From 38ac02fe61a5df1e7898e37a4bc961abcdb7b5ca Mon Sep 17 00:00:00 2001
From: nperez <nperez@bscearth372.int.bsc.es>
Date: Fri, 8 May 2020 11:29:10 +0200
Subject: [PATCH 01/17] Use case 2.9 Mask for chunking in spatial dimensions

---
 inst/doc/usecase.md           |   9 +-
 inst/doc/usecase/ex2_9_mask.R | 159 ++++++++++++++++++++++++++++++++++
 2 files changed, 167 insertions(+), 1 deletion(-)
 create mode 100644 inst/doc/usecase/ex2_9_mask.R

diff --git a/inst/doc/usecase.md b/inst/doc/usecase.md
index 9ffbee4..65dbd2d 100644
--- a/inst/doc/usecase.md
+++ b/inst/doc/usecase.md
@@ -51,4 +51,11 @@ The problem may occur when the dimension number of the splitted selector is more
    7. [Calculate the ensemble-adjusted Continuous Ranked Probability Score (CRPS)](inst/doc/usecase/ex2_7_seasonal_forecast_crps.R)  
       Use `SpecsVerification::EnsCrps` to calculate the ensemble-adjusted Continuous Ranked Probability Score (CRPS) for ECWMF experimental data, and do ensemble mean. Use `s2dverification::PlotEquiMap` to plot the CRPS map.  
    8. [Use CSTools Calibration function](inst/doc/usecase/ex2_8_calibration.R)  
-      Use `CSTools:::.cal`, the interior function of `CSTools::CST_Calibration`, to do the bias adjustment for ECMWF experimental monthly mean data.  
+      Use `CSTools:::.cal`, the interior function of `CSTools::CST_Calibration`, to do the bias adjustment for ECMWF experimental monthly mean data. 
+   9. [Use a mask to apply different methods to different gridpoints](inst/doc/usecase/ex2_9_mask.R) If you need to apply your analysis in a few gridpoints, you may want to consider use case 1.6, but if you need to load a lot of grid points, maybe this a better solution.
+
+
+
+
+
+ 
diff --git a/inst/doc/usecase/ex2_9_mask.R b/inst/doc/usecase/ex2_9_mask.R
new file mode 100644
index 0000000..13be878
--- /dev/null
+++ b/inst/doc/usecase/ex2_9_mask.R
@@ -0,0 +1,159 @@
+# Use a mask for applying different methods in different gridpoints
+# Author: Núria Pérez-Zanón
+# ------------------------------------------------------------------
+# This use case has two parts:
+# A) create a mask 
+# B) the startR workflow using the mask
+# Notice that you can skip step A if you already have a mask, for instance, the Sea-Land Mask of a model, and you want to apply different analysis in the land than in the ocean.
+# Notice too that this strategy allows you to chunk in the spatial dimensions.
+
+library(startR)
+
+#####################################################################
+# Step A)
+
+# This is an example using toy data. 
+#I read one file of system5_m1 to get the latitudes and longitudes in a region, to create a consistent mask:
+repos <- '/esarchive/exp/ecmwf/system5_m1/monthly_mean/$var$_f6h/$var$_$sdate$.nc'
+data <- Start(dat = repos,
+              var = 'tas',
+              sdate = '20170101',
+              ensemble = indices(1),
+              time = 'first',
+              latitude = indices(300:341),
+              longitude = indices(1:40),
+              return_vars = list(latitude = 'dat',
+                                 longitude = 'dat'),
+              retrieve = FALSE)
+
+lats <- attributes(data)$Variables$dat1$longitude 
+lons <- attributes(data)$Variables$dat1$latitude
+
+# I create a fake mask with one's and zero's:
+mask <- rep(c(rep(1, 21), rep(0, 21)), length(lats))
+dim(mask) <- c(latitude = length(lats), longitude = length(lons))
+
+attr(mask, 'longitude') <- lons
+attr(mask, 'latitude') <- lats
+
+# Save the mask in a ncdf file:
+library(ncdf4)
+dims_var <- NULL
+dim_lon <- ncdim_def(name = 'longitude', units = 'degrees',
+                     vals = as.vector(attributes(data)$Variables$dat1$longitude),
+                     longname = 'longitude')
+dims_var[[1]] <- dim_lon
+dim_lat <- ncdim_def(name = 'latitude', units = 'degrees_north',
+                     vals = as.vector(attributes(data)$Variables$dat1$latitude),
+                     longname = 'latitude')
+dims_var[[2]] <- dim_lat
+datanc  <- ncvar_def(name = 'mask',
+                     units = 'adimensional',
+                     dim = dims_var, missval = -99999)
+file_nc <- nc_create("/esarchive/scratch/nperez/mask_system5_m1_harvestmonth.nc",
+                     datanc)
+ncvar_put(file_nc, datanc, mask)
+nc_close(file_nc)
+
+#####################################################################
+# --------------------------------------------------------------------------------
+#####################################################################
+# Step B)
+
+# Read data:
+repos <- '/esarchive/exp/ecmwf/system5_m1/monthly_mean/$var$_f6h/$var$_$sdate$.nc'
+data <- Start(dat = repos,
+              var = 'tas',
+              sdate = c('20170101', '20180101'),
+              ensemble = indices(1:20),
+              time = 'all',
+              latitude = indices(300:341),
+              longitude = indices(1:40),
+              return_vars = list(latitude = 'dat',
+                                 longitude = 'dat',
+                                 time = 'sdate'),
+              retrieve = FALSE)
+
+# Read mask:
+path <- '/esarchive/scratch/nperez/$var$_system5_m1_harvestmonth.nc'
+mask <-  Start(dat = path,
+              var = 'mask',
+              latitude = 'all',
+              longitude = 'all',
+              return_vars = list(latitude = 'dat',
+                                 longitude = 'dat'),
+              retrieve = FALSE)
+
+# The function does the mean if the mask is 1 or write an NA
+MeanMask <- function(x, mask) {
+  if (mask == 1) {
+    ind <- mean(x)
+  } else {
+    ind <-  NA
+  }
+  return(ind)
+}
+
+# It is necessary to specify one dimension for mask,
+# that's why I have added 'dat' dimension:
+stepMask <- Step(fun = MeanMask,
+                target_dims = list(x = c('dat', 'ensemble', 'sdate', 'time'),
+                                   mask = c('dat')),
+                output_dim = NULL)
+
+# Now, there are two data inputs:
+wf_mask <- AddStep(list(data, mask), stepMask)
+
+res <- Compute(workflow = wf_mask,
+                chunks = list(latitude = 2,
+                              longitude = 2))
+#####################################################################
+# --------------------------------------------------------------------------------
+#####################################################################
+# Extra lines for output verification:
+# Output verification:
+
+summary(res$output1)
+dim(res$output1)
+head(res$output1)
+
+mask_loaded <-  Start(dat = path,
+                      var = 'mask',
+                      latitude = 'all',
+                      longitude = 'all',
+                      return_vars = list(latitude = 'dat',
+                                         longitude = 'dat'),
+                      retrieve = TRUE)
+summary(res$output1[mask_loaded == 0]) # All are NA's: correct
+summary(res$output1[mask_loaded == 1]) # There is no NA's: correct
+sum(mask_loaded == 0) # The number of NA's are 840: correct
+
+# compare values:
+data_loaded <- Start(dat = repos,
+                     var = 'tas',
+                     sdate = c('20170101', '20180101'),
+                     ensemble = indices(1:20),
+                     time = 'all',
+                     latitude = indices(300:341),
+                     longitude = indices(1:40),
+                     return_vars = list(latitude = 'dat',
+                                        longitude = 'dat',
+                                        time = 'sdate'),
+                     retrieve = TRUE)
+mean(data_loaded[1,1, , , ,1,1])
+res$output1[1,1,1]
+mean(data_loaded[1,1, , , ,1,2])
+res$output1[1,1,2]
+
+out <- mask_loaded
+for (i in 1:(dim(data_loaded)['latitude'])) {
+    for (j in 1:(dim(data_loaded)['longitude'])) {
+  if (mask_loaded[1,1, i, j] == 1) {
+     out[1,1,i, j] <- mean(data_loaded[,,,,,i,j])
+  } else {
+     out[1,1,i,j] <- NA
+  }
+    }
+}
+
+
-- 
GitLab


