update readme with additional options for runs described

README.md

@@ -61,7 +61,7 @@ To run simulations from the root directory:
 
 * random_parameters.txt: file with the fitted 200 parameter sets for IU 4629. Change to whichever parameter sets we want to run.
 
-3) run the executable with the file input and other required parameters
+3) run the executable with the file input and other required parameters. The basic running of the model is done as follows:
 
 	`src/transfil\_N -s sample_inputs/scenario.xml -n sample_inputs/population_distribution.csv -p sample_inputs/random_parameters.txt -r 200 -t 1 -o sample_results`
 
@@ -79,6 +79,23 @@ To run simulations from the root directory:
 
 	* -t 1: the simulation time step, in months
 
+There are several optional inputs when running the model:
+
+	* -x 1 or 0 (0 is default): set to 1 is we will reduce importation via the input xml file, the reduction will be replaced on map data
+
+ 	* -g seeds.csv: input a file containing integer seeds for the simulations. There must be at least as many seeds as runs to complete if any are provided.
+
+  	* -c coverageReductionFile.csv: file which gives the proportion to which we will reduce the historical MDA coverage by, e.g. a 0.5 will half the historical MDA coverages
+
+   	* -e 1 or 0 (0 is default): set to 1 if we want to output data for IHME.
+
+     	* -D 2026: year from which to output IHME data from. Change to whatever year we want to do this from. Default is 2000.
+
+      	* -m 0 : indicator for outputting NTDMC data. If this is omitted it will be output. If set to 0, this will not be done. Any other integer input will lead to it being output. 
+
+       	* -N 2000: year from which to output NTDMC data from. Change to whatever year we want to do this from. Default is 2000
+
+
 ### Setting the seed for simulations
 
 Random seeds are set per simulation through a .txt file. Each line of the text file should contain the random seed for the corresponding simulation. For example, if line 30 of the file is "123456", then for simulation number 30, the random seed is set to "123456". The number of lines must equal the input `-r` above. e.g. 200 for the command above. This file is passed in with the argument `-g`, e.g.