Spatio-temporal modelling of dengue cases in the city of Bucaramanga, Colombia, for

the period 2008 to 2013

Martnez Bello, D.A.1*; Lopez Qulez A.2 ; Torres Prieto, A.3
*dadymar@uv.es
1
MV, MSc, doctoral student, Departament dEstadstica i Investigacio Operativa, Facultat de
Ciencies Matem`atiques, Universitat de Val`encia, Spain
2
Statistician, PhD, Departament dEstadstica i Investigacio Operativa, Facultat de Ci`encies
Matem`atiques, Universitat de Val`encia, Spain
3
Odontologo, Especialista en Epidemiologa, Coordinacion de Epidemiologa, Secretara de Salud del
Departamento de Santander, Colombia
Abstract
Disease mapping is an important tool to understand the disease distribution in space and time, and to evaluate the public health measures impact to counteract the disease burden. Hierarchical
Bayesian disease mapping is at the core of the geo-spatial representation of the disease. The objective of the study was to apply spatio-temporal hierarchical Bayesian disease mapping models to
aggregated dengue cases from the city of Bucaramanga for the period 2008 to 2013, searching for a model which could be used as a representation of the disease spread and dynamics in
Bucaramanga, and to supply information in the search of a predictive model. Dengue cases in the city of Bucaramanga for the period 2008 to 2013 were geocoded, and allocated to one of 295
sections, extracted from the Census 2005 according to the national statistical office (DANE) by epidemiological periods of 4 epidemiological weeks. Spatio-temporal Bayesian hierarchical models
type I, II, III and IV were fitted to model relative risk of every census section. The full model contained spatial and temporal heterogeneity and clustering effects and interaction random effects.
Models were fitted using the software OpenBUGS and the R package R2openBUGS. Model convergence was established using Gelman and Brooks test and Geweke test and line plots, and model
selection was accomplished using the Deviance Information Criteria (DIC). The results showed from several several fitted models, that the interaction type III models exhibited the smallest DIC, and
from these, the model containing spatial heterogeneity and clustering effect in every epidemiological period was the selected model to produce relative risk maps for Dengue cases in Bucaramanga.

Introduction

Materials and methods

Dengue is one of the most important tropical disease for the XXI century.
Dengue is endemic in more than hundred countries from Africa, Asia and
America. Dengue virus belongs to the Flaviviridae family and Flavivirus genus,
and it is conformed by four serotypes denominated DEN1, DEN2, DEN3, DEN4.
In Colombia is responsible of 839013 , 71239 and 740 dengue cases, severe
dengue cases and deaths respectively, in the period 1995 to 2012. World Health
Organization prioritized in 1999 the strategy to fight against the disease, directing
three main efforts: strengthening of epidemiological surveillance, conceptual
standardization of dengue disease, and clinical guides for disease control and the
implementation of community strategies directed to the modification of individual
practices (Maestre-Serrano, Gomez-Camargo, 2013). An important point to help
the efforts of the dengue control is the representation of the disease in space and
time . For this representation Bayesian Disease Mapping methods are known in
the statistical and epidemiological sciences to provide a valuable and efficient
technique of spatial analysis. The Besag, York and Mollie (BYM) model (Besag
et al, 1991) is the starting point to provide smoothed estimates of the relative
risk of a disease, and estimates for other effects like the heterogeneity or the
clustering effect of a disease, and also to the inclusion of temporal effects, and
the interaction between spatial and temporal effects. Moreover, following the
framework established by Knorr-Held (2000), the BYM model can be extended to
include the interaction model type I (unstructured interaction), type II (temporal
interaction), type III (spatial interaction) and type IV (full spatio - temporal
interaction). The objective of the study was to apply spatio-temporal hierarchical
Bayesian disease mapping models to aggregated dengue cases from the city of
Bucaramanga for the period 2008 to 2013, searching for a model which could be
used as a representation of the disease spread and dynamics in Bucaramanga.

