MALSWOTS WEB APP V 0.1  README FILE 


MALSWOTS - MALARIA SPATIOTEMPORAL WIND-OUTBREAK TRAJECTORY SIMULATION 
This project is funded by a Wellcome Trust Seed Award (212501/Z/18/Z) 

Project principal investigator	Dr Chris Jones, Liverpool School of Tropical Medicine and Hygiene
Project co-investigator:	Dr Luigi Sedda, Lancaste Medical School


INTRODUCTION

MALSWOTS uses wind speed and direction data to predict the spread of Malaria, accordingly to 
the Anopheles flight type of movement, for the systematic implementation of malaria control 
interventions across pre-defined geographic scales.

MALSWOTS WEB APP is a stand-alone framework which provides a web-interface between the user and the
original MALSWOTS R code using the DesktopDeployR framework developed by HJ Lee. It requires
javascript and Shiny web app development tools to compile  the original R code within an 
independent R distribution (R Portable).

MINIMUM SYSTEM REQUIREMENTS:
1. Windows 10  
2. 1GHZ Pentium Atom processor or equivalent
3. 4GB RAM
4. JAVA V.16 
5. 2GB Hard drive space

Please extract the entire folder before starting.


QUICKSTART:
1. Open the folder SWOTS_DEPLOYABLE and double-click on MALSWOTS.bat
2. Observe the pop-up instructions and upload data in the first tab
3. Select  
3. Wait until the analysis is complete, and click OK to see output in the second tab 'Results'
4. Outputs saved in the selected output folder.


USAGE:
1. Select input data files **in .csv format **:
	MANDATORY: wind speed, wind direction, known infection locations
	OPTIONAL: predictor 1, predictor 2, locations known to have no infections.
	
	The data names are:
	Windspeed: Wspeed.csv
	Wind direction: Wdirection.csv
	Predictor 1: Prec.csv
	Predictor 2: Temp.csv
	Mosquito counts: Ento.csv
	x,y infections: xd.csv
	x,y uninfected: xd0.csv

	For a quick one, you can simply run with wind speed, direction, x,y infection and uninfected,

2. Ensure input data files are in .csv format
3. Adjust paratmeters to suit your analyis
	i) Run record number - a user-defined number to record the analysis output, it's 'name'.
	ii) Number of Monte Carlo permutations (a large numnber, i.e. more than 99, may cause long computation)
	iii)Number of simulations (a large numnber, i.e. more than 99, may cause long computation)
	iv) Maxmimum number of days prior to infection before transmissibility. 
	v) Maximum number of days of mosquito flight
	vi) Maximum number of hourse of continuous flight
	vii) Maxmimum distance of flight (m) in one day of typical mosquito
	viii) Distance around each house (m) where mosquitos are present.
	ix) Mosquito flight speed (ms-1) - average.
	x) Distance at which the mosquito can detect the host (m)
	xi) Wind speed limit at which a mosquito cannot take off (ms-1)
	xii) Wind speed limit at which a mosquit can fly (ms-1)
4. Select output folder (default is current working directory) - good folder structure is recommended.
5. Click on 'Run SWOTS' to perform analysis.
6. Please remember the analysis may take some time. 
7. Observe the progress bar in the middle of the screen.
8. You can click 'Quit SWOTS' at any time to cancel the analysis.

TROUBLESHOOTING:
1. Please ensure you have an up-to-date version of Java installed.
2. Please ensure the package is unzipped before running.
3. Google Chrome and MS Edge are tested browsers. Please try using these browsers. 


CREDITS:
The initial version of SWOTS was developed by Dr Luigi Sedda and Colleagues at the University of Oxford.
Dr Luigi Sedda developed it further in the current MALSWOTS version.
DesktopDeployR framework developed by HJLee (https://github.com/wleepang/DesktopDeployR)
MALSWOTS WEB produced by Dr Russell Cain. 

CONTACTS:
Dr Luigi Sedda (Lancaster University): l.sedda@lancaster.ac.uk


LICENSE:
Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
The third-parties copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.