SPATIAL ANALYSIS APPLIED TO...
Transcript of SPATIAL ANALYSIS APPLIED TO...
SPATIAL ANALYSIS
APPLIED TO
EPIDEMIOLOGY Seminar final report
Ana Carolina Cuéllar
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Index
1. Introduction ......................................................................................................................................................... 2
1.1. What is Spatial Analysis? ..................................................................................................................... 2
1.2. Epidemiology and Spatial Analysis ................................................................................................ 3
1.3. Basics concepts in spatial analysis ................................................................................................. 3
1.4 Data for Spatial Epidemiological Studies ..................................................................................... 5
2. Spatial analysis techniques ......................................................................................................................... 7
2.1 Point Pattern Analysis ............................................................................................................................ 7
2.1.1 Ripley´s K-function ........................................................................................................................ 8
2.1.2 Kernel estimation ....................................................................................................................... 11
2.2 Areal Patterns: ......................................................................................................................................... 13
2.2.1 Spatial autocorrelarion indexes ......................................................................................... 13
2.2.1.1 Global indexes ................................................................................................................... 13
2.2.1.2. Local autocorrelation ................................................................................................... 16
2.3 Geostatistics .............................................................................................................................................. 17
2.3.1 Kriging .............................................................................................................................................. 18
3. Disease mapping ............................................................................................................................................ 20
3.1. Why disease mapping is important? .......................................................................................... 22
4. Some Spatial Analysis softwares that can be used in Epidemiology. ................................ 23
5. Some applications of Spatial Analysis (SA) in Epidemiology ................................................ 24
6. Referencias bibliográficas ........................................................................................................................ 29
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1. Introduction
1.1 What is Spatial Analysis?
Spatial analysis is a broad term that comprises both statistical (spatial statistical) and
non-statistical methods, and starts with the application of exploratory techniques to seek a
good description of the data (like any traditional analysis), and thus help the definition of
hypothesis as well as the choice of the appropriate models. The main characteristic of
spatial statistical analysis, compared to the traditional statistical models, is that the places
where the events occurred are, in an explicit way, presented in the analysis (Pina et al.,
2010).
Spatial analysis (SA) is sometimes defined as a collection of techniques for analyzing
geographical events where the results of analysis depend on the spatial arrangement of the
events. By the term ‘geographical event’ (henceforth, ‘event’) is meant a collection of point,
line or area objects, located in geographical space, attached to which are a set of (one or
more) attribute values. In contrast to other forms of analysis, therefore, SA requires
information both on attribute values and the geographical locations of the objects to which
the collection of attributes are attached.
Based on the systematic collection of quantitative information, the aims of SA are: (1)
the careful and accurate description of events in geographical space (including the
description of pattern); (2) systematic exploration of the pattern of events and the
association between events in space in order to gain a better understanding of the
processes that might be responsible for the observed distribution of events; (3) improving
the ability to predict and control events occurring in geographical space (Haining, 1994).
1.2 Epidemiology and Spatial Analysis
As in any area of applied statistics, the definition and application of appropriate
inferential techniques require a balanced understanding of the questions of interest, the
data available or attainable, and probabilistic models defining or approximating the data
generating process. The central question of interest in most studies in epidemiology is the
identification of factors increasing or decreasing the individual risk of disease as observed
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in at-risk populations or samples from the at-risk population. In spatial studies, we refine
this central question to explore spatial variations in the risk of disease in order to identify
locations (and more importantly, individuals) associated with higher risk of the disease
(Waller, 2010)
Geographical epidemiology can be defined as the description of spatial patterns of
disease morbidity and mortality, part of descriptive epidemiological studies, with the aim of
formulating hypotheses about the etiology of diseases. An other definition for the same
concept that relates epidemiology to Spatial Analysis is Spatial epidemiology. This is the
description and analysis of geographic variations in disease with respect to demographic,
environmental, behavioral, socioeconomic, genetic, and infectious risk factors. Spatial
epidemiology extends the rich tradition of ecologic studies that use explanations of the
distribution of diseases in different places to better understand the etiology of disease.
1.3 Basics concepts in spatial analysis
The important role of location for special data, both in terms of absolute location (i.e.
coordinates in a space) as well as in terms of relative location (spatial arrangement,
topology), has major implications for the way in which statistical analyses may be carried
out. In fact, location leads to two different types of so called spatial effects: Spatial
dependence and spatial heterogeneity. The former results directly from the First Law of
Geography. This Law will tend to result in observations that are spatially clustered or, n
other words, will yield samples of geographical data that will not be independent. From a
geographical perspective, this spatial dependence is the rule rather than the exception, and
it conflicts with the usual assumption of independent observations in statistics. The
dependence in spatial data is often referred to spatial autocorrelation. The second, but
equally important spatial effect is related to spatial (or regional) differentiation which
follows from the intrinsic uniqueness of each location, such spatial heterogeneity (or, non
stationrity) may be evidenced in spatial regimes for variables, functional forms or model
coefficients (Anselin, 1993).
The calculation expression of the concept of spatial dependence is the spatial
autocorrelation. This term is derived from the statistical concept of correlation, which is
used to measure the relationship between two random variables. The preposition "auto"
indicates that the measurement of correlation is done with the same random variable,
measured at various locations in the space. We can use different indicators to measure the
spatial autocorrelation, all of them based in how the spatial dependence varies by
comparing the values of a sample and its neighbors. Its value varies from -1 to 1. Values
close to zero, indicate the absence of significant spatial autocorrelation between the objects
values and their neighbors. Positive Values for the index, indicate positive spatial
autocorrelation, i.e. the value of the attribute of an object
its neighbors. Negative Values for the index, in turn, indi
(Figure 1).
Figure 1. Spatial association an
An other important concept is
spatialized occurrence is been studied, is not approximately constant through all the region
equally, it it is said that the process does not have “
process is a non stationary one
The “stationarity” concept leads us to a
isotropy and anisotropy. A process is isotropic when its behavior is
directions. That is, when the spatial dependence is equal in north
west direction. An example of an anisotropic process is the population density of Bra
East-West density decrease, to the inner country, is more intense than that one found in
North-South direction (Figure 2).
Figure 2. Isotropy and Anisotropy (Extracted from
values and their neighbors. Positive Values for the index, indicate positive spatial
autocorrelation, i.e. the value of the attribute of an object tends to be similar to the values of
Negative Values for the index, in turn, indicate negative auto
Spatial association and correlation (Extracted from Lai, So & Chan
An other important concept is “Stationarity”. If the mean of a process, which its
spatialized occurrence is been studied, is not approximately constant through all the region
is said that the process does not have “stationarity”, this means
ionary one.
concept leads us to a concept which is exclusive of spatial statistics:
. A process is isotropic when its behavior is the same in all
directions. That is, when the spatial dependence is equal in north-south direction or in east
An example of an anisotropic process is the population density of Bra
West density decrease, to the inner country, is more intense than that one found in
(Figure 2).
Isotropy and Anisotropy (Extracted from Santos & Souza, 2007).
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values and their neighbors. Positive Values for the index, indicate positive spatial
tends to be similar to the values of
cate negative auto-correlation
Chan, 2009)
process, which its
spatialized occurrence is been studied, is not approximately constant through all the region
means that this
exclusive of spatial statistics:
the same in all
south direction or in east-
An example of an anisotropic process is the population density of Brazil. An
West density decrease, to the inner country, is more intense than that one found in
2007).
