update README

README.md

@@ -1,5 +1,5 @@
 # covate #
-Covate forecasts time series for lineages that are common to a specified list of regions. The selection of either a VAR or VECM model is automated on a per lineage basis, based on the results of a cointegration test. The selection of parameters for the chosen model is also automated based on the results of stats tests.
+Covate forecasts time series for lineages that are common to a specified list of regions. The selection of either a VAR or VECM model is automated on a per lineage basis, based on the results of a cointegration test. The selection of parameters for the chosen model is also automated.
 
 ## Install ##
 ```
@@ -16,7 +16,8 @@ covate -i metadata.csv -o output_dir
 Help message:
 ```
 usage: covate [-h] -i METADATA -o OUTPUT [-r REGIONS] [-a ADM]
-              [-l LINEAGETYPE] [-t TIMEPERIOD] [-e ENDDATE]
+              [-l LINEAGETYPE] [-t TIMEPERIOD] [-e ENDDATE] [-v VALIDATE]
+              [-m MAXLAGS] [-n NSTEPS]
 
 optional arguments:
   -h, --help            show this help message and exit
@@ -32,9 +33,15 @@ optional arguments:
   -l LINEAGETYPE, --lineage-type LINEAGETYPE
                         Select either lineage or uk_lineage
   -t TIMEPERIOD, --time-period TIMEPERIOD
-                        Select time period in months to take from metadata
+                        Select time period in weeks to take from metadata
   -e ENDDATE, --end-date ENDDATE
                         Select end date to take from metadata. Format: d/m/Y
+  -v VALIDATE, --validate VALIDATE
+                        Run validation forecast. True or False
+  -m MAXLAGS, --max-lags MAXLAGS
+                        Maximum number of lags to investigate
+  -n NSTEPS, --n-steps NSTEPS
+                        Number of days to predict
 ```
 
 ### Arguments ###
@@ -43,18 +50,21 @@ optional arguments:
 * **--region-list** <br /> Input list of regions to compare. Default **UK-WLS, UK-ENG**
 * **--adm** <br /> Select adm the regions belong to (adm1 or adm2). Default **adm1**
 * **--lineage-type** <br /> Select whether to compare global or uk lineages (lineage or uk_lineage). Default **uk_lineage**
-* **--time-period** <br /> Select time period in months to take from the input metadata csv. Default **3**
+* **--time-period** <br /> Select time period in weeks to take from the input metadata csv. Default **12**
 * **--end-date** <br /> The end date of the time period to take from the input metadata csv. Expected format is d/m/Y, e.g. 31/7/2021. Default **latest date in the metadata -7 days** (to account for lag in data)
+* **--validate** <br /> Select whether to run the validation forecasts (True or False). Default **True**
+* **--max-lags** <br /> Select maximum number of lags to investigate. Default **14**
+* **-n-steps** <br /> Number of days to predict. Default **14**
 
 ## Workflow ##
 <img height="600" src="https://github.com/Pathogen-Genomics-Cymru/covate/blob/main/covate-workflow.png" />
 
 ## Output ##
-A date-stamped output directory is created with sub-directories for each common lineage. At the top level you will find a csv of the timeseries and an error log file. In a lineage sub-directory you should find the following directories and plots:
+A date-stamped output directory is created with sub-directories for each common lineage. At the top level you will find a csv of the timeseries and error log files. In a lineage sub-directory you should find the following directories and plots:
 * **prediction** The forecasted time series for each region
-* **validation** A validation forecast for each region (plots the time series for the last two weeks prior to the set end date with a forecast)
-* **logs** A log file containing results of the stats tests
-* **additional-plots** Time series for the lineage and ACF plots for each region
+* **validation** A validation forecast for each region (plots the time series for the last nsteps prior to the set end date with a forecast)
+* **logs** Log files containing results of the stats tests. There will be a prediction and validation log file (provided --validate True)
+* **additional-plots** Time series for the lineage and ACF plots for each region. There may be additional VAR plots if relevant
 
 ### Error Log ###
-The error log will likely contain ERROR and WARN messages for some lineages. ERROR messages indicate a fatal error where the code was unable to build a model for a lineage due to poor quality data. WARN messages indicate a non-fatal error, in this case the model should build for a lineage, but the message may indicate that the model might not be accurate (e.g. A WARN message is recorded if causality is not found). These ERROR and WARN messages are also duplicated in the individual log file for each lineage.
+There are separate error log files for prediction and validation. The error log will likely contain ERROR and WARN messages for some lineages. ERROR messages indicate a fatal error where the code was unable to build a model for a lineage due to poor quality data. WARN messages indicate a non-fatal error, in this case the model should build for a lineage, but the message may indicate that the model might not be accurate (e.g. A WARN message is recorded if causality is not found). These ERROR and WARN messages are also duplicated in the individual log files for each lineage.