Outbreak Investigation EPIET Introductory course 2011 Lazareto, Menorca, Spain Maaike van Veen.
Analysis & graphical display of surveillance data EPIET Introductory Course October 2010.
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Transcript of Analysis & graphical display of surveillance data EPIET Introductory Course October 2010.
Analysis & graphical display of surveillance data
EPIET Introductory Course
October 2010
2
Health Care Services Public Health Authority
Indicator Data
InformationIntervention
Reporting
Collection
Collation, Analysis,
Interpretation & Presentation
Dissemination
Surveillance system
Purpose of surveillance
Monitor trends (PPT)
Monitor control programmes
Detect unusual events
Objectives
Define steps in surveillance analysis
Perform descriptive analysis
Use surveillance data for alert
Understand mechanisms of more
complex analysis
Knowledge of surveillance system / surveillance data
– Changes over time– Multiple sources of information– Data entry and validation– Problem of quality and completeness
Evaluation of the system
Surveillance indicators & Denominator issues
Choice of indicator according to availability
of denominator :
• no denominator available:
crude number of cases
proportional morbidity
• denominator available:
calculation of rates
standardisation
Denominators
Albanian and refugee populations, Albania, week 16/1999
Surveillance indicators Distribution of attendance at health facility by diagnosis
Albania, Week 19 (10-16/05/1999)
Diarrhoea by age groups, weeks 15-19, 1999, Albania
Number of notified cases
Week
0
200
400
600
800
1000
1200
1400
15 16 17 18 19
< 5 years5 years and +
Notifying healh-care centres and notified out-patientsAlbania, weeks 15-19, 1999
0
5000
10000
15000
20000
25000
30000
15 16 17 18 19
Number of out-patients
Week
Number of health centres
Week
0
20
40
60
80
100
120
140
15 16 17 18 19
NGO MoH
Diarrhoea by age groups, weeks 15-19, 1999, Albania
Number of notified cases
Week
0
200
400
600
800
1000
1200
1400
15 16 17 18 19
< 5 years5 years and +
Proportional morbidity
0
10
20
30
15 16 17 18 19
< 5 years 5 years and +
Diarrhoea / cardiovasc.
0
1
2
15 16 17 18 19
Surveillance indicators& denominator issues
Choice of indicator according to availability
of denominator :
• no denominator available:
crude number of cases
proportional morbidity
• denominator available:
calculation of rates
standardisation
Standardisation
Disease frequency varies according to age
Age structure of the 2 populations is different
Incidence Rate of Disease = XX.X / 1000
Incidence Rate of Disease = YY.Y / 1000
Compare XX.X to YY.Y
14
Descriptive Analysis of Person Characteristics
Frequency distributions– Tables– Histograms for quantitative classification: age…– Bars for ordinal or nominal qualitative
classification: uneven age-groups, suspect-confirmed…
– Pie for nominal qualitative classification: sex, strain, region
Descriptive analysis- Place -
Mapping– Dot/Spot map– Chloropleth map
Choice of– Colors– Scale
Mediterranean sea
3
4
2
5
1 10
9
7 8
6
Asthma cases in Barcelona by district January 21, 1986
17
H1N1 Map by number of confirmed cases
Wikipedia May 9, 2009
50 000+ confirmed cases
5 000+ confirmed cases
500+ confirmed cases
50+ confirmed cases
5+ confirmed cases
1+ confirmed cases
18
Combination?
