home.md

 ## Introduction
 
+[The documentation in this wiki applies to the new merge, coming soon!]
+
 Auto-S2S is the GitLab repository for the ESS Verification Suite, a modular tool for subseasonal to seasonal to decadal forecast verification workflows. It is intended to have a modularized structure, where each module is a separate part of the code that performs a specific task, so that parts of the workflow can be skipped or reordered. 
 The datasets, forecast horizon, time period, skill metrics to compute and other parameters are specified by the user in a configuration file, called "recipe".
 
@@ -55,13 +57,17 @@ Analysis:
     Calibration:
       method: mse_min # Mandatory, str: Calibration method.
     Skill:
-      metric: RPSS CRPSS EnsCorr # Mandatory, str: Skill metric or list of skill metrics, separated by commas or spaces.
+      metric: RPSS CRPSS # Mandatory, str: List of skill metrics.
     Probabilities:
-      percentiles: [[1/3, 2/3], [1/10, 9/10], [1/4, 2/4, 3/4]] # Optional: Thresholds for quantiles and probability categories. Each set of thresholds should be enclosed within brackets.
+      percentiles: [[1/3, 2/3], [1/10, 9/10], [1/4, 2/4, 3/4]] # Optional: Thresholds 
+      # for quantiles and probability categories. # Each set of thresholds should be
+      # enclosed within brackets.
     Indicators:
       index: no # This feature is not implemented yet
-  ncores: 4 # Optional, int: number of cores to be used in parallel computation. If left empty, defaults to 1.
-  remove_NAs: TRUE # Optional, bool: Whether to remove NAs. If left empty, defaults to FALSE.
+  ncores: 4 # Optional, int: number of cores to be used in parallel computation.
+            # If left empty, defaults to 1.
+  remove_NAs: TRUE # Optional, bool: Whether to remove NAs. 
+                   # If left empty, defaults to FALSE.
   Output_format: S2S4E # This feature is not implemented yet
 Run:
   Loglevel: INFO # This feature is not implemented yet
@@ -72,7 +78,7 @@ Run:
 
 ## List of /esarchive/ datasets
 
-Here is a list of the datasets that can currently be loaded by the tool. To request that an additional dataset be added, please open an issue.
+Here is a list of the datasets that can currently be loaded by the tool. To request that an additional dataset be added, please [open an issue](https://earth.bsc.es/gitlab/es/auto-s2s/-/issues).
 
 ### Seasonal datasets
 
@@ -182,13 +188,15 @@ The output of compute_skill_metrics() is a list containing one or more arrays wi
 
 **compute_probabilities()** returns a list of two elements with arrays containing the values corresponding to the thresholds in Workflow:Probabilities:percentiles (\$percentiles), as well as their probability bins (\$probs). Each list contains arrays with named dimensions ‘time’, ‘longitude’ and ‘latitude’.
 For example, if the extremes (1/10, 9/10) are requested, the output will be:
+
 `$percentiles`:
-   `percentile_10`: The 10th percentile, or lower extreme.
-   `percentile_90`: The 90th percentile, or upper extreme.
+ - `percentile_10`: The 10th percentile, or lower extreme.
+ - `percentile_90`: The 90th percentile, or upper extreme.
+
 `$probs`:
-   `prob_b10`: Probability of falling below the 10th percentile.
-   `prob_10_to_90`: Probability of falling inbetween the 10th and 90th percentile.
-   `prob_a90`: Probability of falling above the 90th percentile.
+- `prob_b10`: Probability of falling below the 10th percentile.
+- `prob_10_to_90`: Probability of falling inbetween the 10th and 90th percentile.
+- `prob_a90`: Probability of falling above the 90th percentile.
 
 **Note**: When naming the variables, the probability thresholds are converted to percentiles and rounded to the nearest integer to avoid dots in variable or file names. However, this is just a naming convention; the computations are performed based on the original thresholds specified in the recipe.
 
@@ -221,7 +229,7 @@ The file containing the requested quantiles is named `<var>-percentiles_month<mm
 
 **Can a new metric/method/module/functionality be added to the ESS Verification Suite?**
 
-To request a new feature, please open an issue in the Auto-S2S repository describing what you need and adding any information you think could be of use. The dev team will assess its viability and priority status and work to implement it whenever possible.
+To request a new feature, please [open an issue](https://earth.bsc.es/gitlab/es/auto-s2s/-/issues) in the Auto-S2S repository describing what you need and adding any information you think could be of use. The dev team will assess its viability and priority status and work to implement it whenever possible.
 
 **How can I interpolate my data to a personalized grid?**