From f2781fa00f0673eff0590a66051a68e335257c33 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Mon, 11 May 2020 14:06:34 +0200
Subject: [PATCH 02/17] Improve the explanation of usecase ex1_7 and FAQ
 how-to-17.

---
 inst/doc/faq.md                      | 21 +++++++++++++++++++--
 inst/doc/usecase/ex1_7_split_merge.R | 28 +++++++++++++++++++---------
 2 files changed, 38 insertions(+), 11 deletions(-)

diff --git a/inst/doc/faq.md b/inst/doc/faq.md
index 66df1e1..bcb937a 100644
--- a/inst/doc/faq.md
+++ b/inst/doc/faq.md
@@ -588,7 +588,7 @@ List of 1
 
 ### 17. Use parameter 'split_multiselected_dims' in Start()
 The selectors can be not only vectors, but also multidimensional array. For instance, the 'time' dimension 
-can be assigned by a two-dimensional array `[sdate = 12, time = 31]`, which is the daily data of 12 months. 
+can be assigned by a two-dimensional array `[sdate = 12, time = 31]`, which is 31 timesteps for 12 start dates. 
 You may want to have both 'sdate' and 'time' in the output dimension, even though 'sdate' is not explicitly specified in Start(). 
 The parameter 'split_multiselected_dims' is for this goal. It is common in the case that uses experimental data attributes to get the corresponding observational data. 
 
@@ -636,7 +636,7 @@ It is important to check if **the order of file_date is in line with dates dimen
 Regardless 'time', which is explicitly specified in Start(), the vector should list 'sdate' first, then 'syear'. 
 As you can see below, the first element '199607' is sdate = 1, and the second element '199612' is sdate = 2. If the order is wrong, you will still get a 
 return data but with mixed dimensions. Because 'sdate' and 'syear' are only 
-implied in the given selectors, Start() cannot check if the order of file_date and dates are consistent or not.
+implied in the given selector vector without any attributes, Start() cannot check if the order of file_date and dates are consistent or not.
 
 ```r
 dates <- attr(hcst, 'Variables')$common$time
@@ -649,6 +649,23 @@ file_date <- sort(unique(gsub('-', '',
 print(file_date)
 #[1] "199607" "199612" "199701" "199707" "199712" "199801" "199807" "199812"
 #[9] "199901"
+
+obs <- Start(dat = path.obs,
+             var = var_name,
+             file_date = file_date,   # a vector with the information of sdate and syear
+             latitude = indices(1:10),
+             longitude = indices(1:10),
+             time = values(dates),    # a 3-dim array (sdate, syear, time)
+             time_across = 'file_date',
+             merge_across_dims = TRUE,
+             merge_across_dims_narm = TRUE,
+             split_multiselected_dims = TRUE,
+             synonims = list(latitude = c('lat','latitude'),
+                             longitude = c('lon','longitude')),
+             return_vars = list(latitude = 'dat',
+                                longitude = 'dat',
+                                time = 'file_date'),
+             retrieve = T)
 ```
 
 
diff --git a/inst/doc/usecase/ex1_7_split_merge.R b/inst/doc/usecase/ex1_7_split_merge.R
index e72ccee..86a704d 100644
--- a/inst/doc/usecase/ex1_7_split_merge.R
+++ b/inst/doc/usecase/ex1_7_split_merge.R
@@ -1,11 +1,17 @@
 #---------------------------------------------------------------------
 # This usecase shows the things to be noticed when the parameters 
 # 'split_multiselected_dims' and 'merge_across_dims' are both used.
-# The problem may occur when the dimension number of the splitted selector 
-# is more than two. 
-
-# If you're not familiar with the usage of these parameters, please see usecases ex1_2 and ex1_3 first, which are less complicated.
+# The problem may occur when the dimension number of the splitted selector is 
+# more than two. If you're not familiar with the usage of these parameters, 
+# please see usecases ex1_2 and ex1_3 first, which are less complicated.
 # See FAQ How-to-#17 for more explanation.
+
+# In this example, hindcast data corresponding to 2 start dates ('20160704', '20161222') 
+# is retrieved. The hindcasts consist of daily values for the 47 following days 
+# after each start date (in this case only the first 12 days are retrieved) and 
+# for the 20 years of hindacst (in this case only the first 3 years are retrieved). 
+# Once the hindacst data is retrieved/read, the corresponding ERA5 values for each 
+# hindcast time and year are retrieved using the 'dates' metadata from the hindcast object.
 #---------------------------------------------------------------------
 
 library(startR)
@@ -18,7 +24,7 @@ path.exp <- '/esarchive/exp/ecmwf/s2s-monthly_ensforhc/daily/$var$_f24h/$sdate$/
 hcst <- Start(dat = path.exp,
               var =  var_name,
               sdate = c('20160704', '20161222'),
-              syear = indices(1:3),  #2016:2018
+              syear = indices(1:3),  #1996:1998
               syear_depends = 'sdate',
               time = indices(1:12),  #4th-15th Jul; 22nd Dec-2nd Jan
               latitude = indices(1:10),
@@ -44,11 +50,15 @@ dim(dates)
 #-----------------------------------------------------------------------
 # This two lines should NOT be used!! It is an example showing the potential
 # problem when using 'split_multiselected_dims' and 'merge_across_dims'.
-# If 'dates' is reordered to 'syear' ahead of 'sdate', while 'file_date' below
-# remains the same, the result will have mixed dimension.
+# If 'dates' is reordered to the order that 'syear' ahead of 'sdate', while 
+# 'file_date' below remains the same, the result will have mixed dimension.
+# The order of 'time', which is the name of the inner dimension `time = values(dates)` 
+# below, is not important. We only need to pay attention on 'sdate' and 'syear' 
+# because they are relavent of the required files (i.e., 'file_date' below).
+# See more explanation in FAQ How-to-#17.
 