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1.4 Data for Spatial Epidemiological Studies
There are usually two important types of spatial data: point and area data. Each item of
health data (including population, environmental exposure, mortality and morbidity) may
be connected with a point, or precise spatial position such as a home, a street address or an
area, which could be defined as a spatial region by postcode, ward, local authority, province
and country. A public health specialist may also come across spatial data in the form of
continuous surface, such as the statistical surfaces of pollution interpolated from fixed-point
characteristic (Rezaeian et al.,2006).
Although it is possible to obtain point-based data representing disease occurrences, a
point distribution map is difficult to interpret and often not a desirable option for policy
makers. Moreover, such detailed data are not suitable for public release, given concerns
over personal privacy and data confidentiality. Units of aggregation typically used by many
public health agencies are census enumeration units. These not only provide an acceptable
solution to ensure the protection of data privacy and the individual’s anonymity but also
allow for the incorporation of demographic and socioeconomic analysis of the enumeration
units within which disease events take place.
Point representation is used to portray health data at the most detailed level of
geographic space. In spatial epidemiological studies, the plotting of disease locations as
points may reveal its distributional pattern, but points are not sufficient to disclose the
possible causes or interactions with other factors. Further analyses incorporating
sociodemographic and environmental factors are usually desirable. These analyses can
require disease counts by locations to be aggregated to some census enumeration units
(e.g., province or state, county, township, village) where summary statistics on the
socioeconomic composition of these units (e.g., age and gender groups, median income,
educational attainment) can be studied to supplement the analyses.
The aggregation of point data into areal data “ignores” a large amount of locational
information in the observed point distribution. This aggregation may inadvertently mask
true hot spots as high frequencies. The process may also result in a more “uniform” or
smoothed areal distribution of events across space than would have been observed through
point patterns (Figure 3).
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Figure 3. Aggregation of epidemiological observations for mapping (Extracted from Lai, So
& Chan, 2009)
2. Spatial analysis techniques
2.1 Point Pattern Analysis
That the basic working units of disease data in a GIS include point (e.g., patient location),
line (e.g., transmission route), and area (e.g., disease rate by country). Among these three
data units, point data representing disease locations are basic and most fundamental in
spatial epidemiological studies. Point pattern analysis in spatial epidemiology concerns the
distribution of disease events in space. At the elementary level, the spread o a disease in a
community is revealed through the plotting of disease occurrences (at the residential
locations of infected individuals) enabled with geocoding or address matching function in
GIS. Point-by-point plotting is the simplest form of mapping disease occurrences (Lai, So &
Chan, 2009)
Pattern is the feature of a set of points which describe the location of these points in
terms of the relative distance between each point and the others (Upton and Fingleton,
1985). A central aspect for understanding the spatial statistical is the notion of random
pattern. A random pattern implies that any region of the plane has the same probability to
contain a point, the same definition of the Poisson distribution. In general, the assumption is
that the point pattern presents a random distribution ("complete spatial randomness", CSR)
will be the null hypothesis for the analysis. The alternative scenarios will be contagious
distribution or aggregated, and overdispersed
Figure 4: random pattern or Poisson pattern (left), aggregated pattern (center), r
pattern (right)
The nature of pattern generated by biological processes can be affected by the scale at
which the process is observed. Most of the natural environments show heterogeneity at a
scale large enough to allow the emergence of patterns aggregates. On a smaller scale, the
environmental variation may be less pronounced and the pattern will be determined by the
intensity and the nature of the i
Under the assumption of stationary (t
and isotropic (the process is invariant to rotation), the main features of a point process can
be summarize by its first order property (λ or intensity: the expected number of points per
unit of area in any locality), and by their ownership of second order, which describes the
relationships between pairs of points (e.g. , the probability of finding a point in the vicinity
of another). In the case of regular or uniform patterns, the probability of finding a
the vicinity of another is less than would have a random pattern while the
patterns the probability is greater. The estimator of the most popular second
properties is the Ripley's K function
ill be the null hypothesis for the analysis. The alternative scenarios will be contagious
ted, and overdispersed or regular (Figure 4) (Rot, 2006)
dom pattern or Poisson pattern (left), aggregated pattern (center), r
pattern (right) (extracted from Rot, 2006).
The nature of pattern generated by biological processes can be affected by the scale at
which the process is observed. Most of the natural environments show heterogeneity at a
the emergence of patterns aggregates. On a smaller scale, the
environmental variation may be less pronounced and the pattern will be determined by the
intensity and the nature of the interactions between individuals.
Under the assumption of stationary (the process is uniform or invariant to translation)
and isotropic (the process is invariant to rotation), the main features of a point process can
be summarize by its first order property (λ or intensity: the expected number of points per
y locality), and by their ownership of second order, which describes the
relationships between pairs of points (e.g. , the probability of finding a point in the vicinity
of another). In the case of regular or uniform patterns, the probability of finding a
the vicinity of another is less than would have a random pattern while the
is greater. The estimator of the most popular second
Ripley's K function, which gives an estimation at all scales (Rot, 2006
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ill be the null hypothesis for the analysis. The alternative scenarios will be contagious
).
dom pattern or Poisson pattern (left), aggregated pattern (center), regular
The nature of pattern generated by biological processes can be affected by the scale at
which the process is observed. Most of the natural environments show heterogeneity at a
the emergence of patterns aggregates. On a smaller scale, the
environmental variation may be less pronounced and the pattern will be determined by the
he process is uniform or invariant to translation)
and isotropic (the process is invariant to rotation), the main features of a point process can
be summarize by its first order property (λ or intensity: the expected number of points per
y locality), and by their ownership of second order, which describes the
relationships between pairs of points (e.g. , the probability of finding a point in the vicinity
of another). In the case of regular or uniform patterns, the probability of finding a point in
the vicinity of another is less than would have a random pattern while the aggregated
is greater. The estimator of the most popular second-order
Rot, 2006)
2.1.1 Ripley´s K-function
This function is proposed by Ripley in 1971.
extent to which there is spatial dependence in the arrangement of events. We see shortly
how this function can be estimated from an observed event
establish how we would expect it to behave in a particular theoretical situation
Formally, the point process that gives rise to such an arrangement is called a
homogeneous Poisson process. We say that an arrangement of events shows complete
spatial randomness (CSR) if it is a realization of such a process. As far as the K function for a
CSR process is concerned, the important po
event at any point in R is independent of what other events have occurred and is equally
likely over the whole of R. Thus, for a homogeneous
expected number of events within a distance d of a randomly chosen
other words, K(d) =πd2 .
If there is clustering of point events, we would expect to see an excess of events at short
distances. Thus, for small values of d, the observed value of K(d) will be greater than πd
Consider a circle centered on event i, passing through the point j, and let wq be the pro
portion of the circumference of this circle which lies within R. Then wq is the conditional
probability that an event is observed in R, given that it is a distance d, from the ith event
suitable estimator for K(d) is then
where R is the area of region R and I
when dij is less than d.