Dengue cases count for the period 2008 to 2013 from Bucaramanga, Colombia, obtained from the Sistema de
Vigilancia Epidemiologica SIVIGILA were aggregated by periods of 4 epidemiological weeks, starting at the first
week of 2008, and by census section according to the Departamento Administrativo Nacional de Estadstica
(DANE), from Census 2005, giving a total of 78 epidemiological periods for the 295 census section. Male and
female population for five years age groups, for every section were obtained from DANE, following Census 2005.
A basal dengue crude rate adjusted by sex and age group was calculated for the 6 year period, and then divided
by the number of study periods (78). The basal dengue crude rate was multiplied by the census section
population by age and sex, to obtain the expected number of dengue cases by section and period. Following
model 1, the observed dengue cases counts Oi in every section were distributed Poisson with parameter i
(relative risk), which depends of the clustering spatial effect ui with intrinsic conditional auto-regressive (CAR)
prior, and uniform hyper prior for the CAR variance, and the heterogeneity spatial effect vi with normal prior and
uniform hyper prior in equation (3). From Model 1 as the basic model for one period, spatio temporal interaction
models were built including terms for temporal heterogeneity , temporal clustering and interaction effect ,
for the 78 periods.
Oi Poisson(Ei i )
Log (
i ) = + vi + ui



2
X wij uj

P
ui |ui N
, P u ; vi N 0, v2 ; v Unif (0, 1); u Unif (0, 1)
j wij
j wij

(1)
(2)
(3)

ji

Hierarchical spatio-temporal models with interaction type I, II, III and IV following Knorr-Held (2000) were fitted
to the data with OpenBUGS (Lunn et al 2009) version 3.2.3 rev 1012, using three chains with a burn-in period
of 10000 iterations, a final run of 10000 iterations, a thinning rate of 2, deriving a final sample of 5000 iterations
for the inference. For every parameter, trace and density plots were done, and Gelman and Geweke test for
convergence were obtained, Model selection was accomplished using Deviance Information Criteria (DIC). R
version 3.1.2 (R Core Team, 2014) produced the maps and served as interface to OpenBUGS.

Results

7.18
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7.12
7.10
7.08

73.16

73.14

73.12

73.10

73.16

(b) Period 2

73.12

73.10

Log. Relative Risk by Epidemiologic period 6

[5.4,6.6)
[4.2,5.4)
[3.0,4.2)
[1.8,3.0)
[0.6,1.8)
[0.6,0.6)
[1.8,0.6)
[3.0,1.8)
[4.2,3.0)
[5.4,4.2)
[6.6,5.4)

[5.4,6.6)
[4.2,5.4)
[3.0,4.2)
[1.8,3.0)
[0.6,1.8)
[0.6,0.6)
[1.8,0.6)
[3.0,1.8)
[4.2,3.0)
[5.4,4.2)
[6.6,5.4)

7.14
7.12

7.14

7.14

73.14

(c) Period 3

Log. Relative Risk by Epidemiologic period 5

[5.4,6.6)
[4.2,5.4)
[3.0,4.2)
[1.8,3.0)
[0.6,1.8)
[0.6,0.6)
[1.8,0.6)
[3.0,1.8)
[4.2,3.0)
[5.4,4.2)
[6.6,5.4)

7.12

7.14

7.16

7.18

73.10

7.18

73.12

[5.4,6.6)
[4.2,5.4)
[3.0,4.2)
[1.8,3.0)
[0.6,1.8)
[0.6,0.6)
[1.8,0.6)
[3.0,1.8)
[4.2,3.0)
[5.4,4.2)
[6.6,5.4)

7.16

73.14

(a) Period 1

7.12

7.14

7.16
7.14
7.12
7.10
7.08

73.16

Log. Relative Risk by Epidemiologic period 4

[5.4,6.6)
[4.2,5.4)
[3.0,4.2)
[1.8,3.0)
[0.6,1.8)
[0.6,0.6)
[1.8,0.6)
[3.0,1.8)
[4.2,3.0)
[5.4,4.2)
[6.6,5.4)

7.18

7.18

73.10

Log. Relative Risk by Epidemiologic period 6

[5.4,6.6)
[4.2,5.4)
[3.0,4.2)
[1.8,3.0)
[0.6,1.8)
[0.6,0.6)
[1.8,0.6)
[3.0,1.8)
[4.2,3.0)
[5.4,4.2)
[6.6,5.4)

7.16

73.12

(c) Period 3

Log. Relative Risk by Epidemiologic period 5

[5.4,6.6)
[4.2,5.4)
[3.0,4.2)
[1.8,3.0)
[0.6,1.8)
[0.6,0.6)
[1.8,0.6)
[3.0,1.8)
[4.2,3.0)
[5.4,4.2)
[6.6,5.4)