 library(s2dv)
-dates <- Reorder(dates, c('syear','time','sdate'))
+dates <- Reorder(dates, c('syear', 'sdate', 'time'))
 #-----------------------------------------------------------------------
 
 #-----------------------------------------------------------------------
@@ -70,7 +80,7 @@ path.obs <- '/esarchive/recon/ecmwf/era5/1hourly/$var$/$var$_$file_date$.nc'
 
 obs <- Start(dat = path.obs,
              var = var_name,
-             file_date = file_date,   # a vector
+             file_date = file_date,   # a vector with the information of sdate and syear
              latitude = indices(1:10),
              longitude = indices(1:10),
              time = values(dates),    # a 3-dim array (sdate, syear, time)
-- 
GitLab


From fd91c1b34d7fef59da15d28837d1fb0b7247dda3 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Thu, 21 May 2020 22:55:44 +0200
Subject: [PATCH 03/17] Add additional data array rearrangement if
 merge_across_dim + split_multiselected_dims. It corrects the displaced values
 when the values in the same file are called more than 1 time.

---
 R/Start.R | 65 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 65 insertions(+)

diff --git a/R/Start.R b/R/Start.R
index 3c544a4..17d116f 100644
--- a/R/Start.R
+++ b/R/Start.R
@@ -3165,6 +3165,71 @@ Start <- function(..., # dim = indices/selectors,
       data_array_final_dims <- .aperm2(data_array_final_dims, tmp)
       data_array_tmp <- data_array_final_dims[data_array_final_dims != -9999]  # become a vector
       
+ #NOTE: When one file contains values for dicrete dimensions, rearrange the 
+ #      chunks (i.e., work_piece) is necessary.
+      if (split_multiselected_dims) {
+      # shape the vector into the array without split_dims
+        split_dims_pos <- match(split_dims, final_dims_fake)
+        new_dims <- c()
+        if (split_dims_pos[1] > 1) {
+          new_dims <- c(new_dims, final_dims_fake[1:(split_dims_pos[1] - 1)])
+        }
+        new_dims <- c(new_dims,  prod(split_dims))
+        names(new_dims)[split_dims_pos[1]] <- across_inner_dim
+        if (split_dims_pos[length(split_dims_pos)] < length(final_dims_fake)) {
+          new_dims <- c(new_dims, final_dims_fake[(split_dims_pos[length(split_dims_pos)] + 1):length(final_dims_fake)])
+        }
+        final_dims_fake_no_split <- new_dims
+        data_array_no_split <- array(data_array_tmp, dim = final_dims_fake_no_split)
+      # seperate 'time' dim into each work_piece length
+        data_array_seperate <- list()
+        tmp <- cumsum(unlist(length_inner_across_dim))
+        tmp <- c(0, tmp)
+        for (i in 1:length(length_inner_across_dim)) {
+          data_array_seperate[[i]] <- Subset(data_array_no_split, across_inner_dim,
+                                             (tmp[i] + 1):tmp[i + 1])
+        }
+      # generate the correct order list from indices_chunk 
+        final_order_list <- list()
+        i <- 1
+        j <- 1
+        a <- indices_chunk[i]
+        while (i < length(indices_chunk)) {
+          while (indices_chunk[i+1] == indices_chunk[i] & i < length(indices_chunk)) {
+            a <- c(a, indices_chunk[i+1])
+            i <- i + 1
+          }
+          final_order_list[[j]] <- a
+          a <- indices_chunk[i+1]
+          i <- i + 1
+          j <- j + 1
+        }
+        names(final_order_list) <- sapply(final_order_list, '[[', 1)
+        final_order_list <- lapply(final_order_list, length)
+
+      # re-build the array: chunk 
+        which_chunk <- as.numeric(names(final_order_list))
+        how_many_indices <- unlist(final_order_list)
+        array_piece <- list()
+        ind_in_array_seperate <- as.list(rep(1, length(data_array_seperate)))
+        for (i in 1:length(final_order_list)) {
+          array_piece[[i]] <- Subset(data_array_seperate[[which_chunk[i]]],
+                                     across_inner_dim,
+                                     ind_in_array_seperate[[which_chunk[i]]]:(ind_in_array_seperate[[which_chunk[i]]] + how_many_indices[i] - 1))
+          ind_in_array_seperate[[which_chunk[i]]] <- ind_in_array_seperate[[which_chunk[i]]] + how_many_indices[i]
+        }
+        
+        # re-build the array: paste
+        data_array_tmp <- array_piece[[1]]
+        along_pos <- which(names(dim(data_array_tmp)) == across_inner_dim)
+        if (length(array_piece) > 1) {
+          for (i in 2:length(array_piece)) {
+          data_array_tmp <- abind::abind(data_array_tmp, array_piece[[i]],
+                                        along = along_pos)
+          }
+        }
+      }        
+        
       data_array <- array(data_array_tmp, dim = final_dims_fake)
       
     } else {  # merge_across_dims_narm = F (old version)
-- 
GitLab


From 90a4c78e9bddbcd490b2b6134d305ab25db9d7c7 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Thu, 21 May 2020 23:55:57 +0200
Subject: [PATCH 04/17] Remove the indices_chunk part to the first, so if the
 array doesn't need reorganization, the new development is skipped.

---
 R/Start.R | 42 ++++++++++++++++++++++++------------------
 1 file changed, 24 insertions(+), 18 deletions(-)