We can visualize the estimation of a K function as shown
that an event is 'visited' and that around this event a set of concentric circles at a fine
spacing is constructed. The cumulative number of events within each of these distance
'bands' is counted. Every other event is similarly 'visited' and the cumulative number o
events within dis- tance bands up to a radius d around all events becomes the estimate of
K(d) when scaled by R/n2.
function
his function is proposed by Ripley in 1971. Essentially, the K function describes the
extent to which there is spatial dependence in the arrangement of events. We see shortly
ow this function can be estimated from an observed event distribution but, first, we
establish how we would expect it to behave in a particular theoretical situation
Formally, the point process that gives rise to such an arrangement is called a
us Poisson process. We say that an arrangement of events shows complete
spatial randomness (CSR) if it is a realization of such a process. As far as the K function for a
CSR process is concerned, the important point is that the probability of the occurrenc
event at any point in R is independent of what other events have occurred and is equally
likely over the whole of R. Thus, for a homogeneous process with no spatial depen
expected number of events within a distance d of a randomly chosen event is simply
If there is clustering of point events, we would expect to see an excess of events at short
distances. Thus, for small values of d, the observed value of K(d) will be greater than πd
red on event i, passing through the point j, and let wq be the pro
portion of the circumference of this circle which lies within R. Then wq is the conditional
probability that an event is observed in R, given that it is a distance d, from the ith event
suitable estimator for K(d) is then
where R is the area of region R and Id(dij) is an indicator function that takes the value 1
e can visualize the estimation of a K function as shown in Figure 5. We
ent is 'visited' and that around this event a set of concentric circles at a fine
spacing is constructed. The cumulative number of events within each of these distance
'bands' is counted. Every other event is similarly 'visited' and the cumulative number o
tance bands up to a radius d around all events becomes the estimate of
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Essentially, the K function describes the
extent to which there is spatial dependence in the arrangement of events. We see shortly
istribution but, first, we
establish how we would expect it to behave in a particular theoretical situation.
Formally, the point process that gives rise to such an arrangement is called a
us Poisson process. We say that an arrangement of events shows complete
spatial randomness (CSR) if it is a realization of such a process. As far as the K function for a
ity of the occurrence of an
event at any point in R is independent of what other events have occurred and is equally
process with no spatial dependence, the
event is simply πd2. In
If there is clustering of point events, we would expect to see an excess of events at short
distances. Thus, for small values of d, the observed value of K(d) will be greater than πd2.
red on event i, passing through the point j, and let wq be the pro-
portion of the circumference of this circle which lies within R. Then wq is the conditional
probability that an event is observed in R, given that it is a distance d, from the ith event. A
) is an indicator function that takes the value 1
e may imagine
ent is 'visited' and that around this event a set of concentric circles at a fine
spacing is constructed. The cumulative number of events within each of these distance
'bands' is counted. Every other event is similarly 'visited' and the cumulative number of
tance bands up to a radius d around all events becomes the estimate of
Figure 5. Estimation of a K function
Once calculated, k(d) can be compared with its expected for
theoretical situations. For example, as we noted, we expect K(d)= πd
process with no spatial dependence. Under regularity, K(d) would be less than πd
whereas, under clustering, K(d) would be greater than πd
estimated from the observed data, with πd
against d. Peaks in positive values tend to indicate spatial clustering and troughs of negative
values indicate regularity, at corresponding sc
To assess whether the observed peaks or troughs in this plot are significant simulation
techniques may be used. Under the assumption of CSR, we may perform
simulations of n events in the study region (
point pattern, we can estimate K(d) and use the maximum and minimum of these functions
for the simulated patterns to define an upper and lower simulation envelope. If the
estimated K(d) lies above the upper en
the lower envelope, this is evidence of spatial 'inhibition' or regularity in the arrangement
of events.
In practice, it is used more often the function L(r) = (K(r)/ π )
constant variance and allows an easier interpretation of the test (Fig
Under CSR, L(r) = r and therefore L(r)
place when L(d) -d is significantly greater than zero and a regular patte
significantly less than zero (Rot, 2006
Estimation of a K function (extracted from Gatrell et al., 1996)
Once calculated, k(d) can be compared with its expected form according to particular
theoretical situations. For example, as we noted, we expect K(d)= πd2 for a homogeneous
process with no spatial dependence. Under regularity, K(d) would be less than πd
whereas, under clustering, K(d) would be greater than πd2. So we can compare K(d),
estimated from the observed data, with πd2. This may be done through a plot of k(d)
against d. Peaks in positive values tend to indicate spatial clustering and troughs of negative
values indicate regularity, at corresponding scales of distance (Gatrell et al., 1996).
To assess whether the observed peaks or troughs in this plot are significant simulation
techniques may be used. Under the assumption of CSR, we may perform m
events in the study region (where m might be, say, 99). For each simulated
point pattern, we can estimate K(d) and use the maximum and minimum of these functions
for the simulated patterns to define an upper and lower simulation envelope. If the
estimated K(d) lies above the upper envelope, we can speak of aggregation. If it lies below
the lower envelope, this is evidence of spatial 'inhibition' or regularity in the arrangement
In practice, it is used more often the function L(r) = (K(r)/ π )1/2 ,that in addition, has a
stant variance and allows an easier interpretation of the test (Figure 6C
Under CSR, L(r) = r and therefore L(r) - r = 0 can be tested in each distance r. A cluster takes
d is significantly greater than zero and a regular pattern when L(d)
Rot, 2006).
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(extracted from Gatrell et al., 1996)
m according to particular
for a homogeneous
process with no spatial dependence. Under regularity, K(d) would be less than πd2,
So we can compare K(d),
. This may be done through a plot of k(d)- πd2
against d. Peaks in positive values tend to indicate spatial clustering and troughs of negative
(Gatrell et al., 1996).
To assess whether the observed peaks or troughs in this plot are significant simulation
m independent
where m might be, say, 99). For each simulated
point pattern, we can estimate K(d) and use the maximum and minimum of these functions
for the simulated patterns to define an upper and lower simulation envelope. If the
velope, we can speak of aggregation. If it lies below
the lower envelope, this is evidence of spatial 'inhibition' or regularity in the arrangement
,that in addition, has a
ure 6C, Figure 7).
A cluster takes
rn when L(d) -d is
Figure 6. Point pattern distribution (left), K function for the same point pattern. The red
indicates the k function for a random process. The black line shows the K function
calculated, dotted blue lines are the max and min values obtained from 99 Monte
simulations (center). L function of the same point pattern.
Figure 7. L function for the point patterns of figure 4: Ran
pattern (left), aggregated pattern (cente
2.1.2 Kernel estimation
The kernel density estimation is a method for examining large
pattern analysis. It analyzes disease patterns and detects hot spots
window technique linked to a quartic kernel algorithm. The
how event frequencies vary continuously across
Kernel estimation is a generalization of this idea, where the window is
moving three-dimensional function (the kernel) which weights events within its sphere of
influence according to their distance from the point at which the intensity is being
Point pattern distribution (left), K function for the same point pattern. The red
indicates the k function for a random process. The black line shows the K function
d blue lines are the max and min values obtained from 99 Monte
simulations (center). L function of the same point pattern.
. L function for the point patterns of figure 4: Random pattern or Poisson
pattern (left), aggregated pattern (center), regular pattern (right).
