sdate_dim' must be a character string."
+  Corr(exp1, obs1, time_dim = c('sdate', 'a')),
+  "Parameter 'time_dim' must be a character string."
   )
   expect_error(
-  Corr(exp1, obs1, sdate_dim = 'a'),
-  "Parameter 'sdate_dim' is not found in 'exp' or 'obs' dimension."
+  Corr(exp1, obs1, time_dim = 'a'),
+  "Parameter 'time_dim' is not found in 'exp' or 'obs' dimension."
   )
   expect_error(
   Corr(exp1, obs1, comp_dim = c('sdate', 'ftime')),
@@ -71,8 +71,8 @@ test_that("1. Input checks", {
                   "integers smaller than the length of paramter 'comp_dim'.")
   )
   expect_error(
-  Corr(exp1, obs1, siglev = -1),
-  "Parameter 'siglev' must be a numeric number between 0 and 1."
+  Corr(exp1, obs1, conf.lev = -1),
+  "Parameter 'conf.lev' must be a numeric number between 0 and 1."
   )
   expect_error(
   Corr(exp1, obs1, method = 1),
@@ -98,7 +98,7 @@ test_that("1. Input checks", {
   expect_error(
   Corr(exp = array(1:10, dim = c(sdate = 2, member = 5, a = 1)),
        obs = array(1:4, dim = c(a = 1, sdate = 2, member = 2))),
-  "The length of sdate_dim must be at least 3 to compute correlation."
+  "The length of time_dim must be at least 3 to compute correlation."
   )
 
 })
@@ -116,11 +116,11 @@ test_that("2. Output checks: dat1", {
     tolerance = 0.001
   )
   expect_equal(
-    length(which(is.na(Corr(exp1, obs1)$p_val))),
+    length(which(is.na(Corr(exp1, obs1)$p.val))),
     2
   )
   expect_equal(
-    max(Corr(exp1, obs1)$conf_low, na.rm = T),
+    max(Corr(exp1, obs1)$conf.lower, na.rm = T),
     0.6332941,
     tolerance = 0.001
   )
@@ -133,7 +133,7 @@ test_that("2. Output checks: dat1", {
     2
   )
   expect_equal(
-    summary(Corr(exp1, obs1, siglev = 0.99)$conf_high)[1],
+    summary(Corr(exp1, obs1, conf.lev = 0.99)$conf.upper)[1],
     c(Min. = 0.2748),
     tolerance = 0.0001
   )
@@ -154,7 +154,7 @@ test_that("2. Output checks: dat1", {
     c(-0.3, -0.4, -0.6, 0.3, -0.3, 0.2)
   )
   expect_equal(
-    range(Corr(exp1, obs1, method = 'spearman', comp_dim = 'ftime')$p_val, na.rm = T),
+    range(Corr(exp1, obs1, method = 'spearman', comp_dim = 'ftime')$p.val, na.rm = T),
     c(0.0, 0.5),
     tolerance = 0.001
   )
-- 
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