diff --git a/R/Start.R b/R/Start.R
index 17d116f..c04894a 100644
--- a/R/Start.R
+++ b/R/Start.R
@@ -3168,6 +3168,28 @@ Start <- function(..., # dim = indices/selectors,
  #NOTE: When one file contains values for dicrete dimensions, rearrange the 
  #      chunks (i.e., work_piece) is necessary.
       if (split_multiselected_dims) {
+
+      # generate the correct order list from indices_chunk 
+        final_order_list <- list()
+        i <- 1
+        j <- 1
+        a <- indices_chunk[i]
+        while (i < length(indices_chunk)) {
+          while (indices_chunk[i+1] == indices_chunk[i] & i < length(indices_chunk)) {
+            a <- c(a, indices_chunk[i+1])
+            i <- i + 1
+          }
+          final_order_list[[j]] <- a
+          a <- indices_chunk[i+1]
+          i <- i + 1
+          j <- j + 1
+        }
+        names(final_order_list) <- sapply(final_order_list, '[[', 1)
+        final_order_list <- lapply(final_order_list, length)
+        
+        if (!all(diff(as.numeric(names(final_order_list))) > 0)) {
+
+
       # shape the vector into the array without split_dims
         split_dims_pos <- match(split_dims, final_dims_fake)
         new_dims <- c()
@@ -3189,23 +3211,6 @@ Start <- function(..., # dim = indices/selectors,
           data_array_seperate[[i]] <- Subset(data_array_no_split, across_inner_dim,
                                              (tmp[i] + 1):tmp[i + 1])
         }
-      # generate the correct order list from indices_chunk 
-        final_order_list <- list()
-        i <- 1
-        j <- 1
-        a <- indices_chunk[i]
-        while (i < length(indices_chunk)) {
-          while (indices_chunk[i+1] == indices_chunk[i] & i < length(indices_chunk)) {
-            a <- c(a, indices_chunk[i+1])
-            i <- i + 1
-          }
-          final_order_list[[j]] <- a
-          a <- indices_chunk[i+1]
-          i <- i + 1
-          j <- j + 1
-        }
-        names(final_order_list) <- sapply(final_order_list, '[[', 1)
-        final_order_list <- lapply(final_order_list, length)
 
       # re-build the array: chunk 
         which_chunk <- as.numeric(names(final_order_list))
@@ -3229,7 +3234,8 @@ Start <- function(..., # dim = indices/selectors,
           }
         }
       }        
-        
+      }
+  
       data_array <- array(data_array_tmp, dim = final_dims_fake)
       
     } else {  # merge_across_dims_narm = F (old version)
-- 
GitLab


From 54064a5c5f77a33eea1ea1d831b465cf81044f34 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Fri, 22 May 2020 14:36:25 +0200
Subject: [PATCH 05/17] Revise the documents for the new development

---
 NEWS.md                              |  5 +++++
 inst/doc/faq.md                      | 13 +++----------
 inst/doc/usecase/ex1_7_split_merge.R | 17 +++--------------
 3 files changed, 11 insertions(+), 24 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 1206070..a153e77 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,8 @@
+# startR v1.0.3 (Release date: 2020-)
+- Bugfix for requiring the repetitive values from a single file when using 
+'merge_across_dims' and 'split_multiselected_dims'. The value positions were not 
+correct before.
+  
 # startR v1.0.2 (Release date: 2020-05-11)
 - Bugfix for longitude transformation when the required grid point across the borders. The bug apprears at v1.0.0 and v1.0.1.  
 - Add one new parameter 'merge_across_dims_narm' in Start(). If it is TRUE,
diff --git a/inst/doc/faq.md b/inst/doc/faq.md
index bcb937a..932ee59 100644
--- a/inst/doc/faq.md
+++ b/inst/doc/faq.md
@@ -627,16 +627,9 @@ print(attr(obs, 'Dimensions'))
 #    1     1     4     3   256   512 
 ```
 
-Notice that when 'split_multiselected_dims' and 'merge_across_dims' are both used, 
-and dimension number of the splitted selector is more than two, a potential 
-problem of mixed dimension might occur. The following script is from part of 
-the usecase [ex1_7_split_merge.R](inst/doc/usecase/ex1_7_split_merge.R). 
-
-It is important to check if **the order of file_date is in line with dates dimensions order!** 
-Regardless 'time', which is explicitly specified in Start(), the vector should list 'sdate' first, then 'syear'. 
-As you can see below, the first element '199607' is sdate = 1, and the second element '199612' is sdate = 2. If the order is wrong, you will still get a 
-return data but with mixed dimensions. Because 'sdate' and 'syear' are only 
-implied in the given selector vector without any attributes, Start() cannot check if the order of file_date and dates are consistent or not.
+The splited dimension can have more than two dimensions. 
+The following example comes from the usecase [ex1_7_split_merge.R](inst/doc/usecase/ex1_7_split_merge.R). 
+The 'time' selector has three dimensions 'sdate', 'syear', and 'time'.
 
 ```r
 dates <- attr(hcst, 'Variables')$common$time
diff --git a/inst/doc/usecase/ex1_7_split_merge.R b/inst/doc/usecase/ex1_7_split_merge.R
index 86a704d..539a24d 100644
--- a/inst/doc/usecase/ex1_7_split_merge.R
+++ b/inst/doc/usecase/ex1_7_split_merge.R
@@ -48,26 +48,15 @@ dim(dates)
 #-----------------------------------------------------------------------
 
 #-----------------------------------------------------------------------
-# This two lines should NOT be used!! It is an example showing the potential
-# problem when using 'split_multiselected_dims' and 'merge_across_dims'.
-# If 'dates' is reordered to the order that 'syear' ahead of 'sdate', while 
-# 'file_date' below remains the same, the result will have mixed dimension.
-# The order of 'time', which is the name of the inner dimension `time = values(dates)` 
-# below, is not important. We only need to pay attention on 'sdate' and 'syear' 
-# because they are relavent of the required files (i.e., 'file_date' below).
-# See more explanation in FAQ How-to-#17.
-
+# If you need to reorder the dimensions of the 'time' selector, you can use
+# s2dv::Reorder function. These two lines are not used in the following example.
 library(s2dv)
 dates <- Reorder(dates, c('syear', 'sdate', 'time'))
 #-----------------------------------------------------------------------
 
 #-----------------------------------------------------------------------
 # Use 'dates' generated above to get the required files. 
-# It is important to check if the order of file_date is in line with 
-# dates dimensions! Regardless 'time', the vector should list 'sdate' first,
-# then 'syear'. As you can see below, the first element '199607' is sdate = 1,
-# and the second element '199612' is sdate = 2.
-
+# The order of file_date is not important. sort() is not necessary to use.
 file_date <- sort(unique(gsub('-', '', 
                               sapply(as.character(dates), substr, 1, 7))))
 print(file_date)
-- 
GitLab


From f52225f93767302ae11535cdfea8a1149802e9de Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Fri, 22 May 2020 15:17:00 +0200
Subject: [PATCH 06/17] Create unit test for multiple sdates

