Free GIS Software meets zoonotic diseases: From raw data to ecological indicators

FOSS4G 2008 Open Source Geospatial: an option for Developing Nations 29 Sep-3 Oct 2008, Cape Town, South Africa Free GIS Software meets zoonotic diseases: From raw data to ecological indicators M. Neteler Fondazione Mach - Centre for Alpine Ecology 38100 Viote del Monte Bondone (Trento), Italy http://www.cealp.it http://www.grassbook.org neteler * cealp.it

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[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],J. Lindsey CDC

[object Object],Data enhancements in complex Alpine terrain: ... interpolating meteo data? Vallarsa near Rovereto (Northern Italy) Lagorai Trento

[object Object],Data enhancements in complex Alpine terrain

What is the MODIS sensor? Approach: replace climatic station data with satellite data MODIS sensor on Terra and Aqua satellites Typical MODIS overpass: data coverage ,[object Object],[object Object],MODIS/Terra (EOS-AM): - launched Dec. 1999 - passes at approx 10:30 + 22:30 local time MODIS/Aqua (EOS-PM): - launched May 2002 - passes at approx 13:30 + 01:30 local time 4 overpasses per 24h Tile h18_v04

MODIS products and processing ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Batch processing on PBS and SGE: 1460 LST maps/year Linux cluster

[object Object],Minimum/maximum temperatures [°C] - Meteo: 2 values per day (min/max) - MODIS: 4 values per day (2*day, 2*night) Temperature dynamics: daily min/max temperatures Station/pixel: Temperature [°C] Speccheri (860m; GB 1666033E 5070563N)

[object Object],10 days aggregates: time series processing (GRASS GIS) Comparison of meteo station and MODIS Note: Land surface temperature != air temp. Wilcox.test: W = 679, p-value = 0.9572 minimum/maximum temperatures mean temperatures Station Speccheri (860m; GB 1666033E 5070563N) Station/pixel: Temperature [°C] 10-days period Station/pixel: Temperature [°C] 10-days period

Raw MODIS Land Surface Temperature map °C ,[object Object]

°C ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Reconstructed MODIS LST map

°C ,[object Object],Difference map: filtered MODIS LST – RST3D interpolated MODIS LST n: 448514 minimum: -16.104 maximum: 10.111 range: 26.215 mean: -0.388 mean of abs. values: 1.469 standard deviation: 2.037 variance: 4.149

[object Object],MODIS sensors night data (22:30, 01:30) Todo: - more fine grain seasonal model - avoid winter outliers Continuous time series

[object Object],MODIS sensors day data (10:30, 13:30) Continuous time series Todo: - more fine grain seasonal model - avoid winter outliers

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Land Surface Temperature [°C] Trentino LST map 28 June 2006 from Aqua satellite at ~13:30 local time (Deg. Celsius)

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

[object Object],3 1 2 ,[object Object],1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 5 10 15 20 0.1 0.2 0.3 0.4 0.5 0.6 0.7 10day periods (2003) 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 1 2 3 Cavedine (570m a.s.l) Val di Non (610m a.s.l) Levico (760m a.s.l) April EVI Vegetation greening 10km

[object Object],[object Object],MODIS sensor based map (satellite, every 8 days) => the “easy way” Situation 24 th Oct. 2004 Pergine, Valsugana (Trentino), Italy Endrizzi, Bertoldi, Neteler, Rigon, 2005. EGU ,[object Object],GEOtop snow-model based map (using climate data)

Situation 17 th Nov. 2004 Pergine, Valsugana (Trentino), Italy Endrizzi, Bertoldi, Neteler, Rigon, 2005. EGU MODIS sensor based map (satellite, every 8 days) => the “easy way” ,[object Object],[object Object],[object Object],GEOtop snow-model based map (using climate data)

[object Object],Use of new remote sensing variables in machine learning EVI Snow Use of Machine Learning algorithms (ensemble methods) to create spatio-temporal risk models Rizzoli et al. 2002: Bagging of Trees Furlanello et al. 2003: RandomForest, DSC Benito Garzón et al. 2006: Predicting habitat suitability. Ecol. Mod. Rizzoli et al. 2007, Geospatial Health ABIOTIC BIOTIC GIS data Ticks and host density maps LST

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Markus Neteler Fondazione Mach - Centre for Alpine Ecology 38100 Viote del Monte Bondone (Trento), Italy http://www.cealp.it/ - neteler AT cealp.it

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[object Object],[object Object],Rizzoli et al. 2007, Geospatial Health Significant correlation of TBE SEROPOSITIVE with COOLING RATE of previous year (GLM with binom. error, p<0.05): predictive modelling Mean TBE seroprevalence 7.87  0.93 (PRNT)

Free GIS Software meets zoonotic diseases: From raw data to ecological indicators

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Free GIS Software meets zoonotic diseases: From raw data to ecological indicators