The kernel density estimation is a method for examining large-scale trends
pattern analysis. It analyzes disease patterns and detects hot spots through a movi
window technique linked to a quartic kernel algorithm. The approach attempts to estimate
how event frequencies vary continuously across the study area based on the point patterns
Kernel estimation is a generalization of this idea, where the window is replaced with a
dimensional function (the kernel) which weights events within its sphere of
influence according to their distance from the point at which the intensity is being
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Point pattern distribution (left), K function for the same point pattern. The red
indicates the k function for a random process. The black line shows the K function
d blue lines are the max and min values obtained from 99 Monte-Carlo
dom pattern or Poisson
scale trends in point
through a moving
approach attempts to estimate
the study area based on the point patterns.
replaced with a
dimensional function (the kernel) which weights events within its sphere of
influence according to their distance from the point at which the intensity is being
estimated. The method is commonly used in
smooth estimates of univariate (or multivariate) probability densities from an observed
sample of observations. Formally, if s represents a vector location anywhere in R and s, ..., s,
are the vector locations of the n observed events,
Here, k() represents the kernel weighting function which, for convenience, is expressed
in standardized form (that is, cent
curve). This is then centered on s and 'stretched' according to the parameter z > 0, which is
referred to as the band width. The value of z is chosen to provide the required degree of
smoothing in the estimate. Graphically, we may imagine a three
'visits' each point s on the fine grid (Figure
within the region of influence (as controlled by z), are measured and contribute to the
intensity estimate at s according to how close they are to s. We may then u
contouring algorithm, or some form of raster display, to represent the resulting intensit
estimates as a continuous surface showing how intensity varies over the
Figure 8. Kernel estimation of a point pattern
The incident hot spots can then be verified and tested for their statistical significance
against a random distribution.
estimated. The method is commonly used in a more general statistical context to obtain
smooth estimates of univariate (or multivariate) probability densities from an observed
Formally, if s represents a vector location anywhere in R and s, ..., s,
are the vector locations of the n observed events, then the intensity, 2(s), at s is estimated as
Here, k() represents the kernel weighting function which, for convenience, is expressed
in standardized form (that is, centered at the origin and having a total volume of 1 under the
red on s and 'stretched' according to the parameter z > 0, which is
referred to as the band width. The value of z is chosen to provide the required degree of
smoothing in the estimate. Graphically, we may imagine a three-dimensional function that
h point s on the fine grid (Figure 8). Distances to each observed event
within the region of influence (as controlled by z), are measured and contribute to the
intensity estimate at s according to how close they are to s. We may then u
contouring algorithm, or some form of raster display, to represent the resulting intensit
face showing how intensity varies over the entire
Kernel estimation of a point pattern (extracted from Gatrell et al., 1996)
The incident hot spots can then be verified and tested for their statistical significance
against a random distribution. The data collected at sampled locations are representative of
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text to obtain
smooth estimates of univariate (or multivariate) probability densities from an observed
Formally, if s represents a vector location anywhere in R and s, ..., s,
then the intensity, 2(s), at s is estimated as
Here, k() represents the kernel weighting function which, for convenience, is expressed
red at the origin and having a total volume of 1 under the
red on s and 'stretched' according to the parameter z > 0, which is
referred to as the band width. The value of z is chosen to provide the required degree of
dimensional function that
). Distances to each observed event Si that lies
within the region of influence (as controlled by z), are measured and contribute to the
intensity estimate at s according to how close they are to s. We may then use a suitable
contouring algorithm, or some form of raster display, to represent the resulting intensity
entire area.
Gatrell et al., 1996)
The incident hot spots can then be verified and tested for their statistical significance
data collected at sampled locations are representative of
the spatial distribution. The interpolator will us
variables of interest at other unsampled locations.
The kernel estimate
this is increased, there is more smoothing of the spatial variation in intens
reduced we obtain an increasingly 'spiky' estimate. What value, then should we choose? In
practice, the value of kernel estimation is that one has the flexibilit
different values of z, exploring the surface a,(s) using dif
order to look at the variation in A(s) at different scales. There are
attempt automatically to choose a value of z which optimally balances the reliability of the
estimate against the degree of spatial deta
event locations. We should further note that it is possible to adjust the value of z at different
points in R in order to improve the kernel estimate. Such local adjustment of bandwidth
may be achieved by adaptive kernel estimation. In adaptive smoothing, sub
events are more densely packed than others (and thus where more detailed information on
the variation in intensity is available) are 'visited' by a kernel whose band
than elsewhere, as a means of avoiding smoothing out too much detail.
As a result of a kernel we get a map showing for each point, a value of density according
to the position and the pattern exhibit by the original points. This estima
punctual distribution to a continuous density value map. An example of a map of kernel
density estimator can be seen at figure
Figure 9: Map of kernel density estimator, illustrating the distribution of Canine Visceral
Lishmaniasis cases in each sector of Ihla Solteira (Extracted from Paulan et al., 2012).
the spatial distribution. The interpolator will use these sample points to predict values of
variables of interest at other unsampled locations.
is intended to be sensitive to the choice of bandwidth, r. As
this is increased, there is more smoothing of the spatial variation in intens
reduced we obtain an increasingly 'spiky' estimate. What value, then should we choose? In
practice, the value of kernel estimation is that one has the flexibility to exper
different values of z, exploring the surface a,(s) using different degrees of smoothing in
order to look at the variation in A(s) at different scales. There are also methods which
matically to choose a value of z which optimally balances the reliability of the
estimate against the degree of spatial detail that is retained, given the observed pattern of
event locations. We should further note that it is possible to adjust the value of z at different
points in R in order to improve the kernel estimate. Such local adjustment of bandwidth
adaptive kernel estimation. In adaptive smoothing, sub-areas in which
events are more densely packed than others (and thus where more detailed information on
the variation in intensity is available) are 'visited' by a kernel whose band- width is smaller
an elsewhere, as a means of avoiding smoothing out too much detail. (Gatrell et al., 996).
As a result of a kernel we get a map showing for each point, a value of density according
to the position and the pattern exhibit by the original points. This estimation lead to a
punctual distribution to a continuous density value map. An example of a map of kernel
density estimator can be seen at figure 9.
: Map of kernel density estimator, illustrating the distribution of Canine Visceral
in each sector of Ihla Solteira (Extracted from Paulan et al., 2012).
13
e these sample points to predict values of
sitive to the choice of bandwidth, r. As
this is increased, there is more smoothing of the spatial variation in intensity; as it is
reduced we obtain an increasingly 'spiky' estimate. What value, then should we choose? In
y to experiment with
ferent degrees of smoothing in
also methods which
matically to choose a value of z which optimally balances the reliability of the
il that is retained, given the observed pattern of
event locations. We should further note that it is possible to adjust the value of z at different
points in R in order to improve the kernel estimate. Such local adjustment of bandwidth
areas in which
events are more densely packed than others (and thus where more detailed information on
width is smaller
(Gatrell et al., 996).
As a result of a kernel we get a map showing for each point, a value of density according
tion lead to a
punctual distribution to a continuous density value map. An example of a map of kernel
: Map of kernel density estimator, illustrating the distribution of Canine Visceral
in each sector of Ihla Solteira (Extracted from Paulan et al., 2012).
14
2.2 Areal Patterns:
2.2.1 Spatial autocorrelarion indexes
2.2.1.1 Global indexes
Global indexes measure how the variable being studied is correlated within a region,
and are useful for a holistic characterization providing a single value to the region (Pina et
al., 2010).