---
 tests/testthat/test-Start-multiple-sdates.R | 157 ++++++++++++++++++++
 1 file changed, 157 insertions(+)
 create mode 100644 tests/testthat/test-Start-multiple-sdates.R

diff --git a/tests/testthat/test-Start-multiple-sdates.R b/tests/testthat/test-Start-multiple-sdates.R
new file mode 100644
index 0000000..cd5bac8
--- /dev/null
+++ b/tests/testthat/test-Start-multiple-sdates.R
@@ -0,0 +1,157 @@
+context("Start() multiple sdate with split + merge dim")
+
+# When certain values in one observation file are required more than once,
+# and 'merge_across_dims' + 'split_multiselected_dims' are used, the values may be misplaced. 
+# It might happen when reading experimental data with many start dates, 
+# and the corresponding observations are required to have the same data structure.
+
+ecmwf_path_hc <- paste0('/esarchive/exp/ecmwf/s2s-monthly_ensforhc/daily/$var$_f24h/$sdate$/$var$_$syear$.nc')
+obs_path <-paste0('/esarchive/recon/ecmwf/era5/daily/$var$-r240x121/$var$_$file_date$.nc')
+
+var_name <- 'sfcWind'
+var100_name <- 'windagl100'
+
+sdates.seq <- c("20161222","20161229","20170105","20170112")
+
+test_that("1. ", {
+hcst<-Start(dat = ecmwf_path_hc,
+            var = var_name,
+            sdate = sdates.seq,
+            syear =  'all',
+            time = 'all',            
+            latitude = indices(1),
+            longitude = indices(1),
+            ensemble = 'all',
+            syear_depends = 'sdate',
+            return_vars = list(latitude = 'dat',
+                                 longitude = 'dat',
+                                 time = c('sdate','syear')
+                                  ),
+            retrieve = F)
+dates <- attr(hcst, 'Variables')$common$time
+file_date <- unique(sapply(dates, format, '%Y%m'))
+
+obs <- Start(dat = obs_path,
+             var = var100_name,
+             latitude = indices(1),
+             longitude = indices(1),
+             file_date= file_date,
+             time = values(dates),    # 'sdate' 'syear' 'time'
+             time_var = 'time',
+             time_across = 'file_date',
+             merge_across_dims= TRUE,
+             merge_across_dims_narm = TRUE,
+             split_multiselected_dims = TRUE,
+             synonims = list(latitude=c('lat','latitude'),
+                             longitude=c('lon','longitude')),
+             return_vars = list(latitude = 'dat',
+                                longitude = 'dat',#
+                                time = c('file_date')),
+             retrieve = T)
+
+  expect_equal(
+  dim(obs),
+  c(dat = 1, var = 1, latitude = 1, longitude = 1, sdate = 4, syear = 20, time = 47)
+  )
+  expect_equal(
+  obs[1, 1, 1, 1, 1, 1, 8:15],
+  c(10.727190, 21.909714, 3.220845, 7.524321, 7.308463, 2.337417, 7.127212, 3.592193),
+  tolerance = 0.0001
+  )
+  expect_equal(
+  obs[1, 1, 1, 1, 2, 1, 1:5],
+  c(10.727190, 21.909714,  3.220845,  7.524321,  7.308463),
+  tolerance = 0.0001
+  )
+  expect_equal(
+  obs[1, 1, 1, 1, 2, 1, 31:38],
+  c(10.680604, 4.843633, 4.981896, 4.833428, 1.426522, 3.625800, 7.037229, 2.911440),
+  tolerance = 0.0001
+  )
+  expect_equal(
+  obs[1, 1, 1, 1, 1, 2, 9:15],
+  c(11.189878, 11.198478, 8.868102, 10.766751, 19.929094, 20.872601, 14.304168),
+  tolerance = 0.0001
+  )
+  expect_equal(
+  mean(obs),
+  8.627518,
+  tolerance = 0.0001
+  )
+  expect_equal(
+  length(obs[which(is.na(obs))]),
+  0
+  )
+})
+
+test_that("2. change the file_date order", {
+  hcst<-Start(dat = ecmwf_path_hc,
+              var = var_name,
+              sdate = sdates.seq,
+              syear =  indices(1:20),
+              time = 'all',
+              latitude = indices(1),
+              longitude = indices(1),
+              ensemble = 'all',
+              syear_depends = 'sdate',
+              return_vars = list(latitude = 'dat',
+                                 longitude = 'dat',
+                                 time = c('sdate','syear')
+                                  ),
+              retrieve = F)
+  dates <- attr(hcst, 'Variables')$common$time
+  file_date <- sort(unique(sapply(dates, format, '%Y%m')))
+
+
+obs <- Start(dat = obs_path,
+             var = var100_name,
+             latitude = indices(1),
+             longitude = indices(1),
+             file_date= file_date,
+             time = values(dates),    # 'sdate' 'syear' 'time'
+             time_var = 'time',
+             time_across = 'file_date',
+             merge_across_dims= TRUE,
+             merge_across_dims_narm = TRUE,
+             split_multiselected_dims = TRUE,
+             synonims = list(latitude=c('lat','latitude'),
+                             longitude=c('lon','longitude')),
+             return_vars = list(latitude = 'dat',
+                                longitude = 'dat',#
+                                time = c('file_date')),
+             retrieve = T)
+
+  expect_equal(
+  dim(obs),
+  c(dat = 1, var = 1, latitude = 1, longitude = 1, sdate = 4, syear = 20, time = 47)
+  )
+  expect_equal(
+  obs[1, 1, 1, 1, 1, 1, 8:15],
+  c(10.727190, 21.909714, 3.220845, 7.524321, 7.308463, 2.337417, 7.127212, 3.592193),
+  tolerance = 0.0001
+  )
+  expect_equal(
+  obs[1, 1, 1, 1, 2, 1, 1:5],
+  c(10.727190, 21.909714,  3.220845,  7.524321,  7.308463),
+  tolerance = 0.0001
+  )
+  expect_equal(
+  obs[1, 1, 1, 1, 2, 1, 31:38],
+  c(10.680604, 4.843633, 4.981896, 4.833428, 1.426522, 3.625800, 7.037229, 2.911440),
+  tolerance = 0.0001
+  )
+  expect_equal(
+  obs[1, 1, 1, 1, 1, 2, 9:15],
+  c(11.189878, 11.198478, 8.868102, 10.766751, 19.929094, 20.872601, 14.304168),
+  tolerance = 0.0001
+  )
+  expect_equal(
+  mean(obs),
+  8.627518,
+  tolerance = 0.0001
+  )
+  expect_equal(
+  length(obs[which(is.na(obs))]),
+  0
+  )
+})
-- 
GitLab


From 67a3bfd0c83e76dc455cebab377cf9405c37c05d Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Tue, 26 May 2020 15:38:04 +0200
Subject: [PATCH 07/17] Set time zone to UTC

---
 R/NcDataReader.R | 2 +-
 R/Start.R        | 8 ++++++++
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/R/NcDataReader.R b/R/NcDataReader.R
index 8213128..cba05fa 100644
--- a/R/NcDataReader.R
+++ b/R/NcDataReader.R
@@ -162,7 +162,7 @@ NcDataReader <- function(file_path = NULL, file_object = NULL,
           units <- 'days'
         }
 
