Update README.md with instructions related to peri-domestic and occupational...

Update README.md with instructions related to peri-domestic and occupational mosquito populations and adjust default outputs.

README.md

@@ -45,9 +45,8 @@ g++ -O3 -o Pv_mod/Pv_model.o Pv_mod/Source.cpp Pv_mod/Simulation.cpp Pv_mod/Inte
 ## Use the model
 Currently, arguments passed to the model binary are unnamed and should respect the following order:
 1. General model parameters file
-2. _An. farauti_ parameters file
-3. _An. punctulatus_ parameters file
-4. _An. koliensis_ parameters file
+2. Peri-domestic mosquitos parameters file
+3. Occupational mosqutos parameters file
 5. Intervention parameters file
 6. Model output file
 
@@ -57,8 +56,8 @@ Great care should be taken in generating these parameter files, especially the i
 TODO: write about general model parameters
 
 ### Mosquito parameters
-The three species considered in this model are _An. farauti_, _An. pucntulatus_ and _An. koliensis_. Each species will have its dedicated parameter file.
-TODO: write (more) about mosquito parameters
+In former versions of the model, mosquito species were modeled explicitely and each had one input parameter file. We now model mosquito mosquitos regardless of their species, but assume they are found near houses (peri-domestic exposure) or at places were males are at increased exposure (occupational exposure). The fraction of males that are over-exposed is, for now, kept fixed at 37%, reflecting what can be observed in malaria-endemic countries. 
+These two different mosquito populations make use of two input parameter files, [domestic_mosquitoes.txt](../domestic_mosquitoes.txt) and [occupational_mosquitoes.txt](../occupational_mosquitoes.txt).
 
 ### Intervention parameters
 The [Intervention file generator](../Intervention_file_generator.R) R script will produce an intervention file where each column corresponds to a time where an intervention (or different combinations of interventions) is enforced.
@@ -70,14 +69,14 @@ __Therefore, intervention parameters files are not interchangeable.__
 ### Run the model
 The following line will run the model using input files provided in this repository, assuming the model has been built in `Pv_mod/Pv_model.o` as described above:
 ```bash
-Pv_mod/Pv_model.o model_parameters.txt farauti_parameters.txt punctulatus_parameters.txt koliensis_parameters.txt intervention_coverage.txt model_output.txt
+Pv_mod/Pv_model.o model_parameters.txt domestic_mosquitoes.txt occupational_mosquitoes.txt intervention_coverage.txt model_output.txt
 ```
 The output will be written to `model_output.txt`.
 
 ## Explore model output
 Model output is provided in a text-based format, where each row represent a time step and columns corespond to model parameters. As such, the _i_-th line and _j_-th column will provide the value of parameter _j_ at time step _i_. The model simulates daily events, so that each line corresponds to a different day, with initial value of `365*date_start`.
 
-The burn-in period (10 years) is dropped from model output, as well as some summary statistics that are not relevant for most uses. These can be further explored in section 1.11 of [Source.cpp, around line 1711](../Pv_mod/Source.cpp#L1711) (at the time of writing this ReadMe), where sections are commented out by default for the sake of making the output files a bit smaller.
+The burn-in period (10 years) is dropped from model output, as well as some summary statistics that are not relevant for most uses. These can be further explored in  [Source.cpp, around line 195](../Pv_mod/Source.cpp#L195) (at the time of writing this ReadMe), where sections are commented out by default for the sake of making the output files a bit smaller.
 
 ### Summary statistics
 TODO: write about `Output_overview.R` script
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