In global tests for autocorrelation, it is assumed that the relationship between nearby
or otherwise connected observations will remain the same everywhere in the study area
(referred to as “stationarity” or “structural stability”) (Jerrett, Gale & Kontgis, 2010).
Moran’s I is one of the oldest indicators of spatial autocorrelation. It is a popular
measure and has remained a de facto standard in examining zones or points with
continuous variables associated with them. Moran’s I is similar to the Pearson’s correlation
coefficient and gives a score ranging between –1 and 1. A positive score means a “hot” spot
or that a polygon or point with a high score has other polygons or points with high scores
surrounding it. Conversely, an occurrence of a low score indicates a “cold” spot because of
low scoring occurrences in the neighborhood. A score of zero indicates that nothing can be
assumed about the scores of the neighboring polygons or points. A negative score means a
“spatial outlier” or that the scores of neighboring locations will be the opposite of the
location under examination; that is, a polygon or point with a low score will have high
scoring neighbors, and viceversa. (Lai, So & Chan, 2009).
Moran´s I statistic gives a formal indication of the degree of linear association
between a vector of observed values and a weighted average of the neighboring values, or
spatial lag. It provides an unique value for each dataset. A test that allows to measure the
statistical significance of the space autocorrelation is built. Formally, Moran´s I can be
expressed in matrix notation as:
Where stands for the sum of all elements in the spatial weights matrix. Z
observations are the deviations from de mean
value in an particular spatial units while X
localization, normally its neighbor.
One way of specifying interdependence among observations is to use a spatial
weight matrix. The spatial weight matrix
Wi j > 0 indicates that observation
Wi j > 0 if region i is contiguous to region
neighbors to themselves. Measures of proximity, such as cardinal distance (e.g., kilometers),
ordinal distance (e.g., the m near
border with region j), have been used to specify
how the weight matrix is constructed:
Figure 10. Construction of a weight matrix (W). 1 indicates
indicates
In 1993 Anselin introduced
observe in a scatter graph the behavior of each spatial unit. This novelty was one of the fir
steps toward the local analysis, i.e. the
scatterplot can be augmented with a linear regression w
which can be used to indicate the degree of fit, the presence of outlier
can be divided into four quadrants (
top and following clockwise with the next ones. In the x
a variable for each spatial unit of the studied
the average of the values in neighboring units of the same variable (univariate analysis) or
stands for the sum of all elements in the spatial weights matrix. Z
observations are the deviations from de mean where Xi is the variable
value in an particular spatial units while Xj is the variable value measured in another
calization, normally its neighbor.
One way of specifying interdependence among observations is to use a spatial
weight matrix. The spatial weight matrix W is an n × n exogenous nonnegative matrix where
0 indicates that observation i depends upon neighboring observations j. For example,
is contiguous to region j. Also, Wii = 0, so observations cannot be
neighbors to themselves. Measures of proximity, such as cardinal distance (e.g., kilometers),
nearest neighbors), and contiguity (Wi j > 0, if region
), have been used to specify W. (Pace & LeSage, 2010). Figure
how the weight matrix is constructed:
. Construction of a weight matrix (W). 1 indicates neighboring observations
the observations which are not neighbors.
In 1993 Anselin introduced the Moran scatterplot, an analysis tool that allows to
observe in a scatter graph the behavior of each spatial unit. This novelty was one of the fir
steps toward the local analysis, i.e. the desaggregation of the global value of AE.
scatterplot can be augmented with a linear regression which has Moran´s I
ich can be used to indicate the degree of fit, the presence of outliers, etc. The scatterplot
can be divided into four quadrants (see Figure 11) starting with the first one on the right
top and following clockwise with the next ones. In the x-axis appear standardized values of
a variable for each spatial unit of the studied area, and in the y-axis standardized values of
the average of the values in neighboring units of the same variable (univariate analysis) or
15
stands for the sum of all elements in the spatial weights matrix. Z
is the variable
is the variable value measured in another
One way of specifying interdependence among observations is to use a spatial
exogenous nonnegative matrix where
. For example,
= 0, so observations cannot be
neighbors to themselves. Measures of proximity, such as cardinal distance (e.g., kilometers),
0, if region i shares a
Figure 10 shows
neighboring observations, 0
an analysis tool that allows to
observe in a scatter graph the behavior of each spatial unit. This novelty was one of the first
of AE. The Moran
I a slope, and
The scatterplot
) starting with the first one on the right
axis appear standardized values of
axis standardized values of
the average of the values in neighboring units of the same variable (univariate analysis) or
another variable (bivariate analysis)
values higher than the average that, in turn, also have neighbors with higher values
(situation high-high, also known as hot spots in the scatterplot of Moran). The reverse
situation is recorded in the quadrant III (situation low
quadrants allow to detect clusters of spatial units with similar values to those presented by
its neighbors. In counterpart, outliers respond to space mixed contexts, in other words,
spatial units with low values (lower than the average) with neighbors
(situation low-high) in the quadrant IV. The opposite scenario (situation high
located in the quadrant II. (Anselin, 1993;
Figure 11. A Moran scatterplot in GeoDa.
Local autocorrelation:
In the analysis of spatial association, it has long been recognized that the assumption
of stationarity or structural stability over space may be highly unrealistic
relationships are of less interest than local relationships or clusters that may display non
stationarity. In exploratory spatial data analysis (ESDA), the predominant approach to
assess the degree of spatial association still ignores this potential instability, as it is based
on global statistics such as Moran's
an allowance for local instabilities in overall spatial
more appropriate perspective.
Llocal indicators of spatial association
indicators, such as Moran's I,
1995). These local statistics usually break the study area into smaller regions to determine
if local areas have attribute values that are higher or lower than would be expected based
on the global average or a random expectation for the entire study area.
translate how the variable in one area is correlated to the same variable in a close
another variable (bivariate analysis). In quadrant I we can identify the spatial units with
verage that, in turn, also have neighbors with higher values
high, also known as hot spots in the scatterplot of Moran). The reverse
situation is recorded in the quadrant III (situation low-low, also called cold spots)
to detect clusters of spatial units with similar values to those presented by
its neighbors. In counterpart, outliers respond to space mixed contexts, in other words,
spatial units with low values (lower than the average) with neighbors with
high) in the quadrant IV. The opposite scenario (situation high
(Anselin, 1993; Lai, So & Chan, 2009).
A Moran scatterplot in GeoDa. The slope of the line represents the Moran´s
In the analysis of spatial association, it has long been recognized that the assumption
of stationarity or structural stability over space may be highly unrealistic. Sometimes global
terest than local relationships or clusters that may display non
In exploratory spatial data analysis (ESDA), the predominant approach to
assess the degree of spatial association still ignores this potential instability, as it is based
bal statistics such as Moran's I. A focus on local patterns of association (hot spots) and
an allowance for local instabilities in overall spatial association has been suggested as
more appropriate perspective.
local indicators of spatial association (LISA) allow for the decomposition of global
I, into the contribution of each individual observation (Anselin,
These local statistics usually break the study area into smaller regions to determine
ute values that are higher or lower than would be expected based
on the global average or a random expectation for the entire study area. Local indicators
translate how the variable in one area is correlated to the same variable in a close
16
. In quadrant I we can identify the spatial units with
verage that, in turn, also have neighbors with higher values
high, also known as hot spots in the scatterplot of Moran). The reverse
low, also called cold spots). Both
to detect clusters of spatial units with similar values to those presented by
its neighbors. In counterpart, outliers respond to space mixed contexts, in other words,
higher values
high) in the quadrant IV. The opposite scenario (situation high-low) is
The slope of the line represents the Moran´s I
In the analysis of spatial association, it has long been recognized that the assumption
Sometimes global
terest than local relationships or clusters that may display non-
In exploratory spatial data analysis (ESDA), the predominant approach to
assess the degree of spatial association still ignores this potential instability, as it is based
. A focus on local patterns of association (hot spots) and
association has been suggested as a
allow for the decomposition of global
of each individual observation (Anselin,
These local statistics usually break the study area into smaller regions to determine
ute values that are higher or lower than would be expected based
Local indicators
translate how the variable in one area is correlated to the same variable in a close
neighborhood; they provide a value for each area and allow the identification of clusters.