-        new_array <- rep(as.POSIXct(parts[2]), length(result)) + 
+        new_array <- rep(as.POSIXct(parts[2], tz = 'UTC'), length(result)) + 
                      as.difftime(result[], units = units)
         #new_array <- seq(as.POSIXct(parts[2]), 
         #                  length = max(result, na.rm = TRUE) + 1, 
diff --git a/R/Start.R b/R/Start.R
index c04894a..b23e0eb 100644
--- a/R/Start.R
+++ b/R/Start.R
@@ -1330,11 +1330,19 @@ Start <- function(..., # dim = indices/selectors,
                                                                c(list(x = picked_common_vars[[var_to_read]]), 
                                                                  var_store_indices, 
                                                                  list(value = var_values)))
+                  # Turn time zone back to UTC if this var_to_read is 'time'
+                  if (all(class(picked_common_vars[[var_to_read]]) == c('POSIXct', 'POSIXt'))) {
+                    attr(picked_common_vars[[var_to_read]], "tzone") <- 'UTC'
+                  }
                 } else {
                   picked_vars[[i]][[var_to_read]] <- do.call('[<-', 
                                                              c(list(x = picked_vars[[i]][[var_to_read]]), 
                                                                var_store_indices, 
                                                                list(value = var_values)))
+                  # Turn time zone back to UTC if this var_to_read is 'time'
+                  if (all(class(picked_vars[[i]][[var_to_read]]) == c('POSIXct', 'POSIXt'))) {
+                    attr(picked_vars[[i]][[var_to_read]], "tzone") <- 'UTC'
+                  }
                 }
                 if (var_to_read %in% names(first_found_file)) {
                   first_found_file[var_to_read] <- TRUE
-- 
GitLab


From bf35c2befb3d8cb96aa8ae1e1b95edf344857e4c Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Tue, 26 May 2020 15:50:41 +0200
Subject: [PATCH 08/17] Revise use cases for the change of UTC time zone

---
 inst/doc/usecase/ex1_2_exp_obs_attr.R | 12 ++++++------
 inst/doc/usecase/ex1_3_attr_loadin.R  |  7 ++++++-
 2 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/inst/doc/usecase/ex1_2_exp_obs_attr.R b/inst/doc/usecase/ex1_2_exp_obs_attr.R
index 5a906f3..acff7c9 100644
--- a/inst/doc/usecase/ex1_2_exp_obs_attr.R
+++ b/inst/doc/usecase/ex1_2_exp_obs_attr.R
@@ -97,12 +97,12 @@ print(attr(exp, 'Variables')$common$time)
 #[11] "2007-03-16 13:14:44 CET" "2008-03-16 13:14:44 CET"
 
 print(attr(obs, 'Variables')$common$time)
-# [1] "2005-01-31 18:00:00 CET"  "2006-01-31 18:00:00 CET" 
-# [3] "2007-01-31 18:00:00 CET"  "2008-01-31 18:00:00 CET" 
-# [5] "2005-02-28 18:00:00 CET"  "2006-02-28 18:00:00 CET" 
-# [7] "2007-02-28 18:00:00 CET"  "2008-02-29 18:00:00 CET" 
-# [9] "2005-03-31 19:00:00 CEST" "2006-03-31 19:00:00 CEST"
-#[11] "2007-03-31 19:00:00 CEST" "2008-03-31 19:00:00 CEST"
+# [1] "2005-01-31 18:00:00 UTC" "2006-01-31 18:00:00 UTC"
+# [3] "2007-01-31 18:00:00 UTC" "2008-01-31 18:00:00 UTC"
+# [5] "2005-02-28 18:00:00 UTC" "2006-02-28 18:00:00 UTC"
+# [7] "2007-02-28 18:00:00 UTC" "2008-02-29 18:00:00 UTC"
+# [9] "2005-03-31 18:00:00 UTC" "2006-03-31 18:00:00 UTC"
+#[11] "2007-03-31 18:00:00 UTC" "2008-03-31 18:00:00 UTC"
 
 ##-----lat-----
 print(attr(exp, 'Variables')$common$lat[1:3])
diff --git a/inst/doc/usecase/ex1_3_attr_loadin.R b/inst/doc/usecase/ex1_3_attr_loadin.R
index 3dca648..a918e16 100644
--- a/inst/doc/usecase/ex1_3_attr_loadin.R
+++ b/inst/doc/usecase/ex1_3_attr_loadin.R
@@ -113,7 +113,7 @@ erai[1, 1, 2, 31, 1, 1]  # 1st March also, since June only has 30 days
 
  dates <- attr(system4, 'Variables')$common$time
  dates[2, 31]
-#[1] "1994-07-01 CEST"
+#[1] "1994-07-01 UTC"
  dates[2, 31] <- NA  # Jun
  dates[5, 31] <- NA  # Sep
  dates[7, 31] <- NA  # Nov
@@ -141,4 +141,9 @@ erai[1, 1, 2, , 1, 1] # June
 # [9] 270.5395 272.0379 272.5489 271.1494 270.7764 270.5678 272.0331 273.7856
 #[17] 273.9849 274.5904 273.4369 273.8404 274.4068 274.2292 274.7375 275.5104
 #[25] 275.4324 274.9408 274.8679 276.5602 275.0995 274.6409       NA
+erai[1, 1, 5, , 1, 1] # Sep
+# [1] 270.0656 270.7113 268.4678 271.6489 271.2354 269.7831 269.8045 268.7994
+# [9] 266.3092 262.2734 265.0124 261.8378 265.3950 257.1690 255.8402 264.8826
+#[17] 267.8663 266.6875 262.5502 258.5476 258.9617 263.6396 257.1111 264.8644
+#[25] 261.0085 256.7690 256.5811 256.4331 256.1260 256.4716       NA
 #------------------------------
-- 
GitLab


From 1c9819f68ce22b934d7bb7811497bee70ba1fa7f Mon Sep 17 00:00:00 2001
From: nperez <nperez@bscearth372.int.bsc.es>
Date: Fri, 29 May 2020 18:45:32 +0200
Subject: [PATCH 09/17] nes faq about files formatting problems

---
 inst/doc/faq.md | 30 +++++++++++++++++++++++++++++-
 1 file changed, 29 insertions(+), 1 deletion(-)

diff --git a/inst/doc/faq.md b/inst/doc/faq.md
index 932ee59..a965827 100644
--- a/inst/doc/faq.md
+++ b/inst/doc/faq.md
@@ -27,7 +27,8 @@ This document intends to be the first reference for any doubts that you may have
    1. [No space left on device](#1-no-space-left-on-device)
    2. [ecFlow UI remains blue and does not update status](#2-ecflow-ui-remains-blue-and-does-not-update-status)  
    3. [Compute() successfully but then killed on R session](#3-compute-successfully-but-then-killed-on-r-session)
-   4. [My jobs work well in workstation and fatnodes but not on Power9 (or vice versa)](#4-my-jobs-work-well-in-workstation-and-fatnodes-but-not-on-power9-or-vice-versa) 
+   4. [My jobs work well in workstation and fatnodes but not on Power9 (or vice versa)](#4-my-jobs-work-well-in-workstation-and-fatnodes-but-not-on-power9-or-vice-versa)
+   5. [Errors related to wrong file formatting](#5-errors-related-to-wrong-file-formatting) 
 
 
 ## 1. How to
@@ -722,3 +723,30 @@ have one, go to [usecase.md](https://earth.bsc.es/gitlab/es/startR/tree/develop-
 If it fails, it means that your connection to machine or the ecFlow setting has 
 some problem.
 