73.14

7.18

(b) Period 2

Log. Relative Risk by Epidemiologic period 4

7.18
7.14
7.12
7.10
7.08

73.16

7.16

73.10

Log. Relative Risk by Epidemiologic period 3

[5.4,6.6)
[4.2,5.4)
[3.0,4.2)
[1.8,3.0)
[0.6,1.8)
[0.6,0.6)
[1.8,0.6)
[3.0,1.8)
[4.2,3.0)
[5.4,4.2)
[6.6,5.4)

7.12

73.12

7.18

(a) Period 1

73.14

7.16

7.18
7.14
7.12
7.10
7.08

73.16

Log. Relative Risk by Epidemiologic period 2

[5.4,6.6)
[4.2,5.4)
[3.0,4.2)
[1.8,3.0)
[0.6,1.8)
[0.6,0.6)
[1.8,0.6)
[3.0,1.8)
[4.2,3.0)
[5.4,4.2)
[6.6,5.4)

7.16

73.10

7.16

73.12

Log. Relative Risk by Epidemiologic period 1

[5.4,6.6)
[4.2,5.4)
[3.0,4.2)
[1.8,3.0)
[0.6,1.8)
[0.6,0.6)
[1.8,0.6)
[3.0,1.8)
[4.2,3.0)
[5.4,4.2)
[6.6,5.4)

7.16

7.18
7.14
7.12
7.10
7.08

73.14

Figure 4: Relative risk logarithm of dengue cases, year 2013

Log. Relative Risk by Epidemiologic period 3

[5.4,6.6)
[4.2,5.4)
[3.0,4.2)
[1.8,3.0)
[0.6,1.8)
[0.6,0.6)
[1.8,0.6)
[3.0,1.8)
[4.2,3.0)
[5.4,4.2)
[6.6,5.4)

7.16

7.18
7.16
7.14
7.12
7.10
7.08

73.16

7.18

%
Total
10.3
15.0
14.6
12.3
10.3
8.1
5.7
4.2
3.9
3.6
3.2
2.5
2.1
1.4
1.2
0.8
0.9
0.0
100

Log. Relative Risk by Epidemiologic period 2

[5.4,6.6)
[4.2,5.4)
[3.0,4.2)
[1.8,3.0)
[0.6,1.8)
[0.6,0.6)
[1.8,0.6)
[3.0,1.8)
[4.2,3.0)
[5.4,4.2)
[6.6,5.4)

7.16

Column
F
M
10.5 10.2
15.8 14.3
14.3 14.9
11.1 13.3
10.4 10.2
7.7 8.5
5.8 5.6
4.2 4.2
3.7 4.1
3.4 3.7
3.4 3.0
2.9 2.1
2.4 1.8
1.6 1.2
1.2 1.3
0.8 0.8
0.9 0.9
0.0 0.0
100 100

Log. Relative Risk by Epidemiologic period 1

7.12

600

Row %
Total
F
M
0 to 4
1976 49.2 50.8
5 to 9
2866 51.1 48.9
10 to 14
2787 47.6 52.4
15 to 19
2347 44.1 55.9
20 to 24
1968 49.0 51.0
25 to 29
1546 46.2 53.8
30 to 34
1090 49.1 50.9
35 to 39
801 48.6 51.4
40 to 44
748 46.1 53.9
45 to 49
683 46.9 53.1
50 to 54
612 51.5 48.5
55 to 59
481 56.3 43.7
60 to 64
400 56.0 44.0
65 to 69
262 56.1 43.9
70 to 74
238 48.3 51.7
75 to 79
149 49.0 51.0
80 or greater 167 49.1 50.9
N.A.
3
33.3 66.7
Total
19124 48.6 51.4

Figure 2: Relative risk logarithm of dengue cases, year 2010

7.14

Figure 1: Dengue cases for census

section by epidemiological period
and auto-correlation plot, 2008 to
2013

Table 1: Total count, row and column

percentage of dengue cases in the period 2008
to 2013

7.12

Figure 1(a) shows dengue cases by

epidemiological period in the years
2008 to 2013. Year 2010 had the
highest number of cases, and the
cases peak was presented between
the periods 3 and 8, with around
500 cases by epidemiological
period. The auto - correlation plot
displays (Figure 1(b)) high
auto-correlation for the dengue
cases between epidemiological
period.