Local indicators are more sensitive to variations of the values of the variable
Kontgis, 2010). Local spatial clusters, sometimes referred to as
as those locations or sets of contiguous locations for which the LISA is significant.
indicates the presence of spatial dependency (clusters) in some areas, i.e., areas where the
incidence rates were significantly correlated (p < 0.05
neighbors. This is shown in a map called by Anselin “LISA map” (Anselin, 1995).
is shown in figure 12:
Figure 12. LISA Maps showing c
Legionellosis incidence rates by age and by
2.3 Geostatistics
D. G. Krige was for many years a professor at the University of the Witwatersrand,
South Africa. He promoted the use of
Krige (1951), set the seeds for the lat
at L’ ´ Ecole des Mines in Fontainbleau, France, of the branch of spatial statistics known as
geostatistics. The spatial prediction method known
different scientific setting, the objective analysis of
tool for constructing spatially continuous weather maps from spatially discrete
observations on the ground and in th
ey provide a value for each area and allow the identification of clusters.
Local indicators are more sensitive to variations of the values of the variable (Jerrett,
Local spatial clusters, sometimes referred to as hot spots, may be i
those locations or sets of contiguous locations for which the LISA is significant.
indicates the presence of spatial dependency (clusters) in some areas, i.e., areas where the
nificantly correlated (p < 0.05) with the incidence rates of its
own in a map called by Anselin “LISA map” (Anselin, 1995).
LISA Maps showing clusters for men (left) and women (right) of standardized
e rates by age and by city council in Spain (Extracted from Gomez
Barrosoa et al., 2011).
D. G. Krige was for many years a professor at the University of the Witwatersrand,
South Africa. He promoted the use of statistical methods in mineral exploration and, in
Krige (1951), set the seeds for the later development, by Georges Mathéron and colleagues
at L’ ´ Ecole des Mines in Fontainbleau, France, of the branch of spatial statistics known as
patial prediction method known as kriging is named in his honor. In a
different scientific setting, the objective analysis of kriging, was for a long time the standard
for constructing spatially continuous weather maps from spatially discrete
the ground and in the air (Diggle, 2010).
17
ey provide a value for each area and allow the identification of clusters.
Jerrett, Gale &
may be identified
those locations or sets of contiguous locations for which the LISA is significant. The LISA
indicates the presence of spatial dependency (clusters) in some areas, i.e., areas where the
idence rates of its
own in a map called by Anselin “LISA map” (Anselin, 1995). An example
lusters for men (left) and women (right) of standardized
in Spain (Extracted from Gomez-
D. G. Krige was for many years a professor at the University of the Witwatersrand,
statistical methods in mineral exploration and, in
ron and colleagues
at L’ ´ Ecole des Mines in Fontainbleau, France, of the branch of spatial statistics known as
as kriging is named in his honor. In a
kriging, was for a long time the standard
for constructing spatially continuous weather maps from spatially discrete
In geostatistics, use is made of the phenomenon of spatial dependence: the tendency
for proximate observations to be more similar than more distant ones. Spatial dependence
may be represented by a range of
z(xi) on property z at locations
estimated for a set of discrete lag (distance and direction) vectors
where N(h) is the number of paired comparisons at the set of discrete lags
represents the spatial dependence (the tendency for proximate points to be more related
than more distant ones) in the data.
display of semivariance (γ) versus distance
of spatial dependence or autocorrelation between samples. To
we need to determine how variance behaves
model levels out. The distance where the model first flattens out is known as the range and
the corresponding value on the y axis is called the sill. Samples separated by distances
closer than the range are spatially autocorrelated, whereas locations farther apart than t
range are not. The range is thus the distance beyond which the deviation in z values does
not depend on distance. Once the sample variogram has been estimated, it is necessary to fit
a continuous mathematical model to it to allow statistical inference (
exponential, Gaussian, linear)
used to estimate distance weights for interpolation
Figure 13. Semivariogram:
In geostatistics, use is made of the phenomenon of spatial dependence: the tendency
for proximate observations to be more similar than more distant ones. Spatial dependence
may be represented by a range of functions. Here, we focus on the variogram. Given
at locations xi, i = 1, 2, . . . , n, the sample variogram
estimated for a set of discrete lag (distance and direction) vectors h using:
of paired comparisons at the set of discrete lags h. The variogram
represents the spatial dependence (the tendency for proximate points to be more related
than more distant ones) in the data. (Graham et al., 2004). A semivariogram is a graphic
) versus distance or lag. Semivariance is a measure of the
of spatial dependence or autocorrelation between samples. To compute a semivariogram,
we need to determine how variance behaves against distance.. At a certain distance, the
t. The distance where the model first flattens out is known as the range and
the corresponding value on the y axis is called the sill. Samples separated by distances
closer than the range are spatially autocorrelated, whereas locations farther apart than t
range are not. The range is thus the distance beyond which the deviation in z values does
Once the sample variogram has been estimated, it is necessary to fit
a continuous mathematical model to it to allow statistical inference (e.g., spherical, cubic,
exponential, Gaussian, linear) (Figure 13). Once the semivariogram has been developed, it is
weights for interpolation.
Semivariogram: graphic display of semivariance (γ) versus distance or la
18
In geostatistics, use is made of the phenomenon of spatial dependence: the tendency
for proximate observations to be more similar than more distant ones. Spatial dependence
functions. Here, we focus on the variogram. Given n data
, the sample variogram γ(h) may be
. The variogram
represents the spatial dependence (the tendency for proximate points to be more related
A semivariogram is a graphic
or lag. Semivariance is a measure of the degree
compute a semivariogram,
At a certain distance, the
t. The distance where the model first flattens out is known as the range and
the corresponding value on the y axis is called the sill. Samples separated by distances
closer than the range are spatially autocorrelated, whereas locations farther apart than the
range are not. The range is thus the distance beyond which the deviation in z values does
Once the sample variogram has been estimated, it is necessary to fit
e.g., spherical, cubic,
Once the semivariogram has been developed, it is
) versus distance or lag
2.3.1 Kriging
The modelled variogram can be used in a wide range of geostatistical operations.
The geostatistical method for spatial prediction known as
prediction variance and unbiased) under the cons
x0 is a linear weighted sum of j
where the λj are the j weights. Optimality is obtained by selecting the weights based on the
variogram: proximate neighbours receive more weight than more distant data, and the
exact weights are determined from the fitted mathematical (variogram) model.
Unbiasedness is achieved by setting the su
2004).