+###  5. Errors related to wrong file formatting
+
+Several errors could be return when the files are not correctly formatted. If you see one of this errors, review the coordinates in your files:
+
+```
+Error in Rsx_nc4_put_vara_double: NetCDF: Numeric conversion not representable
+Error in ncvar_put(ncdf_object, defined_vars[[var_counter]]$name, arrays[[i]], : 
+ C function Rsx_nc4_put_vara_double returned error
+```
+
+```
+Error in dim(x$x) <- dim_bk :
+  dims [product 1280] do not match the length of object [1233]  <- this '1233' changes every time
+```
+
+```
+Error in s2dverification::CDORemap(data_array, lons, lats, ...) : 
+  Found invalid values in 'lons'.
+```
+
+```
+ERROR: invalid cell
+ 
+Aborting in file clipping.c, line 1295 ...
+Error in s2dverification::CDORemap(data_array, lons, lats, ...) : 
+  CDO remap failed.
+```
-- 
GitLab


From a61a3965112bb9208c715ff95a76c251b26f2ca9 Mon Sep 17 00:00:00 2001
From: nperez <nperez@bscearth372.int.bsc.es>
Date: Thu, 18 Jun 2020 18:13:28 +0200
Subject: [PATCH 10/17] Errors moving to Nord3 in FAQ

---
 inst/doc/faq.md | 46 +++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 45 insertions(+), 1 deletion(-)

diff --git a/inst/doc/faq.md b/inst/doc/faq.md
index a965827..9319ffa 100644
--- a/inst/doc/faq.md
+++ b/inst/doc/faq.md
@@ -29,7 +29,7 @@ This document intends to be the first reference for any doubts that you may have
    3. [Compute() successfully but then killed on R session](#3-compute-successfully-but-then-killed-on-r-session)
    4. [My jobs work well in workstation and fatnodes but not on Power9 (or vice versa)](#4-my-jobs-work-well-in-workstation-and-fatnodes-but-not-on-power9-or-vice-versa)
    5. [Errors related to wrong file formatting](#5-errors-related-to-wrong-file-formatting) 
-
+   6. [Errors using a new cluster: setting Nord3](#6Errors-using-a-new-cluster-setting-nord3)
 
 ## 1. How to
 
@@ -750,3 +750,47 @@ Aborting in file clipping.c, line 1295 ...
 Error in s2dverification::CDORemap(data_array, lons, lats, ...) : 
   CDO remap failed.
 ```
+
+
+###  6.Errors using a new cluster: setting Nord3
+
+When using a new cluster, some errors could happen. Here, there are some behaviours detected from issue #64.
+
+- whether running Compute(), request password:
+
+```
+Password:
+```
+
+Check that the host name for the cluster has been include in the ´.ssh/config´. 
+Check also that the passwordless access has been properly set up. You can check that you can access the cluster without providing the password by using the host name ´ssh nord3´ (see more infor in the [**Practical guide**](inst/doc/practical_guide.md)).
+
+- alias may not be available, such as 'enas' for 'esarchive'
+
+In this case, the error ´No data files found for any of the specified datasets.´ will be returned.
+
+- repetitive prints of modules loading:
+
+```
+load UDUNITS/2.1.24 (PATH)
+load NETCDF/4.1.3 (PATH, LD_LIBRARY_PATH, NETCDF)
+load R/2.15.2 (PATH, LD_LIBRARY_PATH)
+```
+
+The .bashrc in your Nord 3 home must be edit with the information from [BSC ES wiki](https://earth.bsc.es/wiki/doku.php?id=computing:nord3) to load correct modules. However, if you add a line before those, the result will be the one above.
+
+Check your .bashrc to avoid loading modules before define the department ones.
+
+
+- R versions: Workstation version versus remote cluster version
+
+Some functions depends on the R version used and they should be compatible in workstation and in the remote cluster. If the error:
+
+```
+cannot read workspace version 3 written by R 3.6.2; need R 3.5.0 or newer
+```
+
+change the R version used in your workstation to one newer.
+
+
+
-- 
GitLab


From c0af0587e5a3f358c88437d0dfc442cef38bd492 Mon Sep 17 00:00:00 2001
From: nperez <nperez@bscearth372.int.bsc.es>
Date: Thu, 18 Jun 2020 18:15:49 +0200
Subject: [PATCH 11/17] edits to links

---
 inst/doc/faq.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/inst/doc/faq.md b/inst/doc/faq.md
index 9319ffa..f9573aa 100644
--- a/inst/doc/faq.md
+++ b/inst/doc/faq.md
@@ -29,7 +29,7 @@ This document intends to be the first reference for any doubts that you may have
    3. [Compute() successfully but then killed on R session](#3-compute-successfully-but-then-killed-on-r-session)
    4. [My jobs work well in workstation and fatnodes but not on Power9 (or vice versa)](#4-my-jobs-work-well-in-workstation-and-fatnodes-but-not-on-power9-or-vice-versa)
    5. [Errors related to wrong file formatting](#5-errors-related-to-wrong-file-formatting) 
-   6. [Errors using a new cluster: setting Nord3](#6Errors-using-a-new-cluster-setting-nord3)
+   6. [Errors using a new cluster: setting Nord3](#6-Errors-using-a-new-cluster-setting-nord3)
 
 ## 1. How to
 
@@ -752,7 +752,7 @@ Error in s2dverification::CDORemap(data_array, lons, lats, ...) :
 ```
 
 
-###  6.Errors using a new cluster: setting Nord3
+###  6. Errors using a new cluster: setting Nord3
 
 When using a new cluster, some errors could happen. Here, there are some behaviours detected from issue #64.
 
-- 
GitLab


From 7ce9a2b7bc06145e4bc7447fad2b7ce61fe540cc Mon Sep 17 00:00:00 2001
From: nperez <nperez@bscearth372.int.bsc.es>
Date: Thu, 18 Jun 2020 18:19:24 +0200
Subject: [PATCH 12/17] edits to links

---
 inst/doc/faq.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/doc/faq.md b/inst/doc/faq.md
index f9573aa..ffd0115 100644
--- a/inst/doc/faq.md
+++ b/inst/doc/faq.md
@@ -29,7 +29,7 @@ This document intends to be the first reference for any doubts that you may have
    3. [Compute() successfully but then killed on R session](#3-compute-successfully-but-then-killed-on-r-session)
    4. [My jobs work well in workstation and fatnodes but not on Power9 (or vice versa)](#4-my-jobs-work-well-in-workstation-and-fatnodes-but-not-on-power9-or-vice-versa)
    5. [Errors related to wrong file formatting](#5-errors-related-to-wrong-file-formatting) 
-   6. [Errors using a new cluster: setting Nord3](#6-Errors-using-a-new-cluster-setting-nord3)
+   6. [Errors using a new cluster: setting Nord3](#6-Errors-using-a-new-cluster:-setting-nord3)
 