• Equal frequency scale : (30 / 3)
INCIDENCE | Freq Percent Cum--------------+--------------------- 1 – 30 | 10 33.3% 33.3% 31 – 39 | 10 33.3% 66.6% 40 – 120 | 10 33.3% 100.0%--------------+--------------------- Total | 30 100.0%
• Equal amplitude scale : (120 / 4)INCIDENCE | Freq Percent Cum--------------+--------------------- 1 – 30 | 10 33.3% 33.3% 31 – 60 | 16 53.3% 86.6% 61 – 90 | 2 6.7% 93.3% 91 – 120 | 2 6.7% 100.0%--------------+--------------------- Total | 30 100.0%
• Convenience scaleINCIDENCE | Freq Percent Cum--------------+--------------------- < 100 | 28 93.3% 93.3% >= 100 | 2 6.7% 100.0%--------------+--------------------- Total | 30 100.0%
Seasonal influenza: incidence rate (%) by regionFrance, January-March 2003
Equal amplitude scale Equal frequency scale
0,00 – 2,85
2,86 – 5,69
5,70 – 8,54
Incidence Rate (%)
0,00 – 1,02
1,03 – 2,52
2,53 – 8,54
Incidence Rate (%)
Diarrhoea, week 40, 2008Estimated number of cases / 100,000
Descriptive analysis- Time -
Descriptive analysis of time
Graphical analysis
Requires aggregation on appropriate time unit
Choice of time variable
Date of onset
Date of notification
Use rates when denominator changes over time
Describe trend, seasonality
24
Descriptive analysis – Time – Graphical analysis
17
1211
17
9
12
6566
12
15
9
68
12
8
32
544
5544
23
7
4244
313
8
24
86
1112
7
1616
11
6
1416
13
0
12
767
4
75
14
6781012
12
10
776
3332
544
5
1
43234
98
3456
10
6
1210
7
15
11
15
1112
6
19
1210
87
111011
14
3
9
37 50 11 24 37 50 11 24 37
Weeks
0
5
10
15
20
25
Number of cases
Foodborne Intoxications Clusters
37 50 11 24 37 50 11 24 37
Weeks
0
5
10
15
20
25Number of cases
Descriptive analysis – Time – Graphical analysis
Descriptive Analysis of TimeComponents of Surveillance Data
0
25
50
-25
Seasonality
0
25
50 Residuals
0
25
50Trend
0
20
40
60
80
100
Signal
Smoothing techniques:Moving average
2005 2006 2007 2008
26 39 52 13 26 39 52 13 26 39 52 13 26 39 52 13
0 -
5 -
10 -
15 -
20 -
25 -
30 -
Moving average of 52 weeks
Moving average of 12 weeks
Notifications
Number of notified cases
Weeks
Descriptive Analysis of TimeSmoothing Techniques
JanFebMar
Jun
AugJul
SepOct
Dec
AprMay
Nov
869726
945834
465
822654
872
546728
692890
0
500
1000
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
3622/5=724,43690/5=738.03728/5=745.6
29
Effect of the Moving Average Window SizeWeekly Notifications of Salmonellosis, Georgia, 1993-1994
3 weeks
7 weeks
5 weeks
10 weeks
30
Steps in Surveillance Analysis
Prerequisite to Surveillance Analysis – Knowledge of surveillance system (evaluation)
• Nature of surveillance data
• Data quality
– Choice of indicator & Denominator issue
Analysis– Descriptive (PPT)
– Detection of unusual variations / test hypothesis
Methodological considerationswhen testing for time hypothesis
Surveillance data
– Does not result from sampling cases
– Can be viewed as a sample of time units
“Ecological analysis”
– Time units are not independent
“Correlated over time”
– Specific testing methods need to be applied
Testing for time hypothesis
Convert to rates (if needed)
Remove time dependency
– Trend and seasons
– By restriction or modelling
Test for detection of outbreaks
– More cases than expected?
Test for changes in trend
– Departure from historical trend?
0
100
200
300
400
500
600
700
1 10 19 28 37 46 55 64 73 82 91 100 109 118 127 136
Accounting for Time Dependency
Is the red dot consistent with the data?
Tests not accounting for time dependencyMean + 1.96 Standard Deviations
0
100
200
300
400
500
600
700
-10 10 30 50 70 90 110 130 150
Yes
95% CI
Mean
Randomly ordered data
Chronologically ordered data
Tests accounting for time dependency
0
100
200
300
400
500
600
700
1 10 19 28 37 46 55 64 73 82 91 100 109 118 127 136
No95% CI
Residuals, after removing trend and seasonality
-0,4
-0,3
-0,2
-0,1
0,0
0,1
0,2
0,3
1 12 23 34 45 56 67 78 89 100 111 122Mois
95% CI
Mean
Statistical tests for time series
For time series with no trend and seasonality: random series– Tests not accounting for time dependency (TD)– Chi square, Poisson
For time series with seasonality and no trend – Tests accounting for TD by restriction– Similar historical period mean/median
For all time series – Tests accounting for TD by modeling
37
Olympic Games Surveillance, Athens 2004Septic Shocks, Syndromic Surveillance
Poisson test– Count of cases/average previous 7 days ()
between 1-4% <1%P-value
Restriction approach:Historical mean
X = Xi / 15
Mean and standard deviation
Test
X0 >X + 1.96*Std(X)
Std(X) = (Xi-X)² / n
2009 X0
2008 X1 X2 X3
2007 X4 X5 X6
2006 X7 X8 X9
2005 X10 X11 X12
2004 X13 X14 X15
12-15 16-19 20-23 Only applicable if data does not present a significant trend
Conclusion
Know the system / the data– role of artefacts, errors, …
First step = graphic description– PPT
More complex analysis– Statistical testing
– Chance, bias, truth?
Data analysis by epidemiologist– Added value +++
Hypothesis must be validated– Specific investigation / study
41
Analysis of surveillance data= Translating data into information
Provides the basis for public health action
Requires sound analysis and interpretation
Extracts meaningful, actionable findings
Requires clear presentation of complex
issues
42
To know moreabout surveillance
data analysistaking into account time dependency
…
EPIET TSA Module!