400

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7.08

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7.08

73.12

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(d) Period 4

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73.12

73.10

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(e) Period 5

73.14

73.12

73.10

(f) Period 6

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(d) Period 4

73.14

73.12

(e) Period 5

73.10

73.12

73.16

73.10

73.14

73.12

73.10

(c) Period 3
Spatial Effect (u)

[2.7,3.3)
[2.1,2.7)
[1.5,2.1)
[0.9,1.5)
[0.3,0.9)
[0.3,0.3)
[0.9,0.3)
[1.5,0.9)
[2.1,1.5)
[2.7,2.1)
[3.3,2.7)

7.14
7.12
7.08

7.10

7.12

7.14

73.14

(d) Period 4

7.18

73.10

[2.7,3.3)
[2.1,2.7)
[1.5,2.1)
[0.9,1.5)
[0.3,0.9)
[0.3,0.3)
[0.9,0.3)
[1.5,0.9)
[2.1,1.5)
[2.7,2.1)
[3.3,2.7)

7.18

[2.7,3.3)
[2.1,2.7)
[1.5,2.1)
[0.9,1.5)
[0.3,0.9)
[0.3,0.3)
[0.9,0.3)
[1.5,0.9)
[2.1,1.5)
[2.7,2.1)
[3.3,2.7)

73.16

7.16
7.14
7.12
7.10
7.08

73.12

Spatial Effect (u)

7.12
73.10

73.14

(b) Period 2

7.10
73.12

73.16

Spatial Effect (u)

7.08
73.14

(f) Period 6

7.18

73.10

7.18

73.12

7.14

7.18

73.14

(a) Period 1

[2.7,3.3)
[2.1,2.7)
[1.5,2.1)
[0.9,1.5)
[0.3,0.9)
[0.3,0.3)
[0.9,0.3)
[1.5,0.9)
[2.1,1.5)
[2.7,2.1)
[3.3,2.7)

73.16

7.16
7.14
7.12
7.10
7.08

73.16

[2.7,3.3)
[2.1,2.7)
[1.5,2.1)
[0.9,1.5)
[0.3,0.9)
[0.3,0.3)
[0.9,0.3)
[1.5,0.9)
[2.1,1.5)
[2.7,2.1)
[3.3,2.7)

7.16

73.10

7.16

73.12

Spatial Effect (u)

[2.7,3.3)
[2.1,2.7)
[1.5,2.1)
[0.9,1.5)
[0.3,0.9)
[0.3,0.3)
[0.9,0.3)
[1.5,0.9)
[2.1,1.5)
[2.7,2.1)
[3.3,2.7)

73.16

7.18
7.14
7.12
7.10
7.08

73.14

(c) Period 3

Spatial Effect (u)

[2.7,3.3)
[2.1,2.7)
[1.5,2.1)
[0.9,1.5)
[0.3,0.9)
[0.3,0.3)
[0.9,0.3)
[1.5,0.9)
[2.1,1.5)
[2.7,2.1)
[3.3,2.7)

73.12

73.16

(b) Period 2

Spatial Effect (u)

73.14

7.18

73.10

7.10

73.12

Spatial Effect (u)

[2.7,3.3)
[2.1,2.7)
[1.5,2.1)
[0.9,1.5)
[0.3,0.9)
[0.3,0.3)
[0.9,0.3)
[1.5,0.9)
[2.1,1.5)
[2.7,2.1)
[3.3,2.7)

7.08

73.14

7.18

(a) Period 1

73.16

7.16
7.14
7.12
7.10
7.08

73.16

Spatial Effect (u)

[2.7,3.3)
[2.1,2.7)
[1.5,2.1)
[0.9,1.5)
[0.3,0.9)
[0.3,0.3)
[0.9,0.3)
[1.5,0.9)
[2.1,1.5)
[2.7,2.1)
[3.3,2.7)

7.16

73.10

7.16

73.12

7.14

Based on the interaction type III model, with

different hyper prior, maps of the smoothed
relative risk (logarithm) were built to show the
areas with clusters of high risk of dengue cases,
and maps of the spatial clustering effect over
the relative risk by section. Figures 2 and 4
show a sample for the epidemiological periods 1
to 6 of the logarithm of the relative risk, for
year 2010 and 2013, and Figures 3 and 5 show
in the same periods, maps of the spatial effect
influencing the relative risk.