 ## 1. How to
 
-- 
GitLab


From 279837fc7d449d3f3151bdaa270bc8df9a18472f Mon Sep 17 00:00:00 2001
From: nperez <nperez@bscearth372.int.bsc.es>
Date: Thu, 18 Jun 2020 18:22:37 +0200
Subject: [PATCH 13/17] edits to links

---
 inst/doc/faq.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/doc/faq.md b/inst/doc/faq.md
index ffd0115..fdbe32f 100644
--- a/inst/doc/faq.md
+++ b/inst/doc/faq.md
@@ -29,7 +29,7 @@ This document intends to be the first reference for any doubts that you may have
    3. [Compute() successfully but then killed on R session](#3-compute-successfully-but-then-killed-on-r-session)
    4. [My jobs work well in workstation and fatnodes but not on Power9 (or vice versa)](#4-my-jobs-work-well-in-workstation-and-fatnodes-but-not-on-power9-or-vice-versa)
    5. [Errors related to wrong file formatting](#5-errors-related-to-wrong-file-formatting) 
-   6. [Errors using a new cluster: setting Nord3](#6-Errors-using-a-new-cluster:-setting-nord3)
+   6. [Errors using a new cluster: setting Nord3](#6-Errors-using-a-new-cluster-:-setting-nord3)
 
 ## 1. How to
 
-- 
GitLab


From 10d969413004b66613a124768e574d6c8358fecb Mon Sep 17 00:00:00 2001
From: nperez <nperez@bscearth372.int.bsc.es>
Date: Thu, 18 Jun 2020 18:27:00 +0200
Subject: [PATCH 14/17] edits to links

---
 inst/doc/faq.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/inst/doc/faq.md b/inst/doc/faq.md
index fdbe32f..da8cd05 100644
--- a/inst/doc/faq.md
+++ b/inst/doc/faq.md
@@ -29,7 +29,7 @@ This document intends to be the first reference for any doubts that you may have
    3. [Compute() successfully but then killed on R session](#3-compute-successfully-but-then-killed-on-r-session)
    4. [My jobs work well in workstation and fatnodes but not on Power9 (or vice versa)](#4-my-jobs-work-well-in-workstation-and-fatnodes-but-not-on-power9-or-vice-versa)
    5. [Errors related to wrong file formatting](#5-errors-related-to-wrong-file-formatting) 
-   6. [Errors using a new cluster: setting Nord3](#6-Errors-using-a-new-cluster-:-setting-nord3)
+   6. [Errors using a new cluster (setting Nord3)](#6-Errors-using-a-new-cluster-setting-nord3)
 
 ## 1. How to
 
@@ -752,7 +752,7 @@ Error in s2dverification::CDORemap(data_array, lons, lats, ...) :
 ```
 
 
-###  6. Errors using a new cluster: setting Nord3
+###  6. Errors using a new cluster (setting Nord3)
 
 When using a new cluster, some errors could happen. Here, there are some behaviours detected from issue #64.
 
-- 
GitLab


From 29bc63e714ed7ed093fbbb0335fa9e95eae02003 Mon Sep 17 00:00:00 2001
From: nperez <nperez@bscearth372.int.bsc.es>
Date: Thu, 18 Jun 2020 18:28:33 +0200
Subject: [PATCH 15/17] edits to links remove capitals

---
 inst/doc/faq.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/doc/faq.md b/inst/doc/faq.md
index da8cd05..bebf4a8 100644
--- a/inst/doc/faq.md
+++ b/inst/doc/faq.md
@@ -29,7 +29,7 @@ This document intends to be the first reference for any doubts that you may have
    3. [Compute() successfully but then killed on R session](#3-compute-successfully-but-then-killed-on-r-session)
    4. [My jobs work well in workstation and fatnodes but not on Power9 (or vice versa)](#4-my-jobs-work-well-in-workstation-and-fatnodes-but-not-on-power9-or-vice-versa)
    5. [Errors related to wrong file formatting](#5-errors-related-to-wrong-file-formatting) 
-   6. [Errors using a new cluster (setting Nord3)](#6-Errors-using-a-new-cluster-setting-nord3)
+   6. [Errors using a new cluster (setting Nord3)](#6-errors-using-a-new-cluster-setting-nord3)
 
 ## 1. How to
 
-- 
GitLab


From 8e6d8005344be947ec3aaf416fcc9452569b33f2 Mon Sep 17 00:00:00 2001
From: Andrea <andrea.manrique@bsc.es>
Date: Thu, 18 Jun 2020 19:06:26 +0200
Subject: [PATCH 16/17] Update faq.md

---
 inst/doc/faq.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/doc/faq.md b/inst/doc/faq.md
index bebf4a8..6f1d1ac 100644
--- a/inst/doc/faq.md
+++ b/inst/doc/faq.md
@@ -765,7 +765,7 @@ Password:
 Check that the host name for the cluster has been include in the ´.ssh/config´. 
 Check also that the passwordless access has been properly set up. You can check that you can access the cluster without providing the password by using the host name ´ssh nord3´ (see more infor in the [**Practical guide**](inst/doc/practical_guide.md)).
 
-- alias may not be available, such as 'enas' for 'esarchive'
+- alias may not be available, such as 'esnas' for 'esarchive'
 
 In this case, the error ´No data files found for any of the specified datasets.´ will be returned.
 
-- 
GitLab


From 8bb3e8d636089b161f2d24c04fa37e620464d13e Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Fri, 19 Jun 2020 14:18:33 +0200
Subject: [PATCH 17/17] Update version number to v1.0.3

---
 DESCRIPTION | 2 +-
 NEWS.md     | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ed168c0..0cda1ba 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: startR
 Title: Automatically Retrieve Multidimensional Distributed Data Sets
-Version: 1.0.2
+Version: 1.0.3
 Authors@R: c(
     person("BSC-CNS", role = c("aut", "cph")),
     person("Nicolau", "Manubens", , "nicolau.manubens@bsc.es", role = c("aut")),
diff --git a/NEWS.md b/NEWS.md
index a153e77..baf436e 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,7 +1,9 @@
-# startR v1.0.3 (Release date: 2020-)
+# startR v1.0.3 (Release date: 2020-06-19)
 - Bugfix for requiring the repetitive values from a single file when using 
 'merge_across_dims' and 'split_multiselected_dims'. The value positions were not 
 correct before.
+- Specify the time zone to be 'UTC' regarding time attributes retrieval. The time zone 
+was not specified before and it caused problems when the time crosses daylight saving.
   
 # startR v1.0.2 (Release date: 2020-05-11)
 - Bugfix for longitude transformation when the required grid point across the borders. The bug apprears at v1.0.0 and v1.0.1.  
-- 
GitLab