Advances in Predictive Modeling
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1 Advances in Predictive Modeling Scott A. sard Professor of Aerobiology Departments of Plant Pathology and Meteorology Pennsylvania State University & Les J. Szabo Research Geneticist USDA, ARS Cereal Disease Laboratory 2009 National Soybean Rust Symposium
2 Collaborators Charles Barnes - Equador Albert Tenuta - OMAFRA Sarah Hambleton - Agriculture and Agri-Food Canada Joe Russo ZedX nc Jeremy Zydek ZedX nc Julie Golod - PSU Annalisa Ariatti PSU and The many U.S., Canadian, and Mexican Extension Pathologists and their assistants who collected data on soybean rust from sentinel plots and through mobile scouting Funded by the USB and USDA
3 Focus of Presentation Validation of short term forecasts of long-distance soybean rust spread ntegrated Aerobiology Modeling Systems (AMS) output NADP Rainwater spore collections Sentinel plot and mobile scouting soybean rust observations What we have learned about forecasting long-distance transport of soybean rust to the continental interior of North America Expectations for 2010 season
4 Synoptic Scale Airflows Govern Transport Direction and Speed Ultraviolet Radiation Turbulent Diffusion and Wind Shear Govern Dilution Turbulent Transport and Dilution in the Atmosphere Survival of Spores while Airborne Temperature and Relative Humidity Vertical Distribution of Spores in Canopy Canopy Density & Structure Wind & Turbulence Time of Spore Release Soybean Plant Growth Stage of Disease Weather Escape of Spores from Canopy Spore Production AMS is a deterministic model of soybean rust transport process Deposition of Spores into a Soybean Crop Colonization of Soybean Crop Dry Deposition Due to Wind and Turbulence Wet Deposition Due to Washout by Precipitation Temperature & Leaf Wetness Soybean Crop Growth Stage
5 Data Sources Doppler Radar NOAA Models (winds, temperatures ) Rapid Update Cycle Forecast (RUC) North American Mesoscale (NAM) Global Forecast System (GFS) NEXRAD stage-4 radar (precipitation) NOAA satellites (precipitation) USDA crop statistics (e.g., soybean acreage for counties) Sentinel plot and mobile scout observations (e.g., crop stage, disease incidence and severity) Epidemiology field studies (aerobiological and epidemiological relationships)
6 AMS Output Maps Wind speed and direction Precipitation and humidity Deposition of viable spores Ensemble risk forecast
7 National Atmospheric Deposition Network Rainwater collector Potential collection sites
8 Time Series of Positive SBR Observations Number of Positives May June July Aug. Sept.
9 Geographic Distribution of Positive SBR Observations
10 Sentinel plot The total number of observations were 22,176 and 26,103 in 2007 and 2008 respectively throughout the U.S., southern Canada, and Mexico from more than 2000 different geographic locations each year.
11 Counties (#) Month of Year
12 Map showing counties where soybean rust is present generated from sentinel plot and mobile scouting observations
13 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (30 May - 06 June 2007) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p Prediction levels considered in analysis Arbitrary demarcation of continental interior SBR Spore Collections Positive, 1-20very few spores Low Moderate Collection levels considered in analysis High >321 Positive, # of # spores of spores unknown unknown
14 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (06-12 June 2007) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 p SBR Spore Collections Positive, 1-20very few spores Low Moderate very low low moderate high Positive, # of # spores of spores unknown unknown May was a particularly dry month in the southeast reinforcing an on-going drought that continued until late August. High >321
15 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (13-19 June 2007) Confusion Matrix AMS Yes No Spore Collections No Yes SBR Spore Collections County with SBR infected sites Positive, 1-20very few spores Low AMS Wet Deposition Output Moderate Viable SBR Spores/Land Area p(#/ha) High > ^0 very low 10^1low10^2 10^3 10^4 moderate 10^5 10^6 high Positive, # of # spores of spores unknown unknown n contrast, rainfall was generally above normal in the southwestern portion of the Mississippi basin during late spring and early summer.