The result of this process is a map showing the values for a certain variable in all the
geographic space (Figure 14).
The modelled variogram can be used in a wide range of geostatistical operations.
The geostatistical method for spatial prediction known as kriging is optimal (minimum
prediction variance and unbiased) under the constraint that the prediction ˆz(x
is a linear weighted sum of j neighbouring data z(xj):
weights. Optimality is obtained by selecting the weights based on the
variogram: proximate neighbours receive more weight than more distant data, and the
exact weights are determined from the fitted mathematical (variogram) model.
is achieved by setting the sum of the kriging weights to one (Graham et al.,
The result of this process is a map showing the values for a certain variable in all the
geographic space (Figure 14).
19
The modelled variogram can be used in a wide range of geostatistical operations.
is optimal (minimum
z(x0) at location
weights. Optimality is obtained by selecting the weights based on the
variogram: proximate neighbours receive more weight than more distant data, and the
exact weights are determined from the fitted mathematical (variogram) model.
m of the kriging weights to one (Graham et al.,
The result of this process is a map showing the values for a certain variable in all the
20
Figure 14. Map of kriged risk of Childhood Cancer in the West Midlands, England (Extracted
from Webster et al., 1994)
3. Disease mapping
Tobler´s first law of geography, which states that “Things that are closer are more
related”, is central to core spatial analytical techniques as well as analytical conceptions of
geographic space. In the case of disease spread, individuals near or exposed to a contagious
person or a tainted environmental setting are deemed more susceptible to certain types of
illnesses. Cartographic design and mapping techniques can draw attention to these
locations by displaying an aggregation and design has the following framework: 1)-
geographic feature classification, 2) scale determination, 3) symbol categorization, and 4)
graphic primitives (figure 15). The basic working units of disease data include point (e.g.,
patient locations), line (e.g., transmission route), and area (e.g, disease rate by country).
Depending on the data scaling and level of measurement (whether nominal, ordinal,
interval, or ratio), the use of certain combinations of symbols and graphic primitives is more
effective in conveying spatial distributions.
Figure 15. A framework of cartographic design
In spatial epidemiology, point-based data representing disease or patient locations are
the bases of data collection. Geocoded point data derived from address matching form the
essential input for disease mapping. Very often, disease mapping involves making maps of
point and choropleth patterns (Figure 3.5). Although it is appropriate in secure research
settings to represent locations of disease incidence at the local scale, for example, to search
for possible disease clusters, point maps for public distribution and consumption may be
deemed too revealing and sensitive.
Although point pattern representation is a quasi-accurate account of a health event, its
use is undesirable in portraying disease occurrences of acute sensitivity (such as AIDS and
21
SARS). To safeguard personal privacy and curtail social segregation, point-based data are
collapsed by enumeration units for visual presentation (as in choropleth, proportional
symbol, and cartogram methods). Aggregating point data by a set of areal units allows
distributional maps to be created to reveal new insights. The point-in-polygon operation in
a GIS, for example, can aggregate point data by administrative zones.
Identification and discrimination between map symbols are necessary to represent data
in a meaningful way. Clear and intuitive map symbols are the main components to allow
map viewers a visual understanding of the resultant pattern or intended message. Other
than point pattern maps, the most commonly used mapping technique is by means of
choropleth or shaded area mapping (Figure 16). This method involves grouping numerical
values (e.g., disease rate per 1,000, standard deviation) associated with some enumeration
units (e.g., census tracts) into ordinal classes (e.g., five ranked classes representing very
high, high, medium, low, and very low readings). Each group is assigned a color in which the
darker color represents a higher value and lighter color a lower value. Each enumeration
area is shaded the color of its corresponding class containing the value. To reduce adverse
visualization effects projected by small areas of high values or large areas of small values, it
is recommended that this technique be used to map rates instead of raw readings.
The remaining mapping techniques illustrated in Figure 3.5 are used to portray results
of spatial analytical functions. The examples show a variation of mapping techniques arising
from point-based data. They offer uniquely different visualization of disease or health-
related patterns, development, and trends. For example, the kernel density method is a
means of summarizing points by quadrants or grids of a uniform size (instead of some
administrative zones) through a moving window approach. This method of presentation not
only addresses the issue of data privacy but also diminishes the effects of MAUP (Modifiable
areal unit problem) and area dependence. Point buffers may also be used to indicate more
clearly the patterns of spatial clustering of points and delineate possible hot spot areas. The
choice of suitable mapping techniques relies largely on cartographic experience and
geographic understanding, in addition to creativity on the part of the spatial analyst.
22
Figure 16. Types of spatial analytical map outputs (Extracted from Lai, So & Chan, 2009)
23
3.1. Why disease mapping is important?
Disease mapping is the first step toward understanding the spatial aspects of health-related
problems because particular types of information are high-lighted in maps. Disease
distributions can be shown through different cartographic symbolization as points, lines,
and patterns. Associative analyses can then be formulated through visual inspection of the
disease maps in conjuction with statistical deduction. Although disease mapping seems only
a tool for preliminary data exploration, it nonetheless offers useful hints in terms of
informing needs for further statistical and empirical analyses as well as different
visualization techniques.
Disease maps provide a rapid visual summary of complex geographic information and
may identify subtle patterns in the data that are missed in tabular presentations. They are
used variously for descriptive purposes, to generate hypotheses as to etiology, for
surveillance to highlight areas at apparently high risk, and to aid policy formation and
resource allocation. They are also useful to help place specific disease clusters and results of
point-source studies in proper context.
4. Some Spatial Analysis softwares that can be used in Epidemiology.
• SaTScan is a free software that analyzes spatial, temporal and space-time data using
the spatial, temporal, or space-time scan statistics.
It is designed for any of the following interrelated purposes:
- Perform geographical surveillance of disease, to detect spatial or space-
time disease clusters, and to see if they are statistically significant.
- Test whether a disease is randomly distributed over space, over time or
over space and time.
- Evaluate the statistical significance of disease cluster alarms.
-Perform prospective real-time or time-periodic disease surveillance for the
early detection of disease outbreaks.
SaTScan is a software available for Windows, Linux and Mac. Download is
done trough the software website: http://www.satscan.org/ . In the website we can
find a list of published papers related to the epidemiological field sorted
thematically.
24
• GeoDa is an interactive environment that combines maps with statistical charts and
graphics, using the technology of dynamically linked windows. It was developed by
Luc Anselin of the Spatial Analysis Laboratory of the University of Illinois, Urbana–
Champaign. Along with its mapping functionality, GeoDa contains the usual EDA
graphs (i.e., EDA graphics including histogram, box plot, scatterplot, etc.) and
implements brushing for bothmaps and statistical plots. The beta release is free for
download for noncommercial use only from http://geodacenter.asu.edu/ .
• R has many spatial analysis packages, e.g gstat package
• GRASS GIS, commonly referred to as GRASS (Geographic Resources Analysis
Support System), is a free and open source Geographic Information System (GIS)
software suite used for geospatial data management and analysis, image processing,
graphics and maps production, spatial modeling, and visualization.
For more information about spatial analysis softwares see the next link
http://en.wikipedia.org/wiki/List_of_spatial_analysis_software
5. Some applications of Spatial Analysis (SA) in Epidemiology
One of the most important applications of SA in Epidemiology are diseases mapping,
ecologic studies, cluster identification and environment surveillance (Santos & Souza,
2007).