73.14

7.12

3551.0
5020.0

7.18
7.14

73.16

Spatial Effect (u)

[2.7,3.3)
[2.1,2.7)
[1.5,2.1)
[0.9,1.5)
[0.3,0.9)
[0.3,0.3)
[0.9,0.3)
[1.5,0.9)
[2.1,1.5)
[2.7,2.1)
[3.3,2.7)

7.10

337.8
487.0
2016.0
981.8

[2.7,3.3)
[2.1,2.7)
[1.5,2.1)
[0.9,1.5)
[0.3,0.9)
[0.3,0.3)
[0.9,0.3)
[1.5,0.9)
[2.1,1.5)
[2.7,2.1)
[3.3,2.7)

7.16

7.18

[2.7,3.3)
[2.1,2.7)
[1.5,2.1)
[0.9,1.5)
[0.3,0.9)
[0.3,0.3)
[0.9,0.3)
[1.5,0.9)
[2.1,1.5)
[2.7,2.1)
[3.3,2.7)

Figure 5: Spatial effect of dengue cases, year 2013

Spatial Effect (u)

7.16

Spatial Effect (u)

7.12

-2067.0
-1696.0
-2265.0
-622.3

Spatial Effect (u)

7.08

There was 19124 dengue cases in

Bucaramanga in the study period.
Fifty one percent of the cases
corresponds to people under 24
years of age. The highest
percentage of cases was presented
in the 5 to 9 years category (Table
1). Table 2 shows DIC for the
interaction models fitted to the
data, demonstrating that the
interaction type III model,
assuming different hyper prior for
clustering and heterogeneity effect
for every period is the model with
the lowest DIC.

73.14

Figure 3: Spatial effect of dengue cases, year 2010

7.10

(b) Autocorrelation plot

73.16

(f) Period 6

7.08

1.0

6360.0
6966.0
6592.0
-2583.0
7625.0

7.18

0.8

73.10

pD

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0.6
Lag

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0.4

73.14

(e) Period 5

7.12

0.2

73.16

7.10

0.0

73.10

7.08

0.4
0.2

0.0

0.2

ACF

0.6

0.8

1.0

Autocorrelation of Dengue cases by epidemiologic period

Dbar Dhat DIC

Interaction type I (unstructured)
+ vi + ui + k + k + ik 42600 36240 48960
+ ui + k + k + ik
42600 35640 49570
+ vi + ui + k + ik
42600 36010 49190
+ vi + ui + k + k
63210 65790 60630
+ ui + k + k
42610 34980 50230
Interaction type II (temporal)
+ vi + ui + k + k + ik 51030 53090 48960
+ ui + k + k + ik
51030 52730 49340
+ vi + ui + k + ik
50980 53250 48720
+ vi + ui + k + k + ik 51100 51720 50480
Interaction type III (spatial)
+ uik + vik
42630 42290 42960
+ vik + ui
42560 42070 43050
+ vi + u i
42140 40120 44150
+ vi + uik
42240 41260 43230
Interaction type IV (spatio - temporal)
+ ui + ik
41710 38160 45260
+ ui + vi + ik
41700 36680 46720

73.12

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Models

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(d) Period 4

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(a) Count

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7.12

10

Epidemiologic period

7.10

7.08

200

7.18

2013

Table 2: DIC for interaction models type I, II,

III and IV. u: spatial clustering, v : spatial
heterogeneity, : temporal heterogeneity,
:temporal clustering, :interaction effect. i:
spatial index, k: temporal index

7.16

2012

7.14

2011

7.12

2010

7.10

2009

7.08

Dengue cases

2008

7.10

year

73.16

73.14

73.12

(e) Period 5

73.10

73.16

73.14

73.12

73.10

(f) Period 6

Discusion
Disease mapping using hierarchical Bayesian models is currently well developed and under continuous research. It is applied for many health problems around the world, but there are not many
reports using the technique to show dengue cases in a region in space and time, as we do in the present report. The main difficulty applying the technique is to find actualized information of
population, for the required aggregation level, discriminated by sex, age and socioeconomical status, to provide accurate estimates of the basal risk, but, this is not a problem of the technique,
being more a problem for obtaining epidemiological information useful to provide adequate products for the public health decision process, it is an opportunity to make a call to the different actors
of the health system to share information, joining efforts to provide better health services for people.
References
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Departamento Nacional de Estadstica (DANE). (2013) Censo General 2005. Republica de Colombia. URL: https://www.dane.gov.co/index.php/poblacion-y-demografia/sistema-de-consulta
Knorr-Held, Leonhard (2000) Bayesian modelling of inseparable space-time variation in disease risk, Statistics in Medicine,19: 255-2567

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