16 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (20-26 June 2007) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
17 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (27 June - 03 July 2007) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
18 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (04-10 July 2007) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p AMS predicted transport and SBR Spore deposition Collections up the Mississippi River valley but not as far as Positive, 1-20very few spores the continental interior Low Moderate High >321 First set of spatially clumped positive observations Positive, # of # spores of spores unknown unknown
19 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (04-10 July 2007) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
20 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (11-17 July 2007) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
21 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (18-24 July 2008) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
22 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (25-31 July 2007) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
23 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (01-07 August 2007) Confusion Matrix AMS Yes No Spore Collections No Yes AMS predicted moderate spore deposition in 2 counties in Kansas AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
24 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (08-14 August 2007) Confusion Matrix Spore Collections No Yes AMS Yes No AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 very low low moderate high Positive, # of # spores of spores unknown 42 infected counties in South, mostly west of the Mississippi River unknown Strong mid-latitude cyclone traversed Midwest advecting heat, moisture, and SBR spores from TX and LA
25 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (15-21 August 2007) Confusion Matrix Spore Collections No Yes AMS Yes No SBR Spore Collections County with SBR infected sites Positive, 1-20very few spores Low AMS Wet Deposition Output Moderate Viable SBR Spores/Land Area p(#/ha) High > ^0 very low 10^1low10^2 10^3 10^4 moderate 10^5 10^6 high Positive, # of # spores of spores unknown Tropical Storm Erin made landfall in TX traversed 20 counties with fields infected unknown with SBR SBR found in continental interior about 5 weeks later
26 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (22-28 August 2007) Confusion Matrix Spore Collections No Yes AMS Yes No SBR Spore Collections County with SBR infected sites Positive, 1-20very few spores Low AMS Wet Deposition Output Moderate Viable SBR Spores/Land Area p(#/ha) High > ^0 very low 10^1low10^2 10^3 10^4 moderate 10^5 10^6 high Positive, # of # spores of spores unknown Low pressure center became established over the Great Lakes with strong winds blowing from unknown northern TX and OK northeastward
27 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (29 August - 04 September 2007) Confusion Matrix Spore Collections No Yes AMS Yes No AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
28 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (05-11 September 2007) Confusion Matrix Spore Collections No Yes AMS Yes No AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Lack of correspondence Last week in 2007 for which we have spore collections Positive, # of # spores of spores unknown unknown
29 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (07-13 May 2008) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p Soybean rust spread more slowly in 2008 then Disappeared from the winter monitoring sites in coastal LA and eastern TX SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
30 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (14-20 May 2008) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high Weather was generally dry throughout the South p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
31 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (21-27 May 2008) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
32 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (28 May - 03 June 2008) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
33 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (04-10 June 2008) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
34 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (11-17 June 2008) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
35 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (18-24 June 2008) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
36 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (25 June - 01 July 2008) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
37 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (01-08 July 2008) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
38 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (09-15 July 2008) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
39 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (16-22 July 2008) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
40 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (06-12 August 2008) Confusion Matrix AMS Yes No Spore Collections No Yes SBR Spore Collections County with SBR infected sites Positive, 1-20 very few spores Low AMS Wet Deposition Output Moderate Viable SBR Spores/Land Area p(#/ha) High > ^0 very low 10^1low10^2 10^3 10^4 moderate 10^5 10^6 high Positive, # of # spores of unknown spores unknown By the end of July, outside of the state of FL, SBR was only known to be present in 3 counties west of the Mississippir River, 1 county in extreme southern GA, and in 2 counties along the AL coast
41 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (13-19 August 2008) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
42 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (20-26 August 2008) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high p Tropical storm Fay brought abundant rain to the southeast in late August SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
43 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (27 August - 02 September 2008) Confusion Matrix AMS Yes No Spore Collections No Yes AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 very low low moderate high Positive, # of # spores of spores unknown unknown SBR found in west-central Mississippi and shortly thereafter in other counties in the Delta
44 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (03-09 September 2008) Confusion Matrix Spore Collections No Yes AMS Yes No AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high Hurricane Gustov made landfall in Louisiana SBR found in continental interior about 1 month later p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Positive, # of # spores of spores unknown unknown
45 Comparison of AMS Spore Deposition Predictions and SBR Spore Collections (10-16 September 2008) Confusion Matrix Spore Collections No Yes AMS Yes No AMS Wet Deposition Output Viable SBR Spores/Land Area (#/ha) 0 County with SBR infected sites 10^0 10^1 10^2 10^3 10^4 10^5 10^6 very low low moderate high Hurricane ke made landfall in eastern Texas p SBR Spore Collections Positive, 1-20very few spores Low Moderate High >321 Last week in 2007 for which we have spore collections Positive, # of # spores of spores unknown unknown
46 Weeks when AMS predictions and rainwater spore collections caused confusion
47 Scenario for SBR Long-Distance Aerial Spread into Continental nterior 1. Pathogen overwinters on kudzu (and perhaps other hosts) along Gulf Coast and perhaps on islands in the Caribbean basin 2. Disease spreads into commercial soybean fields in South Appears to occur when 3 conditions are met: Host is available Prolonged periods of wet weather Temperatures not too hot
48 3. noculum levels increase to high levels in commercial soybean fields in South Combination of conditions occur: continuation of wet weather onset of cool weather maturation of crop beyond stage that requires fungicide application for maintaining yield 4. P. pachyrhizi spores are blown to commercial fields in the interior of North American Requires: large scale southerly airflow associated with either tropical or mid-latitude storm system
49
50 Week of initial transport event
51 Plenty of inoculum in MS but no transport event for over 1 month
52
53
54 Week of initial transport event
55
56
57 Week of initial transport event SBR already found in continental interior Week of initial transport event
58 SBR is found in continental interior 5 wks after likely transport event
59
60 SBR is found in continental interior 3 wks after transport event
61 SBR is found in continental interior 6 wks after initial transport event
62
63
64 Complementary Nature of Aerobiology Models and Rainwater Spore Collections Aerobiology models are strongly dependent on knowing the geographic distribution and strength of inoculum sources. Rainwater spore collections are not. Rainwater spore collections cannot distinguish between viable and non-viable spores. Aerobiology models keep track of spore viability. Rainwater spore collections are point measurements of spore deposition. Aerobiology models predict geographic patterns of spore deposition.
65 Summary 1. Correspondence between AMS model predictions and rainwater spore collections for continental interior is good. 2. We are able to predict long-distance transport of SBR spores into North American continental interior with reasonable accuracy. 3. Length of time between predicted deposition of viable spores and detection of SBR symptoms in continental interior is many weeks and variable (3 wks in 2006, 5 wks in 2007, and 6 wks in 2008)
66 Prospects for SBR Monitoring/Prediction Components in 2010 Reduced funding for sentinel plots No funding for SBR rainwater spore trapping No funding for SBR ensemble forecasting program No funding for SBR national coordinator/data manager position
67 Thank You Advances in Predictive Modeling 2009 National Soybean Rust Symposium
A PRESENTATION BY THE AMERICAN ACADEMY OF ACTUARIES TO THE NAIC S CLIMATE CHANGE AND GLOBAL WARMING (C) WORKING GROUP
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