Updating README

Author: Melsteroni

README.md

@@ -1,15 +1,15 @@
 ohi-global
 ==========
 
-### Global assessments (EEZ, Antarctica, and High Seas) and scenarios (2012-2016) of the Ocean Health Index 
+### Global assessments (EEZ, Antarctica, and High Seas) and scenarios of the Ocean Health Index 
 
 #### Anatomy of the file structure
 
 General information about file structure is here: http://ohi-science.org/manual/#file-system-organization
 
 Three OHI assessments (for a range of scenario years) are included in this folder:
 
-* eez (scenarios: 2012 - 2016): OHI for 220 country/territorial EEZ regions, this is typically considered the "OHI global assessment"
+* eez (scenarios: 2012 - 2017): OHI for 220 country/territorial EEZ regions, this is typically considered the "OHI global assessment"
 * antarctica (scenarios: 2014 - 2015): OHI for Antarctica CCAMLR regions (includes the high seas/FAO and EEZ regions)
 * high seas (scenarios: 2014 - 2015): OHI for high seas regions (FAO regions without the EEZ regions or Antarctica/CCAMLR regions)
 
@@ -18,8 +18,8 @@ Additional files/folders include:
 
 * eez_layers_meta_data: Database for the EEZ data layers (data sources, names, etc.) and functions to create different data formats
 * global_supplement: Descriptions of data layers and goals 
-* global (2014-2016): Post assessment analysis and visualization of data
-* calculate\_scores_??.R: These files provide the code to calculate scores for the corresponding OHI assessment
+* global (2015-2017): Post assessment analysis and visualization of data
+* calculate\_scores_??.R: These files provide the code to calculate scores for the corresponding OHI assessment (the calculate_scores.R for the eez regions is located in the eez folder)
 * layers\_??.csv: These files provide the location of the data layers used to calculate the OHI assessments.  This file is created by data and functions in the eez_layers_meta_data folder, and they are used by calculate_scores_??.R.  
 * other files can be ignored
 
@@ -35,43 +35,5 @@ Important files within the "eez", "antarctica", and "high seas" folders include:
     - pressure_categories: Defines the pressure category for each pressure layer
     - resilience_matrix.csv: Indicates which resilience layers affect which goals
     - resilience_categories: Defines the resilience category for each resilience layer
-   
-
-### Creating a new scenario within an assessment (e.g., eez2012, eez2016, etc.)
-1. Copy the folder of a previous scenario and change the year
-2. Update the eez_layers_meta_data/layers_eez_file_locations.csv with the file paths and names of the data for each scenario
-3. Update conf/goals.csv with appropriate status_year information (which year in the data layer is used for the scenario)
-4. Update the calculate_scores_??.R as follows:
-   - Add the "scenario" to the scenario list (we might want to move this information to a table at some point):
-   - And update the sync functions so the functions.R files stay consistent
-
-```
- # scenario list (need to add new scenarios here)
-scenarios = list(
-  eez2015     = list(
-    layer   = 'layers_eez',
-    fld_dir      = 'dir_2015a',
-    fld_fn       = 'fn_2015a',
-    f_spatial    = c('../ohiprep/Global/NCEAS-Regions_v2014/data/regions_gcs.js'),
-    do           = T),  
-  eez2014     = list(
-    layer   = 'layers_eez',
-  
-```
-
-```
- ### sync functions.R: 
-# overwrite eez2012, eez2014, eez2015, with eez2013
-for (dir in c('eez2012','eez2014', 'eez2015')){
-  stopifnot(file.copy('eez2013/conf/functions.R', file.path(dir, 'conf/functions.R'), overwrite=T))
-}
-# overwrite antarctica2015 with antarctica2014
-for (dir in c('antarctica2015')){
-  stopifnot(file.copy('antarctica2014/conf/functions.R', file.path(dir, 'conf/functions.R'), overwrite=T))
-}
-# overwrite highseas2015 with highseas2014
-for (dir in c('highseas2015')){
-  stopifnot(file.copy('highseas2014/conf/functions.R', file.path(dir, 'conf/functions.R'), overwrite=T))
-}
-
-```
+    - scenario_data_years.csv: Links the scenario year to the corresponding year of the data for each data layer
+