In literature there are hundreds of paper studies that use SA in some aspect related
to Epidemiology. Here, three papers that use different SA techniques were selected from the
literature to be given as examples of application of SA in Epidemiology.
Porcasi et al. (2006) studied the Infestation of Rural Houses by Triatoma Infestans
(Hemiptera: Reduviidae) in Southern Area of Gran Chaco in Argentina (Porcasi et al., 2006).
They analyzed of the spatial pattern of house infestations by T. infestans before and after
house spraying with deltamethrin in the San Martín Department (an arid Chaco region of
central Argentina). Before house spraying, all houses within this department were
inspected and infestation by T. infestans in the domestic and peridomestic structures was
recorded. All houses within the department were treated with deltamethrin. House
spraying was carried out between November 2003 and June 2004. Latitude and longitude
coordinates of 151 localities were recorded with a GPS and used to build a geographic
database. These localities were the units of analysis and were considered infested if at least
one house of the group was infested by T. infestans. One year after spraying the houses
localities recorded before the insecticide application were visited to carry out an active
25
search for T. infestans. A locality was considered infested if at least one peridomestic
structure was positive for T. infestans. Spatial analysis of the house infestation rate was
carried out with the Bernoulli model of the SaTScan, version 4.0 statistics (Information
Management Services 2003). This point-pattern analysis seeks the existence of groups of
localities with significantly higher or lower infestation rates than the departmental average.
To carry out the analysis, the scan statistics calculate the number of infested houses in
circles of increasing radii and compares this number with the expected number of houses
predicted by the binomial probability distribution.
The pattern of house infestation before the insecticide application showed two
clusters of high house infestation rate. A primary cluster was identified to the southwest of
the department, where 15 localities showed a house infestation rate of 68.4% (n _ 52
houses). A secondary cluster of high house infestation rate, composed by four localities with
100% of infested houses (n_12) was located at the northwest of the department. A cluster of
low house infestation rate (11.4%) was located at the northeast of the department,
including four localities (with 35 houses); (Figure 17 A). Another cluster of low house
infestation (20.7%) was located east of the department, including 150 houses in 48
localities (Figure 17 B). A comparison of house infestation before and after the spraying
intervention of 89 localities showed that 47 localities that were infested before the
spraying, 46.8% (n _ 22) remained infested 1 yr later. Of the 42 localities that were not
infested before the spraying, 69% (n _ 29) remained uninfested 1 yr later (Fig. 2).
All localities included in the cluster of low infestation recorded before spraying were
included in the low infestation cluster after spraying to the east of the San Martín
Department.
Figure 17. (A) Cluster of high infestation (primary and secondary clusters: 100 and 68.4%
infestation, respectively), as closed squares and cluster of low infestation (11.4%) as open
squares before the insecticide application. (B) Cluster of high infestation (46.9%), as closed
circles and cluster of low infestation (20.7%) as open circles after the insecticide
application.
26
The results observed in this study confirm that the identification of the infestation
rate clustering at the departmental level by using a geographic information system offers
several advantages over the traditional reporting system currently in use by the vector
control programs in Argentina. It allows for a clear identification of heterogeneity in the
infestation rate distribution that could be used as a basis for risk stratification and
differential allocation of resources. The GIS database also allows a more efficient
mechanism for monitoring vector control activities, compared with procedures based on
hard-copy forms. Other activities carried out by the Chagas disease control program (e.g.,
parasitological treatments) or not connected with the program (e.g., vaccination programs)
could use the same information base.
In a study carried out by Chen et al. (2007), he purpose is to present kriging based
on data from a few sites as a solution to the problem of predicting the spatial distribution of
S. japonicum infection over Dangtu county, China. They established population-based
database containing the human prevalence of schistosomiasis at the village level from 2001
to 2004. Spatial correlation analysis was performed by the semivariogram model, which
provides a measure of variance as a function of distance between data points. The
semivariance was calculated. They used the spatial analyst module of ArcGIS 9.0 and
selected the exponential model to fit the spatial correlation of infection rate with S.
japonicum. They investigated the direction trend of the infection to identify the
presence/absence of trends at a certain direction in the input dataset, and select the
suitable order for the ordinary kriging analysis for the next step. By using the geostatistical
module of ArcGIS 9.0 they selected the suitable order to carry out the ordinary kriging
analysis and developed the prediction map based on the human infection rate for each
endemic village. They then categorized the predicted infection rate to create the
schistosomiasis endemic map with classified strata, based on the “Chinese Operational
Scheme of Schistosomiasis Control” enacted by the Ministry of Health (MoH) in 2004. At the
same time, the map of the standard error of the prediction, i.e. the uncertainty of the
prediction, was produced to qualify the prediction result enabling they to put forward a
particular control strategy for each endemic stratum according to their specific
environmental characteristics.
Based on the result of directional trend analysis, they developed a prediction map by using
ordinary kriging, which is shown in Figure 18. The darker the colour, the higher the
predicted S. japonicum infection rate. The apparent spatial pattern of S. japonicum infection
in Dangtu county presented an infection situation which was the most serious in the north-
west and south-east, while the south-western, north-eastern and central areas were much
less affected with medium infection rates in the transition areas. From the category map,
developed as part of the study, we found that most endemic villages in Dangtu county fell in
the 4th and 5th epidemic strata accounting for 72.7% of all the endemic villages in the
north-west and south-east part of the county. This was followed by the 3
accounting for 14.1% of all the endemic
of the endemic villages which were found i
Figure 18. Prediction map of
Fig. 19. Category map of epidemic strata of
It is suitable to predict the spatial distributi
infection with population-based prevalence data for each endemic village.
this study stated that the directional trend and moderate spatial correlation
part of the county. This was followed by the 3
accounting for 14.1% of all the endemic villages, and the 2nd stratum, accounting for 13.2%
of the endemic villages which were found in the centre of the county (Figure 19
Prediction map of S. japonicum infection in Dangtu county, China
. Category map of epidemic strata of S. japonicum infection in Dangtu county.
It is suitable to predict the spatial distribution of the prevalence of
based prevalence data for each endemic village. The authors of
the directional trend and moderate spatial correlation resulting from
27
part of the county. This was followed by the 3rd stratum,
villages, and the 2nd stratum, accounting for 13.2%
ure 19).
county, China
infection in Dangtu county.
the prevalence of S. japonicum
The authors of
resulting from
28
the study is partially due to the spatially correlated distribution of vegetation and
temperature as well as the water-contact behavior related to the Yangtze River and its
branches. Since different control strategies can be defined according to the principle of the
national schistosomiasis control strategy, they recommend that the control strategy be
defined based on the local environmental settings as well as epidemic strata at base level or
village level, at least in the Dangtu county.
According to Hay, Graham and Rogers (2006): “Geostatistical kriging has been
applied to a variety of disease prediction problems. For example, Oliver et al. (1992) and
Webster et al. (1994) were one amongst the first to apply geostatistics to characterize and
map disease pattern. Kelsall and Wakefield (2002) used kriging to map colorectal cancer in
Birmingham, UK. Geostatistical cokriging has been applied to map the risk of childhood
cancer (Oliver et al., 1998) and tick habitats from NOAA AVHRR imagery (Estrada-Pena,
1998)”.
29
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